Département Ecologie aquatique

Modern plankton high-throughput monitoring relies on deep learning classifiers for species recognition in water ecosystems. Despite satisfactory nominal performances, a significant challenge arises from dataset shift, which causes performances to drop during deployment. In our study, we integrate the ZooLake dataset, which consists of dark-field images of lake plankton (Kyathanahally et al. 2021a), with manually annotated images from 10 independent days of deployment, serving as test cells to benchmark out-of-dataset (OOD) performances. Our analysis reveals instances where classifiers, initially performing well in in-dataset conditions, encounter notable failures in practical scenarios. For example, a MobileNet with a 92% nominal test accuracy shows a 77% OOD accuracy. We systematically investigate conditions leading to OOD performance drops and propose a preemptive assessment method to identify potential pitfalls when classifying new data, and pinpoint features in OOD images that adversely impact classification. We present a three-step pipeline: (i) identifying OOD degradation compared to nominal test performance, (ii) conducting a diagnostic analysis of degradation causes, and (iii) providing solutions. We find that ensembles of BEiT vision transformers, with targeted augmentations addressing OOD robustness, geometric ensembling, and rotation-based test-time augmentation, constitute the most robust model, which we call BEsT. It achieves an 83% OOD accuracy, with errors concentrated on container classes. Moreover, it exhibits lower sensitivity to dataset shift, and reproduces well the plankton abundances. Our proposed pipeline is applicable to generic plankton classifiers, contingent on the availability of suitable test cells. By identifying critical shortcomings and offering practical procedures to fortify models against dataset shift, our study contributes to the development of more reliable plankton classification technologies.

Ökologische Gemeinschaften in Flüssen und Seen reagieren ähnlich auf den Klimawandel wie Gemeinschaften an Land. Das zeigt der erste umfassende Vergleich von Süsswasser- und Landökosystemen weltweit unter der Leitung von Eawag und WSL. Steigen die Temperaturen, profitieren vor allem wärmeliebende Arten. Eine überraschende Ausnahme könnte das Plankton sein.

Les communautés écologiques des lacs et rivières réagissent aux changements climatiques à peu près comme les communautés terrestres. C’est ce que montre la première comparaison des écosystèmes limniques et terrestres, réalisée à l’échelle de la planète sous la houlette de l’Eawag et du WSL. L’augmentation des températures profite surtout aux espèces thermophiles. Le plancton pourrait être une exception surprenante.

Nonliving resources frequently flow across ecosystem boundaries, which can yield networks of spatially coupled ecosystems. Yet the significance of resource flows for ecosystem function has predominantly been understood by studying two or a few coupled ecosystems, overlooking the broader resource flow network and its spatial structure. Here, we investigate how the spatial structure of larger resource flow networks influences ecosystem function at metaecosystem scales by analyzing metaecosystem models with homogeneously versus heterogeneously distributed resource flow networks but otherwise identical characteristics. We show that metaecosystem function can differ strongly between metaecosystems with contrasting resource flow networks. Differences in function generally arise through the scaling up of nonlinear local processes interacting with spatial variation in local dynamics, the latter of which is influenced by network structure. However, we find that neither network structure guarantees the greatest metaecosystem function. Rather, biotic (organism traits) and abiotic (resource flow rates) properties interact with network structure to determine which yields greater metaecosystem function. Our findings suggest that the spatial structure of resource flow networks coupling ecosystems can be a driver of ecosystem function at landscape scales. Furthermore, our study demonstrates how modifications to the structural, biotic, or abiotic properties of metaecosystem networks can have nontrivial large-scale effects on ecosystem function.

Phytoplankton is an essential resource in aquatic ecosystems, situated at the base of aquatic food webs. Plastic pollution can impact these organisms, potentially affecting the functioning of aquatic ecosystems. The interaction between plastics and phytoplankton is multifaceted: while microplastics can exert toxic effects on phytoplankton, plastics can also act as a substrate for colonisation. By reviewing the existing literature, this study aims to address pivotal questions concerning the intricate interplay among plastics and phytoplankton/phytobenthos and analyse impacts on fundamental ecosystem processes (e.g. primary production, nutrient cycling). This investigation spans both marine and freshwater ecosystems, examining diverse organisational levels from subcellular processes to entire ecosystems. The diverse chemical composition of plastics, along with their variable properties and role in forming the "plastisphere", underscores the complexity of their influences on aquatic environments. Morphological changes, alterations in metabolic processes, defence and stress responses, including homoaggregation and extracellular polysaccharide biosynthesis, represent adaptive strategies employed by phytoplankton to cope with plastic-induced stress. Plastics also serve as potential habitats for harmful algae and invasive species, thereby influencing biodiversity and environmental conditions. Processes affected by phytoplankton–plastic interaction can have cascading effects throughout the aquatic food web via altered bottom-up and top-down processes. This review emphasises that our understanding of how these multiple interactions compare in impact on natural processes is far from complete, and uncertainty persists regarding whether they drive significant alterations in ecological variables. A lack of comprehensive investigation poses a risk of overlooking fundamental aspects in addressing the environmental challenges associated with widespread plastic pollution.

Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.
Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

The adaptation of marine fish to freshwater environments includes prodigious examples of rapid evolution.Given the scarcity of ω-3 long-chain polyunsaturated fatty acids (LC-PUFA) in freshwater, we expect selection to be strong on fish transitioning to freshwater habitats and yet the underlying ecological causes of genomic and phenotypic differentiation are poorly understood for traits associated with lipid content and composition. Threespine stickleback Gasterosteus aculeatus have repeatedly colonized, and adapted to, freshwater habitats across the Northern Hemisphere. These freshwater populations often show elevated copy number of the fatty acid desaturase 2 gene (FADS2), which increases the biosynthetic capacity of LC-PUFA. The starkly lower content of LC-PUFA in freshwater compared to marine prey, especially docosahexaenoic acid (DHA), likely imposes strong positive selection on freshwater fish for either increased biosynthesis or greater dietary acquisition of LC-PUFA. The recently colonized and relatively undisturbed threespine stickleback populations in postglacial coastal lakes of southern Greenland offer an exceptional opportunity to study how variation in the copy number of FADS2 is related to abiotic and biotic conditions of lakes and their morphometry. As expected, given its position on the stickleback X chromosome, we found strong sexual dimorphism in FADS2 copy number in all populations (19 freshwater, 1 marine and 1 brackish), and an increased dimorphism in some freshwater populations. We also found that FADS2 copy number was negatively correlated, for both males and females, with the abundance of copepods, which are a DHA-rich food source in the zooplankton community. Overall, our results suggest that the prey community context of lakes might influence the process of metabolic adaptation of marine fish colonizing freshwater ecosystems.

Climate projections for continental Europe indicate drier summers, increased annual precipitation, and less snowy winters, which are expected to cause shifts in species' distributions. Yet, most regions/countries currently lack comprehensive climate-driven biodiversity projections across taxonomic groups, challenging effective conservation efforts. To address this gap, our study evaluated the potential effects of climate change on the biodiversity of an alpine country of Europe, Switzerland. We used a state-of-the art species distribution modeling approach and species occurrence data that covered the climatic conditions encountered across the full species' ranges to help limiting niche truncation. We quantified the relationship between baseline climate and the spatial distribution of 7291 species from 12 main taxonomic groups and projected future climate suitability for three 30-year periods and two greenhouse gas concentration scenarios (RCP4.5 and 8.5). Our results indicated important effects of projected climate changes on species' climate suitability, with responses varying by the taxonomic and conservation status group. The percentage of species facing major changes in climate suitability was higher under RCP8.5 (68%) compared to RCP4.5 (66%). By the end of the century, decreases in climate suitability were projected for 3000 species under RCP8.5 and 1758 species under RCP4.5. The most affected groups under RCP8.5 were molluscs, algae, and amphibians, while it was molluscs, birds, and vascular plants under RCP4.5. Spatially, by 2070–2099, we projected an overall decrease in climate suitability for 39% of the cells in the study area under RCP8.5 and 10% under RCP4.5, while projecting an increase for 50% of the cells under RCP8.5 and 73% under RCP4.5. The most consistent geographical shifts were upward, southward, and eastward. We found that the coverage of high climate suitability cells by protected areas was expected to increase. Our models and maps provide guidance for spatial conservation planning by pointing out future climate-suitable areas for biodiversity.

While it is commonly accepted that ecosystem dynamics are nonlinear, what is often not acknowledged is that nonlinearity implies scale-dependence. With the increasing availability of high-resolution ecological time series, there is a growing need to understand how scale and resolution in the data affect the construction and interpretation of causal networks—specifically, networks mapping how changes in one variable drive changes in others as part of a shared dynamic system ("dynamic causation"). We use Convergent Cross Mapping (CCM), a method specifically designed to measure dynamic causation, to study the effects of varying temporal and taxonomic/functional resolution in data when constructing ecological causal networks. As the system is viewed at different scales relationships will appear and disappear. The relationship between data resolution and interaction presence is not random: the temporal scale at which a relationship is uncovered identifies a biologically relevant scale that drives changes in population abundance. Further, causal relationships between taxonomic aggregates (low-resolution) are shown to be influenced by the number of interactions between their component species (high-resolution). Because no single level of resolution captures all the causal links in a system, a more complete understanding requires multiple levels when constructing causal networks.

Parasites spend at least a part of their lives in or on host organisms from which they obtain resources. Many parasites have complex life cycles, requiring transmission through multiple host species to mature and reproduce. In order to increase the likelihood of successful transmission between hosts via predation events, some parasites alter the phenotype of the host. Fishes are common hosts in the aquatic environment and are often the targets of manipulation. Diplostomid eye flukes and the tapeworm Schistocephalus solidus have been well studied for their ability to alter fish phenotypes, increasing transmission via predation.

Die Erhaltung der Biodiversität ist eine gesellschaftliche Herausforderung. Die gesetzten Schutzziele werden bisher oft nur unvollständig oder nicht erreicht. Kann ein stärkerer Wissenstransfer zwischen Forschung und Praxis dazu beitragen, Antworten auf Fragen aus der Naturschutzpraxis zu finden? Das Synthesezentrum Biodiversität probiert es aus.

The processing of organic matter is a central ecosystem function in freshwater ecosystems that allows the integration of terrestrial plant material into aquatic heterotrophic food webs. From an energetic perspective, many temperate aquatic systems fundamentally depend on such allochthonous inputs. Current research established that this central ecosystem function may be linked to population density of few yet dominant invertebrate detritivores, showing a negative density-dependent relationship. Here, we extended the current knowledge and experimentally assessed the processing of leaf litter by freshwater amphipods, using broad density gradients, interspecific competition, and laboratory and field experiments. We used two species of dominant amphipods, namely the native Gammarus fossarum and the non-native Gammarus roeselii, varying their density by two orders of magnitude, both in single-species and two-species treatments. Results from 252 mesocosms in the lab and 97 mesocosms in a natural stream show that per capita leaf litter processing rates are strongly negatively dependant on population density in monocultures. Interspecific competition in two-species treatments corroborated the negative density-dependent ecosystem function and highlighted the functional redundancy of the two detritivore species. We identified a flattening in the processing rates at previously unreported but well-defined breakpoints. These breakpoints may reflect minimal metabolic requirements at which survival takes precedence over any other process, such as interference competition. The breakpoints were consistent across both species, indicating that they must process leaf litter equalling one fifth to one fourth of their dry body weight per day as a minimal nutritional threshold. Our results suggest the need for integrating nonlinear density-dependencies and breakpoint population densities in key ecosystem functions in aquatic ecosystem modelling alongside classical biodiversity–ecosystem functioning relationships. Depending on the population density the corresponding ecosystem functioning could differ significantly. This corroborates the need to better understand biodiversity–abundance relationships when protecting aquatic ecosystems.

1. Global environmental change will cause shifts in species communities, with non-native species likely replacing native ones at an unprecedented rate. This will have consequences for biodiversity and ecosystem services, in addition to the ecological and economic damage caused by those non-native species that are invasive. Understanding general patterns driving distributions of native and non-native species is therefore vital, but no study has compared yet whether environmental variables that correlate with a species' presence differ between the two groups other than at local scale and often with very limited sample size.
2. In this study, we focus on 141 native and non-native congeneric plant species pairs at the scale of Switzerland. In the framework of correlative species distribution models, we used newly developed methods for efficient automated selection of a parsimonious number of predictor environmental variables to determine which ones, out of a large candidate set in eight classes, have the strongest explanatory power for both species groups.
3. Our results indicated that variables influence the two groups in significantly different ways. Climate was by far the strongest determinant of both native and non-native species distributions, although it had significantly more explanatory power in native species models.
4. Models for non-native species were significantly more influenced by anthropogenic factors, land use variables and forest cover. The presence of non-native species was also associated with habitats with a significantly lower mean naturality value than native species.
5. These findings provide novel empirical evidence for the different environmental factors driving native and non-native plants' distributions and guidance for non-native species management.
6. Practical implications: species distribution models are an increasingly frequently advised tool for conservation management and our results provide guidelines on which covariates should be specifically considered to assess the habitat suitability of non-native versus native species. The distributions of the former group of species are particularly important to research, as, in time, they may turn invasive. In addition, areas close to infrastructure should be scanned regularly for incipient colonizations by non-native species, especially in as yet uninvaded areas, such as high mountains.

Terrestrial and aquatic ecosystems are tightly linked, with direct implications for applied resource management and conservation. It is well known that human land use change and intensification of terrestrial systems can have large impacts on surface freshwater ecosystems. Contrastingly, the study and understanding of such land use impacts on groundwater communities is lagging behind. Both the impact strength of land use on groundwater communities and the spatial extents at which such interlinkages are operating are largely unknown, despite our reliance on groundwater for drinking water extraction as a key ecosystem service. Here, we analyzed groundwater amphipod occurrence from several hundred shallow groundwater aquifers used for drinking water extraction across a region of varying agricultural intensity and human population density in Switzerland. Despite drinking water extraction sites being generally built at locations with expected minimal aboveground impacts on water quality, we found a direct correlation between land use type and intensity within the surrounding catchment area and the locally measured nitrate concentrations, which is a direct proxy for drinking water quality. Furthermore, groundwater amphipods were more likely to be found at sites with higher forest coverage than at sites with higher crop and intensive pasture coverages, clearly indicating a tight connection between aboveground land use and groundwater biodiversity. Our results indicate that land use type effects on groundwater communities are most relevant and pronounced to spatial scales of about 400–1000 m around the groundwater sampling site. Importantly, the here identified spatial scale is 1.2- to 3-fold exceeding the average extent of currently defined groundwater protection zones. We postulate that incorporating an ecosystem perspective into groundwater management strategies is needed for effective protection of groundwater quality and biodiversity.

Implementing and optimizing biodiversity monitoring is crucial given the current, worldwide biodiversity decline. Compared to other ecosystems, monitoring of biodiversity is lagging behind in groundwater ecosystems, both because of sparse taxonomic knowledge and methodological constraints. We here assessed temporal variation in the occurrence and abundance of macroinvertebrates collected systematically from shallow groundwater aquifers of Switzerland to establish general principles on seasonality and repeatability of assessment outcomes. We found no seasonal abundance pattern for obligate groundwater amphipods and isopods, indicating temporal consistency. In contrast, other macroinvertebrates (predominantly stygophiles and stygoxenes) showed pronounced seasonality in their detection rate. However, we found variability in detection rates across groundwater amphipod species and especially across sampling sites. For groundwater communities, characterized by narrowly-distributed and rare species, our results highlight the need for tailored and extensive sampling strategies. When setting up monitoring programs on groundwater fauna, detection probability, temporal autocorrelation, and standardization of sampling effort should be carefully considered. Applying novel, systematic approaches, can offer promising methodologies for understanding and conserving groundwater ecosystems.

Human land-use intensification threatens arthropod (for example, insect and spider) biodiversity across aquatic and terrestrial ecosystems. Insects and spiders play critical roles in ecosystems by accumulating and synthesizing organic nutrients such as polyunsaturated fatty acids (PUFAs). However, links between biodiversity and nutrient content of insect and spider communities have yet to be quantified. We relate insect and spider richness to biomass and PUFA-mass from stream and terrestrial communities encompassing nine land uses. PUFA-mass and biomass relate positively to biodiversity across ecosystems. In terrestrial systems, human-dominated areas have lower biomass and PUFA-mass than more natural areas, even at equivalent levels of richness. Aquatic ecosystems have consistently higher PUFA-mass than terrestrial ecosystems. Our findings reinforce the importance of conserving biodiversity and highlight the distinctive benefits of aquatic biodiversity.

Der Übergangsbereich zwischen Wasser und Land beherbergt vielfältige Lebensräume und zahlreiche Arten: Die dort vorhandene Biodiversität ist besonders hoch und über die blaugrüne Grenze hinweg laufen zahlreiche ökologische Prozesse ab und Stoffe werden ausgetauscht. Der Mensch hat die blaugrünen Lebensräume schon immer genutzt, ja manche verdanken ihre Entstehung dem Menschen. Auch in Zukunft wird der Mensch blaugrüne Landschaftselemente vielfältig nutzen, aber auch vonihnen abhängig sein, sei dies zur Wasserrückhaltung unter dem Klimawandel oder für die Erholung.

Aim: Seagrass meadows represent a key marine ecosystem owing to the significant biodiversity they host. Protection actions are often implemented without considering connectivity between habitats. In this article, we project and prioritise Mediterranean seagrass habitats (Posidonia oceanica and Cymodocea nodosa) based on their potential as sources/retention and stepping stones for dispersal propagules of the associated biotic communities. We use this information to identify gaps in the protection of highly ranked habitats.
Location: Mediterranean Sea.
Methods: We related seagrass observations with marine environmental predictors to run species distribution models and infer the distribution of Mediterranean seagrasses. We then used a network-based approach (CONEFOR) to rank patches of seagrass suitable areas based on their contribution to the seascape in terms of patch area, potential as source/retention of propagules and stepping stone. Finally, by overlaying our ranking with the spatial distribution of marine protected areas (MPAs), we identified potential gaps in the protection of important seagrass habitats across the Mediterranean and its basins.
Results: Most of the identified patches of seagrass suitable areas are not included in MPAs, only reaching a maximum protection coverage of ~50% in the Northwestern Mediterranean. Relatively few patches contribute disproportionately to connectivity, but top-ranked habitat patches are not included within the existing MPAs network, both at the Mediterranean scale and for most basins. The largest gaps for the source/sink role are in the Aegean and Ionian Sea, and largest gaps for the stepping stone role are in the Adriatic, Ionian and Tyrrhenian Sea.
Main Conclusions: Our results suggest that the current MPAs network fails to protect highly relevant patches of seagrass suitable areas in most of the Mediterranean basins. However, this gap could be filled by a few well-placed MPAs. Overall, we provide novel insights for the identification of key habitats and planning novel coastal MPAs in the region.

Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we used inhibitors to disrupt the gut microbiota of juvenile Epibolus pulchripes (tropical, CH₄-emitting) and Glomeris connexa (temperate, non-CH₄-emitting) and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, with Bacteroidota dominant in E. pulchripes and Pseudomonadota in G. connexa. Sodium-2-bromoethanesulfonate treatment halted CH₄ emissions in E. pulchripes, but it resumed after returning to normal feeding. Employing ¹³C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede’s nutrition.

Biodiversity loss is increasing worldwide, necessitating effective approaches to counteract negative trends. Here, we assessed aquatic macroinvertebrate biodiversity in two river catchments in Switzerland; one significantly degraded and associated with urbanisation and instream barriers, and one in a near-natural condition. Contrary to our expectations, environmental heterogeneity was lower in the near-natural stream, with enhanced productivity in the degraded system resulting in a greater range of environmental conditions. At face value, commonly employed alpha, beta and gamma biodiversity metrics suggested both catchments constituted healthy systems, with greater richness or comparable values recorded in the degraded system relative to the near-natural one. Further, functional metrics considered to be early indicators for anthropogenic disturbance, demonstrated no anticipated differences between degraded and near-natural catchments. However, investigating the identity of the taxa unique to each river system showed that anthropogenic degradation led to replacement of specialist, sensitive species indicative of pristine rivers, by generalist, pollution tolerant species. These replacements reflect a major alteration in community composition in the degraded system compared with the near-natural system. Total nitrogen and fine sediment were important in distinguishing the respective communities. We urge caution in biodiversity studies that employ numerical biodiversity metrics alone. Assessing just one aspect of diversity, such as richness, is not sufficient to track biodiversity changes associated with environmental stress. We advocate that biodiversity monitoring for conservation and management purposes must go beyond traditional richness biodiversity metrics, to include indices that incorporate detailed nuances of biotic communities that relates to taxon identity.

Introgressive hybridization is a pivotal force influencing genetic diversity and adaptive potential of invasive species, however to date has received less attention for even the most globally destructive species. Golden apple snails (Pomacea spp.), one of the world’s worst invasive species, were first introduced during the 1980s into Taiwan for commerce and have since emerged as a significant threat to regional biodiversity. Two of the most destructive invasive species of Pomacea, P. canaliculata and P. maculata, have been reported to hybridize in its native and non-native range, the latter of which has been posited to facilitate an adaptive advantage for increasing invasiveness. Thus, our study combined mitochondrial COI (Cytochrome c oxidase subunit I) barcoding and nuclear EF1-α (elongation factor 1-alpha) gene analysis to identify putative hybridization among 254 samples collected across 14 cities/counties in Taiwan. Our investigation confirmed hybridization within the sympatric but heterogeneous distribution of P. canaliculata and P. maculata in Taiwan. The results indicated that 18.9% of the total sampled population consists of hybrids, whereas 81.1% of the samples demonstrated pure P. canaliculata genetics. Remarkably, no pure P. maculata were detected across the island, and all P. maculata mtDNA samples appeared to be genetically introgressed. The dearth of pure P. maculata populations, despite the prevalence of canaliculata-maculata hybrids, invites speculation about introduction mechanisms, genetic drift and maybe the nuanced influence of environmental factors on distribution dynamics, all of which required further investigation. These findings contribute significant scientific insights into the invasive dynamics of Pomacea in Taiwan, and the results underline findings applicable for devising targeted and effective conservation strategies in regions grappling with the challenges posed by invasive species.

Als Folge des Klimawandels etablieren sich immer mehr wärmeliebende Arten in Schweizer Gewässern. Da wirbellose Kleinlebewesen als Bioindikatoren für die Qualität von Fliessgewässern dienen, könnte diese Entwicklung die biologische Gewässerbeurteilung verfälschen. Simulationen zeigen, dass die Vielfalt der Wirbellosen tatsächlich zunehmen wird, jedoch auf Kosten kälteliebender Arten. Soweit sich das beurteilen lässt, sind die verwendeten Indizes aber robust genug, um ihre Aussagekraft zur Gewässerqualität für die nächsten Jahrzehnte zu behalten.

Plant–insect trophic systems should be particularly sensitive to processes altering species spatial co-occurrences, as impacts on one level can cascade effectively through the strong trophic reliance to the other level. Here, we predicted the biogeography of Lepidoptera–plant communities under global-change scenarios, exploiting spatially resolved data on 423 Lepidoptera species and their 848 food plants across the German state of Baden-Württemberg (ca. 36,000 km²). We performed simulations of plant extinction and Lepidoptera expansion, and respectively assessed their cascading consequences—namely secondary extinction of Lepidoptera and change in functional distance of plants—on the interaction networks. Importantly, the simulations were spatially explicit, as we accounted for realistic landscape contexts of both processes: Plant extinctions were simulated as "regional" (a species goes extinct in the whole region at once) vs. "isolation-driven" (a species gradually goes extinct from the peripheral or isolated localities according to its real regional distribution); Lepidoptera expansions were simulated with random, northward, and upward directions according to real topography. The consequences were assessed based on empirical community composition and trophic relationships. When evaluated by regional richness, the robustness of Lepidoptera assemblages against secondary extinctions was higher under isolation-driven plant extinctions than regional plant extinction; however, this relationship was reversed when evaluated by averaged local richness. Also, with isolation-driven plant extinctions, Lepidoptera at the central sub-region of Baden-Württemberg appeared to be especially vulnerable. With Lepidoptera expansions, plants' functional distances in local communities dropped, indicating a possible increase of competition among plants, yet to a lesser extent particularly with upward movements. Together, our results suggested that the communities' composition context at the landscape scale (i.e., how communities, with respective species composition, are arranged within the landscape) matters when assessing global-change influences on interaction systems; spatially explicit consideration of such context can reveal localised consequences that are not necessarily captured via a spatially implicit, regional perspective.

Der Bau von Weihern hat sich als wirksame Massnahme erwiesen, um die Bestände von Amphibien zu fördern und ihre Bestände zu stabilisieren. Im Kanton Aargau zeigen Ergebnisse aus zwei Jahrzehnten Weiherbau und begleitendem Monitoring, was eine funktionierende ökologische Infrastruktur für Amphibien ausmacht: Es braucht gut vernetzte Amphibienlaichgebiete aus mehreren Weihern mit grosser Wasserfläche.

L'aménagement d'étangs s'est révélé efficace pour promouvoir et stabiliser les populations de batraciens. Dans le canton d'Argovie, les résultats de deux décennies d'aménagement et de suivi d'étangs montrent ce qu'est une infrastructure écologique pour batraciens fonctionnelle: il faut que les sites de reproduction soient interconnectés et comprennent plusieurs étangs dotés d'une importante surface aquatique.

Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated by combining the diversity and dispersion. ENDP estimates β-variation independently of estimates of within-sample α-variation, although β-and α-estimates could statistically correlate to some extent. This new concept differs from the existing standard where β-diversity is estimated based on the “partition of variation” scheme (beta = gamma − alpha or beta = gamma∕alpha), so that estimates of β-diversity directly depend on the corresponding values of α-diversity. ENDP estimates are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. The analysis is complicated by geographically coexisting cryptic species and the potential mixed-mating system of this hermaphroditic parasite. Analyses with subsampled data demonstrated that ENDP estimates are robust. Number of loci used for genotyping has much stronger effect on variation of point ENDP estimates than sample size.

A central goal in evolutionary biology is to understand how different evolutionary processes cause trait change in wild populations. However, quantifying evolutionary change in the wild requires linking trait change to shifts in allele frequencies at causal loci. Nevertheless, datasets that allow for such tests are extremely rare and existing theoretical approaches poorly account for the evolutionary dynamics that likely occur in ecological settings. Using a decade-long integrative phenome-to-genome time-series dataset on wild threespine stickleback (Gasterosteus aculeatus), we identified how different modes of selection (directional, episodic, and balancing) drive microevolutionary change in correlated traits over time. Most strikingly, we show that feeding traits changed by as much 25% across 10 generations which was driven by changes in the genetic architecture (i.e., in both genomic breeding values and allele frequencies at genetic loci for feeding traits). Importantly, allele frequencies at genetic loci related to feeding traits changed at a rate greater than expected under drift, suggesting that the observed change was a result of directional selection. Allele frequency dynamics of loci related to swimming traits appeared to be under fluctuating selection evident in periodic population crashes in this system. Our results show that microevolutionary change in a wild population is characterized by different modes of selection acting simultaneously on different traits, which likely has important consequences for the evolution of correlated traits. Our study provides one of the most thorough descriptions to date of how microevolutionary processes result in trait change in a natural population.

DNA methylation (DNAm) is a mechanism for rapid acclimation to environmental conditions. In natural systems, small effect sizes relative to noise necessitates large sampling efforts to detect differences. Large numbers of individually sequenced libraries are costly. Pooling DNA prior to library preparation may be an efficient way to reduce costs and increase sample size, yet there are to date no recommendations in ecological epigenetics research. We test whether pooled and individual libraries yield comparable DNAm signals in a natural system exposed to different pollution levels by generating whole-epigenome data from two invasive molluscs (Corbicula fluminea, Dreissena polymorpha) collected from polluted and unpolluted localities (Italy). DNA of the same individuals were used for pooled and individual epigenomic libraries and sequenced with equivalent resources per individual. We found that pooling effectively captures similar genome-wide and global methylation signals as individual libraries, highlighting that pooled libraries are representative of the global population signal. However, pooled libraries yielded orders of magnitude more data than individual libraries, which was a consequence of higher coverage. We would therefore recommend aiming for a high initial coverage of individual libraries (15×) in future studies. Consequently, we detected many more differentially methylated regions (DMRs) with the pooled libraries and a significantly lower statistical power for regions from individual libraries. Computationally pooled data from the individual libraries produced fewer DMRs and the overlap with wet-lab pooled DMRs was relatively low. We discuss possible causes for discrepancies, list benefits and drawbacks of pooling, and provide recommendations for future epigenomic studies.

Amphibien sind aus vielen Gründen stark gefährdet, sowohl global, national als auch lokal: Lebensräume gehen verloren und verlieren an Qualität, standortfremde Fische fressen Amphibienlarven, Pestizide beeinträchtigen die Populationen, auf der Wanderung zu den Laichgebieten stellen Straßen eine Gefahr dar, neue Krankheitserreger machen den Tieren zu schaffen, und das sich ändernde Klima führt zu Trockenheit - die Liste könnte noch erweitert werden. Trotz dieser negativen Faktoren ist wirkungsvoller Amphibienschutz möglich, wie die Ergebnisse des Weiherbauprogramms des Schweizer Kantons Aargau zeigen.

Anthropogene Einflüsse auf die Umwelt wirken sich auf das Plankton und seine Rolle im See aus und beeinträchtigen so Nahrungsnetze, Ökosystemleistungen und Wasserqualität. In der Schweiz wird das traditionelle Planktonmonitoring durch taxonomische Fachpersonen mittels Mikroskopie aufgrund von Ressourcen- und Personalmangel zunehmend eingeschränkt. Diese Studie untersucht das Potenzial automatisierter Bildgebungsverfahren wie dem Aquascope und zeigt die Defizite und Chancen für zukünftige Entwicklungen auf.

Host–parasite interactions are influenced by present and past eco-evolutionary interactions and the local environment. An ecological community defines the potential host range of each parasite and the potential parasite diversity of each host species. Past and present processes translate potential to realised interaction niches of parasite and host species. Host–parasite interactions are antagonistic, which may slow the saturation of their interaction niches. Intervality, a property of bipartite networks, measures saturation of interaction niches. Intervality of a community increases as the interaction niches of species of one guild (e.g. hosts) become saturated for their interactions with another guild (e.g. parasites). Characteristics driving intervality in host and parasite communities are largely unknown, as well as the effect of environmental change on intervality of these communities. In our study, we assess if the characteristics 'phylogenetic relatedness' and 'overlap in ecological interactions' explain intervality of rodent host–helminth parasite communities. In addition, we contrast intervality of these communities from habitats that differ in their history of human-driven modification. We performed the analyses for the interaction niches of both parasites and hosts, independently. Our results indicated that host and parasite communities were non-interval or significantly less interval than expected by chance. Phylogenetic relatedness and overlap in ecological interactions did not explain the maximum values of intervality. We speculate that antagonistic coevolution in host–parasite communities may hinder communities to reach saturation, which would explain why it is difficult to find the characteristics that explain intervality of a community. Interestingly, intervality of the interaction niche of parasites (host range) increased with habitat modification (i.e. saturation increased), whereas intervality of the interaction niche of hosts (parasite diversity) decreased as habitat modification increased. These opposite trends suggest that interaction niches of parasites and hosts respond differently to habitat modification.

1. Freshwater and terrestrial biodiversity are linked through spatial resource flows. Key examples are detrital subsidies from the riparian vegetation that form the base of food webs in small streams. Despite the central role of detritivores in these food webs, the consequences of altered riparian vegetation type and resource availability on their trophic strategies are less known.
2. Therefore, we experimentally tested direct and indirect effects of riparian vegetation type (i.e. riparian forests present vs. absent) on trophic interactions and dietary imbalances of aquatic detritivores. To characterise trophic strategies, we used stoichiometric and isotopic differences between consumers and resources as functional measures of trophic link strength in leaf litter bags naturally colonised by stream decomposers and detritivores.
3. Our results show that an absence of riparian forests affected stoichiometric and isotopic properties in stream detrital food webs. Where local riparian forests were absent, leaf litter showed lower C:N ratios, which only trichopteran detritivores mirrored, whereas plecopteran and crustacean detritivores showed differences in their isotopic signatures. Diverging patterns between resources and consumers could lead to a rewiring of energy flow paths and weaken the coupling between aquatic detritivores and terrestrial detritus.
4. Consequently, our findings demonstrate that riparian forests are essential for aquatic food webs by not only influencing organisms themselves but also their trophic interactions and energy flow paths. Aquatic detritivores depending on terrestrial subsidies can be highly sensitive to local changes in their resource environment. Therefore, functionally divergent patterns between resources and consumers in recipient systems highlight how habitat properties of the donor system can affect food webs connected across ecosystem boundaries. Read the free Plain Language Summary for this article on the Journal blog.

More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.

Cyanobacterial blooms require monitoring, as they pose a threat to ecosystems and human health, especially by the release of toxins. Along with widely reported microcystins, cyanobacteria coproduce other bioactive metabolites; however, information about their dynamics in surface waters is sparse. We investigated dynamics across full bloom successions throughout a five-year lake monitoring campaign (Greifensee, Switzerland) spanning 150 sampling dates. We conducted extensive suspect screening of cyanobacterial metabolites using the database CyanoMetDB. Across all 850 samples, 35 metabolites regularly co-occurred. Microcystins were present in 70% of samples, with [d-Asp³,(E)-Dhb⁷]MC-RR reaching concentrations of 70 ng/L. Anabaenopeptins, meanwhile, were detected in 95% of all samples with concentrations of Oscillamide Y up to 100-fold higher than microcystins. Based on LC-MS response and frequency, we identified indicator metabolites exclusively produced by one of three cyanobacteria isolated from the lake, these being [d-Asp³,(E)-Dhb⁷]MC-RR from Planktothrix sp. G2020, Microginin 761B from Microcystis sp. G2011, and Ferintoic acid B from Microcystis sp. G2020. These indicators showed distinct temporal trends and peaking seasons that reflect the variance in either the abundance of the producing cyanobacteria or their toxin production dynamics. Our approach demonstrates that selecting high LC-MS response and frequent and species-specific indicator metabolites can be advantageous for cyanobacterial monitoring.

Rivers are biodiverse ecosystems that play an essential role in the processing of organic matter from headwaters to the lower reaches. The biodiversity within these spatially complex ecosystems is often subject to huge seasonal variation, particularly in temperate regions, for example seasonal peaks in emergence of aquatic insects or migration of fish through the river network. However, these ecosystems are also subject to strong anthropogenic pressures that affect not only the biodiversity within this system, but the functions this biodiversity provides to key ecosystem processes. Therefore, spatial and temporally dynamics must be considered to effectively assess and understand the biodiversity and functioning within an ecosystem. Here, we assessed ecosystem function at a high spatial and temporal resolution across a large river network, specifically focussing on standardised organic–matter decomposition. Our results show—even when correcting for temperature—significant effects of both season and water chemistry parameters on microbial decomposition. However, we found no effect of space (i.e., site location within the network) on ecosystem function, contrary to expectations. We also found no imprint of the microbial community richness assessed in the water column (α–diversity and Shannon Index) on the patterns of organic–matter decomposition, however, this may be due to our focus on potential colonising microbes rather than benthic communities. Our study highlights the need to include functional indicators for the assessment of ecosystems.

Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves, or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.

Crop protection from algal grazers is a key area of concern, as grazing zooplankton and flagellates can decimate microalgae crops and impede economic viability of cultivation for biofuels and bioproducts. Inhibition of grazing by chemical and physical interference is one promising solution; however, there have been few empirical tests of this approach that use defense traits innate to algal crop species. Botryococcus braunii is of particular interest because a) it excretes high levels of hydrocarbons and exopolysaccharides and b) forms colonies and possesses chemical defenses. Here we conduct a controlled laboratory experiment to test whether B. braunii can mitigate losses to grazing by two distinct grazers, Daphnia magna and Poterioochromonas malhamensis, due to both chemical inhibition and physical interference linked to large/inedible colonies. We show that chemical and physical defenses interactively reduce the total effect of grazing, thus significantly increasing the biomass and growth rates of cultures of B. braunii and Nannochloropsis limnetica when either grazer is present. We also find that B. braunii medium enhances the growth of N. limnetica. Our study demonstrates how community engineering can identify synergies arising from algal co-cultivation (e.g., by using industrially relevant strains for crop protection). While our lab study serves as a proof-of-concept, future research should test this strategy at pilot scale; if successful, such ecological discoveries may help to reduce the costs of large-scale deployment of algal cultivation for sustainable foods, fuels, bioproducts (e.g., bioplastics), and carbon capture.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N_e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N_e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N_e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

Environmental DNA (eDNA) has revolutionized ecological research, particularly for biodiversity assessment in various environments, most notably aquatic media. Environmental DNA analysis allows for non-invasive and rapid species detection across multiple taxonomic groups within a single sample, making it especially useful for identifying rare or invasive species. Due to dynamic hydrological processes, eDNA samples from running waters may represent biodiversity from broad contributing areas, which is convenient from a biomonitoring perspective but also challenging, as hydrological knowledge is required for meaningful biological interpretation. Hydrologists could also benefit from eDNA to address unsolved questions, particularly concerning water movement through catchments. While naturally occurring abiotic tracers have advanced our understanding of water age distribution in catchments, for example, current geochemical tracers cannot fully elucidate the timing and flow paths of water through landscapes. Conversely, biological tracers, owing to their immense diversity and interactions with the environment, could offer more detailed information on the sources and flow paths of water to the stream. The informational capacity of eDNA as a tracer, however, is determined by the ability to interpret the complex biological heterogeneity at a study site, which arguably requires both biological and hydrological expertise. As eDNA data has become increasingly available as part of biomonitoring campaigns, we argue that accompanying eDNA surveys with hydrological observations could enhance our understanding of both biological and hydrological processes; we identify opportunities, challenges, and needs for further interdisciplinary collaboration; and we highlight eDNA's potential as a bridge between hydrology and biology, which could foster both domains.

The loss of biodiversity in freshwater environments is becoming an increasing problem globally. As a result, many tools have been developed and improved to reduce this decline. However, there is still a need for the identification and evaluation of precise restoration measures to improve habitats and preserve sentinel freshwater species, such as brown trout. This paper provides an up-to-date viewpoint about the life history, habitat characteristics, suitability conditions, and metapopulation dynamic modelling of brown trout, aiming to identify and discuss gaps and propose possible improvements based on collating and reinterpreting literature data. Results suggest that habitat suitability curves for environmental and hydraulic variables possess some degree of universality, for spawning habitat, fry, juvenile and adult trout. Further, an improved method to estimate the amount of suitable area by including the role of stream obstacles (i.e., macro-roughness with characteristic size in the order of the mean water depth) is proposed and discussed. This approach can be integrated into advanced metapopulation models and will allow experts to evaluate the best measures towards restoring and preserving freshwater riverine environments.

Aquatische und terrestrische Lebensräume sind eng miteinander verknüpft. Zahlreiche Pflanzen- und Tierarten nutzen während ihres Lebens beide Lebensräume: zwischen «Wasser» und «Land» herrscht ein reger Austausch von Stoffen und Organismen. Auch die menschliche Nutzung und Gestaltung der Landschaft wird vom Wechselspiel zwischen aquatischen und terrestrischen Lebensräumen geprägt. Das vorliegende Buch lädt dazu ein, auf acht Exkursionen die Funktionsweise dieser Lebensräume und ihre Biodiversität aktiv zu erkunden.

Alpine landscapes are notable regarding their sensitivity to environmental change. Surface waters are especially sensitive as many are influenced by glacial meltwaters that are diminishing with the retreat of glaciers worldwide. The Macun Lakes region, Swiss National Park, is an alpine cirque landscape housing a number of lakes interconnected by streams. The area has been non-glaciated for decades, although rock glaciers are still present in the south basin. Surface waters, 10 stream sites in the present study, have been monitored in mid-summer since the year 2001 for physico-chemistry, periphyton and macroinvertebrates (including 74 species of chironomids). Water physico-chemistry revealed that the two main basins in the catchment differed, reflecting the inputs of rock glacier waters in the south basin. However, trends suggest that waters are becoming more similar as rock glacier inputs diminish over time along with a general decrease in nitrogen levels in all waters. Periphyton biomass showed some spatial differences among sites and a general decrease after 2010. Macroinvertebrate assemblages, including chironomids, clearly differed among basins and spatially along the stream network in each basin. Notably, no significant temporal trend was observed in the long-term data for macroinvertebrates, including chironomids, at the monitored sites. The results suggest that lotic macroinvertebrates may be buffered by the interconnectedness of streams and lakes in the landscape, which mitigates major response patterns of running waters to environmental change.

Aim: groundwater ecosystems harbour a unique biodiversity, but remain poorly studied, mainly due to difficulties in accessibility and imperfect species detection. Consequently, knowledge on the state and change of groundwater biodiversity remains highly deficient. In the context of global warming and excessive groundwater extraction, understanding groundwater from an ecosystem-perspective, including organism diversity and distribution, is essential. This study presents the largest ever systematic assessment of groundwater amphipods, which are a key component of European groundwater biodiversity.
Location: Switzerland (41,285 km²), including data from 906 sampling sites.
Taxon: groundwater amphipods, genera Niphargus and Crangonyx (Crustacea, Amphipoda).
Methods: we applied a highly standardized citizen science approach to collect repeated groundwater fauna samples in collaboration with municipal drinking water providers. Using detection–nondetection data of the genetically identified groundwater amphipod species, we assessed the overall species diversity of both rare and common species. The distribution of commonly found species was predicted using multispecies occupancy modelling.
Results: we retrieved 3882 samples from 906 sites, yielding 2350 groundwater amphipod individuals. We identified a remarkable species diversity, comprising few commonly and many rarely found species. Considering commonly found species, we identified distinct distribution ranges, low local species richness and a predominance of negative co-occurrences. In contrast, a major portion of species were found rarely (generally at just one or two sites each), distributed uniformly throughout the study area and unrelated to common species' recognized hotspots. Many of these rarely found species are not yet formally described.
Main conclusions: Our results give robust emphasis on the rare occurrence and narrow distribution of many groundwater dwellers. Our systematic and standardized sampling data of groundwater amphipods suggest that rarity is particularly prominent and inherent to groundwater organisms. We emphasize the need of systematic data to integrate rare groundwater species in biodiversity assessments, especially in times of global change.

The collection of environmental DNA (eDNA) and subsequent metabarcoding are useful tools for assessing marine fish biodiversity noninvasively. It is of particular importance to evaluate biodiversity in regions that are hard to access and thus less well studied. Sampling and preservation methods tailored to the specific circumstances are required. Aquatic eDNA is often captured on filters made of different materials and pore sizes, and subsequently stored under divergent conditions for varying periods of time. Previous studies on multispecies detection in marine systems have primarily focused on capture and extraction effects. Our study, in contrast, examined the effects of filter type, storage method, and storage time on DNA yield, alpha (i.e., ZOTU richness) and beta diversity (i.e., ZOTU composition) recovered from a marine ecosystem in Shark Bay, Western Australia. We compared two different filter types (cellulose-nitrate filters with pore sizes of 0.45 μm; glass-fiber filters with pore sizes of 0.1 μm), two storage methods (preservation in Longmire's solution and drying, respectively), various storage times (30–68 days) on two metabarcoding assays using different fish-specific primers. Our results showed that storage time decreased DNA yield and affected alpha and beta diversity estimates. Cellulose-nitrate filters stored in Longmire's solution proved to be the best combination with the smallest decrease in DNA yield, no effect on alpha diversity and consistent community compositions. Storing glass-fiber filters in Longmire's solution led to a decrease in eDNA yield and alpha diversity estimates with increasing storage time. Furthermore, the largest change in beta diversity for each metabarcode was found for glass-fiber filters regardless of storage method. Our results highlight the importance of considering storage time and interactions between storage method and filter when analyzing eDNA results, especially when storing samples for an extended time period or comparison of samples stored for different durations.

1. Global change drives multiple facets of biodiversity including interaction diversity, which is fundamental for ecosystem functioning. However, studying trophic interactions is challenging in meta-ecosystems, that is ecosystems connected by spatial flows of energy, materials and organisms across ecosystem boundaries. While analytical methods based on abundances of polyunsaturated fatty acids (PUFAs) and stable isotopes of amino acids (AAs) are being increasingly used, it has never been explored if both approaches could be: (i) combined in mixing models to enhance precision in dietary inference (ii) compared to disentangle transfers of various PUFAs and proteins in food webs in the wild.
2. We explore the utility of analytical approaches based on PUFA abundances and AA isotopes to resolve resource transfers in a natural riparian food web. We focus on spiders and their potential prey from blue, green and brown sources to address three important and persisting methodological issues in food-web ecology, namely whether (i) essential AA carbon isotopes can resolve protein origin from blue, green and brown resources, (ii) PUFA relative abundance and AA isotopes can be combined in a mixing model to provide higher precision estimates (i.e. narrower intervals) and (iii) combining the two approaches can unveil the coupling of protein and PUFA transfers in food webs. 3. Our research demonstrates the power of AA isotopes and PUFAs to distinguish blue, green, and brown sources and their transfer up to consumers. We show that combining PUFA relative abundance and AA isotopes in a mixing model provides overall estimates similar to the individual estimates but significantly increases precision. In addition, we showcase how combining approaches unveil the coupling of protein and PUFA transfers. For instance, we show that most PUFAs are less concentrated from prey to predators, relative to proteins, highlighting uncoupling of PUFAs and protein transfer along food chains.
4. We show for the first time the effectiveness of combining AA isotopes and PUFA abundances, particularly relevant for complex trophic interactions in a meta-ecosystem context. Our study illustrates the trophic uncoupling of proteins and PUFAs, highlighting the necessity in combining both approaches.

The monitoring and management of aquatic ecosystems depend on precise estimates of biodiversity. Metabarcoding analyses of environmental nucleic acids (eNAs), including environmental DNA (eDNA) and environmental RNA (eRNA), have garnered attention for their cost-effective and non-invasive biomonitoring capabilities. However, the accuracy of biodiversity estimates obtained through eNAs can vary among different organismal groups. Here we evaluate the performance of eDNA and eRNA metabarcoding across nine organismal groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections of the Yangtze River, China. We observe robust complementarity between eDNA and eRNA data. The relative detectability of eNAs was notably influenced by major taxonomic groups and organismal sizes, with eDNA providing more robust signals for larger organisms. Both eDNA and eRNA exhibited similar cross-sectional and longitudinal patterns. However, the detectability of larger organisms declined in eRNA metabarcoding, possibly due to differential RNA release and decay among different organismal groups or sizes. While underscoring the potential of eDNA and eRNA in large river biomonitoring, we emphasize the need for differential interpretation of eDNA versus eRNA data. This highlights the importance of careful method selection and interpretation in biomonitoring studies.

Rivers exhibit hierarchical spatial structures of habitat and physical attributes, providing directed pathways for biological population and community dynamics and thus shaping the meta-ecosystems therein. While the River Continuum Concept has generalized the spatial patterns of abiotic and biotic components along rivers, a mechanistic understanding of how river networks' shape may constrain the attributes of riverine meta-ecosystems remains lacking. Here, we address this gap with an in silico study. We integrate the Optimal Channel Network concept (and the well-established scaling of river geomorphological and hydrological attributes) with a meta-ecosystem model (with trait-based food-web dynamics and spatial dynamics of species and inorganic resources) to explore how distinct river network shapes (elongated vs. compact) may drive the spatial patterns of biodiversity and community trophic structure. We analyse metrics of biomass distribution, trophic structure and composition of locally realized food webs and show that elongated and compact networks foster very different upstream-downstream biological patterns, and even more contrasting patterns are often observed between the long and short paths of elongated networks. Overall, we observe a transition from prevailing detritus-based to nutrient-based trophic channels moving downstream, leading to peaks in alpha diversity at intermediate river size, where both channels are more balanced. Higher spatial heterogeneity in community composition and lower biomass levels are observed in elongated than in compact networks, driven by higher variability in nutrient input loads and higher water volumes, respectively. Together, our findings associate river shapes to the emergent riverine meta-ecosystems properties and help reveal the underpinning physical attributes-driven mechanisms.

The Anthropocene has driven a transformative era where human activities exert unprecedented influence on Earth's biosphere. Consequently, synanthropic organisms, adept at thriving in human-modified environments, have emerged. While well studied in terrestrial ecosystems, the presence and ecological importance of synanthropic species in aquatic ecosystems, specifically among cyanobacteria, are less understood. Cyanobacteria blooms, notorious for their detrimental effects on ecosystems and human health, are increasing in frequency and intensity globally. In this perspective, we explore the evidence supporting this rise of cyanobacteria blooms, emphasizing the roles of human-induced eutrophication and climate change on select cyanobacteria genera. Cyanobacteria are not a monolith, with certain genera showing an observable increase within anthropogenically modified environments. We propose the establishment of a new sub-branch of phycology that explicitly investigates the ecology and physiology of synanthropic cyanobacteria. Understanding the intricate interactions between synanthropic species and human populations is imperative for managing human-altered ecosystems and conserving freshwater resources, particularly in the face of increasing global water insecurity.

Practitioner Points:
• The rise in cyanobacteria blooms is driven by a small subset of human-adapted genera—synanthropic cyanobacteria.
• Research is needed to characterize synanthropic cyanobacteria, which will aid in developing tailored management approaches.
• A paradigm shift from domesticating to "rewilding" landscapes and modifying behaviors to facilitate cohabitation are solutions to reducing risks.

Ongoing global climate change will shift nature towards Anthropocene's unprecedented conditions by increasing average temperatures and the frequency and severity of extreme events, such as heatwaves. While such climatic changes pose an increased threat for freshwater ecosystems, other stressors like pesticides may interact with warming and lead to unpredictable effects. Studies that examine the underpinned mechanisms of multiple stressor effects are scarce and often lack environmental realism. Here, we conducted a multiple stressors experiment using outdoor freshwater mesocosms with natural assemblages of macroinvertebrates, zooplankton, phytoplankton, macrophytes, and microbes. The effects of the neonicotinoid insecticide imidacloprid (1 µg/L) were investigated in combination with three temperature scenarios representing ambient, elevated temperatures (+4 °C), and heatwaves (+0 to 8 °C), the latter two having similar energy input. We found similar imidacloprid dissipation patterns for all temperature treatments with lowest average dissipation half-lives under both warming scenarios (DT₅₀: 3 days) and highest under ambient temperatures (DT₅₀: 4 days) throughout the experiment. Amongst all communities, only the zooplankton community was significantly affected by the combined treatments. This community demonstrated low chemical sensitivity with lagged and significant negative imidacloprid effects only for cyclopoids. Heatwaves caused early and long-lasting significant effects on the zooplankton community as compared to elevated temperatures, with Polyarthra, Daphnia longispina, Lecanidae, and cyclopoids being the most negatively affected taxa, whereas Ceriodaphnia and nauplii showed positive responses to temperature. Community recovery from imidacloprid stress was slower under heatwaves, suggesting temperature-enhanced toxicity. Finally, microbial and macrofauna litter degradation were significantly enhanced by temperature, whereas the latter was also negatively affected by imidacloprid. A structural equation model depicted cascading food web effects of both stressors with stronger relationships and significant negative stressor effects at higher than at lower trophic levels. Our study highlights the threat of a series of heatwaves compared to elevated temperatures for imidacloprid-stressed freshwaters.

Understanding spatial patterns of biodiversity within the context of long-term climatic shifts is of high importance, particularly in the face of contemporary climate change. In comparison to aboveground taxa, subterranean organisms respond to changing climates with generally much lower dispersal and recolonization potential, yet possible persistence in refugial groundwater habitats under ice-shields. However, knowledge on general and geographically large-scale effects of glaciation on contemporary groundwater biodiversity patterns is still very limited. Here, we tested how Late Pleistocene glaciation influenced the diversity and distribution of 36 groundwater amphipod species in Alpine and peri-Alpine regions, characterized by extensive glaciation cycles, and how its legacy explains contemporary diversity patterns. We based our analysis on an unprecedented density of ~ 1000 systematic sampling sites across Switzerland. Using presence–absence data, we assessed biodiversity and species' ranges, and calculated for each site within-catchment distance to the Last Glacial Maximum (LGM) glacier extent. We then applied a sliding window approach along the obtained distance gradient from LGM ice-covered to ice-free sites to compute biodiversity indices reflecting local richness, regional richness, and differentiation, respectively. We found a strong signal of the LGM ice extent on the present-day distribution of groundwater amphipods. Our findings revealed pronounced species turnover and spatial envelopes of individual species' occurrences in formerly ice-covered, ice-free, or transitional zones, respectively. While local richness remained constant and low along the LGM distance gradient, groundwater communities in LGM ice-covered areas were more similar to each other and had lower gamma diversities and decreased occurrence probabilities per sliding window compared to communities in Pleistocene ice-free areas. These results highlight the significant impact of Pleistocene glaciation on shaping biodiversity patterns of subterranean communities and imprinting contemporary distribution of groundwater organisms.

The genus Niphargus is the most diverse subterranean amphipod genus in the western Palearctic region but, owing to the presence of cryptic species and homoplasy, its taxonomy and biogeographic scenarios are complex, making molecular methods essential to understand its evolution. We conducted a study combining dna-based taxonomy with traditional morphotaxonomy to investigate Niphargus bihorensis Schellenberg, 1940, known from the Western Alps and Carpathians. We redescribed the type material of N. bihorensis from Bihor County, Romania, and revealed the presence of a cryptic species, N. absconditus n. sp., in the same karstic area (Pădurea Craiului Mountains). Additionally, the Alpine populations previously attributed to N. bihorensis turned out to belong to a new, not so closely related species, N. tizianoi n. sp. Phylogenetic analyses based on a concatenated dataset of one mitochondrial and two nuclear markers suggest that the N. bihorensis species complex belongs to a strongly supported clade, together with several species distributed from Switzerland to Iran.

Freshwater macroinvertebrates are a diverse group and play key ecological roles, including accelerating nutrient cycling, filtering water, controlling primary producers, and providing food for predators. Their differences in tolerances and short generation times manifest in rapid community responses to change. Macroinvertebrate community composition is an indicator of water quality. In Europe, efforts to improve water quality following environmental legislation, primarily starting in the 1980s, may have driven a recovery of macroinvertebrate communities. Towards understanding temporal and spatial variation of these organisms, we compiled the TREAM dataset (Time seRies of European freshwAter Macroinvertebrates), consisting of macroinvertebrate community time series from 1,816 river and stream sites (mean length of 19.2 years and 14.9 sampling years) of 22 European countries sampled between 1968 and 2020. In total, the data include >93 million sampled individuals of 2,648 taxa from 959 genera and 212 families. These data can be used to test questions ranging from identifying drivers of the population dynamics of specific taxa to assessing the success of legislative and management restoration efforts.

Rivers and streams contribute to global carbon cycling by decomposing immense quantities of terrestrial plant matter. However, decomposition rates are highly variable and large-scale patterns and drivers of this process remain poorly understood. Using a cellulose-based assay to reflect the primary constituent of plant detritus, we generated a predictive model (81% variance explained) for cellulose decomposition rates across 514 globally distributed streams. A large number of variables were important for predicting decomposition, highlighting the complexity of this process at the global scale. Predicted cellulose decomposition rates, when combined with genus-level litter quality attributes, explain published leaf litter decomposition rates with high accuracy (70% variance explained). Our global map provides estimates of rates across vast understudied areas of Earth and reveals rapid decomposition across continental-scale areas dominated by human activities.

Insects are frequently infected with heritable bacterial endosymbionts. Some of them confer resistance to parasitoids. Such defensive symbionts are sensitive to variation in temperature. Drawing predominantly from the literature on aphids and flies, we show that temperature can affect the reliability of maternal transmission and the strength of protection provided by defensive symbionts. Costs of infection with defensive symbionts can also be temperature-dependent and may even turn into benefits under extreme temperatures, for example, when defensive symbionts increase heat tolerance. Alone or in combination, these mechanisms can drive temperature-associated (latitudinal) clines of infection prevalence with defensive symbionts. This has important consequences for host–parasitoid coevolution, as the relative importance of host-encoded vs. symbiont-provided defenses will shift along such clines.

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. Individually, both approaches are used in ecological studies to characterize biodiversity, yet they are rarely combined. Here, we integrated high-resolution habitat suitability models with eDNA-based assessments of aquatic invertebrates in riverine networks to understand their individual and combined capacity to inform on species' occurrence. We used eDNA sampling data from 172 river sites and combined the detection of taxa from three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) with suitable habitat predictions at a subcatchment level (2 km²). Overall, we find congruence of habitat suitability and eDNA-based detections. Yet, the models predicted suitable habitats beyond the number of detections by eDNA sampling, congruent with the suitable niche being larger than the realized niche. For local mismatches, where eDNA detected a species but the habitat was not predicted suitable, we calculated the minimal distance to upstream suitable habitat patches, indicating possible sources of eDNA signals from upstream sites subsequently being transported along the water flow. We estimated a median distance of 1.06 km (range 0.2–42 km) of DNA transport based on upstream habitat suitability, and this distance was significantly smaller than expected by null model predictions. This estimated transport distance is in the range of previously reported values and allows extrapolations of transport distances across many taxa and riverine systems. Together, the combination of eDNA and habitat suitability models allows larger scale and spatially integrative inferences about biodiversity, ultimately needed for the management and protection of biodiversity.

Marine heatwaves (MHWs) are episodes of anomalous warming in the ocean that can last from a few days to years. MHWs have different characteristics in terms of intensity, duration and frequency and generate thermal stress in marine ecosystems. In reef ecosystems, they are one of the main causes of the decreased presence and abundance of corals, invertebrates and fish. The deleterious capacity of thermal stress often depends on biotic factors, such as the trophic control of predators on prey. Despite the evidence of thermal stress and biotic factors affecting individual species, the combined effects of both stressors on entire reef ecosystems are much less studied. Here, using a food web modelling approach, we estimated the rate of change in species' biomass due to different MHW characteristics. Specifically, we modelled the mechanistic link between species' consumption rate and seawater temperature (thermal stressor), simulating species' biomass dynamics for different MHW characteristics under different trophic control assumptions (top-down, mixed trophic control and bottom-up). We find that total reef ecosystem biomass declined by 10% ± 5% under MHWs with severe intensity and a top-down control assumption. The bottom-up control assumption moderates the total ecosystem biomass reduction by 5% ± 5%. Irrespective of the MHW characteristics and the trophic control assumption, the most substantial biomass changes occur among top, mesopredators and corals (5% to 20% ± 10%). We show that reef ecosystems where predators exert top-down control on prey are prone to suffer species abundance declines under strong MHW events. We identify food web trophic control as a crucial driver that modulates the impacts of MHWs. Overall, our results provide a unified understanding of the interplay between abiotic stressors and biotic factors in reef ecosystems under extreme thermal events, offering insights into present baselines and future ecological states for reef ecosystems.

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20–35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Spatial truncation in species distribution models (SDMs) might cause niche truncation and model transferability issues, particularly when extrapolating models to non-analog environmental conditions. While broad calibration extents reduce truncation issues, they usually overlook local ecological factors driving species distributions at finer resolution. Spatially-nested hierarchical SDMs (HSDMs) address truncation by merging (a) a global model calibrated with broadly extended, yet typically low-resolution, basic, and imprecise data; and (b) a regional model calibrated with spatially restricted but more precise and reliable data. This study aimed to examine HSDMs' efficacy to overcome spatial truncation in national-scale studies. We compared two hierarchical strategies (‘covariate', which uses the global model output as a covariate for the regional model, and ‘multiply', which calculates the geometric mean of the global and regional models) and a non-hierarchical strategy. The three strategies were compared in terms of niche truncation, environmental extrapolation, model performance, species' predicted distributions and shifts, and trends in species richness. We examined the consistency of the results over two study areas (Spain and Switzerland), 108 tree species, and four future climate scenarios. Only the non-hierarchical strategy was susceptible to niche truncation, and environmental extrapolation issues. Hierarchical strategies, particularly the ‘covariate' one, presented greater model accuracy than non-hierarchical strategies. The non-hierarchical strategy predicted the highest overall values and the lowest decreases over time in species distribution ranges and richness. Differences between strategies were more evident in Switzerland, which was more affected by niche truncation issues. Spain was more negatively affected by climate change and environmental extrapolation. The ‘covariate' strategy exhibited higher model performance than the ‘multiply' one. However, uncertainties regarding model temporal transferability advocate for adopting and further examining multiple hierarchical approaches. This research underscores the importance of adopting spatially-nested hierarchical SDMs given the compromised reliability of non-hierarchical approaches due to niche truncation and extrapolation issues.

Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.

Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Biodiversity generally increases productivity in ecosystems; however, this is mediated by the specific functional traits that come with biodiversity loss or gain and how these traits interact with environmental conditions. Most biodiversity studies evaluate the effects of species richness alone, despite our increasing understanding that intraspecific diversity can have equally strong impacts. Here, we manipulate both species richness and intraspecific richness (i.e., number of distinct strains) in marine diatom communities to explicitly test the relative importance of species and strain richness for biomass and trait diversity in six distinct temperature/nutrient environments. We show that species and strain richness both have significant effects on biomass and growth rates, but more importantly, they interact with each other, indicating that cross-species diversity effects depend on within-species diversity and vice versa. This intertwined relationship thus calls for more integrative approaches quantifying the relative importance of distinct biodiversity components and environmental context on ecosystem functioning.

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

The success of ponds constructed to restore ecological infrastructure for pond-breeding amphibians and benefit aquatic biodiversity depends on where and how they are built. We studied effects of pond and landscape characteristics, including connectivity, on metapopulation dynamics of 12 amphibian species in Switzerland. To understand the determinants of long-term occupancy (here summarized as incidence), environmental effects on both colonization and persistence should be considered. We fitted dynamic occupancy models to 20 years of monitoring data on a pond construction program to quantify effects of pond and landscape characteristics and different connectivity metrics on colonization and persistence probabilities in constructed ponds. Connectivity to existing populations explained dynamics better than structural connectivity metrics, and simple metrics (distance to the nearest neighbor population, population density) were useful surrogates for dispersal kernel-weighted metrics commonly used in metapopulation theory. Population connectivity mediated the persistence of conservation target species in new ponds, suggesting source–sink dynamics in newly established populations. Population density captured this effect well and could be used by practitioners for site selection. Ponds created where there were 2–4 occupied ponds within a radius of ∼0.5 km had >3.5 times higher incidence of target species (median) than isolated ponds. Species had individual preferences regarding pond characteristics, but breeding sites with larger (≥100 m²) total water surface area, that temporarily dried, and that were in surroundings with maximally 50% forest benefitted multiple target species. Pond diversity will foster amphibian diversity at the landscape scale.

Changes in climate and land use represent significant risks of biodiversity loss globally, affect ecological stability, impact nature's contributions to people (NCP, i.e. ecosystem services) and compromise human livelihood. As framings of conservation evolve to consider the interdependence between species and human needs, there is a growing recognition of the importance of NCP and biodiversity in conservation actions. However, knowledge on the interactions and spatial repartition of NCP and biodiversity remains limited. Here we show a comprehensive spatial assessment for 15 NCP and one biodiversity – distribution of threatened species – indicators in Switzerland. Indicators values were computed using a panel of mapping and modelling methods extracted from the literature, or specifically developed for this study. Through the analysis of their relationships, we reveal significant trade-offs and synergies in the spatial repartition of these indicators. Results from a spatial bundle analysis performed on the 16 indicators revealed the existence of four bundles showing a heterogeneous repartition over the Swiss landscape. Furthermore, we identified that topography (slope), climate (temperature and precipitations), and habitat (forest and meadows) were among the most influential factors to explain the spatial distribution of the four bundles. We conclude that various significant relationships exist between NCP and biodiversity indicators in Switzerland, emphasizing the importance of informed conservation approaches considering both NCP and biodiversity supply. This work helps fill the gap in our understanding of the links among different NCP, between NCP and biodiversity, and highlight their relationship to climate and land use, providing key insights for optimizing conservation efforts.

Blue-green infrastructure (BGI), combining semi-natural and engineered elements, offers multifaceted benefits like stormwater management, water purification, heat mitigation, and habitat provision. However, current BGI designs prioritize engineering goals, overlooking its ecological potential. Here we advocate for integrating engineering and ecological objectives into BGI design to enhance performance and biodiversity. Through an interdisciplinary literature review, we emphasize the importance of species diversity, abundance, and ecological processes, to improve engineering performance and resilience, and lower management costs. We emphasize the importance of interdisciplinary collaboration to navigate trade-offs between engineering and ecological objectives, ultimately enabling us to engineer both for and with biodiversity.

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

The impacts of global change—from shifts in climate to overfishing to land use change—can depend heavily on local abiotic context. Building an understanding of how to downscale global change scenarios to local impacts is often difficult, however, and requires historical data across large gradients of variability. Such data are often not available—particularly in peer reviewed or gray literature. However, these data can sometimes be gleaned from casual records of natural history—field notebooks, data sheet marginalia, course notes, and more. Here, we provide an example of one such approach for the Gulf of Maine, as we seek to understand how environmental context can influence local outcomes of region-wide shifts in subtidal community structure. We explore a decade of hand-drawn algal cover maps around Appledore Island made by Dr. Art Borror while teaching at the Shoals Marine Lab. Appledore's steep wave exposure gradient—from exposed to the open ocean to fully protected—provides a living laboratory to test interactions between global change and local conditions. We then recreate Borror's methods two and a half decades later. We show that overfishing-driven urchin outbreaks in the 1980s were slowed or stopped by wave exposure and benthic topography. Similarly, local variation appears to have curtailed current invasions by filamentous red algae. Last, some formerly dominant kelps have disappeared over the past 40 years—an observation verified by subtidal surveys. Global change is altering life in the seas around us. While underutilized, solid natural history observations stand as a key resource for us to begin to understand how global change will translate to the heterogeneous mosaic of life in a future Gulf of Maine and other ecosystems around the world.

Patella caerulea (Linnaeus, 1758) is a mollusc limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered a keystone species due to its primary role in structuring and regulating the ecological balance of tidal and subtidal habitats. It is currently being used as a bioindicator to assess the environmental quality of coastal marine waters and as a model species to understand adaptation to ocean acidification. Here, we provide a high-quality reference genome assembly and annotation for P. caerulea. We generated ∼30 Gb of Pacific Biosciences high-fidelity data from a single individual and provide a final 749.8 Mb assembly containing 62 contigs, including the mitochondrial genome (14,938 bp). With an N50 of 48.8 Mb and 98% of the assembly contained in the 18 largest contigs, this assembly is near chromosome-scale. Benchmarking Universal Single-Copy Orthologs scores were high (Mollusca, 87.8% complete; Metazoa, 97.2% complete) and similar to metrics observed for other chromosome-level Patella genomes, highlighting a possible bias in the Mollusca database for Patellids. We generated transcriptomic Illumina data from a second individual collected at the same locality and used it together with protein evidence to annotate the genome. A total of 23,938 protein-coding gene models were found. By comparing this annotation with other published Patella annotations, we found that the distribution and median values of exon and gene lengths was comparable with other Patella species despite different annotation approaches. The present high-quality P. caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.

1. Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups and the assessment of ecological indices. Yet, most current approaches are not exploiting the full potential of eDNA data, largely interpreting results in a localized perspective. In riverine networks, by explicitly modelling hydrological transport and associated DNA decay, hydrology-based models enable upscaling eDNA-based diversity information, providing spatially integrated inference. To capitalize on these unprecedented biodiversity data and translate it into space-filling biodiversity projections, a streamlined implementation is needed.
2. Here, we introduce the eDITH R-package, implementing the eDITH model to project biodiversity across riverine networks with minimal prior information. eDITH couples a species distribution model relating a local taxon's eDNA shedding rate in streamwater to environmental covariates, a mass balance expressing the eDNA concentration at a river's cross-section as a weighted sum of upstream contributions, and an observational model accounting for uncertainties in eDNA measurements. By leveraging on spatially replicated eDNA measurements and minimal hydro-morphological data, eDITH enables disentangling the various upstream eDNA sources, and produces space-filling maps of a taxon's spatial distribution at any chosen resolution. eDITH is applicable to both eDNA concentration and metabarcoding data, and to any taxon whose DNA can be retrieved in streamwater.
3. The eDITH package provides user-friendly functions for single-run execution and fitting of eDITH to eDNA data with both Bayesian methods (via the BayesianTools package) and non-linear optimization. An interface to the DHARMa package allows model validation via posterior predictive checks. Necessary preliminary steps such as watershed delineation and hydrological characterization are implemented via the rivnet package. We illustrate eDITH's workflow and functionalities with two case studies from published fish eDNA data.
4. The eDITH package provides a user-friendly implementation of eDITH, specifically intended for ecologists and conservation biologists. It can be used without previous modelling knowledge but also allows customization for experienced users. Ultimately, eDITH allows upscaling eDNA biodiversity data for any river globally, transforming how state and change in biodiversity in riverine systems can be tracked at high resolution in a highly versatile manner.

The synthesis of a large body of evidence from field experiments suggests more diverse plant communities are more productive as well as more resistant to the effects of climatic extremes like drought. However, this view is strongly based on data from grasslands due to the limited empirical evidence from tree diversity experiments. Here we report on the relationship between tree diversity and productivity over 10 years in a field experiment established in 2005 that was then affected by the 2018 mega-drought in central Europe. Across a number of years, tree species diversity and productivity were significantly positively related; however, the slope switched to negative in the year of the drought. Net diversity effects increased through time, with complementarity effects making greater contributions to the net diversity effect than selection effects. Complementarity effects were clearly positive in three- and five-species mixtures before the drought (2012–2016) but were found to decrease in the year of the drought. Selection effects were clearly positive in 2016 and remained positive in the drought year 2018 in two-, three-, and five-species mixtures. The survival of Norway spruce (Picea abies) plummeted in response to the drought, and a negative relationship between species diversity and spruce survival was found. Taken together, our findings suggest that tree diversity per se may not buffer communities against the impacts of extreme drought and that tree species composition and the drought tolerance of tree species (i.e., species identity) will be important determinants of community productivity as the prevalence of drought increases.

99 Schweizer Bäche wurden anhand der beiden Bioindikatoren Fische und Makrozoobenthos untersucht. Die Mehrzahl der Bäche zeigt wesentliche Defizite beim ökologischen Zustand. So fehlen beispielsweise in über 70% der Gewässer ein Teil der pestizidempfindlichen Insektenlarven und andere Kleinlebewesen. Statistische Auswertungen deuten darauf hin, dass sich eine beeinträchtigte Ökomorphologie sowie ein grosser Anteil Ackerland, Obstkulturen und Reben im Einzugsgebiet besonders negativ auf das Vorkommen dieser empfindlichen Kleinlebewesen auswirken.

Invasive species are pervasive around the world and have profound impacts on the ecosystem they invade. Invasive species, however, can also have impacts beyond the ecosystem they invade by altering the flow of non-living materials (for example, nutrients or chemicals) or movement of organisms across the boundaries of the invaded ecosystem. Cross-ecosystem interactions via spatial flows are ubiquitous in nature, for example, connecting forests and lakes, grasslands and rivers, and coral reefs and the deep ocean. Yet, we have a limited understanding of the cross-ecosystem impacts invasive species have relative to their local effects. By synthesizing emerging evidence, here we demonstrate the cross-ecosystem impacts of invasive species as a ubiquitous phenomenon that influences biodiversity and ecosystem functioning around the world. We identify three primary ways by which invasive species have cross-ecosystem effects: first, by altering the magnitude of spatial flows across ecosystem boundaries; second, by altering the quality of spatial flows; and third, by introducing novel spatial flows. Ultimately, the strong impacts invasive species can drive across ecosystem boundaries suggests the need for a paradigm shift in how we study and manage invasive species around the world, expanding from a local to a cross-ecosystem perspective.

Moths and other insects are attracted by artificial light sources. This flight-to-light behaviour disrupts their general activity focused on finding resources, such as mating partners, and increases predation risk. It thus has substantial fitness costs. In illuminated urban areas, spindle ermine moths Yponomeuta cagnagella were reported to have evolved a reduced flight-to-light response. Yet, the specific mechanism remained unknown, and was hypothesized to involve either changes in visual perception or general flight ability or overall mobility traits. Here, we test whether spindle ermine moths from urban and rural populations—with known differences in flight-to-light responses—differ in flight-related morphological traits. Urban individuals were found to have on average smaller wings than rural moths, which in turn correlated with a lower probability of being attracted to an artificial light source. Our finding supports the reduced mobility hypothesis, which states that reduced mobility in urban areas is associated with specific morphological changes in the flight apparatus.

How barriers to gene flow arise and are maintained are key questions in evolutionary biology. Speciation research has mainly focused on barriers that occur either before mating or after zygote formation. In comparison, postmating prezygotic (PMPZ) isolation—a barrier that acts after gamete release but before zygote formation—is less frequently investigated but may hold a unique role in generating biodiversity. Here we discuss the distinctive features of PMPZ isolation, including the primary drivers and molecular mechanisms underpinning PMPZ isolation. We then present the first comprehensive survey of PMPZ isolation research, revealing that it is a widespread form of prezygotic isolation across eukaryotes. The survey also exposes obstacles in studying PMPZ isolation, in part attributable to the challenges involved in directly measuring PMPZ isolation and uncovering its causal mechanisms. Finally, we identify outstanding knowledge gaps and provide recommendations for improving future research on PMPZ isolation. This will allow us to better understand the nature of this often-neglected reproductive barrier and its contribution to speciation.

Plant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems.

Although the general impacts of zooplankton grazing on phytoplankton communities are clear, we know comparatively less about how specific grazing strategies interact with environmental conditions to shape the size structure of phytoplankton communities. Here, we present a new data-driven, size-based model that describes changes in the size composition of lake phytoplankton under various environmental constraints. The model includes an ecological trade-off emerging from observed allometric relationships between (1) phytoplankton cell size and phytoplankton growth and (2) phytoplankton cell size and zooplankton grazing. In our model, phytoplankton growth is nutrient-dependent and zooplankton grazing varies according to specific grazing strategies, namely, specialists (targeting a narrow range of the size-feeding spectrum) vs. generalists (targeting a wide range of the size-feeding spectrum). Our results indicate that grazing strategies shape the size composition of the phytoplankton community in nutrient-rich conditions, whereas inorganic nutrient concentrations govern phytoplankton biomass. Under oligotrophic regimes, the phytoplankton community is dominated by small cell sizes and the grazers have little to no impact. Under eutrophic regimes, dominating specialist grazers push phytoplankton towards small cells, whereas dominating generalist grazers push phytoplankton towards large cells. Our work highlights that trait-based modeling, based on realistic eco-physiological trade-offs, represents a valuable tool for disentangling the interactive roles played by nutrient regimes and grazing strategies in determining the size compositions of lake phytoplankton. Ultimately, our study offers a quantitative basis for understanding how communities of lake phytoplankton may reorganize in the future in response to changes in nutrient levels and zooplankton grazing strategies.

How does diversity in nature come about? One factor contributing to this diversity are species interactions; diversity on one trophic level can shape diversity on lower or higher trophic levels. For example, parasite diversity enhances host immune diversity. Insect protective symbionts mediate host resistance and are, therefore, also engaged in reciprocal selection with their host's parasites. Here, we applied experimental evolution in a well-known symbiont-aphid-parasitoid system to study whether parasitoid diversity contributes to maintaining symbiont genetic diversity. We used caged populations of black bean aphids (Aphis fabae), containing uninfected individuals and individuals infected with different strains of the bacterial endosymbiont Hamiltonella defensa, which protects aphids against parasitoids. Over multiple generations, these populations were exposed to three different species of parasitoid wasps (Aphidius colemani, Binodoxys acalephae or Lysiphlebus fabarum), simultaneous or sequential mixtures of these species or no wasps. Surprisingly, we observed little selection for H. defensa in most treatments, even when it clearly provided protection against a fatal parasitoid infection. This seemed to be caused by high induced costs of resistance: aphids surviving parasitoid attacks suffered an extreme reduction in fitness. In marked contrast to previous studies looking at the effect of different genotypes of a single parasitoid species, we found little evidence for a diversifying effect of multiple parasitoid species on symbiont diversity in hosts.

Die noch wenig bekannte Grundwasserfauna ist ein bedeutender Bestandteil der Biodiversität und trägt zum Funktionieren der Grundwasserökosysteme bei. Mittels Proben aus der ganzen Schweiz wurde erstmals ein Überblick über die Vielfalt und Biomasse von Makroinvertebraten in Grundwasserökosystemen der Schweiz erarbeitet. Eine hohe Diversität an ober- und unterirdischen Makroinvertebraten im Grundwasser weist auf die Wechselwirkungen zwischen Oberfläche und Grundwasser hin.

Die Quaggamuschel wurde 2015 erstmalig im Genfersee nachgewiesen. Seitdem hat sich
diese ursprünglich aus dem Dnepr stammende invasive Art in den voralpinen Seen rasant ausgebreitet. Was bedeutet das für die Ökosysteme und die regionale Wasserversorgung?

Rising temperatures are leading to increased prevalence of warm-affinity species in ecosystems, known as thermophilisation. However, factors influencing variation in thermophilisation rates among taxa and ecosystems, particularly freshwater communities with high diversity and high population decline, remain unclear. We analysed compositional change over time in 7123 freshwater and 6201 terrestrial, mostly temperate communities from multiple taxonomic groups. Overall, temperature change was positively linked to thermophilisation in both realms. Extirpated species had lower thermal affinities in terrestrial communities but higher affinities in freshwater communities compared to those persisting over time. Temperature change’s impact on thermophilisation varied with community body size, thermal niche breadth, species richness and baseline temperature; these interactive effects were idiosyncratic in the direction and magnitude of their impacts on thermophilisation, both across realms and taxonomic groups. While our findings emphasise the challenges in predicting the consequences of temperature change across communities, conservation strategies should consider these variable responses when attempting to mitigate climate-induced biodiversity loss.

Facing climate change and biodiversity loss, it is critical that ecology advances so that processes, such as species interactions and dynamics, can be correctly estimated and skillfully forecasted. As different processes occur on different time scales, the sampling frequency used to record them should intuitively match these scales. Yet, the effect of data sampling frequency on ecological forecasting accuracy is understudied. Using a simple simulated dataset as a baseline and a more complex high-frequency plankton dataset, we tested how different sampling frequencies impacted abundance forecasts of different plankton classes and the estimation of their interactions. We then investigated whether plankton growth rates and body sizes could be used to select the most appropriate sampling frequency. The simple simulated dataset showed that the optimal sampling frequency scaled positively with growth rate. This finding was not repeated in the analyses of the plankton time series, however. There, we found that a reduction in sampling frequency worsened forecasts and led us to both over- and underestimate plankton interactions. This suggests that forecasting can be used to determine the ideal sampling frequency in scientific and monitoring programs. A better study design will improve theoretical understanding of ecology and advance policy measures dealing with current global challenges.

Aim: Climate is a major driver of large-scale variability in biodiversity, as a likely result of more intense biotic interactions under warmer conditions. This idea fuelled decades of research on plant-herbivore interactions, but much less is known about higher-level trophic interactions. We addressed this research gap by characterizing both bird diversity and avian predation along a climatic gradient at the European scale.
Location: Europe.
Taxon: Insectivorous birds and pedunculate oaks. Methods: We deployed plasticine caterpillars in 138 oak trees in 47 sites along a 19° latitudinal gradient in Europe to quantify bird insectivory through predation attempts. In addition, we used passive acoustic monitoring to (i) characterize the acoustic diversity of surrounding soundscapes; (ii) approximate bird abundance and activity through passive acoustic recordings; and (iii) infer both taxonomic and functional diversity of insectivorous birds from recordings.
Results: The functional diversity of insectivorous birds increased with warmer climates. Bird predation increased with forest cover and bird acoustic activity but decreased with mean annual temperature and functional richness of insectivorous birds. Contrary to our predictions, climatic clines in bird predation attempts were not directly mediated by changes in insectivorous bird diversity or acoustic activity, but climate and habitat still had independent effects on predation attempts.
Main Conclusions: Our study supports the hypothesis of an increase in the diversity of insectivorous birds towards warmer climates but refutes the idea that an increase in diversity would lead to more predation and advocates for better accounting for activity and abundance of insectivorous birds when studying the large-scale variation in insect-tree interactions.

Rivers are an important component of the global carbon cycle and contribute to atmospheric carbon exchange disproportionately to their total surface area. Largely, this is because rivers efficiently mobilize, transport and metabolize terrigenous organic matter (OM). Notably, our knowledge about the magnitude of globally relevant carbon fluxes strongly contrasts with our lack of understanding of the underlying processes that transform OM. Ultimately, OM processing en route to the oceans results from a diverse assemblage of consumers interacting with an equally diverse pool of resources in a spatially complex network of heterogeneous riverine habitats. To understand this interaction between consumers and OM, we must therefore account for spatial configuration, connectivity, and landscape context at scales ranging from local ecosystems to entire networks. Building such a spatially explicit framework of fluvial OM processing across scales may also help us to better predict poorly understood anthropogenic impacts on fluvial carbon cycling, for instance human-induced fragmentation and changes to flow regimes, including intermittence. Moreover, this framework must also account for the current unprecedented human-driven loss of biodiversity. This loss is at least partly due to mechanisms operating across spatial scales, such as interference with migration and habitat homogenization, and comes with largely unknown functional consequences. We advocate here for a comprehensive framework for fluvial networks connecting two spatially aware but disparate lines of research on (i) riverine metacommunities and biodiversity, and (ii) the biogeochemistry of rivers and their contribution to the global carbon cycle. We argue for a research agenda focusing on the regional scale—that is, of the entire river network—to enable a deeper mechanistic understanding of naturally arising biodiversity–ecosystem functioning coupling as a major driver of biogeochemically relevant riverine carbon fluxes.

Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape-scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co-occur with arctic char. Overall, our results illustrate how trait variation of predators, alongside other ecosystem properties, can influence the composition of prey communities in nature.

Increasing temperatures caused by anthropogenic climate change are leading to changes in the composition of local communities across biomes. This has implications for ecological assessment methods that rely on macroinvertebrates as bioindicators of water quality. To investigate the influence of changing water temperature on these assessment methods, we analysed macroinvertebrate data from Swiss national monitoring programs. We used a species distribution model to simulate temperature change effects on macroinvertebrate communities and estimated the resulting changes on three biological indices commonly used in Switzerland, namely the species richness of Ephemeroptera, Plecoptera and Trichoptera (EPT), the Swiss biological (IBCH) index along with its components, as well as the species at risk pesticides (SPEAR_pesticides) index. While results vary by temperature scenario and index, our model results for the most realistic water temperature increase scenario of + 2 °C across most sites in Switzerland suggest no, or only a minor, influence of temperature (not accounting for other hydrological changes). Our model projection predicted only a small increase in the probability of occurrence for 70 % of the studied families. The sensitivity to temperature as captured in our model is generally not very high and varies among the biological indices: on average across all sites, a + 2 °C increase in temperature resulted in a 7 % increase in EPT species richness, a 4 % increase in the IBCH index, and a less than 1 % increase in the SPEAR_pesticides index. Our study suggests the robustness of these biological indices to moderate warming and points towards the usefulness of these biological indices for the next few decades as tools for water quality assessment. Despite some limitations of statistical species distribution models (e.g., not accounting for dispersal limitation or biotic interactions, predictive performance varying by taxon), the study provides valuable insights into the complex relationships between environmental factors and macroinvertebrate communities, and the potential impacts of future temperature change. These findings can inform conservation and management efforts for these important ecological systems.

Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.

The EU Nature Restoration Law represents an important opportunity for freshwater habitat restoration and, consequently, freshwater biodiversity protection. However, a number of challenges must be anticipated in its implementation, which may compromise its success. Some aspects, particularly those relating to freshwater ecosystems, require more clarification. We use riverine ecosystems to illustrate existing ambiguities in the proposed legislation and the potential consequences of leaving these aspects open to interpretation during the implementation process. We also discuss potential solutions to these problems which could help ensure that the law's objectives are met. We argue that river network structure and connectivity dimensions, which result into river meta-ecosystems, must be explicitly considered. For that purpose, we ask for clear definitions of the critical terms "free-flowing rivers," "barriers," and "reference areas." In addition, we recommend developing methods for integrated assessment of connectivity across river networks. As a key property of river ecosystems, this must be used to prioritize actions to increase the length and number of free-flowing rivers. Adequate restoration planning at larger spatial scales will benefit from a meta-ecosystem perspective and accurate representation of aquatic-terrestrial linkages, which will significantly improve the efficacy of restoration efforts. Furthermore, stakeholder and citizen engagement offer important opportunities at local, national, and European scales, and should be fostered to ensure inclusive decision-making. The conservation challenges outlined here are particularly important for rivers, but they also have implications for other ecosystems. These considerations are useful for policymakers, conservationists, and other stakeholders involved in the Nature Restoration Law and related policy initiatives.

Host–parasite coevolution is mediated by genetic interactions between the antagonists and may lead to reciprocal adaptation. In the black bean aphid, Aphis fabae fabae, resistance to parasitoids can be conferred by the heritable bacterial endosymbiont Hamiltonella defensa. H. defensa has been shown to be variably protective against different parasitoid species, and different genotypes of the black bean aphid's main parasitoid Lysiphlebus fabarum. However, these results were obtained using haphazard combinations of laboratory-reared insect lines with different origins, making it unclear how representative they are of natural, locally (co)adapted communities. We therefore comprehensively sampled the parasitoids of a natural A. f. fabae population and measured the ability of the five most abundant species to parasitize aphids carrying the locally prevalent H. defensa haplotypes. H. defensa provided resistance only against the dominant parasitoid L. fabarum (70% of all parasitoids), but not against less abundant parasitoids, and resistance to L. fabarum acted in a genotype-specific manner (G × G interactions between H. defensa and L. fabarum). These results confirm that strong species- and genotype-specificity of symbiont-conferred resistance is indeed a hallmark of wild A. f. fabae populations, and they are consistent with symbiont-mediated adaptation of aphids to the parasitoids posing the highest risk.

Subterranean ecosystems (comprising terrestrial, semi-aquatic, and aquatic components) are increasingly threatened by human activities; however, the current network of surface-protected areas is inadequate to safeguard subterranean biodiversity. Establishing protected areas for subterranean ecosystems is challenging. First, there are technical obstacles in mapping three-dimensional ecosystems with uncertain boundaries. Second, the rarity and endemism of subterranean organisms, combined with a scarcity of taxonomists, delays the accumulation of essential biodiversity knowledge. Third, establishing agreements to preserve subterranean ecosystems requires collaboration among multiple actors with often competing interests. This perspective addresses the challenges of preserving subterranean biodiversity through protected areas. Even in the face of uncertainties, we suggest it is both timely and critical to assess general criteria for subterranean biodiversity protection and implement them based on precautionary principles. To this end, we examine the current status of European protected areas and discuss solutions to improve their coverage of subterranean ecosystems.

Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.

Aim: The spatial-structural patterns of plant-insect interaction networks, particularly their associations with landscape-scale environmental factors, remain poorly understood. We apply data-driven network constructions that integrate biogeographic and trophic interaction knowledge to uncover how Lepidoptera-plant networks vary across environmental gradients in a real-world landscape.
Location: The 36,000 km² German state Baden-Württemberg, Central Europe. Taxon: Lepidoptera insects and angiosperm plants.
Materials and Methods: We integrated extensive data of Lepidoptera-plant occurrences and interactions to infer local interaction networks across Baden-Württemberg, encompassing 3148 plant and 980 Lepidoptera species, covering butterflies, Noctuoid moths, Geometrid moths, and Bombycoid moths. We quantified clade- and life-stage-specific network structures and related them to GIS-informed environmental conditions, thereby revealing the spatial (environmental) patterns and potential drivers of network variations. Results: Spanning shared environmental gradients, Lepidoptera clades and life stages formed various interaction structures with plants and exhibit distinct spatial-structural patterns. For all Lepidoptera groups, except Geometrid moths, potential diet across life stages broadened toward low-elevation farmlands. The larval and adult networks of butterflies became less modular with farmland coverage; the same for adult Noctuoid moths, but the inverse for adult Geometrid moths. With increasing elevation, the larval and adult networks of Noctuoid moths became less and more modular, respectively, whereas Geometrid adult networks became more modular. While the adult dietary niche of butterflies overlapped more at low elevation, those of Noctuoid and Geometrid moths further associated with land cover and overlapped more toward low- and high-elevation farmlands, respectively.
Main Conclusions: The spatial-structural patterns of Lepidoptera-plant networks vary along geo-climate and land-cover gradients in ways depending on the Lepidoptera's clade and life stage. The driving mechanisms likely include both evolutionary (e.g., resource-consumer [co-]evolution) and ecological (e.g., competitive exclusion) processes, and differentially affect Lepidoptera across clades and life stages. These findings pinpoint conservation implications at both species and community levels, with potential trade-offs for managing different Lepidoptera-plant communities under environmental changes.

The logistic growth model is one of the most frequently used formalizations of density dependence affecting population growth, persistence and evolution. Ecological and evolutionary theory, and applications to understand population change over time often include this model. However, the assumptions and limitations of this popular model are often not well appreciated. Here, we briefly review past use of the logistic growth model and highlight limitations by deriving population growth models from underlying consumer–resource dynamics. We show that the logistic equation likely is not applicable to many biological systems. Rather, density-regulation functions are usually non-linear and may exhibit convex or concave curvatures depending on the biology of resources and consumers. In simple cases, the dynamics can be fully described by the Schoener model. More complex consumer dynamics show similarities to a Maynard Smith–Slatkin model. We show how population-level parameters, such as intrinsic rates of increase and equilibrium population densities are not independent, as often assumed. Rather, they are functions of the same underlying parameters. The commonly assumed positive relationship between equilibrium population density and competitive ability is typically invalid. We propose simple relationships between intrinsic rates of increase and equilibrium population densities that capture the essence of different consumer–resource systems. Relating population level models to underlying mechanisms allows us to discuss applications to evolutionary outcomes and how these models depend on environmental conditions, like temperature via metabolic scaling. Finally, we use time-series from microbial food chains to fit population growth models as a test case for our theoretical predictions. Our results show that density-regulation functions need to be chosen carefully as their shapes will depend on the study system's biology. Importantly, we provide a mechanistic understanding of relationships between model parameters, which has implications for theory and for formulating biologically sound and empirically testable predictions.

In times of rapid environmental changes, baseline biodiversity data are crucial for management. In freshwaters, fish inventories are commonly based on the capture and morphological identification of specimens. The sampling of environmental DNA (eDNA) provides an alternative to assess diversity across large catchments. Here, we used extensive historic data of fish communities collected across 89 river sites in all major catchments of Switzerland and compared their diversity and community composition to a single campaign of eDNA and electrofishing, respectively. Locally, we found that eDNA provided diversity estimates similar to the integrated historic richness, while the electrofishing campaign captured a significantly lower local richness. Fish species locally recorded by electrofishing were nested (Jaccard's dissimilarity index) within the respective eDNA community for most sites. Finally, eDNA sequence reads positively correlated with the overall electrofishing biomass. Despite the congruences, the eDNA data did not correlate well with the electrofishing water quality index. Overall, eDNA was more accurately assessing overall diversity than a simultaneous electrofishing campaign, but yet cannot be directly used to calculate fish-based water quality indices.

Numerous biodiversity–ecosystem functioning (BEF) experiments have shown that plant community productivity typically increases with species diversity. In these studies, diversity is generally quantified using metrics of taxonomic, phylogenetic, or functional differences among community members. Research has also shown that the relationships between species diversity and functioning depends on the spatial scale considered, primarily because larger areas may contain different ecosystem types and span gradients in environmental conditions, which result in a turnover of the species set present locally. A fact that has received little attention, however, is that ecological systems are hierarchically structured, from genes to individuals to communities to entire landscapes, and that additional biological variation occurs at levels of organization above and below those typically considered in BEF research. Here, we present cases of diversity effects at different hierarchical levels of organization and compare these to the species-diversity effects traditionally studied. We argue that when this evidence is combined across levels, a general framework emerges that allows the transfer of insights and concepts between traditionally disparate disciplines. Such a framework presents an important step towards a better understanding of the functional importance of diversity in complex, real-world systems.

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

Human activities have facilitated the invasion of freshwater ecosystems by various organisms. Especially, invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae, and colonize various substrates. They have invaded various waterbodies across the Northern Hemisphere. In Central Europe, they have invaded multiple large and deep perialpine lakes with first recordings in Lake Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, quagga mussels quickly colonized the littoral zone but are also abundant deeper (>80 m), where they are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes, and all populations showed high genetic diversity and effective population size. In Lake Constance, we detected no genetic differentiation amongst quagga mussels sampled across different sites and depth habitats. We also did not identify any convincing candidate loci evidential for adaptation along a depth gradient and a transplant experiment showed no indications of local adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than local adaptation to depth. In conclusion, our ddRAD approach revealed insight into the establishment of genetically distinct quagga mussel populations in three perialpine lakes and suggests that phenotypic plasticity and life history traits (broadcast spawner with high fecundity and dispersing pelagic larvae) facilitate the fast spread and colonization of various depth habitats by the quagga mussel.

Biodiversity loss in river ecosystems is much faster and more severe than in terrestrial systems, and spatial conservation and restoration plans are needed to halt this erosion. Reliable and highly resolved data on the state of and change in biodiversity and species distributions are critical for effective measures. However, high-resolution maps of fish distribution remain limited for large riverine systems. Coupling data from global satellite sensors with broad-scale environmental DNA (eDNA) and machine learning could enable rapid and precise mapping of the distribution of river organisms. Here, we investigated the potential for combining these methods using a fish eDNA dataset from 110 sites sampled along the full length of the Rhone River in Switzerland and France. Using Sentinel 2 and Landsat 8 images, we generated a set of ecological variables describing both the aquatic and the terrestrial habitats surrounding the river corridor. We combined these variables with eDNA-based presence and absence data on 29 fish species and used three machine-learning models to assess environmental suitability for these species. Most models showed good performance, indicating that ecological variables derived from remote sensing can approximate the ecological determinants of fish species distributions, but water-derived variables had stronger associations than the terrestrial variables surrounding the river. The species range mapping indicated a significant transition in the species occupancy along the Rhone, from its source in the Swiss Alps to outlet into the Mediterranean Sea in southern France. Our study demonstrates the feasibility of combining remote sensing and eDNA to map species distributions in a large river. This method can be expanded to any large river to support conservation schemes.

Catchment urbanisation results in urban streams being exposed to a multitude of stressors. Notably, stressors originating from diffuse sources have received less attention than stressors originating from point sources. Here, advances related to diffuse urban stressors and their consequences for stream benthic communities are summarised by reviewing 92 articles. Based on the search criteria, the number of articles dealing with diffuse urban stressors in streams has been increasing, and most of them focused on North America, Europe, and China. Land use was the most common measure used to characterize diffuse stressor sources in urban streams (70.7 % of the articles characterised land use), and chemical stressors (inorganic nutrients, xenobiotics, metals, and water properties, including pH and conductivity) were more frequently reported than physical or biological stressors. A total of 53.3 % of the articles addressed the impact of urban stressors on macroinvertebrates, while 35.9 % focused on bacteria, 9.8 % on fungi, and 8.7 % on algae. Regarding ecosystem functions, almost half of the articles (43.5 %) addressed changes in community dynamics, 40.3 % addressed organic matter decomposition, and 33.9 % addressed nutrient cycling. When comparing urban and non-urban streams, the reviewed studies suggest that urbanisation negatively impacts the diversity of benthic organisms, leading to shifts in community composition. These changes imply functional degradation of streams. The results of the present review summarise the knowledge gained to date and identify its main gaps to help improve our understanding of urban streams.

La urbanización de las cuencas expone a los arroyos urbanos a multitud de factores de estrés. Destacan aquellos que tienen su origen en fuentes difusas, los cuales han recibido menos atención que aquellos estresores procedentes de fuentes puntuales. Este estudio resume los avances relacionados con los estresores urbanos difusos y sus consecuencias para las comunidades bentónicas fluviales, a partir de la revisión de 92 artículos. En base a los criterios de búsqueda, el número de artículos que tratan sobre estresores urbanos difusos en arroyos ha ido en aumento, la mayoría de ellos centrados en América del Norte, Europa y China. Los usos del suelo fueron la variable más utilizada para caracterizar las fuentes difusas de estrés (el 70.7 % de los artículos caracterizó los usos del suelo), y los factores de estrés químico (nutrientes inorgánicos o propiedades del agua, como pH o conductividad) se mencionaron con más frecuencia que los factores de estrés físico o biológico. El 53.3 % de los trabajos abordaron el impacto de los estresores urbanos difusos sobre los macroinvertebrados, mientras que el 35.9 % se centraron en bacterias, el 9.8 % en hongos y el 8.7 % en algas. En cuanto al funcionamiento de los ecosistemas, prácticamente la mitad de los trabajos (43.5 %) analizó cambios en la dinámica de las comunidades, el 40.3 % en la descomposición de materia orgánica y el 33.9 % en los ciclos de los nutrientes. Al comparar los arroyos urbanos y no urbanos, los trabajos revisados sugieren que la urbanización afecta negativamente a la diversidad de organismos bentónicos, provocando cambios en la composición de la comunidad. Estos cambios implican la degradación funcional de los arroyos. Los resultados de la presente revisión resumen los conocimientos adquiridos hasta hoy e identifican sus principales carencias a fin de ayudar a mejorar nuestra comprensión de los arroyos urbanos.

Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly, and invasive capture and examination of host species, and require specialized expertise for every host and pathogen of interest. Environmental DNA could provide simultaneous occurrence data for multiple pathogens across different host taxa, valuable for using parasite diversity as, for example, a bioindicator of ecosystem disturbance. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica, and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co-detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA-based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA-based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA-based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

Predicting contemporary and future species distributions is relevant for science and decision making, yet the development of high-resolution spatial predictions for numerous taxonomic groups and regions is limited by the scalability of available modelling tools. Uniting species distribution modelling (SDM) techniques into one high-performance computing (HPC) pipeline, we developed N-SDM, an SDM platform aimed at delivering reproducible outputs for standard biodiversity assessments. N-SDM was built around a spatially-nested framework, intended at facilitating the combined use of species occurrence data retrieved from multiple sources and at various spatial scales. N-SDM allows combining two models fitted with species and covariate data retrieved from global to regional scales, which is useful for addressing the issue of spatial niche truncation. The set of state-of-the-art SDM features embodied in N-SDM includes a newly devised covariate selection procedure, five modelling algorithms, an algorithm-specific hyperparameter grid search, and the ensemble of small-models approach. N-SDM is designed to be run on HPC environments, allowing the parallel processing of thousands of species at the same time. All the information required for installing and running N-SDM is openly available on the GitHub repository https://github.com/N-SDM/N-SDM.

1. Selecting the best subset of covariates out of a panel of many candidates is a key and highly influential stage of the species distribution modelling process. Yet, there is currently no commonly accepted and widely adopted standard approach by which to perform this selection.
2. We introduce a two-step "embedded" covariate selection procedure aimed at optimizing the predictive ability and parsimony of species distribution models fitted in a context of high-dimensional candidate covariate space. The procedure combines a collinearity-filtering algorithm (Step A) with three model-specific embedded regularization techniques (Step B), including generalized linear model with elastic net regularization, generalized additive model with null-space penalization, and guided regularized random forest.
3. We evaluated the embedded covariate selection procedure through an example application aimed at modelling the habitat suitability of 50 species in Switzerland from a suite of 123 candidate covariates. We demonstrated the ability of the embedded covariate selection procedure to provide significantly more accurate species distribution models as compared to models obtained with alternative procedures. Model performance was independent of the characteristics of the species data, such as the number of occurrence records or their spatial distribution across the study area.
4. We implemented and streamlined our embedded covariate selection procedure in the covsel R package, paving the way for a ready-to-use, automated, covariate selection tool that was missing in the field of species distribution modelling. All the information required for installing and running the covsel R package is openly available on the GitHub repository https://github.com/N-SDM/covsel.

Während fünfeinhalb Jahren untersuchten Forschende aus den drei Bodenseeländern den Einfluss und die Wechselwirkung verschiedener Stressfaktoren wie Nährstoffänderungen, invasive Arten und Klimawandel auf das Ökosystem des Sees. Der aktuelle Wandel ist tiefgreifend und mit voraussichtlich weitreichenden Folgen für das komplexe Ökosystemgefüge und die Gewässernutzenden. Am 13. und 14. Juni 2023 schliesst das Projekt mit einem wissenschaftlichen Symposium und einer Informationsveranstaltung für die Praxis ab.

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision-making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long-term plausibility and comparability.

Amphipods are among the most abundant macroinvertebrates in freshwater ecosystems of the Palaearctic and crucial for ecosystem functioning. Furthermore, their high sensitivity to environmental change and pollutants makes them widely used model organisms in environmental sciences and ecotoxicology. In field studies and surveys across Eurasia, species of the genus Gammarus are commonly used, yet laboratory-based studies and ecotoxicological tests are often restricted to the in most parts of the world non-native Hyalella azteca, as Gammarus is much harder to breed and maintain under laboratory conditions. However, for direct comparisons and extrapolations of results of field- vs. laboratory-based studies, the use of the same species would be desirable. Here, we investigated different settings with respect to feeding, shelter and day length to successfully increase survival, juvenile production and their respective growth and survival, and ultimately multi-generation breeding of the amphipod Gammarus fossarum. Amphipod populations persisted and reproduced successfully under optimized husbandry conditions for 12 months and were partially maintained for another year in populations up to a few hundred individuals. Specifically, supplementing diet with protein-rich food sources as well as the provisioning of shelters improved survival rate of G. fossarum significantly. However, we found no significant effect of different day length treatments on the overall relative reproductive activity or on the total amphipod abundance maintained. We conclude that G. fossarum can be kept and reared under standardized conditions. Despite the longer generation times of G. fossarum and higher effort required for maintenance compared to H. azteca, direct ecological relevance and comparability of results to natural systems may justify its future use and development as a study organism for environmental sciences and ecotoxicology.

Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTU) approach of our raw reads and assigned it taxonomically (i) in combination with publicly available reference sequences (open databases) or (ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database. Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.

South America is home to the highest freshwater fish biodiversity on Earth, and the hotspot of species richness is located in the western Amazon basin. The location of this hotspot is enigmatic, as it is inconsistent with the pattern observed in river systems across the world of increasing species richness towards a river’s mouth. Here we investigate the role of river capture events caused by Andean mountain building and repeated episodes of flooding in western Amazonia in shaping the modern-day richness pattern of freshwater fishes in South America, and in Amazonia in particular. To this end, we combine a reconstruction of river networks since 80 Ma with a mechanistic model simulating dispersal, allopatric speciation and extinction over the dynamic landscape of rivers and lakes. We show that Andean mountain building and consequent numerous small river capture events in western Amazonia caused freshwater habitats to be highly dynamic, leading to high diversification rates and exceptional richness. The history of marine incursions and lakes, including the Miocene Pebas mega-wetland system in western Amazonia, played a secondary role.

1. Fragmentation of habitat, for example by intensive agricultural practices, can be detrimental to local biodiversity. However, it often remains unclear whether such biodiversity declines are caused by loss of habitat area or increased fragmentation, and how habitat quality factors into it. In our study system, vegetated vineyards are typically small, and isolated from one another, potentially limiting the distribution and dispersal of organisms.
2. In a full-factorial experiment of a priori selected vegetated vineyard patches of differing size and fragmentation, we aimed to disentangle the effects of habitat area (area of vegetated vineyards), habitat fragmentation (number of vegetated vineyards per 100 ha) and field-scale ground vegetation density on ground beetle, leafhopper and wild bee communities using a combined framework of multiscale and multispecies modelling (Hierarchical Model of Species Communities).
3. We demonstrate variable effects of habitat area, fragmentation and local ground vegetation density on the three insect groups: Increased habitat area at fine scales favours higher species richness of leafhoppers, while local vegetation density boosts species richness of both leafhoppers and ground beetles, whereas no community-level responses were detected for wild bees.
4. We conclude that increased ground vegetation density at both field and landscape scales (i.e. higher habitat area) favours more diverse and abundant insect communities, while fragmentation effects are highly variable and species specific. In addition, our results highlight that mainly ground beetles and leafhoppers will benefit from simple ground greening measures in vineyards, while for wild bees environmental factors other than the ones tested here may drive community structure.
5. We recommend increasing the number and area of vegetated vineyards (even at small spatial scales) requiring more nature-friendly farming practices especially regarding a reduction or renunciation from herbicide applications, while the within-field vegetation density should optimally be intermediate or high to favour a diverse insect community.

Reliable biodiversity data are crucial for environmental research and management. Unfortunately, data paucity prevails for many regions and organismal groups such as aquatic invertebrates. High-throughput DNA-based identification, in particular DNA metabarcoding, has accelerated biodiversity data generation. However, in the process of metabarcoding, specimens are usually destroyed, precluding later specimen-based analyses. Metabarcoding of DNA released into the preservative ethanol has been proposed as a non-destructive alternative, but proof-of-principle studies have yielded ambiguous results, reporting variance in detection probability for various taxa and methodological biases. In this study, we tested the performance of preservative-based metabarcoding of aquatic invertebrates in comparison to a standard morpho-taxonomic assessment based on samples from one of Europe’s last free-flowing rivers, the Vjosa. Multi-habitat samples were collected at 43 sites in two seasons and stored in ethanol, after fixation in formaldehyde for morpho-taxonomic analyses. Preservative-based DNA metabarcoding detected three times more taxa but failed to detect other taxa found using the standard method. In addition to incomplete reference data and primer bias that likely precluded the detection of specific taxa, preservative-based DNA metabarcoding cannot provide accurate abundance estimates. However, the metabarcoding data revealed distinct small-scale and large-scale community patterns in the Vjosa river network, which were also recovered by quantitative data of the standard approach. Overall, our results indicate that preservative-based metabarcoding provides important biodiversity data, which could be further improved by quantitative validation. The method is robust and reliable, even though samples were taken under harsh field-conditions and stored without cooling. Further, our results emphasise the need for reliable DNA barcoding reference libraries. Building those may be supported by preservative-based metabarcoding that maintains intact vouchers for subsequent specimen-based analyses.

Variation in food resources can result in dramatic fluctuations in the body condition of animals dependent on those resources. Decreases in body mass can disrupt patterns of energy allocation and impose stress, thereby altering immune function. In this study, we investigated links between changes in body mass of captive cane toads (Rhinella marina), their circulating white blood cell populations, and their performance in immune assays. Captive toads that lost weight over a three-month period had increased levels of monocytes and heterophils and reduced levels of eosinophils. Basophil and lymphocyte levels were unrelated to changes in mass. Because individuals that lost mass had higher heterophil levels but stable lymphocyte levels, the ratio of these cell types was also higher, partially consistent with a stress response. Phagocytic ability of whole blood was higher in toads that lost mass, owing to increased circulating levels of phagocytic cells. Other measures of immune performance were unrelated to mass change. These results highlight the challenges faced by invasive species as they expand their range into novel environments which may impose substantial seasonal changes in food availability that were not present in the native range. Individuals facing energy restrictions may shift their immune function towards more economical and general avenues of combating pathogens.

Global change assessments have typically ignored synthetic chemical pollution, despite the rapid increase of pharmaceuticals, pesticides and industrial chemicals in the environment. Part of the problem reflects the multifarious origins of these micropollutants, which can derive from urban and agricultural sources. Understanding how micropollutants harm ecosystems is a major scientific challenge due to asymmetries of stress across trophic levels and ecological surprises generated by multiple drivers interacting in human-impacted landscapes. We used field assays above and below municipal wastewater treatment plants (WWTPs) in 60 sampling locations across 20 Swiss streams to test how micropollutants and nutrients originating from WWTPs affect two trophic levels (microbes and detritivores) and their role in leaf litter processing. Wastewater impacts were asymmetric across trophic levels, with the detritivore contribution declining relative to microbial-driven decomposition. The strength of negative impacts were context dependent, peaking at sites with the highest upstream abundances of detritivorous invertebrates. Diffuse pollution from intensive agriculture and wastewater-born micropollutants contributed to reduced litter processing rates, including indirect effects apparently mediated through negative influences of insecticides on detritivores. Asymmetries in stress responses across trophic levels can introduce quantitative changes in consumer–resource dynamics and leaf litter processing. This means functional redundancies at different trophic levels are insufficient to compensate for biodiversity losses, causing environmental stressors such as chemical pollutants to have pervasive ecosystem-level impacts.

The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.

Spatially explicit mathematical models are key to a mechanistic understanding of environmental processes in rivers. Such models necessitate extended information on networks' morphology, which is often retrieved from geographic information system (GIS) software, thus hindering the establishment of replicable script-based workflows. Here I present rivnet, an R package for GIS-free extraction and analysis of river networks based on digital elevation models (DEMs). The package exploits TauDEM's flow direction algorithm in user-provided or online accessible DEMs, and allows for computing covariate values and assigning hydraulic variables across any network node. The package is designed so as to require minimal user input while allowing for customization for experienced users. It is specifically intended for application in models of ecohydrological, ecological or biogeochemical processes in rivers. As such, rivnet aims to make river network analysis accessible to users unfamiliar with GIS-based and geomorphological methods and therefore enhance the use of spatially explicit models in rivers.

Global ecosystems are facing a deepening biodiversity crisis, necessitating robust approaches to quantifying species extinction risk. The lower limit of the macroecological relationship between species range and body size has long been hypothesized as an estimate of the relationship between the minimum viable range size (MVRS) needed for species persistence and the organismal traits that affect space and resource requirements. Here, we perform the first explicit test of this assumption by confronting the MVRS predicted by the range-body size relationship with an independent estimate based on the scale of synchrony in abundance among spatially separated populations of riverine fish. We provide clear evidence of a positive relationship between the scale of synchrony and species body size, and strong support for the MVRS set by the lower limit of the range-body size macroecological relationship. This MVRS may help prioritize first evaluations for unassessed or data-deficient taxa in global conservation assessments.

Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. Although biodiversity patterns can be directly inferred from the structure of these assemblages, an assessment of changes through time and space is needed to understand how organisms initially assembled and how they are responding to local environmental and biotic factors. Small freshwater streams are particularly affected by contemporary anthropogenic activities and biological invasions, yet they are commonly less studied, as studies often focus on lakes and large streams. Here, we conducted a spatially explicit analysis of keystone shredder assemblages across eight years in 12 replicated small tributary streams. In each stream, we monitored multiple sites per kilometer of stream length. By assessing temporal beta diversity dynamics, defined by the gain or loss of species or abundance per species at individual sites, we show that changes in amphipod assemblages occur within the context of the surrounding terrestrial matrix and reflect recent amphipod colonization history. While amphipod composition was mostly constant in streams located in forested catchments, streams embedded in catchments with more extensive agricultural land use displayed more pronounced temporal changes, either driven by colonization of unoccupied upstream locations or by more pronounced but undirected fluctuations in gains and losses of species or abundance per species. Our study thus suggests that agricultural landscapes might destabilize aquatic amphipod assemblages, causing higher temporal changes in community structures and highlighting the vulnerability of aquatic ecosystems to terrestrial land use drivers.

Disturbance can strongly influence ecosystems, yet much remains unknown about the relative importance of key processes (selection, drift, and dispersal) in the recovery of ecological communities following disturbance. We combined field surveys with a field experiment to elucidate mechanisms governing the recovery of aquatic macroinvertebrates in habitats of an alluvial floodplain following flood disturbance. We monitored macroinvertebrates in 24 natural parafluvial habitats over 60 days after a major flood, as well as the colonization of 24 newly-built ponds by macroinvertebrates over 45 days in the same floodplain. We examined the sources of environmental variation and their relative effects on aquatic assemblages using a combination of null models and Mantel tests. We also used a joint species distribution model to investigate the importance of primary metacommunity structuring processes during recovery: selection, dispersal, and drift. Contrary to expectations, we found that beta diversity actually decreased among natural habitats over time after the flood or the creation of the ponds, instead of increasing. This result was despite environmental predictors showing contrasting patterns for explaining community variation over time in the natural habitats compared with the experimental ponds. Flood heterogeneity across the floodplain and spatial scale differences between the experimental ponds and the natural habitats seemingly constrained the balance between deterministic and stochastic processes driving the ecological convergence of assemblages over time. While environmental selection was the dominant structuring process in both groups, biotic interactions also had a prominent influence on community assembly. These findings have profound implications towards understanding metacommunity structuring in riverscapes that includes common linkages between disturbance heterogeneity, spatial scale properties, and community composition.

1. Flow regime is a major determinant of the structure and functioning of aquatic ecosystems. Under climate change, flow intermittency is becoming more prevalent in glaciated alpine catchments, but the effects of increasing dryness on aquatic biodiversity remain largely unknown.
2. We characterised flow intermittency patterns in 30 streams of a glaciated alpine catchment over 15 months and separated these streams into four intermittency categories: perennial streams, winter-drying streams, moderately intermittent streams with occasional drying in summer, and periodically intermittent streams with extensive dry periods throughout the year.
We then examined how these drying patterns affected structural and functional properties of benthic macroinvertebrate communities, and whether these changes were primarily deterministic or stochastic.
3. At the taxonomic level, we observed a response at the highest intermittency levels, with α diversity lower and β diversity higher in periodically intermittent streams than in other stream types. This result suggested that local biota were well adapted to intermediate intermittency levels (mostly during winter) but not to high intermittency during summer. In contrast, functional diversity indices at the α and β levels (based on trait abundances) did not differ across intermittency categories. Considering the moderate level of functional redundancy, we interpreted this as an indication that changes in taxonomic diversity may have resulted primarily from stochastic processes.
4. Analysis of community and trait composition indicated that deterministic selection may indeed have occurred with increased intermittency, but this process was likely to be minor in comparison to stochastic extinctions. Notably, community evenness was highest in periodically intermittent streams and lowest in perennial streams, suggesting that frequent drying prevented competitive exclusion.
5. Our results suggested that most macroinvertebrate populations are resilient to intermediate intermittency levels but are filtered at high intermittency, irrespective of their resilience capacities. However, more research is needed to clarify the specific roles of different facets of flow regimes, specifically frequency, duration, and timing of intermittency. Understanding the consequences of responses in diversity and community evenness with increasing intermittency on the functional properties of communities will allow better prediction of the future ecological status of alpine stream networks to ongoing environmental change.

The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large-scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.

Flow regulation of montane and alpine headwater streams can fundamentally alter food web structure and energy flows through changes in productivity, resource availability, and community assembly. Dam flow-release schemes can be used to mitigate the environmental impacts of flow regulation via environmental flows, which can increase discharge variability and other ecologically important hydrological properties. In particular, managed floods can reintroduce disturbance to the system and stimulate the reactivation of physical habitat dynamics. However, how managed floods might restore ecosystem processes is virtually unknown. In this study, we examined patterns in potential energy fluxes before, during and after a long-term experimental flood program on the river Spöl, a regulated alpine River in southeast Switzerland. We used benthic samples collected during long-term monitoring and stable isotope analysis (δ¹³C and δ¹⁵N) of macroinvertebrates and their potential food sources to reconstruct secondary production, and potential energy fluxes, over a 20-year study period. The experimental floods did not alter the relative importance of basal resources but resulted in a considerable decline in secondary production, which remained low after the discontinuation of the floods. Our data suggest that a lack of recolonization by mosses following the discontinuation of the experimental flood program on the river Spöl may have driven patterns in energy fluxes by limiting macroinvertebrates using mosses for habitat. The effects of environmental flows on energy flows in this system thus depend on flood disturbance and the environmental context following the discontinuation of floods.

Despite being the most important source of liquid freshwater on the planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It is thus extensively monitored for pollutants and declines in quantity. The organisms living in groundwater, however, are rarely the target of surveillance programmes and little is known about the fauna inhabiting underground habitats. The difficulties accessing groundwater, the lack of expertise, and the apparent scarcity of these organisms challenge sampling and prohibit adequate knowledge on groundwater fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome these limitations but is largely unexplored. Here, we sampled water in 20 communal spring catchment boxes used for drinking water provisioning in Switzerland, with a high level of replication at both filtration and amplification steps. We sequenced a portion of the COI mitochondrial gene, which resulted in 4917 ASVs, yet only 3% of the reads could be assigned to a species, genus, or family with more than 90% identity. Careful evaluation of the unassigned reads corroborated that these sequences were true COI sequences belonging mostly to diverse eukaryotic groups, not present in the reference databases. Principal component analyses showed a strong correlation of the community composition with the surface land-use (agriculture vs. forest) and geology (fissured rock vs. unconsolidated sediment). While incomplete reference databases limit the assignment of taxa in groundwater eDNA metabarcoding, we showed that taxonomy-free approaches can reveal large hidden diversity and couple it with major land-use drivers, revealing their imprint on chemical and biological properties of groundwater.

Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.

Molecular techniques using DNA retrieved from community or environmental samples, in particular environmental DNA (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template for population genetics, and several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types of "community-based" samples, such as the possibility to target multiple species at the same time, have generated great enthusiasm and expectations for using eDNA in population genetics. However, not every aspect of population genetics can be addressed by eDNA-based data and some inherent limitations may challenge its conclusions. Here, we firstly review the state of current knowledge of DNA retrieved from environmental and community samples for population genetics. Then, focusing on eDNA, we summarize the opportunities but also detail four main limitations of its use for population-level inferences, namely, (1) the difficulty to retrieve a species-specific dataset, (2) the potential lack of correlation between observed and true allelic frequencies, (3) the loss of individual information in multi-locus genotyping and linkage between loci, and (4) the uncertainty about the individuals contributing to the sampled DNA pool (e.g., number, life-stage, or sex). Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA. Others, however, are inherent, and their effect on the inferences must be thoroughly evaluated. The possibility of gaining insights into genetic diversity and population structure from DNA retrieved from community and environmental samples is appealing for scientists, conservation managers, and other practitioners. Yet, to avoid false expectations and incorrect inferences, it is imperative that these limitations are known and considered alongside the opportunities and advantages.

Choosing to mate with an infected partner has several potential fitness costs, including disease transmission and infection-induced reductions in fecundity and parental care. By instead choosing a mate with no, or few, parasites, animals avoid these costs and may also obtain resistance genes for offspring. Within a population, then, the quality of sexually selected ornaments on which mate choice is based should correlate negatively with the number of parasites with which a host is infected ("parasite load"). However, the hundreds of tests of this prediction yield positive, negative, or no correlation between parasite load and ornament quality. Here, we use phylogenetically controlled meta-analysis of 424 correlations from 142 studies on a wide range of host and parasite taxa to evaluate explanations for this ambiguity. We found that ornament quality is weakly negatively correlated with parasite load overall, but the relationship is more strongly negative among ornaments that can dynamically change in quality, such as behavioral displays and skin pigmentation, and thus can accurately reflect current parasite load. The relationship was also more strongly negative among parasites that can transmit during sex. Thus, the direct benefit of avoiding parasite transmission may be a key driver of parasite-mediated sexual selection. No other moderators, including methodological details and whether males exhibit parental care, explained the substantial heterogeneity in our data set. We hope to stimulate research that more inclusively considers the many and varied ways in which parasites, sexual selection, and epidemiology intersect.

1. Parasite species that use two or more host species during their life cycle depend on successful transmission between these species. These successive host species may have different habitat requirements. For example, one host species may be aquatic while the other is terrestrial. To overcome this complicating factor in transmission, a wide diversity of parasite species have adaptations that alter the habitat preference in one host species to facilitate transmission to the next host species.
2. Two common trematode parasites in New Zealand, Atriophallophorus winterbourni and Notocotylus spp., both have a life cycle with two host species. The aquatic snail Potamopyrgus antipodarum is the intermediate host, from which the parasites require transmission to dabbling ducks or other waterfowl. Of these parasites, A. winterbourni is most frequently found in snails from the shallow-water margin. This may indicate parasite-induced movement of infected snails into the foraging habitat of dabbling ducks.
3. To test whether the parasites manipulate the snails to move into shallow water, we stretched tubular mesh cages across depth-specific ecological habitat zones in a lake. Both infected and healthy snails were released into the cages. After 11 days, significantly higher infection frequencies of A. winterbourni were retrieved from the shallowest end of the cages, while Notocotylus spp. frequencies did not vary with depth.
4. The hypothesis that A. winterbourni induces its snail host to move into the shallow-water habitat cannot be rejected based on the experimental results. Although further research is needed to address alternative explanations, the depth preference of infected snails may be due to a parasite adaptation that facilitates trophic transmission of parasites to dabbling ducks.

To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. Observed individual selfing rates depend on the environment (e.g. differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail Radix balthica by conducting laboratory mating trials that manipulated mate availability (low versus moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%) and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness. Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers and mixed maters. As mate availability did not affect selfing, our ‘moderate’ experimental level of mate availability might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.

Defensive symbiosis describes the interaction between two species where one species protects the other from dangers, in exchange for another benefit. Protagonist of this thesis is Hamiltonella defensa, a vertically transmitted bacterial endosymbiont of aphids. H. defensa can defend its aphid host against parasitoid wasps and in return profits from nutrients and shelter inside the aphid body. In wild aphid populations, H. defensa often occurs at intermediate prevalence, that is, some aphid individuals carry the bacteria, but others do not. This might be explained by balancing selection, as carrying H. defensa has not only benefits but also costs for the aphid. The tripartite interaction between aphids, H. defensa and aphid parasitoids is considered a model system for symbiont-driven hostparasite coevolution and has been studied from various angles during the past twenty years. However, there is still a lack of data on the role of defensive symbiosis in the ecology and evolution of natural communities. With my PhD work, I sought to improve on that by studying patterns and dynamics of H. defensa-conferred resistance in the field. [...]

Symbiose beschreibt das enge Zusammenleben zweier unterschiedlicher Organismen. In sogenannten defensiven Symbiosen bietet eine Art der anderen Schutz oder Resistenz gegen Feinde oder Gefahren. Protagonist der vorliegenden Arbeit ist Hamiltonella defensa, ein endosymbiotisches Bakterium, das im Körper von Blattläusen lebt und von einer zur nächsten Blattlausgeneration vererbt wird. H. defensa kann Blattläusen Resistenz gegen parasitische Schlupfwespen verleihen, welche wichtige natürliche Feinde der Läuse sind. H. defensa ist also ein defensiver Symbiont von Blattläusen. Im Gegenzug profitiert H. defensa von 'Kost und Logis' im Innern der Blattlaus. In natürlichen Blattlauspopulationen leben meist einige Individuen mit, andere ohne symbiotische H. defensa. Das wird damit erklärt, dass H. defensa für die Läuse nicht nur Vorteile bringt, sondern auch Kosten. Diese Kosten kommen besonders dann zur Geltung, wenn keine Schlupfwespen die Blattläuse bedrohen, weil die Resistenz gegen solche dann nichts bringt, H. defensa aber weiterhin von den Blattlausressourcen zehrt. Je nach Situation sind also Blattläuse mit oder solche ohne H. defensa fitter. [...]

Parasite-mediated selection can rapidly drive up resistance levels in host populations, but fixation of resistance traits may be prevented by costs of resistance. Black bean aphids (Aphis fabae) benefit from increased resistance to parasitoids when carrying the defensive bacterial endosymbiont Hamiltonella defensa. However, due to fitness costs that come with symbiont infection, symbiont-conferred resistance may result in either a net benefit or a net cost to the aphid host, depending on parasitoid presence as well as on the general ecological context. Balancing selection may therefore explain why in natural aphid populations, H. defensa is often found at intermediate frequencies. Here we present a 2-year field study where we set out to look for signatures of balancing selection in natural aphid populations. We collected temporally well-resolved data on the prevalence of H. defensa in A. f. fabae and estimated the risk imposed by parasitoids using sentinel hosts. Despite a marked and consistent early-summer peak in parasitism risk, and significant changes in symbiont prevalence over time, we found just a weak correlation between parasitism risk and H. defensa frequency dynamics. H. defensa prevalence in the populations under study was, in fact, better explained by the number of heat days that previous aphid generations were exposed to. Our study grants an unprecedentedly well-resolved insight into the dynamics of endosymbiont and parasitoid communities of A. f. fabae populations, and it adds to a growing body of empirical evidence suggesting that not only parasitism risk, but rather multifarious selection is shaping H. defensa prevalence in the wild.

Motivation: Aquatic insects comprise 64% of freshwater animal diversity and are widely used as bioindicators to assess water quality impairment and freshwater ecosystem health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater biodiversity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database, which includes worldwide geo-referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO).
Main type of variables contained: A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the corresponding drainage basin and sub-catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the protection status of their location.
Spatial location and grain: The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m precision at the equator) in the World Geodetic System 1984 (WGS84) coordinate reference system.
Time period and grain: Sampling years span from 1951 to 2021. Ninety-nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub-datasets, exact dates can be retrieved upon communication with the data contributors.
Major taxa and level of measurement: Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification.
Software format: The entire tab-separated value (.csv) database can be downloaded and visualized at https://glowabio.org/project/epto_database/. Fifty individual datasets are also available at https://fred.igb-berlin.de, while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors.

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

Invasive species have far-reaching consequences for whole ecosystems. The two dreissenids zebra and quagga mussels are two of the most successful invaders in aquatic systems. Quagga mussels can colonize deeper parts of a lake while zebra mussels prefer shallow areas. Both species show large variability in shell morphology, but only quagga mussels show a shallow and deep-water morphotype. The aim of this study is to investigate the depth adaptation of quagga mussels and the potential filtration advantage of the quagga mussel compared to the zebra mussel. We conducted common garden experiments, where we measured filtration rates at different temperatures of quagga mussels collected from different water depths and compared them to zebra mussel from 1m depth. We found filtration rates to be strongly temperature dependent, and in particular, lower at 4 °C. Overall, zebra mussels fed less than quaggas. Quagga mussels collected from 1 m depth fed more at higher temperature than quaggas from 30 and 60 m. We hypothesize that deep-water quagga mussels are less sensitive to lower temperature and/or constrained to modify filtration rates at higher temperatures.

The integration of ecosystem processes over large spatial extents is critical to predicting whether and how local and global changes may impact biodiversity and ecosystem functions. Yet, there remains an important gap in meta-ecosystem models to predict multiple functions (e.g. carbon sequestration, elemental cycling, trophic efficiency) across ecosystem types (e.g. terrestrial-aquatic, benthic-pelagic). We derive a flexible meta-ecosystem model to predict ecosystem functions at landscape extents by integrating the spatial dimension of natural systems as spatial networks of different habitat types connected by cross-ecosystem flows of materials and organisms. We partition the physical connectedness of ecosystems from the spatial flow rates of materials and organisms, allowing the representation of all types of connectivity across ecosystem boundaries. Through simulating a forest-lake-stream meta-ecosystem, our model illustrates that even if spatial flows induced significant local losses of nutrients, differences in local ecosystem efficiencies could lead to increased secondary production at regional scale. This emergent result, which we dub the 'cross-ecosystem efficiency hypothesis', emphasizes the importance of integrating ecosystem diversity and complementarity in meta-ecosystem models to generate empirically testable hypotheses for ecosystem functions.

Parasitoids in the genus Lysiphlebus specialize on ant-tended aphids and have previously been reported to mimic the cuticular hydrocarbon (CHC) profiles of their aphid hosts to avoid detection by ants. However, the precise mechanisms that mediate reduced ant aggression toward Lysiphlebus spp. are not known, nor is it clear whether such mechanisms are broadly effective or specialized on particular aphid hosts. Here we explore the effects of wasp genotype and host environment on Lysiphlebus CHC profiles and ant aggression. Rearing asexual Lysiphlebus lines in different host aphid environments revealed effects of both wasp line and aphid host on wasp CHCs. However, variation in genotype and host affected different features of the CHC profile, with wasp genotype explaining most variation in linear and long-chain methyl alkanes, while aphid host environment primarily influenced short-chain methyl alkanes. Subsequent behavioural experiments revealed no effects of host environment on ant aggression, but strong evidence for genotypic effects. The influence of genotypic variation on experienced ant aggression and relevant chemical traits is particularly relevant in light of recent evidence for genetic divergence among Lysiphlebus parasitoids collected from different aphid hosts.

Introduction: Understanding how species are distributed in space and how they interact with each other is central for scientific and conservation purposes. Species' distributions and interactions result from a complex interplay of local trophic dynamics, dispersal processes, resource availability, and abiotic factors governed by the landscape matrix, which also determines the spatial connectivity for organisms' dispersal and resource fluxes. River networks not only exhibit universal spatial structures, but their dendritic landscape structure is tightly linked to species and metacommunity processes therein.
Methods: Here, using a mechanistic model of spatially connected food webs integrating both essential biological and hydrological aspects, we investigate how food-web properties vary in space, and how these patterns are influenced by key model parameters. We then contrast our predictions with a suite of null models, where different aspects (such as spatial structure or trophic interactions) of the spatial food-web model are alternatively relaxed.
Results: We find that species richness is highest in areas where local nutrient load is maximal (lowland headwaters, according to our default assumption). Overall, species richness is positively associated with link density, modularity and omnivory, and negatively related to connectance, nestedness, and niche overlap. However, for metrics such as connectance and omnivory, stochasticity of trophic interactions is a much stronger predictor than spatial variables such as distance to outlet and drainage area. Remarkably, relationships between species richness and food-web metrics do not generally hold in null models, and are hence the outcome of coupled biological and physical (i.e., hydrological) processes characteristic to river networks.
Discussion: Our model generates realistic patterns of species richness and food-web properties, shows that no universal food-web patterns emerge as a result of the riverine landscape structure, and paves the way for future applications aimed at disentangling metacommunity dynamics in river networks.

Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild-caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population expansion into unoccupied habitats and accelerate invasion success.

In recent years, unexplained declines in lake total phosphorus (TP) concentrations have been observed at northern latitudes (> 42°N latitude) where most of the world's lakes are found. We compiled data from 389 lakes in Fennoscandia and eastern North America to investigate the effects of climate on lake TP concentrations. Synchrony in year-to-year variability is an indicator of climatic influences on lake TP, because other major influences on nutrients (e.g., land use change) are not likely to affect all lakes in the same year. We identified significant synchrony in lake TP both within and among different geographic regions. Using a bootstrapped random forest analysis, we identified winter temperature as the most important factor controlling annual TP, followed by summer precipitation. In Fennoscandia, TP was negatively correlated with the winter East Atlantic Pattern, which is associated with regionally warmer winters. Our results suggest that, in the absence of other overriding factors, lake TP and productivity may decline with continued winter warming in northern lakes.

Riverine exports of silicon (Si) influence global carbon cycling through the growth of marine diatoms, which account for ∼25% of global primary production. Climate change will likely alter river Si exports in biome-specific ways due to interacting shifts in chemical weathering rates, hydrologic connectivity, and metabolic processes in aquatic and terrestrial systems. Nonetheless, factors driving long-term changes in Si exports remain unexplored at local, regional, and global scales. We evaluated how concentrations and yields of dissolved Si (DSi) changed over the last several decades of rapid climate warming using long-term data sets from 60 rivers and streams spanning the globe (e.g., Antarctic, tropical, temperate, boreal, alpine, Arctic systems). We show that widespread changes in river DSi concentration and yield have occurred, with the most substantial shifts occurring in alpine and polar regions. The magnitude and direction of trends varied within and among biomes, were most strongly associated with differences in land cover, and were often independent of changes in river discharge. These findings indicate that there are likely diverse mechanisms driving change in river Si biogeochemistry that span the land-water interface, which may include glacial melt, changes in terrestrial vegetation, and river productivity. Finally, trends were often stronger in months outside of the growing season, particularly in temperate and boreal systems, demonstrating a potentially important role of shifting seasonality for the flux of Si from rivers. Our results have implications for the timing and magnitude of silica processing in rivers and its delivery to global oceans.

The current advances of environmental DNA (eDNA) bring profound changes to ecological monitoring and provide unique insights on the biological diversity of ecosystems. The very nature of eDNA data is challenging yet also revolutionizing how biological monitoring information is analysed. In particular, new metrics and approaches should take full advantage of the extent and detail of molecular data produced by genetic methods. In this perspective, machine learning algorithms are particularly promising as they can capture complex relationships between the multiple environmental pressures and the diversity of biological communities. We investigated the potential of a new generation of biomonitoring tools that implement machine-learning techniques to fully exploit eDNA datasets. We trained a machine learning model to discriminate between reference and impacted communities of freshwater macroinvertebrates and assessed its performances using a large eDNA dataset collected at 64 standard federal monitoring sites across Switzerland. We show that a model trained on eDNA is significantly better than a naive model and performs similarly to a model trained on traditional data. Our proof-of-concept shows that such a combination of eDNA and machine learning approaches has the potential to complement or even replace traditional environmental monitoring, and could be scaled along temporal or spatial dimensions.

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.

Evaluating the impact of future changes in land-use and climate on species communities, especially species richness, is one of the most important challenges of current research in ecology and conservation. The impact of environmental changes on species richness depends on its sensitivity (i.e., how strongly a given level of change influences the ecological community) and its exposure (i.e., the amount of change that occurs). To examine the sensitivity, exposure, and potential impact of future environmental conditions on bird communities, we compiled data on bird species richness for Pakistan-a neglected region in macro- or country-scale studies. Since bird species richness strongly varies across seasons due to the seasonal occurrence of migratory species in winter, we compared both wintering (migratory plus resident species) and breeding (resident species only) bird richness. We found breeding and wintering species richness to be sensitive to temperature, precipitation and rainfed cropland by being positively related to these factors. Exposure varied regionally, with projected temperature changes being most profound in northern regions while the strongest projected precipitation changes occurred in central and southern regions. The projected impact of future environmental change were highly heterogeneous across the country and differed between the wintering and breeding communities. Overall, the most negatively impacted region was projected to be the Khyber Pakhtunkha province in the North of Pakistan, due to reductions in precipitation and rainfed cropland, resulting in a projected negative impact, especially on wintering species richness. By highlighting the regional and seasonal bird communities most at risk, our findings provide useful information for policy makers to help devise new policies for mitigating negative impacts of future environmental changes on birds within Pakistan.

1. Understanding the role of thermal tolerances in determining species distributions is important for assessing species responses to climate change. Two hypotheses linking physiology with species distributions have been put forward—the climatic variability hypothesis and the climatic extreme hypothesis. The climatic variability hypothesis predicts the selection of individuals with broad thermal tolerance in more variable climatic conditions and the climatic extreme hypothesis predicts the selection of individuals with extreme thermal tolerance values under extreme climatic conditions. However, no study has tested the predictions of these hypotheses simultaneously for several taxonomic groups along elevational gradients.
2. Here, we related experimentally measured critical thermal maxima, critical thermal minima and thermal tolerance breadths for 15,187 individuals belonging to 116 species of ants, beetles, grasshoppers, and spiders from mountain ranges in central and northern Pakistan to the limits and breadths of their geographic and temperature range.
3 Across all species and taxonomic groups, we found strong relationships between thermal traits and elevational distributions both in terms of geography and temperature. The relationships were robust when repeating the analyses for ants, grasshoppers, and spiders but not for beetles. These results indicate a strong role of physiology in determining elevational distributions of arthropods in Southern Asia.
4. Overall, we found strong support for the climatic variability hypothesis and the climatic extreme hypothesis. A close association between species' distributional limits and their thermal tolerances suggest that in case of a failure to adapt or acclimate to novel climatic conditions, species may be under pressure to track their preferred climatic conditions, potentially facing serious consequences under current and future climate change.

In river systems worldwide, land cover changes have been identified as major drivers of biodiversity change. Quantifying how terrestrial land cover impacts riverine diversity requires local biodiversity assessments. In this study, we investigated the association of terrestrial land cover and the corresponding riverine fish species communities using eDNA-metabarcoding in the Chinese Shaying River basin. This basin is home to about 37 million people and is largely dominated by a mix of intense agriculture and urban areas, creating a relatively homogeneous, intensely used landscape. We investigated whether the homogeneous landscape is mirrored in the composition and structure of fish communities in the river network. We sampled eDNA in spring and fall of 2018, amplified it with a primer designed for local fish species and used operational taxonomic units (OTU) assigned to fish as proxy for diversity. Furthermore, we used redundancy analysis, general linear models, and distance decay curves to assess the effects of land cover on fish communities. We found that the Shaying River showed relatively high basin-wide richness (63 OTU) and seasonal differences in local richness, but limited community differentiation. Variations in alpha- and beta-diversity, measured as local OTU richness and pairwise distance-decay across the basin were low. Redundancy analysis showed only a weak association between observed aquatic communities and their terrestrial surroundings in a 10 km buffer upstream. The lack of community differentiation assessed by eDNA metabarcoding reflects the homogeneous and intense land-use in this basin.

Subterranean fauna is an important contributor to the global fauna, but it is still understudied and a large part of its taxonomy is not yet resolved. One species complex with unresolved taxonomy is the groundwater amphipod Niphargus ruffoi, endemic to the Alpine chain. Here, we used new samples from across the Alpine arc to review the taxonomic status of the entire clade, including the species N. ruffoi and Niphargus arolaensis. We sequenced four genetic markers from the collected specimens, assessed the phylogenetic position of N. ruffoi within the genus, and studied the structure of this species complex using four molecular species delimitation methods. We tested for recombination using the alignments of the concatenated nuclear rDNA genes. The phylogenetic analyses revealed high support for the monophyly of the studied species complex, defining two lineages (i.e., N. arolaensis and N. ruffoi) within the clade. Molecular species delimitation methods suggested that N. arolaensis is a single species, while N. ruffoi should be considered as a species complex of three (using ITS) to eight (using COI) putative species. Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. present in the genome of N. arolaensis. For the above-mentioned reasons, the internal phylogenetic structure of N. ruffoi s. lat. could not be fully resolved. Moreover, no clear morphological evidence supported the molecular species delimitation. Consequently, no taxonomic changes were proposed. We postulate that this complex scenario was influenced by Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts, making this an interesting study system to investigate the evolution and biogeography of Alpine clades.

Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and 'Diat.barcode', a reference barcode library, enables the identification of more than 90% of the environmental sequences to species level in French rivers. But the completeness of this library is much lower in other regions, such as the tropical French overseas departments. A barcode library completion method using high-throughput sequencing data combined with microscopy count data from natural samples (Rimet et al. Citation2018) was applied and tested in rivers of Martinique and Guadeloupe (West Indies), for which only 45% of the environmental sequences could be identified to species level using Diat.barcode v9. Assigning barcodes to the most abundant species in the islands by this method is illustrated with Ulnaria goulardii and two new species belonging to Nupela and Epithemia, which are also described in this paper. The more complex situation of morphologically similar species is illustrated by reference to Gomphonema designatum and G. bourbonense. Using a combination of molecular and morphological data, their conspecificity, as G. bourbonense, is demonstrated with their reference barcodes. However, when several morphologically similar species and several environmental sequences belonging to the same clade are present, it is not possible to relate the barcodes to corresponding morphological species.
Applying this method enabled the Diat.barcode library (v.10) to be updated, with 84% of the environmental sequences from the West Indies now identifiable at the species level. However, many morphological species still lack barcodes. In these cases, more classical methods, such as cell isolation, Sanger sequencing and morphological observations of cultures, must be applied.

Lignocellulose biomass has recently been considered a cost-effective and renewable energy source within circular economy management. Cellulases are important key enzymes for simple, fast, and clean biomass decomposition. The intestinal tract of millipedes is the environment which can provide promising microbial strains with cellulolytic potential. In the present study, we used the tropical millipede Telodeinopus aoutii as an experimental organism. Within a feeding test in which millipedes were fed with oak and maple leaf litter, we focused on isolating culturable cellulolytic microbiota from the millipede gut. Several growth media selecting for actinobacteria, bacteria, and fungi have been used to cultivate microbial strains with cellulolytic activities. Our results showed that oak-fed millipedes provided a higher number of culturable bacteria and a more diversified microbial community than maple-fed ones. The screening for cellulolytic activity using Congo red revealed that about 30% of bacterial and fungal phylotypes isolated from the gut content of T. aoutii, produced active cellulases in vitro. Actinobacteria Streptomyces and Kitasatospora were the most active cellulolytic genera on Congo red test. In contrast, fungi Aspergillus, Penicillium, Cheatomium, Clonostachys, and Trichoderma showed the highest protein-specific cellulase activity quantified by 4-Methylumbelliferyl β-d-cellobioside (4‐MUC). Our findings provide a basis for future research on the enzyme activities of microbes isolated from the digestive tracts of invertebrates and their biocatalytic role in biomass degradation.

Freshwater systems have undergone drastic alterations during the last century, potentially affecting cross-boundary resource transfers between aquatic and terrestrial ecosystems. One important connection is the export of biomass by emergent aquatic insects containing omega-3 polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA), that is scarce in terrestrial systems. Because of taxon-specific differences in PUFA content and functional traits, the contribution of different insect groups should be considered, in addition to total biomass export. In this context, one important trait is the emergence mode. Stoneflies, in contrast to other aquatic insects, crawl to land to emerge instead of flying directly from the water surface, making them accessible to ground-dwelling predators. Because stoneflies are especially susceptible to environmental change, stream degradation might cause a mismatch of available and required nutrients, particularly for ground-dwelling predators. In this study, we estimated emergent biomass and EPA export along two streams with different levels of habitat degradation. The EPA content in aquatic insects did not differ with different degrees of habitat degradation and total biomass export in spring was with 7.9 ± 9.6 mg m^-2 day^-1 in the degraded and 7.3 ± 8.5 mg m^-2 day^-1 in the natural system, also unaffected. However, habitat degradation substantially altered the contribution of crawling emergence to the total export in spring, with no biomass export by stoneflies at the most degraded sites. The EPA content in ground-dwelling spiders was correlated with emergent stonefly biomass, making up only 16.0 ± 6.2 % of total fatty acids at sites with no stonefly emergence, but 27.3 ± 3.0 % at sites with highest stonefly emergence. Because immune function in ground-dwelling spiders has been connected to EPA levels, reduced crawling emergence might impact spider fitness. Functional traits, like emergence mode as well as nutritional quality, should be considered when assessing the effects of stream degradation on adjacent terrestrial ecosystems.

Quagga mussels have expanded their range across the northern hemisphere in recent decades owing to their dispersal abilities, prolific reproduction rates, and broad ecological tolerances. Their remarkable capacity to filter particulates from the water column has had profound effects on inland aquatic ecosystems. In the North American Great Lakes, quagga mussel populations have increased inexorably since the late 1980's, but it remains unclear whether quagga mussels will follow a similar trajectory in Europe where they have appeared more recently. Here we apply knowledge from a long-term quagga population monitoring effort in the North American lakes to predict future quagga populations in deep European lakes, where quaggas are quickly becoming a conspicuous part of the underwater landscape. We predict that quagga mussel biomass in Lakes Biel, Constance, and Geneva may increase by a factor of 9-20 by 2045. Like in North America, this increase may be characterized by a shift to larger individuals and deeper depths as the population matures. If realized, this rapid expansion of quagga mussels would likely drive the largest aquatic ecosystem change in deep European lakes since the eutrophication period of the mid-20th century.

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host–microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater – potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Immune defence is an important determinant of organismal fitness. While theoretical models based on tradeoffs in resource allocation predict quantitative immune traits to be subject to stabilizing selection due to associated energetic costs and self-harm, empirical studies report mainly positive directional selection. This discrepancy may arise from multiple ecological factors that vary in nature and could influence selection. We examined if selection on immune activity varies depending on immune challenge/infection risk, between immune traits and among populations in the freshwater snail Lymnaea stagnalis. We assessed selection on the phenoloxidase-like and antibacterial activity of snail haemolymph while manipulating the level of immune challenge imposed by environmental microbes. We did this using snails from multiple populations and also quantified within-population family-level variation (i.e. evolutionary potential) in the snails' immune activity. We found that the strength of immune challenge and the examined immune trait determined selection on the snails' immune function. Thus, variation in infection risk can be an important factor in maintaining genetic variation in defence traits. Additionally, immune traits showed low among-population differentiation but high within-population genetic variation. This pattern could arise if natural snail populations are exposed to higher temporal than spatial variation in infection risk.

Human-driven environmental stressors are increasingly threatening species survival and diversity of river systems worldwide. However, it remains unclear how the stressors affect the stability changes across aquatic multiple communities. Here, we used environmental DNA (eDNA) data sets from a human-dominated river in China over 3 years and analyzed the stability changes in multiple communities under persistent anthropogenic stressors, including land use and pollutants. First, we found that persistent stressors significantly reduced multifaceted species diversity (e.g., species richness, Shannon’s diversity, and Simpson’s diversity) and species stability but increased species synchrony across multiple communities. Second, the structures of interaction networks inferred from an empirical meta-food web were significantly changed under persistent stressors, for example, resulting in decreased network modularity and negative/positive cohesion. Third, piecewise structural equation modeling proved that the persistent stress-induced decline in the stability of multiple communities mainly depended upon diversity-mediated pathways rather than the direct effects of stress per se; specifically, the increase of species synchrony and the decline of interaction network modularity were the main biotic drivers of stability variation. Overall, our study highlights the destabilizing effects of persistent stressors on multiple communities as well as the mechanistic dependencies, mainly through reducing species diversity, increasing species synchrony, and changing interaction networks.

The freshwater isopod Asellus aquaticus is an important decomposer of leaf detritus, and its diverse gut microbiome has been depicted as key contributors in lignocellulose degradation as of terrestrial isopods. However, it is not clear whether the individual-level microbiome profiles in the isopod digestive system across different habitats match the implied robust digestion function of the microbiome. Here, we described the bacterial diversity and abundance in the digestive system (hindgut and caeca) of multiple A. aquaticus individuals from two contrasting freshwater habitats. Individuals from a lake and a stream harboured distinct microbiomes, indicating a strong link between the host-associated microbiome and microbes inhabiting the environments. While faeces likely reflected the variations in environmental microbial communities included in the diet, the microbial communities also substantially differed in the hindgut and caeca. Microbes closely related to lignocellulose degradation are found consistently more enriched in the hindgut in each individual. Caeca often associated with taxa implicated in endosymbiotic/parasitic roles (Mycoplasmatales and Rickettsiales), highlighting a complex host–parasite–microbiome interaction. The results highlight the lability of the A. aquaticus microbiome supporting the different functions of the two digestive organs, which may confer particular advantages in freshwater environments characterized by seasonally fluctuating and spatially disparate resource availability.

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H₂′]) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co-occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host–parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%–10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

Microbes often exist in spatially structured environments and many of their interactions are mediated through diffusible metabolites. How does such a context affect microbial coexistence? To address this question, we use a model in which the spatial distributions of species and diffusible interaction mediators are explicitly included. We simulate the enrichment process, examining how microbial species spatially reorganize and how eventually a subset of them coexist. In our model, we find that slower motility of cells promotes coexistence by allowing species to co-localize with their facilitators and avoid their inhibitors. We additionally find that a spatially structured environment is more influential when species mostly facilitate each other, rather than when they are mostly competing. More coexistence is observed when species produce many mediators and consume some (not many or few) mediators, and when overall consumption and production rates are balanced. Interestingly, coexistence appears to be disfavored when mediators are diffusing slowly because that leads to weaker interaction strengths. Overall, our results offer new insights into how production, consumption, motility, and diffusion intersect to determine microbial coexistence in a spatially structured environment.

Dispersal is a central life history trait that affects the ecological and evolutionary dynamics of populations and communities. The recent use of experimental evolution for the study of dispersal is a promising avenue for demonstrating valuable proofs of concept, bringing insight into alternative dispersal strategies and trade-offs, and testing the repeatability of evolutionary outcomes. Practical constraints restrict experimental evolution studies of dispersal to a set of typically small, short-lived organisms reared in artificial laboratory conditions. Here, we argue that despite these restrictions, inferences from these studies can reinforce links between theoretical predictions and empirical observations and advance our understanding of the eco-evolutionary consequences of dispersal. We illustrate how applying an integrative framework of theory, experimental evolution and natural systems can improve our understanding of dispersal evolution under more complex and realistic biological scenarios, such as the role of biotic interactions and complex dispersal syndromes.

1. Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community-weighted approaches (e.g. abundance-weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty.
2. We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community-weighting, two types of bootstrapping).
3. We introduce the traitstrap R package, which contains a modular and extensible set of bootstrapping and weighted-averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill, allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample.
4. Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community-weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%–74% relative to community-weighting. Random sampling across all species outperformed both size- and abundance-biased sampling.
5. Our results suggest randomly sampling ~9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems.

Haplotaxis Hoffmeister, 1843 is a poorly known genus: it is rarely collected because it usually inhabits groundwater, and many species are only known from immature specimens. Even the type species, Haplotaxis gordioides (Hartmann in Oken, 1819) remains poorly defined because of the absence of reference types. Most of the Haplotaxis species have been placed in synonymy with H. gordioides since the end of the 19^th century, a situation that has remained essentially unchanged until now. As a result, the species is supposedly present on all continents, except Antarctica. This observation is all the more questionable as the aquatic subterranean environment is nowadays well known to harbour many species with restricted distribution, due to the strong hydrogeographic isolation and the low dispersal abilities of its inhabitants.
In this study we assessed the hypothesis of H. gordioides as a single species with wide distribution versus a complex of cryptic species with narrow distribution. We used a DNA-barcoding approach based on the COI mitochondrial marker of 46 Haplotaxis specimens collected in Switzerland, mostly as part of a countrywide sampling campaign to study groundwater macroinvertebrates.
Preliminary results suggested that H. gordioides is a complex of at least 6 cryptic species in Switzerland, which has important implications both for the knowledge of the exact identity of the type species and for the synonymy of most of the species described in the 19^th century. However, as it is based on a single-locus approach, this study should be seen as the first step in an integrative taxonomic process that should include additional biological material, the study of complementary markers (especially nuclear), and the morphological study of specimens.

1. The mayfly Prosopistoma pennigerum (Müller, 1785) (Insecta: Ephemeroptera) once occurred in many European river networks. However, observations decreased in the last decades and the species can be considered largely extinct throughout Europe due to river alterations.
2. Only three extant populations are known from Cabriel (southern Spain), Volga (Russia) and Vjosa (Albania) rivers.
3. We recorded the species along a 150 km stretch in the Vjosa River in three sampling seasons (spring 2018, fall 2018 and fall 2019), counting up to 302 P. pennigerum per m², the highest recorded abundance for the species to date. Moreover, we detected traces of environmental DNA in a newly designed targeted eDNA assay.
4. In our modelling approach we define the species' niche in a theoretically available niche space given by the Vjosa River network and predict a high probability of presence (θ) in downstream located sections of this river. Expected abundances (λ) could be related to a set of environmental variables, importantly to higher discharge and increased sediment dynamics.
5. Simultaneous occurrence of larvae of different sizes at individual sites suggests an asynchronous life cycle, which may be advantageous to cope with the highly dynamic river hydrology.
6. The P. pennigerum population in the Vjosa is of key importance for the species' global survival.

Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to four fundamental processes that structure communities: dispersal, speciation, species-level selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and responses to impacts, may differ across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesise (i) how the four processes influence diversity and dynamics in terrestrial versus freshwater communities, specifically whether the relative importance of each process differs among ecosystems, and (ii) the pathways by which human impacts can produce divergent responses across ecosystems, due to differences in the strength of processes among ecosystems we identify. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.

Fast-growing and reproducing sun corals have successfully invaded rocky reefs around the Atlantic Ocean, markedly reducing the diversity of fouling invertebrates and macroalgae, and profoundly changing the composition of reef-associated mobile invertebrates. Here, we address sun-coral rubble depositions and report, for the first time, the effects of sun corals on near-reef soft-bottom invertebrate assemblages. Abundance, richness and diversity were higher at rubble habitats compared to bare sandy grounds, which could be a positive effect of substrate complexity. All those parameters were also higher at rubble patches dominated by sun-coral fragments compared to rubble patches dominated by pebbles or shell fragments, also suggesting possible additive effects of coral-borne chemical attraction (sun-coral specific, as inputs of other coral species were virtually absent). Different epifaunal groups were exclusive of rubble habitats and a subset of those exclusive of sun-coral rubble, explaining the incremental richness across habitats. The relative abundance of the two dominant groups – polychaetes (p) and amphipods (a) – contributed the most to the observed contrasts on community structure, as their proportion (p:a) changed from 10:1 in bare sand to nearly co-dominance in coral rubble. While previous research suggested that spreading sun corals reduce prey supply for fish foraging on reef walls, our results suggest they may increase prey abundance and diversity at the adjacent non-consolidated habitat, possibly reshaping trophic pathways connecting the benthic and the pelagic environment.

Understanding structural and functional changes in plankton communities is essential to predict cascading effects of environmental change on aquatic biodiversity and ecosystem services (e.g., carbon storage and water quality) (Chapter I). External abiotic (environment) and internal biotic processes (taxa interactions) have been suggested to drive plankton community dynamics. Limitations in available data and analytical methods to infer interactions between taxa have made studying the relative importance of biotic and abiotic processes in shaping natural plankton communities difficult. Recent advances in plankton monitoring and equation-free modeling deliver promising tools to investigate natural communities in-situ and eventually make accurate predictions of changes in plankton communities. [...]

Das Verständnis struktureller und funktioneller Veränderungen in Planktongemeinschaften ist unerlässlich für die Vorhersage von kaskadeartigen Auswirkungen von Umweltveränderungen auf die aquatische Artenvielfalt und Ökosystemleistungen (z. B. Kohlenstoffspeicherung und Wasserqualität) (Kapitel I). Es wird vermutet, dass externe abiotische (Umweltfaktoren) und interne biotische Prozesse (Interaktionen zwischen Arten) die Dynamik von Planktongemeinschaften bestimmen. Aufgrund der begrenzten Verfügbarkeit von Daten und Analysemethoden zur Ermittlung von Interaktionen zwischen Arten ist die Untersuchung der relativen Wichtigkeit von biotischen und abiotischen Prozessen bei der Zusammensetzung von natürlichen Planktongemeinschaften schwierig. Jüngste Fortschritte in der Planktonüberwachung und gleichungsfreie Modellierungsverfahren liefern vielversprechende Mittel, um natürliche Gemeinschaften in-situ zu untersuchen und schliesslich genaue Vorhersagen über Veränderungen in Planktongemeinschaften zu ermöglichen. [...]

Climate change interacts with local processes to threaten biodiversity by disrupting the complex network of ecological interactions. While changes in network interactions drastically affect ecosystems, how ecological networks respond to climate change, in particular warming and nutrient supply fluctuations, is largely unknown. Here, using an equation-free modelling approach on monthly plankton community data in ten Swiss lakes, we show that the number and strength of plankton community interactions fluctuate and respond nonlinearly to water temperature and phosphorus. While lakes show system-specific responses, warming generally reduces network interactions, particularly under high phosphate levels. This network reorganization shifts trophic control of food webs, leading to consumers being controlled by resources. Small grazers and cyanobacteria emerge as sensitive indicators of changes in plankton networks. By exposing the outcomes of a complex interplay between environmental drivers, our results provide tools for studying and advancing our understanding of how climate change impacts entire ecological communities.

Im «Wasserschloss» Schweiz fühlten sich Amphibien wohl. In unseren heutigen trockengelegten Landschaen haben sie jedoch einen schweren Stand. Viele Arten sind gefährdet. Der Kanton Aargau hat vorgemacht, was im Amphibienschutz möglich ist. In den letzten 20 Jahren hat er grossflächig neue Weiher gebaut und das mit Erfolg: Die Anzahl der Populationen fast aller Amphibienarten hat sich stabilisiert oder in einer Trendwende sogar zugenommen.

Lineages with independent evolutionary histories often differ in both their morphology and diet. Experimental work has improved our understanding of the links between the biomechanics of morphological traits and foraging performance (trait utility). However, because the expression of foraging-relevant traits and their utility can be highly context-specific, it is often unclear how dietary divergence arises from evolved phenotypic differences. Here, we explore the phenotypic causes of dietary divergence between two genetically and phenotypically divergent lineages of threespine stickleback (Gasterosteus aculeatus) with independent evolutionary histories of freshwater colonization and adaptation. First, using individuals from a line-cross breeding design, we conducted 150 common-garden foraging trials with a community of multiple prey species and performed morphological and behavioral analyses to test for prey-specific trait utility. Second, we tested if the traits that explain variation in foraging performance among all individuals could also explain the dietary divergence between the lineages. Overall, we found evidence for the utility of several foraging traits, but these traits did not explain the observed dietary divergence between the lineages in a common garden. This work suggests that evolved dietary divergence results not only from differences in morphology but also from divergence in behaviors that underlie prey capture success in species-rich prey communities.

Headwater streams harbor diverse macroinvertebrate communities and are hotspots for leaf litter breakdown. The process of leaf litter breakdown mediated by macroinvertebrates forms an important link between terrestrial and aquatic ecosystems. Yet, how the vegetation type in the local riparian zone influences leaf-associated macroinvertebrate assemblages and leaf litter breakdown rates is still not resolved. We investigated how leaf-associated macroinvertebrate assemblages and leaf litter fragmentation rates differ between forested and non-forested sites using experimental leaf litter bags in sixteen sites paired across eight headwater streams in Switzerland. Our results show that sensitive taxa of the invertebrate orders Ephemeroptera, Plecoptera and Trichoptera (EPT) and the functional group of shredders were strongly associated with forested sites with overall higher values of abundance, diversity, and biomass of EPTs in forested compared to non-forested sites. However, the importance of riparian vegetation differed between study regions, especially for shredders. Fragmentation rates, which are primarily the result of macroinvertebrate shredding, were on average three times higher in forested compared to non-forested sites. Our results demonstrate that not only the composition of the aquatic fauna but also the functioning of an essential ecosystem process depend on the vegetation type in the local riparian zone.

Background: MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography.
Motivation/goal: We aim to promote the development of process-based biodiversity models that predict community genetic diversity patterns together with other community-scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community-scale data including a genetic component.
Main conclusions: Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top-down or a bottom-up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.

Migration is ubiquitous and can strongly shape food webs and ecosystems. Less familiar, however, is that the majority of life cycle, seasonal and diel migrations in nature are partial migrations: only a fraction of the population migrates while the other individuals remain in their resident ecosystem. Here, we demonstrate different impacts of partial migration rendering it fundamental to our understanding of the significance of migration for food web and ecosystem dynamics. First, partial migration affects the spatiotemporal distribution of individuals and the food web and ecosystem-level processes they drive differently than expected under full migration. Second, whether an individual migrates or not is regularly correlated with morphological, physiological, and/or behavioural traits that shape its food-web and ecosystem-level impacts. Third, food web and ecosystem dynamics can drive the fraction of the population migrating, enabling the potential for feedbacks between the causes and consequences of migration within and across ecosystems. These impacts, individually and in combination, can yield unintuitive effects of migration and drive the dynamics, diversity and functions of ecosystems. By presenting the first full integration of partial migration and trophic (meta-)community and (meta-)ecosystem ecology, we provide a roadmap for studying how migration affects and is affected by ecosystem dynamics in a changing world.

This paper describes a new diatom species (Orthoseira helvetica sp. nov.) found in the Swiss Alps at an elevation over 2600 m a.s.l. The diatom was recorded at the Macun plateau, Swiss National Park, from samples of terrestrial and wet semi-terrestrial mosses near the stream splash zone. The diatom has a unique set of features and is easily recognized under light and scanning electron microscopy. The most distinctive feature is the presence of a prominent silica collar in a 'rose flower' shape rounding each carinoportulae and an additional silica collar on the areolae (first 3-4 rows) bordering the hyaline area. The valve diameter of O. helvetica sp. nov. is 7.5-26.5 µm and possesses 2-3 (usually 3) carinoportulae. Linking spines at the valve face/mantle junction are present, having a simple basis and being triangular in shape.

Uncovering the demographic basis of population fluctuations is a central goal of population biology. This is particularly challenging for spatially structured populations, which require disentangling synchrony in demographic rates from coupling via movement between locations. In this study, we fit a stage-structured metapopulation model to a 29-year time series of threespine stickleback abundance in the heterogeneous and productive Lake Mývatn, Iceland. The lake comprises two basins (North and South) connected by a channel through which the stickleback disperse. The model includes time-varying demographic rates, allowing us to assess the potential contributions of recruitment and survival, spatial coupling via movement, and demographic transience to the population's large fluctuations in abundance. Our analyses indicate that recruitment was only modestly synchronized between the two basins, whereas survival probabilities of adults were more strongly synchronized, contributing to cyclic fluctuations in the lake-wide population size with a period of approximately 6 years. The analyses further show that the two basins were coupled through movement, with the North Basin subsidizing the South Basin and playing a dominant role in driving the lake-wide dynamics. Our results show that cyclic fluctuations of a metapopulation can be explained in terms of the combined effects of synchronized demographic rates and spatial coupling.

1. Species performance depends on the concerted interplay of their functional traits. Natural selection acts on the performance of the species and influences entire suits of interdependent functional traits, thereby driving the evolution of functional diversity (FD) within a clade.
2. In a given habitat, interdependent functional traits are expected to integrate into only a few adaptive combinations. When a clade diversifies in different habitats, the FD within habitats (herein called α-FD) diversifies in response to local selections, while between the habitats, alternative adaptive combinations of interdependent traits that are specific to the habitat emerge. This multivariate selection leads to two hypotheses. First, realized α-FD within one habitat represents only a small fraction of the variation of functional traits, and second, realized FDs across habitats (hereafter called β-FD) are equal to or greater than would be in the absence of the interdependence of functional traits.
3. We tested these hypotheses using 185 species of the highly diverse subterranean amphipod genus Niphargus living in three habitats: river interstitial, cave lakes, and cave streams. We (i) explored integration of functional traits related to locomotion and feeding biology and tested (ii) if realized α-FD within each habitat is lower than it would be without trait interdependence, and (iii) if realized β-FD in pairwise comparisons of habitats is higher than it would be without trait interdependence.
4. In all three habitats, the length of the appendages as a proxy of the locomotion speed was positively correlated with the trophic position of the species. On the contrary, the body shape correlations were habitat dependent: species in high trophic positions were slender, stout or invariant in shape in interstitial, cave streams and cave lakes, respectively.
5. Using null models, we show that only a fraction of functional trait combinations was realized in each habitat, whereas β-FD between habitats was equal to or greater than the null expectations.
6. The results indicate preserved potential for diversification in species within and between habitats. This potential can be realized through hybridization and can drive diversification in adaptive radiations. Moreover, this perspective on the evolution of FD is compatible with several central ecological and evolutionary concepts, such as adaptive landscape or ecological niche theory. Read the free Plain Language Summary for this article on the Journal blog.

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Host microbiomes play an important role in host-parasite interaction, but few studies integrate hostparasite-microbiome tripartite interactions in the wild. In this thesis, I combine field and laboratory experiments using the water flea Daphnia to investigate the role of host microbiomes in host-parasite interactions. In Chapter I, I surveyed with my co-authors the bacterial communities of eight Daphnia galeata genotypes isolated from Lake Greifensee and found host genotype-specific variation. We additionally found no correlation between host genetic distances based on whole genome sequencing of the hosts, and bacterial community composition, suggesting that host genetic distances do not predict divergence in bacterial communities. In Chapter II, we compared the bacterial communities of Daphnia sp. in Lake Greifensee between hosts infected or not infected with the virulent, eukaryotic gut parasite Caullerya mesnili. We found that infection associates with reduced alpha diversity in the gut (the site of infection) and altered community composition in both the gut and body. In Chapter III we tested longterm dynamics of host-parasite-bacterial community associations between Daphnia and Caullerya in Lake Greifensee. For this, we compared infected and uninfected Daphnia across six natural epidemics spanning 13 years. Here we found that Daphnia bacterial community composition showed substantial temporal variation in both dominant bacterial taxa as well as rare taxa, but that infection by Caullerya only altered the composition of rare taxa. Host bacterial community composition also correlated with parasite infection prevalence, i.e. years with larger epidemics had distinct host bacterial communities than those with smaller epidemics. We further found that the environmental abiotic conditions temperature, dissolved oxygen content and cyanobacterial abundance in lake water, all previously known to drive epidemics all associated with distinct host bacterial community compositions. In Chapter IV, we tested the directionality of infection and host microbiome interaction in a laboratory experiment with Daphnia magna and the fungal parasite Metschnikowia bicuspidata. We found that initial parasite exposure drives host genotype specific changes in bacterial community compositions that correlate with the parasite's life stage. We also found that successful infection drives a loss of bacterial community diversity and abundance shifts in dominant bacterial taxa in the host gut. Overall, the results of this thesis indicate that Daphnia bacterial communities play a significant role in host-parasite interaction.

Wirtsmikrobiome spielen eine wichtige Rolle bei der Interaktion zwischen Wirt und Parasit, aber nur wenige Studien integrieren dreigliedrige Interaktionen zwischen Wirt, Parasit und Mikrobiom in freier Wildbahn. In dieser Arbeit kombinieren wir Feld- und Laborexperimente mit dem Wasserfloh Daphnia, um die Rolle von Wirtsmikrobiomen in Wirt-Parasit-Interaktionen zu untersuchen. In Kapitel I untersuchten wir die Bakteriengemeinschaften von acht Daphnia galeata-Genotypen, die aus dem Greifensee isoliert wurden, und fanden wirtsgenotypspezifische Variationen. Darüber hinaus fanden wir keine Korrelation zwischen den genetischen Distanzen der Wirte, die auf der Gesamtgenomsequenzierung der Wirte basieren, und der Zusammensetzung der Bakteriengemeinschaften, was darauf hindeutet, dass die genetischen Distanzen der Wirte keine Divergenz in den Bakteriengemeinschaften vorhersagen. In Kapitel II verglichen wir die Bakteriengemeinschaften von Daphnia sp. im Greifensee zwischen Wirten, die mit dem virulenten, eukaryotischen Darmparasiten Caullerya mesnili infiziert waren und solchen, die nicht infiziert waren. Wir haben festgestellt, dass eine Infektion mit einer geringeren Alpha-Diversität im Darm (dem Ort der Infektion) und einer veränderten Zusammensetzung der Gemeinschaft sowohl im Darm als auch im Körper einhergeht. In Kapitel III untersuchten wir die Langzeitdynamik von Beziehungen zwischen Wirt, Parasit und Bakteriengemeinschaften zwischen Daphnien und Caullerya im Greifensee. Zu diesem Zweck verglichen wir infizierte und nicht infizierte Daphnien in sechs natürlichen Epidemien über einen Zeitraum von 13 Jahren hinweg. Dabei stellten wir fest, dass die Zusammensetzung der Daphnia-Bakteriengemeinschaft sowohl bei den dominanten Bakterientaxa als auch bei den seltenen Taxa erhebliche zeitliche Schwankungen aufwies, während eine Infektion mit Caullerya nur die Zusammensetzung der seltenen Taxa veränderte. Die Zusammensetzung der Wirtsbakteriengemeinschaft korrelierte auch mit der Prävalenz von Parasiteninfektionen, d. h. Jahre mit größeren Epidemien wiesen andere Wirtsbakteriengemeinschaften auf als solche mit kleineren Epidemien. Wir fanden ferner heraus, dass die abiotischen Umweltbedingungen Temperatur, Gehalt an gelöstem Sauerstoff und Cyanobakterienhäufigkeit im Seewasser, von denen bereits bekannt war, dass sie Epidemien fördern, alle mit unterschiedlichen Zusammensetzungen der Wirtsbakteriengemeinschaft verbunden sind. In Kapitel IV haben wir die Richtungsabhängigkeit der Interaktion zwischen Infektion und Wirtsmikrobiom in einem Laborexperiment mit Daphnia magna und dem Pilzparasiten Metschnikowia bicuspidata getestet. Wir fanden heraus, dass die anfängliche Exposition gegenüber dem Parasiten zu wirtsgenotypspezifischen Veränderungen in der Zusammensetzung der Bakteriengemeinschaft führt, die mit dem Lebensstadium des Parasiten korrelieren. Wir fanden auch heraus, dass eine erfolgreiche Infektion zu einem Verlust der Diversität der Bakteriengemeinschaft und zu Abundanzverschiebungen bei den dominanten Bakterientaxa im Wirtsdarm führt. Insgesamt deuten die Ergebnisse dieser Arbeit darauf hin, dass Daphnien-Bakteriengemeinschaften eine bedeutende Rolle in der Wirt-Parasit-Interaktion spielen.

Predicting the spread of populations across fragmented habitats is vital if we are to manage their persistence in the long term. We applied network theory with a model and an experiment to show that spread rate is jointly defined by the configuration of habitat networks (i.e., the arrangement and length of connections between habitat fragments) and the movement behavior of individuals. We found that population spread rate in the model was well predicted by algebraic connectivity of the habitat network. A multigeneration experiment with the microarthropod Folsomia candida validated this model prediction. The realized habitat connectivity and spread rate were determined by the interaction between dispersal behavior and habitat configuration, such that the network configurations that facilitated the fastest spread changed depending on the shape of the species' dispersal kernel. Predicting the spread rate of populations in fragmented landscapes requires combining knowledge of species-specific dispersal kernels and the spatial configuration of habitat networks. This information can be used to design landscapes to manage the spread and persistence of species in fragmented habitats.

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.

Die drei Felchenarten des Bodensees sind die «Brotfische» der dortigen Berufsfischerei. Sie sind sich äusserlich ähnlich und genetisch nahe verwandt, unterscheiden sich aber stark in ihrer Lebensweise. Gegenüber Veränderungen ihres Lebensraums sind sie empfindlich. Das Projekt «See-Wandel: Leben im Bodensee – gestern, heute und morgen» untersuchte die Bodenseefelchen genetisch und auf Populationsebene. Im Fokus der angewandten Forschung stand der Zusammenhang zwischen dem Auftreten neuer Wirkfaktoren und dem aktuellen Rückgang der Felchenbestände.

Die Bodenseefische waren in den vergangenen 60 Jahren starken Nährstoffschwankungen des Sees unterworfen und sind seit etwas über zehn Jahren auch invasiv ausbreitenden Neozoen und Klimaänderungen wie kontinuierlich ansteigenden Wassertemperaturen ausgesetzt. Diese Faktoren haben das gesamte aquatische Ökosystem Bodensee verändert und mit ihm auch die Fischbestände. «SeeWandel» hat die komplexen Zusammenhänge dieser Entwicklung untersucht und aktuelle Daten zu den Fischbeständen des Bodensees geliefert.

Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator–prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator–prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.

Die Erhaltung der Biodiversität ist eine gesellschaftliche Herausforderung. Die gesetzten Schutzziele werden heute oft nur unvollständig oder nicht erreicht. Ein stärkerer Wissenstransfer zwischen Forschung und Praxis soll dazu beitragen, Antworten auf Fragen aus der Naturschutzpraxis zu finden. Dies erfordert, dass relevante wissenschaftliche Erkenntnisse für die Praxis besser zugänglich gemacht und mit dem Wissen aus der Praxis für die Umsetzung aufbereitet werden.
La préservation de la biodiversité est un défi sociétal et les objectifs de protection ne sont souvent pas atteints. Un transfert de connaissances plus efficace entre la recherche et la pratique peut contribuer à fournir des solutions aux questions de la pratique en matière de conservation de la nature. Cela nécessite que les connaissances scientifiques pertinentes soient rendues plus accessibles pour la pratique et préparées avec les connaissances issues de la pratique en vue de leur mise en oeuvre.

Artificial high flows attempt to simulate natural flood pulses in flow-regulated rivers with the intent to improve their ecological integrity. The long-term use of such high flow events have shown beneficial ecological effects on various rivers globally. However, such responses are often non-linear and characterized by underlying feedback mechanisms among ecosystem components. The question arises as to what happens when such high flow releases are disrupted or even discontinued. Here, we used the long-term (22 years) monitoring dataset from the river Spöl to examine whether discontinuation (2016–2021) of the flood program (annual artificial high flows from 2000 to 2016) resulted in the ecological degradation of the river. We used monitoring data of physico-chemistry, periphyton, benthic organic matter, macroinvertebrates and fish (brown trout, Salmo trutta fario L.) in the analysis. The flood program had no long-term effect on water physico-chemistry with most parameters showing typical variations associated with season and inter-annual weather patterns. The floods were effective at mobilizing bed sediments that reduced periphyton biomass and benthic organic matter following each flood. Increases in periphyton biomass and benthic organic matter occurred between floods, but both parameters showed no significant increase with discontinuation of the flood program. Floods reduced macroinvertebrate densities, but with density increases occurring between floods. The pulsed disturbances, and the progressive change in the habitat template, resulted in shifts in community assembly by reducing densities of Gammarus fossarum, a dominant crustacean, which allowed other taxa to colonize the system. Macroinvertebrate densities remained low after discontinuation of the floods, although G. fossarum densities have increased substantially while other taxa, especially some stoneflies, remained low in abundance. Notably, community assembly returned to a pre-flood composition with discontinuation of the floods. The abundance of brown trout increased substantially during the flood program but returned to low pre-flood numbers with discontinuation of the floods. We conclude that the flood program was beneficial to the ecology of the river Spöl and discontinuation of the floods resulted in degradation of the system after a relatively short lag period. However, the system showed high resilience to an earlier perturbation, a sediment spill in 2013, suggesting a rapid positive response by biota with resumption of the flood program.

Human-mediated dispersal is a major contributor of biological invasions. To reduce impacts induced by the introduction and spread of exotic species, biosecurity interventions are put into place. These interventions often rely on risk-assessment procedures, whereby biosecurity practitioners (which includes researchers, stakeholders such as national park managers, and all other decision makers who determine when and how to protect biodiversity) attempt to preemptively identify and predict which exotic species could potentially become a threat to natural ecosystems. In theory, extensive field and experimental studies would be required to accurately and precisely determine the risks of biological invasion of a species or group of species. However, due to a lack of resources or knowledge, such critical studies are limited. As a result, biosecurity practitioners rarely have a full picture of the extent to which the exotic species has and will spread at the time of decision making. Hence, they instead opt for preventive measures such as identifying and managing potential target exotic species which are likely to be invasive or dispersal pathways through which exotic species are likely to be introduced and spread. As most of the uncertainties pertaining to biosecurity interventions lie in the resolution of data made available to practitioners at the time of decision making, we first present some of the different types of information which are readily available during the risk-assessment procedure. We then highlight how one could exploit these different resolutions of data during the risk-assessment procedure using network analysis to better understand human-mediated dispersal of exotic species. By doing so, our paper puts forward what network analysis has to offer practitioners in the context of biosecurity interventions.

Among a multitude of stressors to which wildlife is exposed, environmental pollution is a pervasive one that poses a serious threat. The permeable skin of amphibians is likely to increase direct contact of the body with pollutants, making them a group worth studying to access environmental quality. Consequently, finding reliable and complementary biomarkers that will present detectable and predictable changes in response to pollutants is essential to identify pollution sublethal effects on amphibians and to investigate whether these are in part responsible for population declines. The glucocorticoid hormone corticosterone (CORT), involved in many metabolic functions, is often used to measure the physiological stress response to environmental stressors in amphibians. In this study, we evaluated whether water-borne CORT can serve as a non-invasive biomarker for nitrate pollution stress in the European common frog (Rana temporaria) by comparing the effect of nitrate exposure on hormone release rates and on other physiological downstream biomarkers, i.e., ultimate physiological effects of the stressor. Specifically, we investigated the effect of different nitrate concentrations (0, 10, 50, and 100 mg/L) on water-borne CORT release rates, age, size, and body condition. Exposure to nitrate pollution significantly increased age at metamorphosis and water-borne CORT release rates, and led to reduced mass and body condition, but only at higher nitrate concentrations (i.e., 50 and 100 mg/L). Considering this similar sensitivity to other acknowledged biomarkers, water-borne CORT was a reliable biomarker of physiological stress in R. temporaria exposed to nitrate pollution stress in a controlled single-stressor laboratory approach. Thus, water-borne CORT is a promising method to be included in more holistic approaches. We recommend that such approaches keep testing multiple biomarker combinations, as species are exposed to several stressors likely to interact and produce varied outcomes in different biomarkers in their natural habitats.

Groundwater is a vast ecosystem harboring a high diversity of specialized taxa. Despite its diversity, groundwater is a still relatively unexplored and threatened ecosystem. Especially the linkage of groundwater with other ecosystems remains largely unknown from the perspective of groundwater fauna. Here, we used citizen science data to get a first baseline knowledge of the occurrence, diversity, and biomass of major macroinvertebrate groups found in shallow groundwater systems of Switzerland. We investigated all organisms collected from the groundwater in 346 spring catchment boxes of municipal drinking water providers. We morphologically identified the organisms on a broad taxonomic level and estimated their biomass and pigmentation using automated image processing. Crustaceans, particularly Niphargus and groundwater isopods, were the most common taxa of obligate groundwater organisms. We also found a surprisingly high number of macroinvertebrates associated with surface and subsurface ecosystems. These taxa might be accidentally entering the groundwater or use it as temporary habitat. In both cases they possibly contribute essential allochthonous energy imports from the surface. We found a positive relationship between the estimated biomass of macroinvertebrates in the samples and the occurrence and abundance of Niphargus. Owing to the widespread occurrences of surface and subsurface macroinvertebrates in our groundwater samples, our study provides evidence for common interactions between groundwater, soil, and surface ecosystems.

Ecoimmunological research on molluscs and other invertebrates frequently quantifies phenoloxidase (PO) activity to estimate the strength of the immune function. PO enzymes form different families whose relative roles in oxidative reactions are typically unknown. Understanding this could allow enzyme-specific assays with higher accuracy than in commonly used nonspecific assays. We tested the contribution of different PO enzyme families to haemolymph PO-like activity in Lymnaea stagnalis snails using substrates specific to enzymes detected in L. stagnalis transcriptome data (p-phenylenediamine, specific to laccases; L-tyrosine, specific to tyrosinases) and compared the reactions to those with a nonspecific substrate (L-dopa). We found laccase-like but no tyrosinase-like activity. However, reactions with L-dopa were the strongest, possibly due to other oxidative enzymes in snail haemolymph. Laccase-like activity is common in molluscs, and we propose the use of enzyme-specific assays in future ecoimmunological studies of this taxon. The lack of tyrosinase-like activity in L. stagnalis contradicts earlier transcriptome data, which calls for investigating the expression of PO enzymes in L. stagnalis at the proteome level.

As alien invasive species are a key driver of biodiversity loss, understanding patterns of rapidly changing global species compositions depends upon knowledge of invasive species population dynamics and trends at large scales. Within this context, the Ponto-Caspian region is among the most notable donor regions for aquatic invasive species in Europe. Using macroinvertebrate time series collected over 52 years (1968–2020) at 265 sites across 11 central and western European countries, we examined the occurrences, invasion rates, and abundances of freshwater Ponto-Caspian fauna. We examined whether: (i) successive Ponto-Caspian invasions follow a consistent pattern of composition pioneered by the same species, and (ii) Ponto-Caspian invasion accelerates subsequent invasion rates. In our dataset, Ponto-Caspian macroinvertebrates increased from two species in 1972 to 29 species in 2012. This trend was parallelled by a non-significant increasing trend in the abundances of Ponto-Caspian taxa. Trends in Ponto-Caspian invader richness increased significantly over time. We found a relatively uniform distribution of Ponto-Caspian macroinvertebrates across Europe without any relation to the distance to their native region. The Ponto-Caspian species that arrived first were often bivalves (46.5% of cases), particularly Dreissena polymorpha, followed secondarily by amphipods (83.8%; primarily Chelicorophium curvispinum and Dikerogammarus villosus). The time between consecutive invasions decreased significantly at our coarse regional scale, suggesting that previous alien establishments may facilitate invasions of subsequent taxa. Should alien species continue to translocate from the Ponto-Caspian region, our results suggest a high potential for their future invasion success highly connected central and western European waters. However, each species' population may decline after an initial 'boom' phase or after the arrival of new invasive species, resulting in different alien species dominating over time.

Aim: Invasive alien species are a growing problem worldwide due to their ecological, economic and human health impacts. The “killer shrimp” Dikerogammarus villosus is a notorious invasive alien amphipod from the Ponto-Caspian region that has invaded many fresh and brackish waters across Europe. Understandings of large-scale population dynamics of highly impactful invaders such as D. villosus are lacking, inhibiting predictions of impact and efficient timing of management strategies. Hence, our aim was to assess trends and dynamics of D. villosus as well as its impacts in freshwater rivers and streams.
Location: Europe.
Methods: We analysed 96 European time series between 1994 and 2019 and identified trends in the relative abundance (i.e. dominance %) of D. villosus in invaded time series, as well as a set of site-specific characteristics to identify drivers and determinants of population changes and invasion dynamics using meta-regression modelling. We also looked at the spread over space and time to estimate the invasion speed (km/year) of D. villosus in Europe. We investigated the impact of D. villosus abundance on recipient community metrics (i.e. abundance, taxa richness, temporal turnover, Shannon diversity and Pielou evenness) using generalized linear models.
Results: Population trends varied across the time series. Nevertheless, community dominance of D. villosus increased over time across all time series. The frequency of occurrences (used as a proxy for invader spread) was well described by a Pareto distribution, whereby we estimated a lag phase (i.e. the time between introduction and spatial expansion) of approximately 28 years, followed by a gradual increase before new occurrences declined rapidly in the long term. D. villosus population change was associated with decreased taxa richness, community turnover and Shannon diversity.
Main Conclusion: Our results show that D. villosus is well-established in European waters and its abundance significantly alters ecological communities. However, the multidecadal lag phase prior to observed spatial expansion suggests that initial introductions by D. villosus are cryptic, thus signalling the need for more effective early detection methods.

Vorfahren des Dreistacheligen Stichlings haben nach der letzten Eiszeit von Atlantik und Ostsee aus die mitteleuropäischen Binnengewässer besiedelt. In einige Schweizer Gewässer konnten sie nur mithilfe des Menschen gelangen. Auch im Bodensee verbreiten sie sich erst seit den 1950er-Jahren. Um 2012 haben dort Stichlinge invasionsartig das Freiwasser besiedelt, fressen überwiegend Zooplankton und konkurrieren so mit den dort lebenden Felchen um dieselbe Nahrungsressource.

In nur fünf Jahren hat die Quaggamuschel den Boden- und den Genfersee vollständig besiedelt, in sechs weiteren Seen wurde sie bereits nachgewiesen. In Wassertiefen von 10 bis 30 Metern findet man mittlerweile bis zu 25 000 Muscheln pro Quadratmeter. Auch an den tiefsten Stellen der Seen gibt es bereits Vorkommen. Die Muscheln verstopfen die Infrastrukturanlagen von Trinkwasserbetrieben und thermischen Nutzungen, was Schäden in Millionenhöhe verursacht. Da das Ausbreitungsmuster der Schweizer Seen vergleichbar mit dem der Grossen Seen in Nordamerika ist, muss mit gravierenden Folgen gerechnet werden.

Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here, we integrate whole-genome sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP based heritability of all measured traits was high (h² = 0.42–0.65), indicating adaptive potential for all traits. Environment-association analyses further identified thousands of loci putatively involved in selection, related to genes linked to, for instance, neuron development and protein phosphorylation. Finally, we found that loci linked to water depth were concurrently associated with pelvic spine length variation - supporting the conclusion that divergence in pelvic spine length occurred in the face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.

The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.

Contaminating organisms (grazers, pathogens, competitors) and self-inhibition by algae-produced allelopathic chemicals are two issues that may limit the productivity of algal cultivation for bioproducts. One potential solution is to identify algal strains that are not affected by allelopathic inhibition even while undesirable organisms are suppressed. Here we used two experiments to test how sensitivity to allelopathy varies across algae. In the first experiment, we tested the sensitivity of five biofuel candidate green algae strains to two allelopathic compounds (i.e., free fatty acids) and found that the degree of inhibition depends strongly on both the species and specific compound. In the second experiment, we exposed one alga (Chlorella) to the sterile-filtered medium of each species, and found that the concentration of free fatty acids released into the media predicted Chlorella's growth response. This provides a better understanding of how the production of, and sensitivity to, allelopathic compounds determines algal productivity.

Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.

Global urbanization trends have led to the widespread increasing occurrence of contaminants of emerging concern (CECs) such as pharmaceuticals, personal care products, pesticides, and micro- and nano-plastics in aquatic systems. Even at low concentrations, these contaminants pose a threat to aquatic ecosystems. To better understand the effects of CECs on aquatic ecosystems, it is important to measure concentrations of these contaminants present in these systems. Currently, there is an imbalance in CEC monitoring, with more attention to some categories of CECs, and a lack of data about environmental concentrations of other types of CECs. Citizen science is a potential tool for improving CEC monitoring and to establish their environmental concentrations. However, incorporating citizen participation in the monitoring of CECs poses some challenges and questions. In this literature review, we explore the landscape of citizen science and community science projects which monitor different groups of CECs in freshwater and marine ecosystems. We also identify the benefits and drawbacks of using citizen science to monitor CECs to provide recommendations for sampling and analytical methods. Our results highlight an existing disparity in frequency of monitoring different groups of CECs with implementing citizen science. Specifically, volunteer participation in microplastic monitoring programs is higher than volunteer participation in pharmaceutical, pesticide, and personal care product programs. These differences, however, do not necessarily imply that fewer sampling and analytical methods are available. Finally, our proposed roadmap provides guidance on which methods can be used to improve monitoring of all groups of CECs through citizen science.

he Research Topic on the 16^th Deep Sea Biology Symposium compiles a range of articles presented during the conference that was held in Brest (France) in September 2021 and hosted by the Institut Français de Recherche pour l’Exploitation de la Mer (Ifremer). This triannual event is the central meeting for deep-sea research, where scientists from all over the world gather together to showcase and discuss the latest advances in their field. For the first time in 2021, this event was held in a hybrid mode with participants attending on site and online. Puccinelli et al. showed that, while meetings organized by the Deep-Sea Biology Society had typically less than 400 participants, the use of a hybrid format increased participation by 33% (581 attendees), 73% of whom joined online.
The 26 articles of this Research Topic span research conducted by 138 authors across all ocean basins, encompassing a range of topics that we classified in four sections: 1) zoology and systematics, 2) biodiversity, 3) ecology and 4) conservation and policy. These works investigated most trophic levels from phytoplankton to benthos, fish and whales, across diverse deep-sea environments such as mesopelagic to abyssal environments, vents, seeps and seamounts. This Research Topic provides novel insights on the largest biome of the planet, while advancing our understanding of the complex interactions between organisms and their physical environment, and how such equilibrium is affected by human-induced activities and climate change.

Bacterial assemblages on amphibian skin may play an important role in protecting hosts against infection. In hosts that occur over a range of environments, geographic variation in composition of bacterial assemblages might be due to direct effects of local factors and/or to evolved characteristics of the host. Invasive cane toads (Rhinella marina) are an ideal candidate to evaluate environmental and genetic mechanisms, because toads have evolved major shifts in physiology, morphology, and behavior during their brief history in Australia. We used samples from free-ranging toads to quantify site-level differences in bacterial assemblages and a common-garden experiment to see if those differences disappeared when toads were raised under standardised conditions at one site. The large differences in bacterial communities on toads from different regions were not seen in offspring raised in a common environment. Relaxing bacterial clustering to operational taxonomic units in place of amplicon sequence variants likewise revealed high similarity among bacterial assemblages on toads in the common-garden study, and with free-ranging toads captured nearby. Thus, the marked geographic divergence in bacterial assemblages on wild-caught cane toads across their Australian invasion appears to result primarily from local environmental effects rather than evolved shifts in the host.

Alpine river biodiversity around the world is under threat from glacier retreat driven by rapid warming, yet our ability to predict the future distributions of specialist cold-water species is currently limited. Here we link future glacier projections, hydrological routing methods and species distribution models to quantify the changing influence of glaciers on population distributions of 15 alpine river invertebrate species across the entire European Alps, from 2020 to 2100. Glacial influence on rivers is projected to decrease steadily, with river networks expanding into higher elevations at a rate of 1% per decade. Species are projected to undergo upstream distribution shifts where glaciers persist but become functionally extinct where glaciers disappear completely. Several alpine catchments are predicted to offer climate refugia for cold-water specialists. However, present-day protected area networks provide relatively poor coverage of these future refugia, suggesting that alpine conservation strategies must change to accommodate the future effects of global warming.

Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about the extent of this spatial association is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km² mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 2.0 km radius. Our findings show that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages.

The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.

Quagga and zebra mussels (Dreissena bugensis and D. polymorpha) are spreading across lakes in Europe and North America. In particular, quagga mussels colonize lakes to great depths (>200 m). To better understand the colonization pattern of quagga mussels in deep lakes, we studied the settlement of quagga mussels along a depth gradient on colonization plates at multiple depths (1–140 m) in the pelagic zone of two recently invaded perialpine lakes, Lake Constance and Lake Geneva. We measured colonization rates every three months over one year on colonization plates deployed in both lakes at defined depths. We also assessed long-term population dynamics from abundance and size distribution using repeated photogrammetry of colonization plates. Highest colonization rates and largest mussel sizes occurred above 8 m depth, and almost no zebra mussels were found. Colonization rates decreased to almost zero below 30 m. Colonization rates on plates were associated with variation in environmental conditions as well as veliger densities in the plankton across season and depth. Temperature was the most important environmental parameter that influenced colonization. Our results will help to better understand the seasonal colonization patterns of invasive quagga mussels in deep lakes.

Global change encompasses many co-occurring anthropogenic drivers, which can act synergistically or antagonistically on ecological systems. Predicting how different global change drivers simultaneously contribute to observed biodiversity change is a key challenge for ecology and conservation. However, we lack the mechanistic understanding of how multiple global change drivers influence the vital rates of multiple interacting species. We propose that reaction norms, the relationships between a driver and vital rates like growth, mortality, and consumption, provide insights to the underlying mechanisms of community responses to multiple drivers. Understanding how multiple drivers interact to affect demographic rates using a reaction-norm perspective can improve our ability to make predictions of interactions at higher levels of organization - that is, community and food web. Building on the framework of consumer–resource interactions and widely studied thermal performance curves, we illustrate how joint driver impacts can be scaled up from the population to the community level. A simple proof-of-concept model demonstrates how reaction norms of vital rates predict the prevalence of driver interactions at the community level. A literature search suggests that our proposed approach is not yet used in multiple driver research. We outline how realistic response surfaces (i.e., multidimensional reaction norms) can be inferred by parametric and nonparametric approaches. Response surfaces have the potential to strengthen our understanding of how multiple drivers affect communities as well as improve our ability to predict when interactive effects emerge, two of the major challenges of ecology today.

Biodiversity is under enormous pressure from multiple threats including climate change, land use change, habitat alterations and hunting pressure. One way to ease this pressure on biodiversity and to mitigate the effects of above-mentioned threats, is to establish protected areas. Importance of protected increases many folds in regions that are considered as biodiversity poor regions i.e. deserts. Protected areas have long been a major pillar of biodiversity conservation strategies; the Houbara Protected Area (HPA) is one of the 13 terrestrial protected areas in Abu Dhabi Emirate officially declared in 2017. However, no information regarding the status of biodiversity in the HPA has been communicated to the research fraternity. During the present study, surveys were conducted to fill this gap. The survey area was divided in to 50 grids of 5 × 5 km² and monitoring surveys were undertaken from January to December 2016. A total of 14 bi-monthly to monthly surveys were conducted within HPA and 196 species of different taxonomical groups were recorded. A year-long survey yielded highly diversified fauna and flora from 19 different habitat types (H) 1.32, (E) 2.28, Shannon Diversity Index). We looked at the influence of habitat breadth and temperature on the species richness and abundance, results shows that in desert setup heterogeneity of habitat is not an important factor in maintaining the biodiversity as total number of individuals as well as species were similar in the grids that have different number of habitat types (df = 34.3, t = -0.472, P = 0.640). However, we did find a positive impact of mean monthly temperature on species richness (df = 154, t = 2.53, P = 0.012). Our study highlights the importance of temperature in driving species abundance and richness in protected area. Abundance and species richness are similar in protected areas indicating that protection is allowing species to explore the heterogenous habitats. Overall, we can conclude that protection is beneficial for species.

À ce jour, dix espèces exotiques ont pu s’établir en Suisse, dont cinq sont considérées comme envahissantes. Certaines de ces espèces ont, en partie, un régime alimentaire de prédateur ou se nourrissent en filtrant l’eau; leurs populations peuvent atteindre des densités très élevées. Jusqu’à présent, les espèces exotiques ne sont toutefois apparues que dans de grand lacs et cours et plans d’eau.

Until now, ten alien amphipod species have become established in Switzerland, of which five are considered invasive. These species are partly predatory or are filter-feeding and can reach very high densities. Until now they have only been found in larger bodies of water, however.

In der Schweiz konnten sich bislang zehn gebietsfremde Arten etablieren. Von diesen zählen fünf zu den invasiven Arten. Einige dieser Arten ernähren sich teilweise räuberisch oder leben filtrierend und können sehr hohe Dichten erreichen. Allerdings sind die gebietsfremden Arten bisher nur in grösseren Gewässern aufgetreten.

Maternal effects have the potential to alter early developmental processes of offspring and contribute to adaptive diversification. Egg size is a major contributor to offspring phenotype, which can influence developmental trajectories and potential resource use. However, to what extent intraspecific variation in egg size facilitates evolution of resource polymorphism is poorly understood. We studied multiple resource morphs of Icelandic Arctic charr, ranging from an anadromous morph—with a phenotype similar to the proposed ancestral phenotype—to sympatric morphs that vary in their degree of phenotypic divergence from the ancestral anadromous morph. We characterized variation in egg size and tested whether egg size influenced offspring phenotype at early life stages (i.e., timing of- and size at- hatching and first feeding [FF]). We predicted that egg size would differ among morphs and be less variable as morphs diverge away from the ancestral anadromous phenotype. We also predicted that egg size would correlate with offspring size and developmental timing. We found morphs had different egg size, developmental timing, and size at hatching and FF. Egg size increased as phenotypic proximity to the ancestral anadromous phenotype decreased, with larger eggs generally giving rise to larger offspring, especially at FF, but egg size had no effect on developmental rate. The interaction between egg size and the environment may have a profound impact on offspring fitness, where the resulting differences in early life-history traits may act to initiate and/or maintain resource morphs diversification.

Regular monitoring of ecosystems can be used for the early detection of invasive alien species (IAS), and provide information for management and preventing them from becoming established or advancing into new areas. Current methods of monitoring freshwater systems for IAS can be both financially costly and time-consuming, with routine monitoring often carried out at low intensity and at only a small number of sites. In this study, we evaluate how environmental DNA (eDNA) metabarcoding for monitoring freshwater macroinvertebrate IAS compares to traditional kick-net sampling as part of a national (Switzerland) and a catchment monitoring programme. Kick-net sampling was more fruitful for the detection of several well-known target macroinvertebrate IAS. However, eDNA samples proved complementary for the detection of IAS that belong to species often being unnoticed by traditional sampling due to methodological or taxonomic reasons. Specifically, the invasive jellyfish Craspedacusta sowerbii, hardly detectable using classic kick-net sampling, was found to be widespread in both the national and the catchment-scale monitoring with the eDNA method only. Our study shows that IAS detection using eDNA is easily implemented in both national- and catchment-scale monitoring campaigns. However, successful detection of target IAS is still highly dependent on primer choice, species' biology, and availability of adequate markers. Specifically, multiple markers should be considered for detecting IAS from several different taxonomic groups, such as those under the 'freshwater macroinvertebrate' umbrella term. While eDNA is still developing in terms of these fundamental methodological requirements, surveillance for both target and non-target IAS using eDNA is likely to increase efficiency in early detection of IAS in freshwater systems.

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases and decreases towards downstream location within the catchment for fish and bacteria, respectively. Meanwhile, invertebrate richness remained spatially unchanged but varied across seasons. The structure of local food webs, such as link density and nestedness, also varied across space and time. However, these patterns did not necessarily mirror those observed for biodiversity and functional feeding characteristics. Our results suggest that biodiversity patterns and food-web dynamics are not directly scalable to each other even at the same spatial and temporal scales. In order to conserve species diversity as well as the functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied.

Aim: Groundwater harbours an exceptional fauna and provides invaluable ecosystem services, yet is among the least explored and consequently least protected ecosystems. Successful protection of its biodiversity depends on complete species inventories, knowledge of species spatial distribution, and quantification of biodiversity patterns, as well as disentanglement of the processes that shaped biodiversity patterns. We studied the hyper-speciose amphipod genus Niphargus as a model system within a global subterranean biodiversity hotspot. We linked the biodiversity patterns with possible underlying processes and discuss the needs to include information on different origins of biodiversity into conservation approaches.
Location: Europe, Western Balkans.
Methods: We analysed biodiversity patterns of Niphargus using two biodiversity metrics, species richness and phylogenetic diversity, on a grid-based approach. To account for high cryptic diversity, we replaced nominal species with taxonomic units identified in unilocus delimitations (MOTUs). We built a time-calibrated multilocus phylogeny of 512 Niphargus MOTUs from within and outside the study area, and calculated Faith's phylogenetic diversity, standardized effect sizes of phylogenetic diversity, and residual of phylogenetic diversity regressed onto species richness.
Results: Within the study area, we recognized 245 MOTUs, belonging to different Niphargus clades. Species richness is highest in a north-western hotspot, although some species-rich cells were detected also in the south-east. High phylogenetic diversity coincides with high species richness in the north-west, while in the south-east it is lower than expected.
Main conclusions: We have shown that species richness does not predictably correlate with phylogenetic diversity. This difference suggests that different processes have led to the formation of species-rich areas in the Western Balkans: through a combination of dispersal and speciation in the north-west, and local radiation in the south-east, respectively. This calls for caution in conservation strategies relying solely on number of species and may change the view on conservation priorities within this region.

Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef's approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial di-versity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef's Mandala with the aim of improving future studies on aquatic microbial ecology.

Macroinvertebrates serve as key indicators in ecological assessments of aquatic ecosystems, where the composition and richness of their communities are indicative of environmental and anthropogenic change. Established monitoring of macroinvertebrates is expensive and time-consuming, and relies on expert taxonomic knowledge. In contrast, biomonitoring based on molecular tools can support faster characterization of aquatic communities but needs validation for the target taxonomic groups and the study region. Here, we used data from a biomonitoring program covering a large biogeographic gradient to compare the routine kick-net method with eDNA metabarcoding. We used two primer pairs targeting COI, one targeting a broad metazoan spectrum (mICOIintF/jgHCO2198) and another more recently developed primer pair optimized for the detection of freshwater invertebrates (fwhF2/EPTDr2n). We used the data of the macroinvertebrate monitoring with a focus on the orders of Ephemeroptera, Plecoptera, and Trichoptera across 92 rivers in Switzerland, covering four continental drainage basins and an elevational range from 198 to 1650 m a.s.l. Across all sample sites, the kick-net detected more distinct taxa than either of the metabarcoding approaches. At a site level, however, both primer pairs detected on average more species. Comparing both primer pairs, the fwhF2/EPTDr2n primer pair captured more species assigned to the indicator groups Ephemeroptera, Plecoptera, and Trichoptera, and showed a significantly larger overlap with the kick-net method. However, the community composition still varied significantly among the different metabarcoding approaches. Fewer Trichoptera species were recovered by eDNA, whereas the fwhF2/EPTDr2n primer pair detected more Plecopterans than the other two approaches. This study highlights the importance of the optimization and validation of novel molecular approaches under consideration of the target organismal group and the study area.

Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.

1. Freshwater is vital to much life on Earth and is an essential resource for humans. Climate change, however, dramatically changes freshwater systems and reduces water quality, poses a risk to drinking water availability and has severe impacts on aquatic ecosystems and their biodiversity.
2. The direct effects of climate change, such as increased temperatures and higher frequency of extreme meteorological events, interact with human responses to climate change, which we refer to here as 'indirect effects'. The latter possibly have even greater impact than the direct effects of climate change. Specifically, changes in land-use practices as responses to climate change, such as adjusted cropping regimes or a shift to renewable hydroelectricity to mitigate climate change, can very strongly affect freshwater ecosystems.
3. Hitherto, these indirect effects and the possibility of idiosyncratic outcomes are under-recognized. Here, we synthesize knowledge and identify threats to freshwater environments in alpine and pre-alpine regions, which are particularly affected by climate change.
4. We focus on the effects of adapted agriculture and hydropower production on freshwater quality and ecological status, as these examples have strong indirect effects that interact with direct effects of climate change (e.g., water temperature, droughts, isolation of populations).
5. We outline how failure to effectively account for indirect effects associated with human responses to climate change may exacerbate direct climate change impacts on aquatic ecosystems. If managed properly, however, human responses to indirect effects offer potential for rapid and implementable leverage to mitigate some of the direct climate change effects on aquatic ecosystems. To better address looming risks, policy- and decisionmakers must account for indirect effects and incorporate them into restoration planning and the respective sectorial policies.

1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna.
2. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study the interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and Daphnia clones originating from two latitudes.
3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones. Infected Daphnia populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modelling results.
4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming. A free Plain Language Summary can be found within the Supporting Information of this article.

Der Greifensee ist ausserhalb des Kantons Zürichs nicht so vielen Leuten bekannt, doch weil das Wasserforschungsinstitut Eawag seit 1970 in Dübendorf den Hauptsitz hat, ist er sehr gut erforscht. Für gewisse Themen, zum Beispiel die Einführung einer einheitlichen Beprobung von kleinen Zuflüssen aus landwirtschaftlich genutzten Einzugsgebieten, kommt ihm für die ganze Schweiz Modellcharakter zu. Zusammen mit anderen Forschungspartnern - wie Empa oder ETH Zürich - sowie mit kantonalen Stellen forscht und entwickelt die Eawag aktuell moderne, automatisierte Untersuchungsmethoden, welche helfen, das «System See» noch besser zu verstehen und wo nötig frühzeitig auf unerwünschte Entwicklungen reagieren zu können.

River networks' universal fractal structure not only defines their hydrology and connectivity, but has also profound biological consequences, especially regarding stability and persistence of organismal populations. While rivers' scaling features are captured by Optimal Channel Networks, knowledge on adequate network topologies has hitherto been only partially transferred across geo- and biosciences. Consequently, ecologists have often studied riverine populations via random networks not respecting real rivers' scaling character. Here we show that an alleged property of such random networks (branching probability) is a scale-dependent quantity that does not reflect any recognized metric of rivers' fractal character, and hence cannot be a driver of ecological dynamics. Moreover, we show that random networks lead to biased estimates of population stability and persistence, while only Optimal Channel Networks yield estimates comparable to real rivers. We hence advocate Optimal Channel Networks as model landscapes for realistic and generalizable projections of ecohydrological dynamics in riverine networks.

Rivers regulated by dams display several ecosystem alterations due to modified flow and sediment regimes. Downstream from a dam, ecosystem degradation occurs because of reduced disturbance, mostly derived from limitations on flow variability and sediment supply. In the last decade, most flow restoration/dam impact mitigation was oriented towards the development of environmental flows. Flow variability (and consequent disturbance) can be reintroduced by releasing artificial high flows (experimental floods). Flow-sediment interactions during experimental floods represent strong ecosystem drivers, influencing nutrient dynamics, and metabolic and functional properties. In river networks, sediment and water inputs from tributaries generate points of discontinuity that can drive major changes in environmental conditions, affecting habitat structure and determining functional differences between upstream and downstream. However, despite the relevance for management, flow/sediment relations during environmental flows - and more importantly during experimental floods - remain poorly understood, mostly due to the lack of empirical evidence. In this study, we examined how a major tributary (source of water and sediments) modified the physical habitat template of a regulated river, thereby influencing ecological and geomorphological responses to experimental floods. Methods combined high-resolution drone mapping techniques with a wide range of biological samples collected in field surveys before, during, and after experimental floods in an alpine river. Data were used to quantify changes in relevant functional and structural ecosystem properties, relating ecological responses to geomorphological dynamics. Results highlight the importance of tributaries in restoring ecosystem properties lost after damming, enhancing the resilience of the system. In addition, we observed that disturbance legacy played a fundamental role in determining ecological conditions of a river prior to experimental floods, thus confirming that considering flow variability and sediment availability is crucial in adaptive dam management and environmental flows design.

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.

Dispersal is a central biological process tightly integrated into life-histories, morphology, physiology and behaviour. Such associations, or syndromes, are anticipated to impact the eco-evolutionary dynamics of spatially structured populations, and cascade into ecosystem processes. As for dispersal on its own, these syndromes are likely neither fixed nor random, but conditional on the experienced environment. We experimentally studied how dispersal propensity varies with individuals' phenotype and local environmental harshness using 15 species ranging from protists to vertebrates. We reveal a general phenotypic dispersal syndrome across studied species, with dispersers being larger, more active and having a marked locomotion-oriented morphology and a strengthening of the link between dispersal and some phenotypic traits with environmental harshness. Our proof-of-concept metacommunity model further reveals cascading effects of context-dependent syndromes on the local and regional organisation of functional diversity. Our study opens new avenues to advance our understanding of the functioning of spatially structured populations, communities and ecosystems.

Changing weather patterns and receding glaciers are predicted to increase flow intermittency in alpine streams. If aquatic macroinvertebrate communities largely comprise taxa adapted to perennial flows, an increase in flow intermittency substantially reduces biodiversity and affects functional processes. We conducted a before-after-control-impact field experiment to examine how macroinvertebrate communities in an alpine headwater stream responded to and recovered from a repeated experimental increase in flow intermittency. Flow in one channel was manipulated to simulate increased summer intermittency (June–September) over two consecutive years, whilst an adjacent channel served as a control. We monitored the density of benthic macroinvertebrates, periphyton and organic matter at approximately monthly intervals over three years during the snow-free period. Before manipulation, both channels had similar ecological properties. The flow manipulation reduced the overall macroinvertebrate density, and especially the proportional rheophile density, across both years. Recovery of the macroinvertebrate community following experimental flow intermittency took more than a year, and longer than our study period. This could be due to long aquatic life stages, dispersal limitation and biotic interactions. We conclude that climate-induced changes in alpine stream flow regimes can lead to a fundamental shift in macroinvertebrate assemblages through local extinctions, mostly of rheophilic species.

Monitoring of aquatic habitats for water quality and biodiversity requires regular sampling, often in off-shore locations and underwater. Such sampling is commonly performed manually from research vessels, or if autonomous, is constrained to permanent installations. Consequentially, high frequency ecological monitoring, such as for harmful algal blooms, are limited to few sites and/or temporally infrequent. Here, we demonstrate the use of MEDUSA, an Unmanned Aerial-Aquatic Vehicle which is capable of performing underwater sampling and inspection at up to 10 m depth, and is composed of a multirotor platform, a tether management unit and a tethered micro Underwater Vehicle. The system is validated in the task of vertical profiling of Chlorophyll-a levels in freshwater systems by means of a custom solid sample filtering mechanism. This mechanism can collect up to two independent samples per mission by pumping water through a pair of glass-fibre GF/F filters. Chlorophyll levels measured from the solid deposits on the filters are consistent and on par with traditional sampling methods, highlighting the potential of using UAAVs to sample aquatic locations at high frequency and high spatial resolution.

The phylogeographic patterns of many taxa on New Zealand's South Island are characterized by disjunct distributions that have been attributed to Pleistocene climatic cycles and the formation of the Southern Alps. Pleistocene glaciation has been implicated in shaping the contemporary genetic differentiation between populations of the aquatic snail Potamopyrgus antipodarum. We investigated whether similar phylogeographic patterns exist for the snail's locally adapted trematode parasite, Atriophallophorus winterbourni. We found evidence for a barrier to gene-flow in sympatry between cryptic, but ecologically divergent species. When focusing on the most common of these species, disjunct geographic distributions are found for mitochondrial lineages that diverged during the Pleistocene. The boundary between these distributions is found in the central part of the South Island and is reinforced by low cross-alpine migration. Further support for a vicariant origin of the phylogeographic pattern was found when assessing nuclear multilocus SNP data. Nuclear and mitochondrial population differentiation was concordant in pattern, except for populations in a potential secondary contact zone. Additionally, we found larger than expected differentiation between nuclear- and mitochondrial-based empirical Bayes F_ST estimates (global F_ST: 0.02 vs. 0.39 for nuclear and mitochondrial data, respectively). Population subdivision is theoretically expected to be stronger for mitochondrial genomes due to a smaller effective population size, but the strong difference here, together with mitonuclear discordance in a putative contact zone, is potentially indicative of divergent gene flow of nuclear and mitochondrial genomes.

Competition for limited resources is a major force in structuring ecological communities. Species minimum resource requirements (R*s) can predict competitive outcomes and evolve under selection in simple communities under controlled conditions. However, whether R*s predict competitive outcomes or demonstrate adaptive evolution in naturally complex communities is unknown. We subjected natural phytoplankton communities to three types of resource limitation (nitrogen, phosphorus, light) in outdoor mesocosms over 10 weeks. We examined the community composition weekly and isolated 21 phytoplankton strains from seven species to quantify responses to the selection of R* for these resources. We investigated the evolutionary change in R*s in the dominant species, Desmodesmus armatus. R*s were good predictors of species changes in relative abundance, though this was largely driven by the success of D. armatus across several treatments. This species also demonstrated an evolutionary change in R*s under resource limitation, supporting the potential for adaptive trait change to modify competitive outcomes in natural communities.

Recently, a plethora of studies reporting insect declines has been published. Even though the common theme is decreasing insect richness, positive trends have also been documented. Here, we analysed nationwide, systematic monitoring data on aquatic insect richness collected at 438 sites in Switzerland from 2010 to 2019. In addition to taxonomic richness, we grouped taxa in accordance with their ecological preferences and functional traits to gain a better understanding of trends and possible underlying mechanisms. We found that in general, richness of aquatic insects remained stable or increased with time. Warm-adapted taxa, common feeding guilds and pesticide-tolerant taxa showed increasing patterns while cold-adapted, rarer feeding guilds and pesticide-sensitive taxa displayed stable trends. Both climate and land-use-related factors were the most important explanatory variables for the patterns of aquatic insect richness. Although our data cover the last decade only, our results suggest that recent developments in insect richness are context-dependent and affect functional groups differently. However, longer investigations and a good understanding of the baseline are important to reveal if the increase in temperature- and pesticide-tolerant species will lead to a decrease in specialized species and a homogenization of biotic communities in the long term.

Lakes are often described as sentinels of global change. Phenomena like lake eutrophication, algal blooms, or reorganization in community composition belong to the most studied ecosystem regime shifts. However, although regime shifts have been well documented in several lakes, a global assessment of the prevalence of regime shifts is still missing, and, more in general, of the factors altering stability in lake status, is missing. Here, we provide a first global assessment of regime shifts and stability in the productivity of 1,015 lakes worldwide using trophic state index (TSI) time series derived from satellite imagery. We find that 12.8% of the lakes studied show regime shifts whose signatures are compatible with tipping points, while the number of detected regime shifts from low to high TSI has increased over time. Although our results suggest an overall stable picture for global lake dynamics, the limited instability signatures do not mean that lakes are insensitive to global change. Modeling the interaction between lake climatic, geophysical, and socioeconomic features and their stability properties, we find that the probability of a lake experiencing a tipping point increases with human population density in its catchment, while it decreases as the gross domestic product of that population increases. Our results show how quantifying lake productivity dynamics at a global scale highlights socioeconomic inequalities in conserving natural environments.

Ecological and evolutionary processes can occur at similar time scales and, hence, influence one another. There has been much progress in developing metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document trait differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between nonevolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait changes are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not meaningful. We suggest three modifications to existing partitioning metrics so they allow quantifying ecological and evolutionary contributions to changes in population and community trait values across spatial locations in landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility of applying eco-evolutionary partitioning metrics to populations and communities in natural landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature.

Übermässige Stickstoff- und Phosphoreinträge in die Umwelt gehören zusammen mit Änderungen der Land- und Gewässernutzung, der Übernutzung natürlicher Ressourcen, der Umweltverschmutzung, invasiven gebietsfremden Arten und dem Klimawandel zu den Hauptgründen des Biodiversitätsrückgangs. Überschüsse dieser Nährstoffe verändern und reduzieren die Artenzahlen, die Zusammensetzung von Lebensgemeinschaften, Interaktionen zwischen Arten sowie Ökosystemprozesse. Die flächendeckenden Einträge, die heute mehrheitlich aus der Landwirtschaft stammen, vereinheitlichen zudem die Standortbedingungen weiträumig, was den Verlust regionaler Besonderheiten verursacht. Dies alles kann nicht nur zum irreversiblen Verschwinden von Arten und zum Verlust genetischer und funktioneller Diversität führen, sondern beeinträchtigt auch Ökosystemleistungen wie zum Beispiel die Trinkwasserqualität und verschiedene Waldfunktionen. Entsprechend können neben der Biodiversität weitere Schutzgüter wie Wasser-, Boden-, Luftqualität, Treibhausgasbilanz und Gesundheit ebenfalls beeinträchtigt werden. Ursachen und Auswirkungen dieser Einträge sind wissenschaftlich gut belegt.
Der vorliegende Artikel soll einen Einstieg in das Thema bieten. Es werden die Wirkungsweisen übermässiger Stickstoff- und Phosphoreinträge auf die Biodiversität thematisiert, diskutiert, wie sich die Stickstoffdeposition über die Luft und Phosphorgehalte in Seen im Laufe der Zeit verändert haben und wie sich aus naturwissenschaftlicher Sicht beurteilen lässt, ob Einträge und Gehalte von Stickstoff und Phosphor übermässig sind. Schlussendlich werden wirkungsvolle Handlungsansätze im Landwirtschafts- und Ernährungssystem präsentiert.

The dreissenids, quagga mussel Dreissena bugensis and zebra mussel D. polymorpha, are invasive freshwater mussels in Europe and North America. These species strongly impact aquatic ecosystems, such as the food web through their high abundance and filtration rate. They spread quickly within and between waterbodies, and have the ability to colonize various substrates and depths. The zebra mussel invaded and established in Swiss lakes in the 1960s, whereas the quagga mussel was not detected until 2014. We collected all available data from cantonal as well as local authorities and other institutions to describe the colonization pattern of quagga mussels in perialpine lakes north of the Alps. We also collected data regarding the distribution of larval stages of the mussels, the so-called veliger larvae. We observed that in lakes colonized by the quagga mussel, veligers are present the whole year round, whereas they are absent in winter in lakes with only zebra mussels. Additionally, we present detailed information about the invasion and colonization pattern of quagga mussels in Lake Constance. Quagga mussels colonized the lakeshore within a few years (~ 2016-2018), outcompeted zebra mussels, and have reached densities > 5000 ind. m^-2 in the littoral zone, even at 80 m densities above 1000 ind. m^-2 were found at some locations. At the end of the article, we discussed possibilities on how the spread of quagga mussels within and among northern perialpine lakes should be monitored and prevented in the future.

1. Shifts in microbial communities and their functioning in response to environmental change result from contemporary interspecific and intraspecific diversity changes. Interspecific changes are driven by ecological shifts in species composition, while intraspecific changes are here assumed to be dominated by evolutionary shifts in genotype frequency. Quantifying the relative contributions of interspecific and intraspecific diversity shifts to community change thus addresses the essential, yet understudied question as to how important ecological and evolutionary contributions are to total community changes. This debate is to date practically constrained by (a) a lack of studies integrating across organizational levels and (b) a mismatch between data requirements of existing partitioning metrics and the feasibility to collect such data, especially in microscopic organisms like phytoplankton.
2. We experimentally assessed the relative ecological and evolutionary contributions to total phytoplankton community changes using a new design and validated its functionality by comparisons to established partitioning metrics. We used a community of coexisting Emiliania huxleyi and Chaetoceros affinis with initially nine genotypes each. First, we exposed the community to elevated CO₂ concentration for 80 days (~50 generations) to induce interspecific and intraspecific diversity changes and a total abundance change. Second, we independently manipulated the induced interspecific and intraspecific diversity changes in an assay to quantify the corresponding ecological and evolutionary contributions to the total change. Third, we applied existing partitioning metrics to our experimental data and compared the outcomes.
3. Total phytoplankton abundance declined to one-fifth in the high CO₂ exposed community compared to ambient conditions. Consistently across all applied partitioning metrics, the abundance decline could predominantly be explained by ecological shifts and to a low extent by evolutionary changes.
4. We discuss potential consequences of the observed community changes on ecosystem functioning. Furthermore, we explain that the low evolutionary contributions likely resulted of intraspecific diversity changes that occurred irrespectively of CO₂. We discuss how the assay could be upscaled to more realistic settings, including more species and drivers. Overall, the presented calculations of eco-evolutionary contributions to phytoplankton community changes constitute another important step towards understanding future phytoplankton shifts, and eco-evolutionary dynamics in general.

Advancing understanding of the complexities and expansive spatial scales of river ecology can be enhanced through the application of remote sensing. We obtained satellite (Quickbird) and airborne (LIDAR, hyperspectral, multispectral, and thermal) imagery data of an alluvial gravel-bed river floodplain in western Montana to quantify both riparian and aquatic habitats and processes. LIDAR data provided a detailed bare earth DEM and vegetation canopy DEM. We classified river hydraulics and aquatic habitats using a combination of the satellite multispectral, airborne hyper-spectral, and LIDAR data coupled with spatially-explicit acoustic Doppler velocity profile data of water depth and velocity. Velocity, depth, and Froude classifications were aggregated into similar hydraulic zones of river habitat classes. Thermal imagery data were coupled with field measurements of temperature and radon gas tracer to identify patterns of water exchange between the alluvial aquifer and the surface. We found a high complexity of aquatic surface temperatures and radon tracer linked to groundwater discharge from the alluvial aquifer. Airborne hyperspectral data were used to identify “hot spots” of periphyton production, which coincided with the complex nature of groundwater–surface water exchange. Airborne hyperspectral data provided differentiation of vegetation patches by dominant species. When the hyperspectral data were coupled to LIDAR first return metrics, we were able to determine vegetation canopy height and relative vegetation patch age classes. The integration of these various remote sensing sources allowed us to characterize the distribution and abundance of floodplain aquatic and riparian species and model processes of change through space and time.

Aphids have evolved tight relationships with heritable endosymbionts, i.e., bacteria hosted within their tissues. Besides the primary endosymbiont Buchnera aphidicola, aphids host many facultative secondary endosymbionts with functions they may or may not benefit from. The different phenologies, lifestyles, and natural enemies of aphid species are predicted to favor the selection for distinct endosymbiont assemblages, as well as the emergence of intra-specific genetic diversity in the symbiotic bacteria. In this study, we (1) investigated the diversity of endosymbionts associated with four species from the genus Aphis in the field, and (2) we characterized the genetic diversity of Hamiltonella defensa, an endosymbiont that protects aphids against parasitoid wasps. We observed strong differences in the composition of endosymbiont communities among the four aphid species. H. defensa was clearly the dominant symbiont, although its abundance in each species varied from 25 to 96%. Using a multilocus sequence-typing approach, we found limited strain diversity in H. defensa. Each aphid species harbored two major strains, and none appeared shared between species. Symbiont phylogenies can thus help to understand the (seemingly limited) mobility of endosymbionts in aphid communities and the selection forces driving strain diversification.

While aquatic (blue) and terrestrial (green) food webs are parts of the same landscape, it remains unclear whether they respond similarly to shared environmental gradients. We use empirical community data from hundreds of sites across Switzerland and a synthesis of interaction information in the form of a metaweb to show that inferred blue and green food webs have different structural and ecological properties along elevation and among various land-use types. Specifically, in green food webs, their modular structure increases with elevation and the overlap of consumers’ diet niche decreases, while the opposite pattern is observed in blue food webs. Such differences between blue and green food webs are particularly pronounced in farmland-dominated habitats, indicating that anthropogenic habitat modification modulates the climatic effects on food webs but differently in blue versus green systems. These findings indicate general structural differences between blue and green food webs and suggest their potential divergent future alterations through land-use or climatic changes.

Biological invasions are globally affecting ecosystems, causing local species loss and altering ecosystem functioning. Understanding how such biological invasions occur and succeed is thus of high priority. Both local properties and the spatial network structure have been shown to be determinants of invasion success, and the identification of spatial invasion hubs directly promoting invasion dynamics is gaining attention. Spatial dynamics, however, could also indirectly alter invasion success by shaping pre-invasion local community structure: in many ecosystems, such as riverine networks, regional properties such as patch size distribution are known drivers of local community structures, which themselves may affect the establishment success of invading species. Using microcosm experiments in dendritic networks, we disentangled how inherent patch size distribution and dispersal along specific network topologies shaped local resident communities, and, subsequently, affected the establishment success of invading species. After controlling for regional scale effects of connectivity on pre-invasion diversity, we find that patch size distributions independently shaped pre-invasion community diversity and invasion success, with no direct effect of pre-invasion diversity on invasion success. Our results suggest that 1) landscape configuration plays an underestimated role in invasion success and that 2) invasion success should follow predictable landscape-scale patterns in riverine networks given non-random patch-size distribution.

The meta-ecosystem concept provides a theoretical framework to study the effect of local and regional flows of resources on ecosystem dynamics. Meta-ecosystem theory has hitherto been applied to highly abstract landscapes, and meta-ecosystem dynamics in real-world landscapes remain largely unexplored. River networks constitute a prime example of meta-ecosystems, being characterized by directional resource flows from upstream to downstream communities and between the terrestrial and the aquatic realm. These flows have been thoroughly described by the River continuum concept (RCC), a seminal concept in freshwater ecology, stating that observed spatial variations in the relative abundances of invertebrate functional groups reflect systematic shifts in types and locations of food resources, which are in turn determined by the physical attributes of river reaches. Hence, the RCC represents a solid conceptual basis for determining how changes in landscape structure and resource flows will translate into local and regional changes in community composition. Here, we develop and analyse a riverine meta-ecosystem model inspired by the RCC, which builds upon a physically-based landscape model of dendritic river networks. We show that the spatial distributions and regional biomass of invertebrate functional groups observed in stream communities are determined by the spatial structure and scaling attributes of dendritic river networks, as well as by specific rates of resource flows. Neglecting any of these aspects in modelling river meta-ecosystems would result in different community patterns. Moreover, we observed that high rates of resource flow, for example due to river anthropization, have a negative effect on the regional biomass of all functional groups studied, and can lead to cascading extinctions at the meta-ecosystem scale. Our work paves the way for the development of physically-based meta-ecosystem models to understand the structure and functioning of real-world ecosystems.

Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.

How infected hosts behave critically affects both their fitness and the transmission, and thus fitness, of their parasites. Understanding host-parasite coevolution therefore requires understanding the factors affecting infected host behaviour. This can usefully be decomposed into the current behavioural expression level and any infection-induced changes in that expression: each of these may have different implications for host and parasite fitness. For example, from the perspective of socially transmitted parasites, the more contacts infected hosts make with susceptible conspecifics, the better, regardless of their pre-infection contact behaviour. For social hosts, however, minimizing infection-induced changes to fitness-enhancing behaviours ('behavioural tolerance') may reduce the risk of social exclusion and its associated costs. Here, we tested how the presence of conspecifics ('social context') affects the behaviour and behavioural tolerance of guppies, Poecilia reticulata, infected with the socially transmitted ectoparasite Gyrodactylus turnbulli. In the absence of a stimulus shoal of three females, males that lost the most mass over the course of infection (i.e. had lowest tissue-specific tolerance) were significantly less active, whereas in the presence of the shoal, male activity levels were high and not correlated with tissue-specific tolerance. Females were consistently active, regardless of their tissue-specific tolerance or social context. Behavioural tolerance, quantified as the per-parasite change in activity level, also differed between the sexes in the absence of the shoal: among females, behavioural tolerance was negatively correlated with tissue-specific tolerance, whereas in males the correlation was strikingly positive. In the presence of the shoal, however, tolerance components were not correlated in either sex. Overall, these sex differences in behaviour and behavioural tolerance indicate that females are highly competent at transmitting this parasite, and that males can conceal their disease when in the presence of females. Our results contribute to the growing literature on factors affecting variation between infected hosts, which fundamentally affects epidemiological predictions.

Endosymbiont-conferred resistance to parasitoids is common in aphids, but comes at a cost to the host in the absence of parasitoids. In black bean aphids (Aphis fabae), costs in terms of reduced lifespan and lifetime reproduction were demonstrated by introducing 11 isolates of the protective symbiont Hamiltonella defensa into previously uninfected aphid clones. Transfection of H. defensa isolates into a common genetic background allows to compare the costs of different endosymbiont isolates unconfounded by host genetic variation, but has been suggested to overestimate the realized costs of the endosymbiont in natural populations, because transfection creates new and potentially maladapted host–symbiont combinations that would be eliminated by natural selection in the field. In this experiment, we show that removing H. defensa isolates from their natural host clones with antibiotics results in a fitness gain that is comparable to the fitness loss from their introduction into two new clones. This suggests that estimating cost by transfecting endosymbiont isolates into a shared host genotype does not lead to gross overestimates of their realized costs, at least not in the two recipient genotypes used here. By comparing our data with data reported in previous publications using the same lines, we show that symbiont-induced costs may fluctuate over time. Thus, costs estimated after extended culture in the laboratory may not always be representative of the costs at the time of collection in the field. Finally, we report the accidental observation that two isolates from a distinct haplotype of H. defensa could not be removed by cefotaxime treatment, while all isolates from two other haplotypes were readily eliminated, which is suggestive of variation in susceptibility to this antibiotic in H. defensa.

Diatom taxonomy has evolved in recent years, with many new species described and new approaches such as molecular genetics showing the existence of cryptic diversity within currently accepted species. This cryptic diversity is not well understood even for common freshwater genera such as Fragilaria and Ulnaria. The purpose of our study was to define taxon-specific ecological profiles and geographical distributions for unique molecular identifiers (amplicon sequence variants, ASVs) linked to curated taxonomy for these genera. Our goal is to contribute to the development of ecological assessment methods, and to the understanding why we often observe so many diatom species co-occurring in a single sample. We filtered a large (770 samples) metabarcoding dataset with linked environmental data covering several countries in Europe for genetic variants (ASVs) assigned to currently accepted species of our target genera. We studied the geographical distribution of the ASVs, and tested for ASV-pair co-occurrence. We modelled ASV-specific preferences for pH, alkalinity, total nitrogen, total phosphorus and conductivity, and analysed their preference for lakes or streams as habitat. Our study confirmed that there seems to be no general geographical barrier for the distribution of freshwater benthic diatom ASVs in Europe, but that dispersal is not rapid enough to hide historical events. The Fragilaria and Ulnaria ASVs in our study showed considerable overlap in geographical distribution, habitat and ecological preferences. We found evidence that only large differences in preferences for the analysed water chemistry variables prevented the co-occurrence of ASVs at the same sites. Instead, Fragilaria and Ulnaria ASVs co-occurred frequently in samples. We found subtle differences in ecological preferences for some ASV pairs, which might in part explain the co-occurrence by the avoidance of direct competition. However, the great overlap in distribution and ecological preferences suggests that other factors not studied here were also responsible for the observed co-occurrences and high richness of ASVs found at many sites. To our knowledge, we are the first to use ASVs in combination with a curated taxonomy to understand co-occurrence, specific ecological profiles and large-scale geographical distribution for unique identifiers not biased by the quality of reference databases, clustering methods, or non-harmonized morphological identification. Thus, our results can now be used in subsequent projects to interpret ASV occurrences, e.g. for development of ecological assessment methods.

Monitoring biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution and species richness models. Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared three different approaches in order to better understand assessments of aquatic macroinvertebrate diversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species richness model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species richness model, that is, a generalized linear model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the kicknet and eDNA approaches, particularly at a local scale. We found the EPT-specific primer set fwhF2/EPTDr2n, detected a greater number of targeted EPT species compared to the more general primer set mlCOIintF/HCO2198. Moreover, we found that the species richness measured by eDNA from either primer set was poorly correlated to the richness measured by kicknet sampling (Pearson correlation = 0.27) and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the species richness model (Pearson correlation = 0.30 and 0.44, respectively). The weak relationships between the traditional kicknet sampling and eDNA with this model indicates inherent limitations in upscaling species richness estimates, and possibly a limited ability of the model to meet real world expectations. It is also possible that the number of replicates was not sufficient to detect ambiguous correlations. Future challenges include improving the accuracy and sensitivity of each approach individually, yet also acknowledging their respective limitations, in order to best meet stakeholder demands and address the biodiversity crisis we are facing.

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho-taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA-based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta-analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

Assessment of biodiversity using metabarcoding data, such as from bulk- or eDNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences, and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the non-detection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate taxonomic assignment inferences. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually non-exclusive list of seven classes of challenges when it comes to selecting, developing, and using a reference database for taxonomic assignment. These are: 1) mislabeling, 2) sequencing errors, 3) sequence conflict, 4) taxonomic conflict, 5) low taxonomic resolution, 6) missing taxon, and 7) missing intraspecific variant. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as Genbank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users’ awareness of the limitations of metabarcoding data and DNA-reference databases, adequate interpretations of these data will be achieved.

Monitoring biodiversity is paramount to manage and protect natural resources. Collecting images of organisms over large temporal or spatial scales is a promising practice to monitor the biodiversity of natural ecosystems, providing large amounts of data with minimal interference with the environment. Deep learning models are currently used to automate classification of organisms into taxonomic units. However, imprecision in these classifiers introduces a measurement noise that is difficult to control and can significantly hinder the analysis and interpretation of data. We overcome this limitation through ensembles of Data-efficient image Transformers (DeiTs), which not only are easy to train and implement, but also significantly outperform the previous state of the art (SOTA). We validate our results on ten ecological imaging datasets of diverse origin, ranging from plankton to birds. On all the datasets, we achieve a new SOTA, with a reduction of the error with respect to the previous SOTA ranging from 29.35% to 100.00%, and often achieving performances very close to perfect classification. Ensembles of DeiTs perform better not because of superior single-model performances but rather due to smaller overlaps in the predictions by independent models and lower top-1 probabilities. This increases the benefit of ensembling, especially when using geometric averages to combine individual learners. While we only test our approach on biodiversity image datasets, our approach is generic and can be applied to any kind of images.

The Smithian-Spathian boundary (SSB) crisis played a prominent role in resetting the evolution and diversity of the nekton (ammonoids and conodonts) during the Early Triassic recovery. The late Smithian nektonic crisis culminated at the SSB, ca. 2.7 Myr after the Permian–Triassic boundary mass extinction. An accurate and high-resolution biochronological frame is needed for establishing patterns of extinction and re-diversification of this crisis. Here, we propose a new biochronological frame for conodonts that is based on the Unitary Associations Method (UAM). In this new time frame, the SSB can thus be placed between the climax of the extinction and the onset of the re-diversification. Based on the study of new and rich conodont collections obtained from five sections (of which four are newly described here) in the Nanpanjiang Basin, South China, we have performed a thorough taxonomical revision and described one new genus and 21 new species. Additionally, we have critically reassessed the published conodont data from 16 other sections from South China, and we have used this new, standardized dataset to construct the most accurate, highly resolved, and laterally reproducible biozonation of the Smithian to early Spathian interval for South China. The resulting 11 Unitary Association Zones (UAZ) are intercalibrated with lithological and chemostratigraphical (δ¹³C_carb) markers, as well as with ammonoid zones, thus providing a firm basis for an evolutionary meaningful and laterally consistent definition of the SSB. Our UAZ_8, which is characterized by the occurrence of Icriospathodus ex gr. crassatus, Triassospathodus symmetricus and Novispathodus brevissimus, is marked by a new evolutionary radiation of both conodonts and ammonoids and is within a positive peak in the carbon isotope record. Consequently, we propose to place the SSB within the separation interval intercalated between UAZ₇ and UAZ₈ thus leaving some flexibility for future refinement and updating.

DNA-based taxon identification is improving the assessment and management of biodiversity in rivers. However, the lack of comprehensive DNA barcode reference libraries and globally highly unequal coverage are still hindering the application prospects of this method worldwide. Here, we analyzed the COI barcode gap in two reference libraries, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on three aquatic animal groups (freshwater fish, aquatic insects and molluscs) in Chinese rivers. Our data show gaps in barcode coverage (e.g., organisms without barcodes) of ca. 40–70% of taxa in these groups in the BOLD or NCBI GenBank database, respectively. These gaps can rise even further if the barcode thresholds are set to contain at least five reference sequences per taxon. Furthermore, most barcodes are from non-local samples, and only 14.4% (BOLD) and 28.8% (NCBI GenBank) of reference sequences were from organisms sampled in China, respectively. The pairwise genetic distance of local barcodes is 3 to 5 times lower than non-local barcodes, indicating that the latter may not be a good substitute. When looking at individual catchments, ca. 60% of the potentially occurring aquatic species have one or more barcodes, yet the barcode coverage varies slightly across ten major river catchments, ranging from 54.3% (Liao River basin) to 68.2% (Huai River basin). The taxa Salmoniformes and Perciformes in freshwater fish, Odonata and Diptera in aquatic insects, and Bivalvia in molluscs have the best barcode coverage in most catchments (mean coverage >70%). This study gives the first overview and current status of barcode reference libraries of three major aquatic animal groups in Chinese rivers. Our results will help to better interpret current metabarcoding studies from China, and also provide a basis to develop a strategy of filling the gaps in the reference libraries of aquatic species in China.

Introduced species can alter the dynamics and structure of a native community. Network analysis provides a tool to study host–parasite interactions that can help to predict the possible impact of biological invasions or other disturbances. In this study, we used weighted bipartite networks to assess differences in the interaction patterns between hosts and helminth parasites of native (Sea of Japan) and invasive (Black Sea and Sea of Azov) populations of Planiliza haematocheilus (Teleostei: Mugilidae). We employed three quantitative network descriptors, connectance, weighted nestedness and modularity, to gain insight into the structure of the host–parasite networks in the native and invaded areas. The role of parasite species in the networks was assessed using the betweenness centrality index. We analyzed networks encompassing the whole helminth community and subsets of species classified by their transmission strategy. The analyses were downscaled to host individual-level to consider intraspecific variation in parasite communities. We found significant differences between networks in the native and invaded areas. The latter presented a higher value of nestedness, which may indicate a co-occurrence between parasite species with many connections in the network and species with fewer interactions within the same individual-host. In addition, modularity was higher in the native area’s networks than those of the invaded area, with subgroups of host individuals that interact more frequently with certain parasite species than with others. Only the networks composed of actively transmitted parasites and ectoparasites did not show significant differences in modularity between the Sea of Azov and the Sea of Japan, which could be due to the introduction of a part of the native community into the invaded environment, with a lower diversity and abundance of species. We show that network analysis provides a valuable tool to illuminate the changes that occur in host–parasite interactions when an invasive species and its parasite community are introduced into a new area.

Spatial dynamics have long been recognized as an important driver of biodiversity. However, our understanding of species' coexistence under realistic landscape configurations has been limited by lack of adequate analytical tools. To fill this gap, we develop a spatially explicit metacommunity model of multiple competing species and derive analytical criteria for their coexistence in fragmented heterogeneous landscapes. Specifically, we propose measures of niche and fitness differences for metacommunities, which clarify how spatial dynamics and habitat configuration interact with local competition to determine coexistence of species. We parameterize our model with a Bayesian approach using a 36-y time-series dataset of three Daphnia species in a rockpool metacommunity covering >500 patches. Our results illustrate the emergence of interspecific variation in extinction and recolonization processes, including their dependencies on habitat size and environmental temperature. We find that such interspecific variation contributes to the coexistence of Daphnia species by reducing fitness differences and increasing niche differences. Additionally, our parameterized model allows separating the effects of habitat destruction and temperature change on species extinction. By integrating coexistence theory and metacommunity theory, our study provides platforms to increase our understanding of species' coexistence in fragmented heterogeneous landscapes and the response of biodiversity to environmental changes.

Flow refugia, locations that maintain substrate stability and low hydraulic stress during periods of high flow, can ensure riverine resilience in the face of increasing hydrological unpredictability. Despite their known importance, they have been overlooked in recent years with work on drought refugia currently seeing greater attention. Moreover, research on the role of flow refugia during artificial flood pulses in regulated rivers, where flood disturbances are no longer part of the hydrograph, is essentially absent. Here, we compared flow refugia for benthic macroinvertebrates among six habitats (main channel, side channel, riffle, margin, lentic including a floodplain pond, and inundated floodplain) within four different sites in response to an artificial flood pulse. We found that the grain-size distribution and macroinvertebrate community composition changed at each site following the flood. Macroinvertebrate assemblages became longitudinally homogeneous, but within-site beta diversity and taxa richness remained temporally stable following the flood pulse, suggesting the presence of flow refugia. In this respect, margin, inundated floodplain and lentic (a floodplain pond) habitats provided important flow refugia locations, particularly for the mobile mayfly Rhithrogena sp. In contrast, low substrate stability in riffle and side channels resulted in limited refugia potential for most taxa. Refuge use was however patchy with high levels of intra-habitat variability being evident for Rhithrogena sp. and the amphipod Gammarus fossarum in margin and side channel habitats. Further work is required to advance our knowledge of flow refugia in rivers with differing flow regimes to enable their integration into management and restoration schemes.

Background: Physiological processes, as immediate responses to the environment, are important mechanisms of phenotypic plasticity and can influence evolution at ecological time scales. In stressful environments, physiological stress responses of individuals are initiated and integrated via the release of hormones, such as corticosterone (CORT). In vertebrates, CORT influences energy metabolism and resource allocation to multiple fitness traits (e.g. growth and morphology) and can be an important mediator of rapid adaptation to environmental stress, such as acidification. The moor frog, Rana arvalis, shows adaptive divergence in larval life-histories and predator defense traits along an acidification gradient in Sweden. Here we take a first step to understanding the role of CORT in this adaptive divergence. We conducted a fully factorial laboratory experiment and reared tadpoles from three populations (one acidic, one neutral and one intermediate pH origin) in two pH treatments (Acid versus Neutral pH) from hatching to metamorphosis. We tested how the populations differ in tadpole CORT profiles and how CORT is associated with tadpole life-history and morphological traits.

Results: We found clear differences among the populations in CORT profiles across different developmental stages, but only weak effects of pH treatment on CORT. Tadpoles from the acid origin population had, on average, lower CORT levels than tadpoles from the neutral origin population, and the intermediate pH origin population had intermediate CORT levels. Overall, tadpoles with higher CORT levels developed faster and had shorter and shallower tails, as well as shallower tail muscles.

Conclusions: Our common garden results indicate among population divergence in CORT levels, likely reflecting acidification mediated divergent selection on tadpole physiology, concomitant to selection on larval life-histories and morphology. However, CORT levels were highly environmental context dependent. Jointly these results indicate a potential role for CORT as a mediator of multi-trait divergence along environmental stress gradients in natural populations. At the same time, the population level differences and high context dependency in CORT levels suggest that snapshot assessment of CORT in nature may not be reliable bioindicators of stress.

Populations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. We here studied genomic adaptation during experimental range expansions of the protist Tetrahymena thermophila in landscapes with a uniform environment or a pH gradient. Specifically, we investigated two aspects of genomic adaptation during range expansion. First, we investigated adaptive genetic change in terms of the underlying numbers of allele frequency changes from standing genetic variation and de novo variants. We focused on how sexual reproduction may alter this adaptive genetic change. Second, we identified genes subject to selection caused by the expanding range itself, and directional selection due to the presence or absence of the pH gradient. We focused this analysis on alleles with large frequency changes that occurred in parallel in more than one population to identify the most likely candidate targets of selection. We found that sexual reproduction altered adaptive genetic change both in terms of de novo variants and standing genetic variation. However, sexual reproduction affected allele frequency changes in standing genetic variation only in the absence of long-distance gene flow. Adaptation to the range expansion affected genes involved in cell divisions and DNA repair, whereas adaptation to the pH gradient additionally affected genes involved in ion balance and oxidoreductase reactions. These genetic changes may result from selection on growth and adaptation to low pH. In the absence of gene flow, sexual reproduction may have aided genetic adaptation. Gene flow may have swamped expanding populations with maladapted alleles, thus reducing the extent of evolutionary adaptation during range expansion. Sexual reproduction also altered the genetic basis of adaptation in our evolving populations via de novo variants, possibly by purging deleterious mutations or by revealing fitness benefits of rare genetic variants.

Success stories are rare in conservation science, hindered also by the research-implementation gap, where scientific insights rarely inform practice and practical implementation is rarely evaluated scientifically. Amphibian population declines, driven by multiple stressors, are emblematic of the freshwater biodiversity crisis. Habitat creation is a straightforward conservation action that has been shown to locally benefit amphibians, as well as other taxa, but does it benefit entire amphibian communities at large spatial scales? Here, we evaluate a landscape-scale pond-construction program by fitting dynamic occupancy models to 20 y of monitoring data for 12 pond-breeding amphibian species in the Swiss state Aargau, a densely populated area of the Swiss lowlands with intensive land use. After decades of population declines, the number of occupied ponds increased statewide for 10 out of 12 species, while one species remained stable and one species further declined between 1999 and 2019. Despite regional differences, in 77% of all 43 regional metapopulations, the colonization and subsequent occupation of new ponds stabilized (14%) or increased (63%) metapopulation size. Likely mechanisms include increased habitat availability, restoration of habitat dynamics, and increased connectivity between ponds. Colonization probabilities reflected species-specific preferences for characteristics of ponds and their surroundings, which provides evidence-based information for future pond construction targeting specific species. The relatively simple but landscape-scale and persistent conservation action of constructing hundreds of new ponds halted declines and stabilized or increased the state-wide population size of all but one species, despite ongoing pressures from other stressors in a human-dominated landscape.

Obwohl aquatische (blaue) und terrestrische (grüne) Ökosysteme eng miteinander verwoben sind, werden sie oft getrennt voneinander betrachtet und verwaltet. Um Biodiversität Ökosystem-übergreifend besser zu schützen, braucht es integrative Ansätze in Forschung, Praxis und Gesetzgebung.

Bien qu’ils soient interdépendants, les écosystèmes aquatiques (bleus) et terrestres (verts) sont trop souvent appréhendés isolément les uns des autres. Pour que la conservation de la biodiversité soit plus efficace, la recherche, la pratique et la législation doivent dépasser cette approche cloisonnée au profit d’une vision inter-écosystémique.

Im Wald gibt es eine Vielfalt von Lebensräumen und Arten, die von Wechselwirkungen zwischen Wasser und Land beeinflusst sind. Ein grösseres Bewusstsein für diese gegenseitige Abhängigkeit ermöglicht effektiveren Biodiversitätsschutz.

Molecular biology protocols have been more and more accessible to researchers for ecological investigations. However, these protocols always require optimization steps for the analysis of specific types of samples. This study aimed to optimize a molecular protocol to analyze cyanobacterial 16S rRNA in Danube Delta shallows lakes. In this regard, several commercial DNA extraction kits were tested compared to the potassium ethyl xanthogenate extraction method on different matrices. The obtained DNA was further used for 16S rRNA PCR optimization. Finally, an optimized protocol is proposed for the molecular analysis of the cyanobacteria group in freshwater samples. The best DNA extraction method was the potassium xanthogenate extraction from dried cyanobacterial biomass. A dynamic in total genomic eDNA was observed, reflecting the seasonal difference in phytoplankton biomass from the studied lakes. The PCR protocol optimized by us can be successfully applied for the identification of a broad range of cyanobacterial genetic markers.

1. Protective symbionts can provide effective and specific protection to their hosts. This protection can differ between different symbiont strains with each strain providing protection against certain components of the parasite and pathogen community their host faces. Protective symbionts are especially well known from aphids where, among other functions, they provide protection against different parasitoid wasps. However, most of the evidence for this protection comes from laboratory experiments.
2. Our aim was to understand how consistent protection is across different symbiont strains under natural field conditions and whether symbiont diversity enhanced the species diversity of colonizing parasitoids, as could be expected from the specificity of their protection.
3. We used experimental colonies of the black bean aphid Aphis fabae to investigate symbiont-conferred protection under natural field conditions over two seasons. Colonies differed only in their symbiont composition, carrying either no symbionts, a single strain of the protective symbiont Hamiltonella defensa, or a mixture of three H. defensa strains. These aphid colonies were exposed to natural parasitoid communities in the field. Subsequently, we determined the parasitoids hatched from each aphid colony.
4. The evidence for a protective effect of H. defensa was limited and inconsistent between years, and aphid colonies harbouring multiple symbiont strains did not support a more diverse parasitoid community. Instead, parasitoid diversity tended to be highest in the absence of H. defensa.
5. Symbiont-conferred protection, although a strong and repeatable effect under laboratory conditions may not always cause the predicted bottom-up effects under natural conditions in the field.

Biological treatment of waterborne viruses, specifically grazing of viruses by protists, can enhance microbial water quality while avoiding the production of toxic byproducts and high energy costs. However, tangible applications are limited by the lack of understanding of the underlying mechanisms. Here, we examined the feeding behavior of Tetrahymena pyriformis ciliates on 13 viruses, including bacteriophages, enteric viruses, and respiratory viruses. Significant differences in virus removal by T. pyriformis were observed, ranging from no removal (Qbeta, coxsackievirus B5) to ≥2.7 log₁₀ (JC polyomavirus) after 48 h of co-incubation of the protist with the virus. Removal rates were conserved even when protists were co-incubated with multiple viruses simultaneously. Video analysis revealed that the extent of virus removal was correlated with an increase in the protists’ swimming speed, a behavioral trait consistent with the protists’ response to the availability of food. Protistan feeding may be driven by a virus’ hydrophobicity but was independent of virus size or the presence of a lipid envelope.

Identifying sublethal pesticide effects on aquatic organisms is a challenge for environmental risk assessment. Long-term population experiments can help assessing chronic toxicity. However, population experiments are subject to stochasticity (demographic, environmental, and genetic). Therefore, identifying sublethal chronic effects from “noisy” data can be difficult. Model-based analysis can support this process.
We use stochastic, age-structured population models applied to data from long-term population experiments with Daphnia galeata in 1L aquaria with and without chronic pesticide treatments (diazinon and diuron) at sublethal concentrations. Posterior analysis following Bayesian inference of model parameters and states helped choosing an adequate description of life-history characteristics under the specific experimental conditions (a zero-inflated negative binomial distribution for reproduction and mortality without density dependence). For the insecticide treatments, the inferred marginal posterior parameter distributions indicated the need for a mortality rate that increases with time, indicating cumulative chronic toxic effects of diazinon on Daphnia populations. With this study, we demonstrate how stochastic models can be used to infer mechanisms from population data to help identifying sublethal pesticide effects.

Games as a didactic tool (e. g., puzzles) are gaining recognition in environmental education to promote skill development, but also to develop a specific understanding of the natural world. However, a children's puzzle containing representations of nature may unwillingly lead to "misconceptions" of biodiversity themes and processes, and an over-simplification of the relationship between people and nature. To solve this problem, positive connotations of biodiversity may prompt a conceptual change to a more nuanced, multifaceted conception of biodiversity.

In this study, we monitored diatom assemblages at various sites along a stream-lake network draining a glaciated alpine cirque landscape (2600 m asl) in the Swiss National Park over 19 years (2001-2020). The primary goal of this study was to examine the long-term changes in diatom assemblages in the running waters at high-elevation influenced by rock glaciers, and particularly the use of diatoms as indicators of environmental change. Because streams in the catchment are interconnected with lakes, another objective was to compare diatom assemblages between lake inlets and lake outlets as well as along the chain of lakes. The Macun cirque comprises two main drainage basins with one influenced by waters from rock glaciers. Lakes are interconnected by stream segments in both basins before merging at an outflow lake. We expected changes in diatom assemblages would reflect changes in long-term physico-chemistry of surface waters between basins, between lake inlets and outlets, and along lake chains. The novelty of this work is that covers a unique heterogeneous aquatic environment in the Alps affected by climate change, an area where the temperature has increased over twofold more than other regions in the northern hemisphere. This long-term study provides the opportunity of forecasting how other alpine freshwater ecosystems globally may change in the future. We combined a classical taxonomic approach and scanning electron microscopy (SEM) along with physico-chemical data across a broad spatio-temporal scale. Diatom assemblages showed distinct spatial differences between basins, reflecting basin-wide differences in water physico-chemistry. Diatoms in both basins displayed a major temporal shift in composition between samples collected pre-2010 with those collected post-2010 that also followed temporal changes in physico-chemistry, suggesting a tipping point occurred in the system. There were subtle differences in diatom assemblages between lake inlets and outlets, most evident in the precipitation/groundwater fed north basin. Lastly, a clear lake order effect was detected in both basins with upper basin sites differing from lower basin sites at similar altitude. We conclude that diatoms were effective in documenting the environmental changes that occurred in these alpine waters, specifically reflecting the abrupt change in physico-chemistry (concurrent tipping point in diatom assemblages) and the concomitant increase in surface water homogeneity and similarity of diatom assemblages over the study period.

Hybrid conferences are in-person events that have an online component. This type of meeting format was rare before the COVID-19 pandemic, but started to become more common recently given the asynchronous global progression of the pandemic, the uneven access to vaccines and different travel regulations among countries that led to a large proportion of participants being unable to attend conferences in person. Here we report the organization of a middle-sized (581 participants: 159 onsite, 422 online) international hybrid conference that took place in France in September 2021. We highlight particular organizational challenges inherent to this relatively new type of meeting format. Furthermore, we surveyed both in-person and online participants to better understand their conference experience and to propose improvements based on the feedback received. Finally, we compare the advantages and disadvantages of three types of conferences (onsite-only, online-only and hybrid) and suggest that hybrid events should be favored in the future because they offer the most flexibility to participants. We conclude by proposing suggestions and ways forward to maximize accessibility and inclusivity of hybrid conferences. Our study brings novel insights on the challenges and opportunities created by hybrid conferences, by reporting not only the organizing committee experience but also by considering the participants’ perspective.

Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.

The Macun lakes form a high-alpine (> 2,600 m asl) cirque landscape (3.6 km2) in the Swiss National Park, comprising 26 small lakes together with a number of temporary ponds. Streams interconnect the four largest lakes, forming the drainage network that flows into the Inn River at the town of Lavin. The drainage network of Macun consists of a north and a south basin that overlie an ortho-gneiss, meta-granitoid bedrock. The south basin is influenced by various rock glaciers. The physico-chemistry of surface waters at 10 sites has been monitored annually in midsummer since 2001. Further, an YSI EXO2 Multiparameter Sonde (Exosonde) with various water quality sensors has been employed since 2016 at the last lake in the network to examine seasonal and diel patterns in physico-chemistry. Results showed clear physico-chemical differences between the two basins, which mostly reflect rockglacier inputs in the south basin. Nitrogen values were two-fold higher and particulate phosphorus values two-fold lower in the south basin than in the north basin. Over time, the physico-chemistry in the two basins became more homogeneous, with a reduction in rock-glacial inputs in the south basin and an overall decrease in nitrogen in the catchment. Data from 30 springs and tributaries sampled in 2002 and 2017 reflected the basin differences and temporal changes observed at the primary study sites. Continuous temperature records showed north basin streams to be ca. 3°C warmer than south-basin streams, but with high inter-annual variation that reflected annual differences in weather and no evidence of a general change over time (increase or decrease). Exosonde data revealed strong seasonality in measured parameters as well as seasonality in diel patterns (e. g., dissolved oxygen, temperature, chlorophyll-a); diel fluctuations were most pronounced in summer and least in winter. The results highlight the importance of long-term monitoring for understanding ecosystem state changes in alpine freshwaters, especially during periods of rapid environmental change.

Environmental stress is a major driver of ecological and evolutionary processes in nature. To cope with stress, organisms can adjust through phenotypic plasticity and/or adapt through genetic change. Here, we compared short-term behavioural (activity) and physiological (corticosterone levels, CORT) responses of Rana arvalis tadpoles from two divergent populations (acid origin, AOP, versus neutral origin, NOP) to acid and predator stress. Tadpoles were initially reared in benign conditions at pH 7 and then exposed to a combination of two pH (acid versus neutral) and two predator cue (predator cue versus no predator cue) treatments. We assessed behavioural activity within the first 15 min, and tissue CORT within 8 and 24 h of stress exposure. Both AOP and NOP tadpoles reduced their activity in acidic pH, but the response to the predator cue differed between the populations: AOP tadpoles increased whereas NOP tadpoles decreased their activity. The AOP and NOP tadpoles differed also in their CORT responses, with AOP being more responsive (CORT levels of NOP tadpoles did not differ statistically across treatments). After 8 h exposure, AOP tadpoles had elevated CORT levels in the acid-predator cue treatment and after 24 h exposure they had elevated CORT levels in all three stress treatments (relative to the benign neutral-no-cue treatment). These results suggest that adaptation to environmental acidification in R. arvalis is mediated, in part, via behavioural and hormonal plasticity.

Aim: Biological invasions are a major threat to biodiversity in aquatic and terrestrial habitats. Insects represent an important group of species in freshwater and terrestrial habitats, and they constitute a large proportion of non-native species. However, while many non-native insects are known from terrestrial ecosystems, they appear to be less represented in freshwater habitats. Comparisons between freshwater and terrestrial habitats of invader richness relative to native species richness are scarce, which hinders syntheses of invasion processes. Here, we used data from three regions on different continents to determine whether non-native insects are indeed under-represented in freshwater compared with terrestrial assemblages.
Location: Europe, North America, New Zealand.
Methods: We compiled a comprehensive inventory of native and non-native insect species established in freshwater and terrestrial habitats of the three study regions. We then contrasted the richness of non-native and native species among freshwater and terrestrial insects for all insect orders in each region. Using binomial regression, we analysed the proportions of non-native species in freshwater and terrestrial habitats. Marine insect species were excluded from our analysis, and insects in low-salinity brackish water were considered as freshwater insects.
Results: In most insect orders living in freshwater, non-native species were under-represented, while they were over-represented in a number of terrestrial orders. This pattern occurred in purely aquatic orders and in orders with both freshwater and terrestrial species. Overall, the proportion of non-native species was significantly lower in freshwater than in terrestrial species.
Main conclusions: Despite the numerical and ecological importance of insects among all non-native species, non-native insect species are surprisingly rare in freshwater habitats. This is consistent across the three investigated regions. We review hypotheses concerning species traits and invasion pathways that are most likely to explain these patterns. Our findings contribute to a growing appreciation of drivers and impacts of biological invasions.

1. The immune system is costly to maintain and use because it requires a lot of energy. This can make parasite resistance dependent on host nutritional state. The dependence of immune function on host condition can have broad ecological (e.g., disease dynamics) and evolutionary (e.g., expression of trade-offs related to parasite resistance) consequences.
2. Research on the dependence of immune function on host condition is typically conducted in laboratory experiments that manipulate either the quantity or composition of available resources. Such studies are essential in establishing conceptual frameworks, but their results are difficult to generalise to natural populations because the experimental treatments may deviate from natural variation in host resource level and use.
3. We examined the condition dependence of immune function in a generalist freshwater snail Lymnaea stagnalis by relating the activity of two immune parameters of snail haemolymph, phenoloxidase (PO)-like and antibacterial activity, to snail resource level and use using field-collected individuals. We measured several variables that reflect the snails' quality based on their recent (i.e., within the past few days; amount and stable isotope composition [δ¹⁵N and δ¹³C] of produced faeces) and longer-term (i.e., weeks to months; stable isotope composition of tissues) resource use.
4. The PO-like activity of the snails' haemolymph was condition-dependent. Snails that had recently consumed food from higher trophic levels, presumably including more animal protein (high δ¹⁵N values of faeces), had a stronger defence. Additionally, snails with low energy (i.e., lipid) reserves in their tissues (high δ¹³C values of tissues) showed higher PO-like activity. The antibacterial activity of the snails' haemolymph was not condition dependent.
5. The finding of the importance of the composition of recently consumed food on immune function (namely PO-like activity) suggests that the parasite resistance of snails may change rapidly depending on the type of resources available in their environment. Thus, environmental variation may influence the outcome of host–parasite interactions on fine spatial and temporal scales. Furthermore, the negative relationship between the snails' energy reserves and PO-like activity suggests substantial energetic costs of immune activity in L. stagnalis.

Globally, the sanitation needs of three billion people are met by non-sewered sanitation. Small-footprint treatment technologies are needed that are appropriate for dense urban areas. Blackwater (BW) (or fecal sludge), contains more than 95% liquid, and dewatering it without conditioning requires large footprints. Chemically-enhanced dewatering with conditioners is a promising option to increase dewatering performance and reduce required footprints. However, before implementation of this solution there is a need for increased knowledge on selection and dosing of conditioners. This study evaluated bio-based and synthetic conditioners (chitosan, tannin-, and starch-based, synthetic with and without poly-acrylamide) with 14 types of BW from five countries. The supernatant after settling with jar-tests was analyzed to quantify optimal dose and dewatering performance. The reduction of total chemical oxygen demand (COD) was >55%, achieved by removal of particulate constituents with mainly soluble COD remaining in the supernatant. A reduction in particulate COD could lead to increased efficiency of soluble COD in supernatant treatment. Bio-based conditioners are as effective as synthetic conditioners, and when performance was variable, it was due to differing properties of TSS, TS, EC and pH. Optimal conditioner dose for synthetic conditioners and chitosan could be predicted using concentrations of total solids (TS) (R² > 0.7), whereas optimal dose for starch- and tannin-based conditioners could be predicted with electrical conductivity (EC) (R² > 0.8), and colloid titration (R² > 0.8). In addition, real-time optical TSS and EC sensors could accurately predict chitosan dose for fresh BW treated at source (R² = 0.97, R² = 0.95). This study validates that use of conditioners for dewatering with highly variable BW can be implemented with real-time measurements for optimal dose, in globally relevant implementations.

Invasive species can facilitate the spread of pathogens by first providing asymptomatic host reservoirs, and then driving disease outbreaks in native populations through pathogen spillover. An example of this are invasive crayfish species in Europe (Faxonius limosus, Pacifastacus leniusculus, Procambarus clarkii), which carry the deadly plague agent (Aphanomyces astaci). Effective disease management requires comprehensive monitoring, however, pathogen detection in carrier populations with low pathogen prevalence and intensities is challenging. We simultaneously collected and analysed crayfish tissue samples of invasive crayfish populations and water samples to compare A. astaci detection in different sample types using quantitative PCR. Combined, the two sampling methods revealed A. astaci presence with DNA concentrations above limit of detection (LOD; the lowest concentration which can be detected with reasonable certainty) in 13 of 23 invasive crayfish populations. In four additional sites, A. astaci DNA concentrations below LOD were found in water. In four populations only were A. astaci concentrations above LOD detected in both sample types and in three populations in concentrations above LOD in tissue but below LOD in water. The likely reason for these discrepancies is the low A. astaci prevalence and concentration in resistant invasive crayfish, which limit detection reliability. Consistency may be improved by timing surveys with seasonal periods of high A. astaci abundance and by increasing water sampling effort. Considering the ease of collecting eDNA samples, compared to crayfish tissue sampling, eDNA methods would facilitate frequent and comprehensive surveys. However, remaining uncertainties in eDNA-based detection reveal the relevance of combining monitoring tools to improve detection of invasive pathogens and their management.

In high-altitude Alpine streams, seasonal cycles of snowmelt, glacial melt, and rainfall drive variation in the availability of algal food resources. Yet, high-altitude streams also exhibit varying degrees of flow intermittency, ranging from solely winter-drying streams to others that dry periodically throughout summer and autumn. These environmental drivers may interact in different ways to determine the functional trophic base of macroinvertebrates inhabiting high-altitude streams. Here, we estimated the proportional contribution of autochthonous resources to the assimilated diets of benthic macroinvertebrates in 26 headwater streams of Val Roseg, a high Alpine glacial catchment, using stable isotope analysis (δ¹³C and δ¹⁵N) of different macroinvertebrate families and their potential food sources. We compared dietary estimates along a gradient of flow intermittency and across three seasons (Alpine spring, summer, and autumn). Assimilation from autochthonous sources was highest for collector-gatherers and filter feeders in spring, and for grazers in summer. Grazers had higher estimated assimilation from autochthonous sources in intermittent streams than in perennial streams, particularly in summer, while collector-gatherers showed little effect of flow intermittency on dietary estimates. However, responses were highly taxon-specific, with different responses to variation in flow intermittency and season across families within functional groups. Our results suggest that frequent summer-drying events represent tradeoffs between greater access to algal food resources and a higher risk of desiccation, but that differing life history and functional feeding traits across macroinvertebrate taxa drive marked variation in the risks or benefits associated with inhabitants of drying streams.

Background: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses.

Results: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models.

Conclusions: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.

Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics – and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.

Erstmals wurde die Verbreitung und Artenvielfalt der Grundwasserflohkrebse im Einzugsgebiet der Töss, unter Einbezug von Bürgerwissenschaft, räumlich hoch aufgelöst untersucht. Bei der durch die Eawag und die Universität Zürich durchgeführten Studie wurden vier in dieser Region bisher noch nicht nachgewiesene Arten gefunden. Auch konnte gezeigt werden, dass die Daten zur Fundwahrscheinlichkeit, die von Wasserversorgungen erhoben wurden, mit denen von Forschenden vergleichbar sind.

Background: Patients with cancer are at high risk for severe coronavirus disease 2019 (COVID-19) infection. Knowledge regarding the efficacy of the messenger RNA (mRNA) vaccines in actively treated cancer patients is limited as they had been excluded from the pivotal studies of these vaccines. We evaluated humoral and cellular immune responses in cancer patients after double vaccination and a booster dose and identified disease- and treatment-related factors associated with a reduced immune response. We also documented the number and outcome of breakthrough infections.
Patients and methods: Patients with metastatic solid malignancies undergoing active treatment were included if they had received two doses of the severe acute respiratory syndrome coronavirus 2 mRNA vaccines BNT162b2 or mRNA-1273 and a booster dose. Other causes of immunosuppression and previous COVID-19 infections (positive anti-nucleocapsid titers) were exclusion criteria. Anti-spike antibodies, neutralizing antibodies (nAbs) and T-cell responses were assessed about 6 months after the two-dose vaccination and 4 weeks after the booster.
Results: Fifty-one patients had pre-booster and 46 post-booster measurements. Anti-spike titers after two vaccine doses were highly variable and significantly lower in older patients, during treatment with chemotherapy compared to targeted and endocrine treatments and in patients with low CD4+ or CD19+ cell counts. The booster dose led to a significant increase in anti-spike antibodies and nAbs, achieving almost uniformly high titers, irrespective of baseline and treatment factors. The cellular immune response was also significantly increased by the booster, however generally more stable and not influenced by baseline factors and treatment type. Seventeen patients (33%) experienced breakthrough infections, but none required hospital care or died from COVID-19.
Conclusions: An mRNA vaccine booster dose is able to increase humoral and cellular immune responses and to overcome the immunosuppressive influence of baseline and treatment factors in cancer patients. Breakthrough infections were uniformly mild in this vaccinated high-risk population.

Microbial life in natural biofilms is dominated by prokaryotes and microscopic eukaryotes living in dense association. In stream ecosystems, microbial biofilms influence primary production, elemental cycles, food web interactions as well as water quality. Understanding how biofilm communities respond to anthropogenic impacts, such as wastewater treatment plant (WWTP) effluent, is important given the key role of biofilms in stream ecosystem function. Here, we implemented 16S and 18S rRNA gene sequencing of stream biofilms upstream (US) and downstream (DS) of WWTP effluents in four Swiss streams to test how bacterial and eukaryotic communities respond to wastewater constituents. Stream biofilm composition was strongly affected by geographic location – particularly for bacteria. However, the abundance of certain microbial community members was related to micropollutants in the wastewater – among bacteria, micropollutant-associated members were found e.g. in Alphaproteobacteria, and among eukaryotes e.g. in Bacillariophyta (algal diatoms). This study corroborates several previously characterized responses (e.g. as seen in diatoms), but also reveals previously unknown community responses – such as seen in Alphaproteobacteria. This study advances our understanding of the ecological impact of the current wastewater treatment practices and provides information about potential new marker organisms to assess ecological change in stream biofilms.

Cereals are very common and widespread crops in Europe. Aphids are a diverse group of herbivorous pests on cereals and one of the most important limiting factors of cereal production. Here, we present an overview of knowledge about the taxonomy, biodiversity, and ecology of cereal aphid parasitoids in Europe, an important group of natural enemies contributing to cereal aphid control. We review the knowledge obtained from the integrative taxonomy of 26 cereal aphid primary parasitoid species, including two allochthonous species (Lysiphlebus testaceipes and Trioxys sunnysidensis) and two recently described species (Lipolexis labialis and Paralipsis brachycaudi). We further review 28 hyperparasitoid species belonging to three hymenopteran superfamilies and four families (Ceraphronoidea: Megaspillidae; Chalcidoidea: Pteromalidae, Encyrtidae; Cynipoidea: Figitidae). We also compile knowledge on the presence of secondary endosymbionts in cereal aphids, as these are expected to influence the community composition and biocontrol efficiency of cereal aphid parasitoids. To study aphid–parasitoid–hyperparasitoid food webs more effectively, we present two kinds of DNA-based approach: (i) diagnostic PCR (mainly multiplex PCR), and (ii) DNA sequence-based methods. Finally, we also review the effects of landscape complexity on the different trophic levels in the food webs of cereal aphids and their associated parasitoids, as well as the impacts of agricultural practices and environmental variation.

Upon starvation diploid cells of the facultative sexual yeast Saccharomyces cerevisiae undergo sporulation, forming four metabolically quiescent and robust haploid spores encased in a degradable ascus. All endosymbionts, whether they provide net benefits or costs, utilize host resources; in yeast, this should induce an earlier onset of sporulation. Here, we tested whether the presence of endosymbiotic dsRNA viruses (M satellite and L-A helper) correspond with higher sporulation rate of their host, S. cerevisiae. We find that S. cerevisiae hosting both the M and L-A viruses (so-called “killer yeasts”) have significantly higher sporulation efficiency than those without. We also found that the removal of the M virus did not reduce sporulation frequency, possibly because the L-A virus still utilizes host resources with and without the M virus. Our findings indicate that either virulent resource use by endosymbionts induces sporulation, or that viruses are spread more frequently to sporulating strains. Further exploration is required to distinguish cause from effect.

Fische, Invertebraten oder Makrophyten – im Gewässermanagement stehen traditionellerweise die aquatischen Lebewesen im Vordergrund. Im vorliegenden Artikel betrachten wir unsere Flüsse und Seen aus der Vogelperspektive – mit speziellem Fokus auf die insektenfressenden Vögel. Wir zeigen, dass aquatische Insekten eine besonders wichtige Nahrungsquelle sind aufgrund der spezifischen Fettsäuren, die sie enthalten. Für insektenfressende Vögel ist es deshalb entscheidend, dass in kritischen Lebensphasen, wie z. B. während der Aufzucht der Jungen, genügend aquatische Insekten vorhanden sind. Menschliche Eingriffe in die Umwelt, wie z. B. die Intensivierung der Landwirtschaft oder der Klimawandel, haben die Menge, Qualität und zeitliche Verfügbarkeit von Insekten verändert und damit auch die Nahrungsgrundlage für insektenfressende Vögel. Wir schliessen mit Überlegungen, wie das Gewässermanagement (z. B. Revitalisierung, Gewässerschutz, Einzugsgebietsmanagement) zum Schutz der Vogelvielfalt und zur Förderung des grün-blauen Nahrungsnetzes beitragen kann.

Poissons, invertébrés ou macrophytes – dans la gestion des cours d'eau, les organismes aquatiques sont traditionnellement au premier plan. Dans le présent article, nous considérons nos rivières et nos lacs du point de vue des oiseaux – avec un accent particulier sur les oiseaux insectivores. Nous montrons que les insectes aquatiques sont une source de nourriture particulièrement importante en raison des acides gras spécifiques qu'ils contiennent. Pour les oiseaux insectivores, il est donc crucial de disposer de suffisamment d'insectes aquatiques durant les phases critiques de leur vie, comme pendant l'élevage des jeunes. Les interventions humaines dans l'environnement, telles que l'intensification de l'agriculture ou le changement climatique, ont modifié la quantité, la qualité et la disponibilité temporelle des insectes, et donc la base alimentaire des oiseaux insectivores. Nous concluons par des réflexions sur la manière dont la gestion des cours d'eau (p. ex. revitalisation, protection des eaux, gestion des bassins versants) peut contribuer à la protection de la diversité des oiseaux et à la promotion du réseau alimentaire vert et bleu.

Gold mining is currently one of the main anthropogenic sources of mercury in the environment. In this study, the total mercury content was measured in bottom sediments, benthic macroinvertebrates (mayfly larvae), and fish (Siberian dace) along the Boroo River in northern Mongolia. There was a gold recovery plant in the middle reaches of the river until the mid-twentieth century; an accident there in the 1950s caused a mercury spill. We found an increased content of mercury in measured ecosystem components near the plant compared to the upper reaches of the river. The mercury content in sediments varied from trace amounts in the upper Boroo to 2200 ng/g dry weight (dw) in the vicinity of the plant ruins. The mercury content in mayfly larvae ranged from 50 to 2940 ng/g dw and had a spatial pattern as sediments, with the highest concentrations near the plant. The mercury content in sediments was lower at the mouth of the Boroo River than near the plant, reflecting the lower boundary of the mercury spill. Maximum values of mercury content in fish muscle were found at the river’s mouth and were several times higher than in other rivers of northern Mongolia. Median mercury content in muscles of dace from the lower Boroo in 2016 has doubled since studies in 2010-2012, which may be the result of current mercury releases from gold mining.

Insect host–parasitoid interactions abound in nature and are characterized by a high degree of host specialization. In addition to their behavioral and immune defenses, many host species rely on heritable bacterial endosymbionts for defense against parasitoids. Studies on aphids and flies show that resistance conferred by symbionts can be very strong and highly specific, possibly as a result of variation in symbiont-produced toxins. I argue that defensive symbionts are therefore an important source of diversifying selection, promoting the evolution of host specialization by parasitoids. This is likely to affect the structure of host–parasitoid food webs. I consider potential changes in terms of food web complexity, although the nature of these effects will also be influenced by whether maternally transmitted symbionts have some capacity for lateral transfer. This is discussed in the light of available evidence for horizontal transmission routes. Finally, I propose that defensive mutualisms other than microbial endosymbionts may also exert diversifying selection on insect parasitoids.

With mounting scientific evidence demonstrating adverse global climate change (GCC) impacts to water quality, water quality policies, such as the Total Maximum Daily Loads (TMDLs) under the U.S. Clean Water Act, have begun accounting for GCC effects in setting nutrient load-reduction policy targets. These targets generally require nutrient reductions for attaining prescribed water quality standards (WQS) by setting safe levels of nutrient concentrations that curtail potentially harmful cyanobacteria blooms (CyanoHABs). While some governments require WQS to consider climate change, few tools are available to model the complex interactions between climate change and benthic legacy nutrients. We present a novel process-based integrated assessment model (IAM) that examines the extent to which synergistic relationships between GCC and legacy Phosphorus release could compromise the ability of water quality policies to attain established WQS. The IAM is calibrated for simulating the eutrophic Missisquoi Bay and watershed in Lake Champlain (2001–2050). Water quality impacts of seven P-reduction scenarios, including the 64.3% reduction specified under the current TMDL, were examined under 17 GCC scenarios. The TMDL WQS of 0.025 mg/L total phosphorus is unlikely to be met by 2035 under the mandated 64.3% reduction for all GCC scenarios. IAM simulations show that the frequency and severity of summer CyanoHABs increased or minimally decreased under most climate and nutrient reduction scenarios. By harnessing IAMs that couple complex process-based simulation models, the management of water quality in freshwater lakes can become more adaptive through explicit accounting of GCC effects on both the external and internal sources of nutrients.

Biogeographical transition zones present good opportunities for studying the effect of the past ice ages on genetic structure of species because secondary contact zones of post-glacial lineages can be formed. In this study, we investigated the population genetic structure of the marbled rock crab, Pachygrapsus marmoratus along the coasts of Turkey. We genotyped 334 individuals from the Black Sea, the Turkish Straits System (TSS), the Aegean, and the Eastern Mediterranean basins. In order to reveal its evolutionary history and its population connectivity, we used mitochondrial CO1 region and five microsatellite loci. CO1 analyzes also included 610 additional samples from Genbank, which covered most of its distribution range. Both microsatellites and mtDNA showed decreased diversity in sampling sites of the TSS and the Black Sea as compared to those along the Aegean and the Levantine coasts. There is an especially strong geographical pattern in distributions of haplotypes in mtDNA, most probably as a result of genetic drift in the Black Sea and the Sea of Marmara (SoM). Microsatellite data analyses revealed two genetically distinct clusters of P. marmoratus (clusters C and M). While individuals belonging to cluster C are present in all the sampling locations, those belonging to cluster M are only detected along the Mediterranean coasts including the Aegean and the Levantine basins. These clusters shared similar haplotypes in the Mediterranean. Haplotypes of two sympatric clusters could be similar due to incomplete lineage sorting of ancestral polymorphisms. In order to retrieve the complex demographic history and to investigate evolutionary processes resulting in sympatric clusters in the Aegean Sea and the Levantine basin, mitochondrial markers with faster mutation rates than CO1 and/or SNP data will be useful.

Knowledge on the diversity and distribution of subterranean organisms is still scattered, even in faunistically relatively well-researched countries such as Switzerland. This is mostly due to the restricted access to these subterranean habitats. Better knowledge on these organisms is needed, because they contribute substantially to overall biodiversity of a region, often contain unique elements of biodiversity, and can potentially be indicative of the ecological status of subterranean ecosystems that are providing important ecosystem services such as drinking water. Past research on subterranean organisms has often used highly specialised sampling techniques and expert knowledge. Here, we show that inclusion of non-professionals can be an alternative and highly promising sampling strategy. We retrieved citizen science-based samples from municipal groundwater wells across Switzerland, mainly from the Swiss Plateau. Opportunistic samples from 313 sites revealed a previously undocumented groundwater fauna including organisms from different major invertebrate groups, with a dominance of crustaceans. Here, we studied amphipods of the genus Niphargus. Among all 363 individuals sampled, we found in total eight nominal species. Two of them, namely N. fontanus and N. kieferi, are reported for Switzerland for the first time. We also found four further phylogenetic lineages that are potentially new species to science. One of them is here formally described as Niphargus arolaensis sp. nov. The description is based on molecular and morphometric data. Our study proves the suitability of citizen science to document subterranean diversity, supports groundwater conservation efforts with data, and raises awareness for the relevance and biodiversity of groundwater amphipods among stakeholders.

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km² riverine network to study the influence of spatial connectivity and dispersal strategies on the spatial distribution of their genetic diversity. We found a significant imprint of the effects of riverine network connectivity on the local and global genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness significantly increased towards more central nodes of the network. This was also seen for observed heterozygosity, yet not for expected heterozygosity. Genetic differentiation increased with instream distance. In simulation models, depending on the mutational model assumed, upstream movement probability and dispersal rate, respectively, emerged as key factors explaining the empirically observed distribution of local genetic diversity and genetic differentiation. Surprisingly, the role of site-specific carrying capacities, for example by assuming a direct dependency of population size on local river size, was less clear cut: while our best fitting model scenario included this feature, over all simulations, scaling of carrying capacities did not increase data-model fit. This highlights the importance of dispersal behaviour along spatial networks in shaping population genetic diversity.

Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km² Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection.

Intermittent rivers and ephemeral streams (IRES) – waterways in which flow ceases periodically or that dry completely – are found worldwide, and their frequency and extent are expected to increase in the future in response to global climate change and growing anthropogenic demand for fresh water. Repeated wet–dry cycles generate highly dynamic settings within river networks composed of aquatic and terrestrial habitats, which act as evolutionary triggers for aquatic and terrestrial biota. Drying also alters functions and processes within river networks, with consequences for ecosystem services. Despite the emergence of promising conceptual and methodological developments, our understanding of the occurrence and diversity of organisms in these ecosystems is limited primarily due to their coupled aquatic–terrestrial characteristics. Novel genomic tools based on high-throughput sequencing have the potential to tackle unanswered questions of pivotal importance to predict future change in IRES. Here, we outline why genomic tools are needed to assess these dynamic ecosystems from the population to the metacommunity scale, and their potential role in bridging ecological–evolutionary dynamics.

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Rivers are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. Traditional monitoring methods for ecological assessments are costly and time-intensive. Here, we compared monitoring of macroinvertebrates based on environmental DNA (eDNA) sampling with monitoring based on traditional kick-net sampling to assess biodiversity patterns at 92 river sites covering all major Swiss river catchments. From the kick-net community data, a biotic index (IBCH) based on 145 indicator taxa had been established. The index was matched by the taxonomically annotated eDNA data by using a machine learning approach. Our comparison of diversity patterns only uses the zero-radius Operational Taxonomic Units assigned to the indicator taxa. Overall, we found a strong congruence between both methods for the assessment of the total indicator community composition (gamma diversity). However, when assessing biodiversity at the site level (alpha diversity), the methods were less consistent and gave complementary data on composition. Specifically, environmental DNA retrieved significantly fewer indicator taxa per site than the kick-net approach. Importantly, however, the subsequent ecological classification of rivers based on the detected indicators resulted in similar biotic index scores for the kick-net and the eDNA data that was classified using a random forest approach. The majority of the predictions (72%) from the random forest classification resulted in the same river status categories as the kick-net approach. Thus, environmental DNA validly detected indicator communities and, combined with machine learning, provided reliable classifications of the ecological state of rivers. Overall, while environmental DNA gives complementary data on the macroinvertebrate community composition compared to the kick-net approach, the subsequently calculated indices for the ecological classification of river sites are nevertheless directly comparable and consistent.

Vector-borne parasites often manipulate hosts to attract uninfected vectors. For example, parasites causing malaria alter host odor to attract mosquitoes. Here, we discuss the ecology and evolution of fruit-colonizing yeast in a tripartite symbiosis—the so-called "killer yeast" system. "Killer yeast" consists of Saccharomyces cerevisiae yeast hosting two double-stranded RNA viruses (M satellite dsRNAs, L-A dsRNA helper virus). When both dsRNA viruses occur in a yeast cell, the yeast converts to lethal toxin‑producing "killer yeast" phenotype that kills uninfected yeasts. Yeasts on ephemeral fruits attract insect vectors to colonize new habitats. As the viruses have no extracellular stage, they depend on the same insect vectors as yeast for their dispersal. Viruses also benefit from yeast dispersal as this promotes yeast to reproduce sexually, which is how viruses can transmit to uninfected yeast strains. We tested whether insect vectors are more attracted to killer yeasts than to non‑killer yeasts. In our field experiment, we found that killer yeasts were more attractive to Drosophila than non-killer yeasts. This suggests that vectors foraging on yeast are more likely to transmit yeast with a killer phenotype, allowing the viruses to colonize those uninfected yeast strains that engage in sexual reproduction with the killer yeast. Beyond insights into the basic ecology of the killer yeast system, our results suggest that viruses could increase transmission success by manipulating the insect vectors of their host.

The current biodiversity crisis calls for appropriate methods for assessing biodiversity. In this respect, environmental DNA (eDNA) holds great promise, especially for aquatic ecosystems. While initial eDNA studies assessed biodiversity at single sites, technology now allows analyzing samples from many points simultaneously. However, the selection of these sites has been mostly motivated on an ad‐hoc basis. To this end, hydrology‐based models might offer a unique guidance on where to sample eDNA to most effectively reconstruct spatial patterns of biodiversity. Here, we performed computer simulations to identify best‐practice criteria for the choice of positioning of eDNA sampling sites in river networks. To do so, we combined a hydrology‐based eDNA transport model with a virtual river network reproducing the scaling features of real rivers. In particular, we conducted simulations investigating scenarios of different number and location of eDNA sampling sites in a riverine network, different spatial taxon distributions, and different eDNA measurement errors. We found that, due to hydrological controls, non‐uniform patterns of eDNA concentration arise even if the taxon distribution is uniform and decay is neglected. Best practices for sampling site selection depend on the taxon's spatial distribution: when taxa are concentrated in some hotspots and only few sampling sites can be placed, it is better to preferentially locate them in the downstream part of the catchment; when taxa are more evenly distributed, and/or many sites can be placed, these should be preferentially located upstream. We also found that uncertainties in eDNA concentration estimates do not necessarily hamper model predictions. Knowledge of eDNA decay rates improves model predictions, highlighting the need for empirical estimates of these rates under relevant environmental conditions. Our simulations help define strategies for designing eDNA sampling campaigns in river networks and can guide the sampling effort of field ecologists and environmental authorities.

For most micropollutants (MPs) present in surface waters, such as pesticides and pharmaceuticals, the contribution of biotransformation to their overall removal from lake ecosystems is largely unknown. This study aims at empirically determining the biotransformation rate constants for 35 MPs at different periods of the year and depths of a meso-eutrophic lake. We then tested statistically the association of environmental parameters and microbial community composition with the biotransformation rate constants obtained. Biotransformation was observed for 14 out of 35 studied MPs for at least one sampling time. Large variations in biotransformation rate constants were observed over the seasons and between compounds. Overall, the transformation of MPs was mostly influenced by the lake's temperature, phytoplankton density and bacterial diversity. However, some individual MPs were not following the general trend or association with microorganism biomass. The antidepressant mianserin, for instance, was transformed in all experiments and depths, but did not show any relationship with measured environmental parameters, suggesting the importance of specific microorganisms in its transformation. The results presented here contribute to our understanding of the fate of MPs in surface waters and thus support improved risk assessment of contaminants in the environment.

Ecological stability refers to a family of concepts used to describe how systems of interacting species vary through time and respond to disturbances. Because observed ecological stability depends on sampling scales and environmental context, it is notoriously difficult to compare measurements across sites and systems. Here, we apply stochastic dynamical systems theory to derive general statistical scaling relationships across time, space, and ecological level of organisation for three fundamental stability aspects: resilience, resistance, and invariance. These relationships can be calibrated using random or representative samples measured at individual scales, and projected to predict average stability at other scales across a wide range of contexts. Moreover deviations between observed vs. extrapolated scaling relationships can reveal information about unobserved heterogeneity across time, space, or species. We anticipate that these methods will be useful for cross-study synthesis of stability data, extrapolating measurements to unobserved scales, and identifying underlying causes and consequences of heterogeneity.

Motivation: We compiled a global database of long-term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones.
Main types of variables contained: The database includes 11,386 time-series of riverine fish community catch data, including 646,270 species-specific abundance records, together with metadata related to the geographical location and sampling methodology of each time-series.
Spatial location and grain: The database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins world-wide.
Time period and grain: The database encompasses the period 1951–2019. Each time-series is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years).
Major taxa and level of measurement: The database includes 944 species of ray-finned fishes (Class Actinopterygii). Software format: csv.
Main conclusion: Our collective effort provides the most comprehensive long-term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm.

Exploitation of hydropower potential in alpine areas undermines the ecological integrity of rivers. Damming and water abstraction substantially alter the physical habitat template of rivers, with strong repercussions on aquatic communities and their resources. Tools are needed to predict and manage the consequences of these alterations on the structure and functioning of macroinvertebrate communities and resource availability in alpine streams. We developed habitat preference models for taxa, functional feeding guilds, and organic resources to quantify the effects of discharge alteration on macroinvertebrate communities in two alpine streams. Our physical habitat model related an indirect measure of bottom hydraulic forces (FST hemispheres) to the distribution of macroinvertebrate taxa and their resources. We observed that flow-dependent habitat availability for macroinvertebrate communities generally decreased with increasing water abstraction. We were able to relate these changes to near-bed hydraulic conditions. Our results suggest, however, the existence of upper discharge thresholds delimiting optimal habitat conditions for taxa. In contrast, we found weak effects of near-bed hydraulic conditions on resource distribution. Overall, our findings contribute towards predicting the impacts of water abstraction on macroinvertebrate communities in small alpine streams and the benefits of baseflow restoration.

Cities are uniquely complex systems regulated by interactions and feedbacks between nature and human society. Characteristics of human society - including culture, economics, technology and politics - underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing research on urban ecology and evolutionary biology has coincided with growing interest in eco-evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco-evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological - and even social - significance. Still, little work fully integrates urban evolutionary biology and eco-evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban "socio-eco-evolutionary dynamics." Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.

River floodplains are spatially diverse ecosystems that respond quickly to flow variations and disturbance. However, it remains unclear how flow alteration and hydrological disturbance impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we examined the spatial and seasonal dynamics of microbial communities in aquatic (benthic) and terrestrial habitats of three hydrologically contrasting (natural flow, residual flow, hydropeaking flow) floodplain systems. Microbial communities (alpha and beta diversity) differed more among floodplain habitats than between riverine floodplains. Microbial communities in all systems displayed congruent seasonal effects. In the residual and hydropeaking systems, an experimental flood was released from a reservoir to mimic a natural high flow event causing hydromorphological disturbance. The experimental flood caused a temporary shift in microbial communities by releasing microbes from the reservoir as well as redistributing communities among floodplain habitats. The flood-mediated shift in community structures had only a transient impact as pelagic bacteria did not persist within floodplain habitats over time after the flood. More frequent pulse disturbances might lead to an alternate structure of bacterial communities in floodplains over time.

To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phosphorus [TP] = 0.06 and total nitrogen [TN] = 0.7 mg L⁻¹), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chlorophyll a (Chl a) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chl a than Boreal lakes, where the temperature anomaly from the long-term average, during a summer heatwave was the highest (+4°C) and showed a significant, exponential relationship with stratification strength. This European survey represents a summer snapshot of phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are both affected by climate change, are better predictors for phytoplankton biomass in nutrient-rich lakes than nutrient concentrations and surface temperature.

The study of ecosystem services requires the integration of different observational points. This is particularly true in Water, as this element continuously cycles, increasing chances of interaction among services originating in different ecosystems. However, aquatic scientists historically approached the study of inland/freshwater and open/marine waters in different ways and this cultural division potentially hampers integrative approaches. Herein, we explored the literature pertaining to ecosystem services across the last 23 years, analysing 4,590 aquatic papers. By aggregating and intersecting topics included in this papers' collection using text-mining and topical network approaches, we saw that the study of local environmental conditions (e.g., river estuary management) and synergies and trade-offs between services (e.g., carbon sequestration and water purification) can display several potential conceptual links between freshwater and marine sciences. Our analyses suggest that to intersect ecosystem services across the aquatic continuum, the conceptual integration between marine and freshwater science must be reinforced, especially at the interface between different "salinity realms." Such integration should adopt a "system thinking" perspective, in which the focus is on multiple socio-ecological processes giving rise to interactions that are (i) biologically mediated, (ii) potentially conflicting, and (iii) entangled within networks.

In Lake Tanganyika, blooms of nitrogen-fixing (diazotrophic) cyanobacteria emerge, when the upper water column re-stratifies after a period of upwelling and convective mixing. During this seasonal transition, diazotrophic cyanobacteria exploit the abundant phosphate and fix nitrogen after other phytoplankton taxa have consumed the available nitrate. However, it remains less clear, which mechanisms favour diazotrophic cyanobacteria under more heavily stratified conditions with lower levels of excess phosphate and persistent nitrate-depletion. Here, we collected profiles of physicochemical parameters, nutrients and photo-pigments, as well as the medium- to large-sized phytoplankton community during two lake-wide cruises to elucidate to what extent the abundance of diazotrophic cyanobacteria in Lake Tanganyika may be controlled by the nitrate resupply through the thermocline into the euphotic zone. At stations where nitrate was depleted, but phosphate remained available near the surface, high densities of diazotrophic cyanobacteria were associated with a low nitrate supply to surface waters. Our data provide first support for two conceptual scenarios, where the relative position of the thermocline and the euphotic depth may create a functional niche for diazotrophic cyanobacteria: when the upward transport of nitrate into the euphotic zone is reduced by a subjacent thermocline, diazotrophic cyanobacteria, comprising Dolichospermum and Anabaenopsis, are key players in the medium-to large-sized phytoplankton community. By contrast, a thermocline located within the euphotic zone allows for a rapid vertical transport of nitrate for a thriving nitrate-assimilating phytoplankton community that evidently outcompetes diazotrophic cyanobacteria. This study highlights that, under nitrogen-depleted conditions, diazotrophic cyanobacteria can also grow in response to a reduced nutrient resupply to the productive surface waters.

Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.
Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes.
Availability and implementation: fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.

Trait based ecology has developed fast in the last decades, aiming to both explain mechanisms of community assembly, and predict patterns in nature, such as the effects of biodiversity shifts on key ecosystem processes. This body of work has stimulated the development of several conceptual frameworks and analytical methods, as well as the production of trait databases covering a growing number of taxa and organizational levels (from individuals to guilds). However, this breeding ground of novel concepts and tools currently lacks a general and coherent framework, under which functional traits can help ecologists organize their research aims, and serve as the common currency to unify several scientific disciplines. Specifically, we see a need to bridge the gaps between community ecology, ecosystem ecology, and evolutionary biology, in order to address the most pressing environmental issues of our time. To achieve this integration goal, we define a trait-integration continuum, which reconciles alternative trait definitions and approaches in ecology. This continuum outlines a coherent progression of biological scales, along which traits interact and hierarchically integrate from genetic information, to whole organism fitness-related traits, to trait syndromes and functional groups. Our conceptual scheme proposes that lower-level trait integration is closer to the inference of ecoevolutionary mechanisms determining population and community properties, whereas higher-level trait integration is most suited to the prediction of ecosystem processes. Within these two extremes, trait integration varies on a continuous scale, which relates directly to the inductive-deductive loop that should characterize the scientific method. With our proposed framework, we aim to facilitate scientists in contextualising their research based on the trait-integration levels that matter most to their specific goals. Explicitly acknowledging the existence of a trait-integration continuum is a promising way for framing the appropriate questions, thus obtaining reliable answers and results that are comparable across studies and disciplines.

Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge.

Food webs are often simulated dynamically to explore how trophic interactions influence resource and consumer abundances. As large trophic networks cannot be simulated in their original size – it would be too computationally expansive – they are shrunk by aggregating species together. However, key species may get lumped during this process, masking their unique role in their ecosystem. Therefore, a more systematic understanding of the aggregation effects on key positions is needed. Here, we study how six aggregation methods change 24 importance indices used to find key species in food webs. Our work was carried out on 76 aquatic food webs from the Ecopath with Ecosim database (EcoBase). The aggregation methods we considered were: 1) hierarchical clustering with the Jaccard index; 2) hierarchical clustering with the REGE index; 3) clustering within classic food web modules, which we refer to as 'density-based' modules; 4) clustering within 'predator-based modules' in which species fed on the same preys; 5) clustering within 'prey-based modules' in which species are fed upon by the same predators; and 6) clustering within 'groups' in which species share the same probability to interact with other groups. Hierarchical clustering with the REGE index produced the best results. Therefore, we recommend using it if we were interested in maintaining the identity of key species. The other algorithms could also be used to study specific network processes. However, we need to consider the bias they produce when masking important species.

The dynamics of coevolution between hosts and parasites are influenced by their genetic interactions. Highly specific interactions, where the outcome of an infection depends on the precise combination of host and parasite genotypes (G × G interactions), have the potential to maintain genetic variation by inducing negative frequency-dependent selection. The importance of this effect also rests on whether such interactions are consistent across different environments or modified by environmental variation (G × G × E interaction). In the black bean aphid, Aphis fabae, resistance to its parasitoid Lysiphlebus fabarum is largely determined by the possession of a heritable bacterial endosymbiont, Hamiltonella defensa, with strong G × G interactions between H. defensa and L. fabarum. A key environmental factor in this system is the host plant on which the aphid feeds. Here, we exposed genetically identical aphids harbouring three different strains of H. defensa to three asexual genotypes of L. fabarum and measured parasitism success on three common host plants of A. fabae, namely Vicia faba, Chenopodium album and Beta vulgaris. As expected, we observed the pervasive G × G interaction between H. defensa and L. fabarum, but despite strong main effects of the host plants on average rates of parasitism, this interaction was not altered significantly by the host plant environment (no G × G × E interaction). The symbiont-conferred specificity of resistance is thus likely to mediate the coevolution of A. fabae and L. fabarum, even when played out across diverse host plants of the aphid.

Species react to environmental change via plastic and evolutionary responses. While both of them determine species' survival, most studies quantify these responses individually. As species occur in communities, competing species may further influence their respective response to environmental change. Yet, how environmental change and competing species combined shape plastic and genetic responses to environmental change remains unclear. Quantifying how competition alters plastic and genetic responses of species to environmental change requires a trait-based, community and evolutionary ecological approach. We exposed unicellular aquatic organisms to long-term selection of increasing salinity - representing a common and relevant environmental change. We assessed plastic and genetic contributions to phenotypic change in biomass, cell shape, and dispersal ability along increasing levels of salinity in the presence and absence of competition. Trait changes in response to salinity were mainly due to mean trait evolution, and differed whether species evolved in the presence or absence of competition. Our results show that species' evolutionary and plastic responses to environmental change depended both on competition and the magnitude of environmental change, ultimately determining species persistence. Our results suggest that understanding plastic and genetic responses to environmental change within a community will improve predictions of species’ persistence to environmental change.

1. Recent studies demonstrate that ecological and evolutionary processes can occur over similar temporal and spatial scales and might thus frequently interact. Although concepts such as the evolving metacommunity, diffuse (co)evolution and community genetics integrate multi-species dynamics, most experimental studies usually consider how evolution affects only one focal species. Hence, our understanding of evolution in multi-species communities is still underdeveloped.
2. We highlight key community and evolutionary mechanisms and their interactions to facilitate a broader understanding of evolution in multi-species communities. We propose a framework that explicitly considers interactions between each of the four analogous processes of evolutionary biology (selection, gene flow, genetic drift and mutation) and community ecology (species sorting, dispersal, ecological drift and speciation).
3. Focusing on interactions between processes of evolutionary biology and community ecology enables explorations of the full range of eco-evolutionary dynamics in multi-species communities and guides the design of novel experiments. Furthermore, the proposed framework develops a shared language between evolutionary biologists and community ecologists and indicates new research avenues.
4. Overall, we propose that explicitly incorporating interactions between these evolutionary and community processes to study eco-evolutionary dynamics in multi-species communities will better inform broader questions about the maintenance of diversity and the resilience of diverse communities to disturbances, both natural and manmade. A free Plain Language Summary can be found within the Supporting Information of this article.

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features. Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary 'hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence) or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.

Surface-groundwater interactions in intermittent rivers and ephemeral streams (IRES), waterways which do not flow year-round, are spatially and temporally dynamic because of alternations between flowing, non-flowing and dry hydrological states. Interactions between surface and groundwater often create mixing zones with distinct redox gradients, potentially driving high rates of carbon and nutrient cycling. Yet a complete understanding of how underlying biogeochemical processes across surface-groundwater flowpaths in IRES differ among various hydrological states remains elusive. Here, we present a conceptual framework relating spatial and temporal hydrological variability in surface water-groundwater interactions to biogeochemical processing hotspots in IRES. We combine a review of theIRES biogeochemistry literature with concepts of IRES hydrogeomorphology to: (i) outline common distinctions among hydrological states in IRES; (ii) use these distinctions, together with considerations of carbon, nitrogen, and phosphorus cycles within IRES, to predict the relative potential for biogeochemical processing across different reach-scale processing zones (flowing water, fragmented pools, hyporheic zones, groundwater, and emerged sediments); and (iii) explore the potential spatial and temporal variability of carbon and nutrient biogeochemical processing across entire IRES networks. Our approach estimates the greatest reach-scale potential for biogeochemical processing when IRES reaches are fragmented into isolated surface water pools, and highlights the potential of relatively understudied processing zones, such as emerged sediments. Furthermore, biogeochemical processing in fluvial networks dominated by IRES is likely more temporally than spatially variable. We conclude that biogeochemical research in IRES would benefit from focusing on interactions between different nutrient cycles, surface-groundwater interactions in non-flowing states, and consideration of fluvial network architecture. Our conceptual framework outlines opportunities to advance studies and expand understanding of biogeochemistry in IRES.

Parasites and pathogens are crucial in shaping immune systems. Many animals and especially insects have outsourced part of their immune function to protective symbionts. There is good evidence that, akin to immune systems, parasites shape the occurrence and diversity of protective symbionts and that likewise, protective symbionts can shape the occurrence and diversity of parasites. Such a relationship should result in a correlation between symbiont and parasite diversity in nature. Aphids are well known for possessing symbionts that provide specific and effective protection against parasitoid wasps. We compared symbiont and parasitoid diversity across multiple populations of different aphid species of the genus Aphis and their parasitoid wasps. The diversity of protective symbionts and parasitoids was indeed positively associated. Even though this association was very noisy, it is in line with the hypothesis that parasitoids and symbionts promote each other’s diversity.

Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and is stocked for conservation management in England, but its impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicate their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and environmental DNA (eDNA) metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding and eDNA metabarcoding. Five 2L water samples and 3min sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e., ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.

Cuticular hydrocarbons (CHCs) have important communicative functions for ants, which use CHC profiles to recognize mutualistic aphid partners. Aphid endosymbionts can influence the quality of their hosts as ant mutualists, via effects on honeydew composition, and might also affect CHC profiles, suggesting that ants could potentially use CHC cues to discriminate among aphid lines harbouring different endosymbionts. We explored how several strains of Hamiltonella defensa and Regiella insecticola influence the CHC profiles of host aphids (Aphis fabae) and the ability of aphid-tending ants (Lasius niger) to distinguish the profiles of aphids hosting different endosymbionts. We found significant compositional differences between the CHCs of aphids with different infections. Some endosymbionts changed the proportions of odd-chain linear alkanes, while others changed primarily methyl-branched compounds, which may be particularly important for communication. Behavioural assays, in which we trained ants to associate CHC profiles of endosymbiont infected or uninfected aphids with food rewards, revealed that ants readily learned to distinguish differences in aphid CHC profiles associated with variation in endosymbiont strains. While previous work has documented endosymbiont effects on aphid interactions with antagonists, the current findings support the hypothesis that endosymbionts also alter traits that influence communicative interactions with ant mutualists.

Methanogens represent the final decomposition step in anaerobic degradation of organic matter, occurring in the digestive tracts of various invertebrates. However, factors determining their community structure and activity in distinct gut sections are still debated. In this study, we focused on the tropical millipede species Archispirostreptus gigas (Diplopoda, Spirostreptidae) and Epibolus pulchripes (Diplopoda, Pachybolidae), which release considerable amounts of methane. We aimed to characterize relationships between physicochemical parameters, methane production rates, and methanogen community structure in the two major gut sections, midgut and hindgut. Microsensor measurements revealed that both sections were strictly anoxic, with reducing conditions prevailing in both millipedes. Hydrogen concentration peaked in the anterior hindgut of E. pulchripes. In both species, the intestinal pH was significantly higher in the hindgut than in the midgut. An accumulation of acetate and formate in the gut indicated bacterial fermentation activities in the digestive tracts of both species. Phylogenetic analysis of 16S rRNA genes showed a prevalence of Methanobrevibacter spp. (Methanobacteriales), accompanied by a small fraction of so-far-unclassified “Methanomethylophilaceae” (Methanomassiliicoccales), in both species, which suggests that methanogenesis is mostly hydrogenotrophic. We conclude that anoxic conditions, negative redox potential, and bacterial production of hydrogen and formate promote gut colonization by methanogens. The higher activities of methanogens in the hindgut are explained by the higher pH of this compartment and their association with ciliates, which are restricted to this compartment and present an additional source of methanogenic substrates.

Winter conditions, such as ice cover and snow accumulation, are changing rapidly at northern latitudes and can have important implications for lake processes. For example, snowmelt in the watershed—a defining feature of lake hydrology because it delivers a large portion of annual nutrient inputs—is becoming earlier. Consequently, earlier and a shorter duration of snowmelt are expected to affect annual phytoplankton biomass. To test this hypothesis, we developed an index of runoff timing based on the date when 50% of cumulative runoff between January 1 and May 31 had occurred. The runoff index was computed using stream discharge for inflows, outflows, or for flows from nearby streams for 41 lakes in Europe and North America. The runoff index was then compared with summer chlorophyll-a (Chl-a) concentration (a proxy for phytoplankton biomass) across 5–53 years for each lake. Earlier runoff generally corresponded to lower summer Chl-a. Furthermore, years with earlier runoff also had lower winter/spring runoff magnitude, more protracted runoff, and earlier ice-out. We examined several lake characteristics that may regulate the strength of the relationship between runoff timing and summer Chl-a concentrations; however, our tested covariates had little effect on the relationship. Date of ice-out was not clearly related to summer Chl-a concentrations. Our results indicate that ongoing changes in winter conditions may have important consequences for summer phytoplankton biomass and production.

Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.

Phytoplankton blooms are complex ecological events that emerge from the dynamics of an entire ecosystem. Increasing efforts to forecast blooms are hampered by inconsistent definitions of what constitutes a bloom event, from both conceptual (mechanistic) and empirical (quantitative) perspectives. By clarifying definitions of blooms using temporal system dynamics, we propose to target modeling and forecasting methods to appropriate settings, and generate testable ecological hypotheses into the underlying processes fueling bloom development. Here, we present a general bloom definition that highlights both growth and loss processes, and identify quantitative metrics of time-series structure associated with several subclasses of blooms. We hypothesize ecological processes that are consistent with these time-series structures, and that suggest promising approaches for forecasting different types of blooms.

Northern lakes are experiencing widespread increases in dissolved organic carbon (DOC) that are likely to lead to changes in pelagic phytoplankton biomass. Pelagic phytoplankton biomass responds to trade-offs between light and nutrient availability. However, the influence of DOC light absorbing properties and carbon–nutrient stoichiometry on phytoplankton biomass across seasonal or spatial gradients has not been assessed. Here, we analyzed data from almost 5000 lakes to examine how the carbon–phytoplankton biomass relationship is influenced by seasonal changes in light availability, DOC light absorbing properties (carbon-specific visual absorbance, SVA₄₂₀), and DOC–nutrient [total nitrogen (TN) and total phosphorus (TP)] stoichiometry, using TOC as a proxy for DOC. We found evidence for trade-offs between light and nutrient availability in the relationship between DOC and phytoplankton biomass [chlorophyll (chl)-a], with the shape of the relationship varying with season. A clear unimodal relationship was found only in the fall, particularly in the subsets of lakes with the highest TOC:TP. Observed trends of increasing TOC:TP and decreasing TOC:TN suggest that the effects of future browning will be contingent on future changes in carbon–nutrient stoichiometry. If browning continues, phytoplankton biomass will likely increase in most northern lakes, with increases of up to 76% for a 1.7 mg L⁻¹ increase in DOC expected in subarctic regions, where DOC, SVA₄₂₀, DOC:TN, and DOC:TP are all low. In boreal regions with higher DOC and higher SVA₄₂₀, and thus lower light availability, lakes may experience only moderate increases or even decreases in phytoplankton biomass with future browning.

A recent global meta-analysis reported a decrease in terrestrial but increase in freshwater insect abundance and biomass (van Klink et al., Science 368, p. 417). The authors suggested that water quality has been improving, thereby challenging recent reports documenting drastic global declines in freshwater biodiversity. We raise two major concerns with the meta-analysis and suggest that these account for the discrepancy with the declines reported elsewhere. First, total abundance and biomass alone are poor indicators of the status of freshwater insect assemblages, and the observed differences may well have been driven by the replacement of sensitive species with tolerant ones. Second, many of the datasets poorly represent global trends and reflect responses to local conditions or nonrandom site selection. We conclude that the results of the meta-analysis should not be considered indicative of an overall improvement in the condition of freshwater ecosystems. This article is categorized under: Water and Life > Conservation, Management, and Awareness.

Secondary endosymbionts of aphids have an important ecological and evolutionary impact on their host, as they provide resistance to natural enemies but also reduce the host’s lifespan and reproduction. While secondary symbionts of aphids are faithfully transmitted from mother to offspring, they also have some capacity to be transmitted horizontally between aphids. Here we explore whether 11 isolates from 3 haplotypes of the secondary endosymbiont Hamiltonella defensa differ in their capacity for horizontal transmission. These isolates vary in the protection they provide against parasitoid wasps as well as the costs they inflict on their host, Aphis fabae. We simulated natural horizontal transmission through parasitoid wasps by stabbing aphids with a thin needle and assessed horizontal transmission success of the isolates from one shared donor clone into three different recipient clones. Specifically, we asked whether potentially costly isolates reaching high cell densities in aphid hosts are more readily transmitted through this route. This hypothesis was only partially supported. While transmissibility increased with titre for isolates from two haplotypes, isolates of the H. defensa haplotype 1 were transmitted with greater frequency than isolates of other haplotypes with comparable titres. Thus, it is not sufficient to be merely frequent—endosymbionts might have to evolve specific adaptations to transmit effectively between hosts.

Background: Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.
Results: We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.
Conclusions: Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host’s obligatory endosymbiont B. aphidicola.

Land use and climate change are anticipated to affect phytoplankton of lakes worldwide. The effects will depend on the magnitude of projected land use and climate changes and lake sensitivity to these factors. We used random forests fit with long-term (1971–2016) phytoplankton and cyanobacteria abundance time series, climate observations (1971–2016), and upstream catchment land use (global Clumondo models for the year 2000) data from 14 European and 15 North American lakes basins. We projected future phytoplankton and cyanobacteria abundance in the 29 focal lake basins and 1567 lakes across focal regions based on three land use (sustainability, middle of the road, and regional rivalry) and two climate (RCP 2.6 and 8.5) scenarios to mid-21st century. On average, lakes are expected to have higher phytoplankton and cyanobacteria due to increases in both urban land use and temperature, and decreases in forest habitat. However, the relative importance of land use and climate effects varied substantially among regions and lakes. Accounting for land use and climate changes in a combined way based on extensive data allowed us to identify urbanization as the major driver of phytoplankton development in lakes located in urban areas, and climate as major driver in lakes located in remote areas where past and future land use changes were minimal. For approximately one-third of the studied lakes, both drivers were relatively important. The results of this large scale study suggest the best approaches for mitigating the effects of human activity on lake phytoplankton and cyanobacteria will depend strongly on lake sensitivity to long-term change and the magnitude of projected land use and climate changes at a given location. Our quantitative analyses suggest local management measures should focus on retaining nutrients in urban landscapes to prevent nutrient pollution from exacerbating ongoing changes to lake ecosystems from climate change.

Polyunsaturated fatty acids (PUFAs) are essential resources unequally distributed throughout landscapes. Certain PUFAs, such as eicosapentaenoic acid (EPA), are common in aquatic but scarce in terrestrial ecosystems. In environments with low PUFA availability, meeting nutritional needs requires either adaptations in metabolism to PUFA-poor resources or selective foraging for PUFA-rich resources. Amphibiotic organisms that emerge from aquatic ecosystems represent important resources that can be exploited by predators in adjacent terrestrial habitats. Here, we traced PUFA transfer from streams to terrestrial ecosystems, considering benthic algae as the initial PUFA source, through emergent aquatic insects to riparian spiders. We combined carbon stable isotope and fatty acid analyses to follow food web linkages across the ecosystem boundary and investigated the influence of spider lifestyle (web building vs. ground dwelling), season, and ecosystem degradation on PUFA relations. Our data revealed that riparian spiders consumed considerable amounts of aquatic-derived resources. EPA represented on average 15 % of the total fatty acids in riparian spiders. Season had a strong influence on spider PUFA profiles, with highest EPA contents in spring. Isotope data revealed that web-building spiders contain more aquatic-derived carbon than ground dwelling spiders in spring, although both spider types had similarly high EPA levels. Comparing a natural with an anthropogenically degraded fluvial system revealed higher stearidonic acid (SDA) contents and Σω3/Σω6 ratios in spiders collected along the more natural river in spring but no difference in spider EPA content between systems. PUFA profiles of riparian spiders where distinct from other terrestrial organism and more closely resembled that of emergent aquatic insects (higher Σω3/Σω6 ratio). We show here that the extent to which riparian spiders draw on aquatic PUFA subsidies can vary seasonally and depends on the spider’s lifestyle, highlighting the complexity of aquatic-terrestrial linkages.

Plankton are effective indicators of environmental change and ecosystem health in freshwater habitats, but collection of plankton data using manual microscopic methods is extremely labor-intensive and expensive. Automated plankton imaging offers a promising way forward to monitor plankton communities with high frequency and accuracy in real-time. Yet, manual annotation of millions of images proposes a serious challenge to taxonomists. Deep learning classifiers have been successfully applied in various fields and provided encouraging results when used to categorize marine plankton images. Here, we present a set of deep learning models developed for the identification of lake plankton, and study several strategies to obtain optimal performances, which lead to operational prescriptions for users. To this aim, we annotated into 35 classes over 17900 images of zooplankton and large phytoplankton colonies, detected in Lake Greifensee (Switzerland) with the Dual Scripps Plankton Camera. Our best models were based on transfer learning and ensembling, which classified plankton images with 98% accuracy and 93% F1 score. When tested on freely available plankton datasets produced by other automated imaging tools (ZooScan, Imaging FlowCytobot, and ISIIS), our models performed better than previously used models. Our annotated data, code and classification models are freely available online.

Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.

Body pigmentation is an evolutionarily diversified and ecologically relevant trait with substantial variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution, including its ecological significance and genetic bases. Pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, and can be under different selective pressures. We decompose Drosophila thorax and abdominal pigmentation, a valuable eco-evo-devo model, into distinct measurable traits related to color and color pattern. We investigate intra- and interspecific variation for those traits and assess its different sources. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate each body part. By focusing on two standard D. melanogaster laboratory populations, we show that pigmentation components vary and covary in distinct manners depending on sex, genetic background, and temperature during development. Studying three natural populations of D. melanogaster along a latitudinal cline and five other Drosophila species, we then show that evolution of lighter or darker bodies can be achieved by changing distinct component traits. Our results paint a much more complex picture of body pigmentation variation than previous studies could uncover, including patterns of sexual dimorphism, thermal plasticity, and interspecific diversity. These findings underscore the value of detailed quantitative phenotyping and analysis of different sources of variation for a better understanding of phenotypic variation and diversification, and the ecological pressures and genetic mechanisms underlying them.

Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time-series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality generate fundamental spatial patterns of synchrony in fish metapopulations, empirical synchrograms can aid knowledge advancement and inform conservation strategies in complex habitats.

Global environmental changes are causing widespread nutrient depletion, declines in the ratio of dissolved inorganic nitrogen (N) to total phosphorus (DIN:TP), and increases in both water temperature and terrestrial colored dissolved organic carbon (DOC) concentration (browning) in high-latitude northern lakes. Declining lake DIN:TP, warming, and browning alter the nutrient limitation regime and biomass of phytoplankton, but how these stressors together affect the nutritional quality in terms of polyunsaturated fatty acid (PUFA) contents of the pelagic food web components remains unknown. We assessed the fatty acid compositions of seston and zooplankton in 33 lakes across south-to-north and boreal-to-subarctic gradients in Sweden. Data showed higher lake DIN:TP in the south than in the north, and that boreal lakes were warmer and browner than subarctic lakes. Lake DIN:TP strongly affected the PUFA contents—especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)—in seston, calanoids, and copepods (as a group), but not in cladocerans. The EPA+DHA contents increased by 123% in seston, 197% in calanoids, and 230% in copepods across a lake molar DIN:TP gradient from 0.17 to 14.53, indicating lower seston and copepod nutritional quality in the more N-limited lakes (those with lower DIN:TP). Water temperature affected EPA+DHA contents of zooplankton, especially cladocerans, but not seston. Cladoceran EPA+DHA contents were reduced by ca. 6% for every 1°C increase in surface water. Also, the EPA, DHA, or EPA+DHA contents of Bosmina, cyclopoids, and copepods increased in lakes with higher DOC concentrations or aromaticity. Our findings indicate that zooplankton food quality for higher consumers will decrease with warming alone (for cladocerans) or in combination with declining lake DIN:TP (for copepods), but impacts of these stressors are moderated by lake browning. Global environmental changes that drive northern lakes toward more N-limited, warmer, and browner conditions will reduce PUFA availability and nutritional quality of the pelagic food web components.

Biological quality elements have been developed worldwide to assess whether a water body is in a good status or not. However, current studies mainly focus on a single taxonomic group or a small set of species, often limited by methods of morphological identification, and lack further aspects of biodiversity (e.g., across taxa and multiple attributes) and ecosystem functions. Here, we advance a framework for assessing the river's ecological status based on complete biodiversity data measured by environmental DNA (eDNA) metabarcoding and measurements of ecosystem functions in addition to physicochemical elements across a large riverine system in China. We identified 40 indicators of biodiversity and ecosystem functions, covering five taxonomic groups from bacteria to invertebrates, and associated with multiple attributes of biodiversity and ecosystem functions. Our data show that human impact on ecosystems could be accurately predicted by these eDNA-based indicators and ecosystem functions, using cross-validation with a known stressor gradient. Moreover, indices based on these indicators of biodiversity and ecosystem functions not only distinguish the physicochemical characteristics of the sites but also improve the assessment accuracy of 20–30% for the river’s ecological status. Overall, by incorporating eDNA-based biodiversity with physicochemical and ecosystem functional elements, the multidimensional perspectives of ecosystem states provide additional information to protect and maintain a good ecological status of rivers.

Developmental plasticity is ubiquitous in natural populations, but the underlying causes and fitness consequences are poorly understood. For consumers, nutritional variation of juvenile diets is probably associated with plasticity in developmental rates, but little is known about how diet quality can affect phenotypic trajectories in ways that might influence survival to maturity and lifetime reproductive output. Here, we tested how the diet quality of a freshwater detritivorous isopod (Asellus aquaticus), in terms of elemental ratios of diet (i.e. carbon : nitrogen : phosphorus; C : N : P), can affect (i) developmental rates of body size and pigmentation and (ii) variation in juvenile survival. We reared 1047 individuals, in a full-sib split-family design (29 families), on either a high- (low C : P, C : N) or low-quality (high C : P, C : N) diet, and quantified developmental trajectories of body size and pigmentation for every individual over 12 weeks. Our diet contrast caused strong divergence in the developmental rates of pigmentation but not growth, culminating in a distribution of adult pigmentation spanning the broad range of phenotypes observed both within and among natural populations. Under low-quality diet, we found highest survival at intermediate growth and pigmentation rates. By contrast, survival under high-quality diet survival increased continuously with pigmentation rate, with longest lifespans at intermediate growth rates and high pigmentation rates. Building on previous work which suggests that visual predation mediates the evolution of cryptic pigmentation in A. aquaticus, our study shows how diet quality and composition can generate substantial phenotypic variation by affecting rates of growth and pigmentation during development in the absence of predation.

Eutrophication is a persistent threat to aquatic ecosystems worldwide. Foundation species, namely those that play a central role in the structuring of communities and functioning of ecosystems, are likely important for the resilience of aquatic ecosystems in the face of disturbance. However, little is known about how interactions among such species influence ecosystem responses to nutrient perturbation. Here, using an array (N = 20) of outdoor experimental pond ecosystems (15,000 L), we manipulated the presence of two foundation species, the macrophyte Myriophyllum spicatum and the mussel Dreissena polymorpha, and quantified ecosystem responses to multiple nutrient disturbances, spread over two years. In the first year, we added five nutrient pulses, ramping up from 10 to 50 μg P/L over a 10-week period from mid-July to mid-October, and in the second year, we added a single large pulse of 50 μg P/L in mid-October. We used automated sondes to measure multiple ecosystems properties at high frequency (15-minute intervals), including phytoplankton and dissolved organic matter fluorescence, and to model whole-ecosystem metabolism. Overall, both foundation species strongly affected the ecosystem responses to nutrient perturbation, and, as expected, initially suppressed the increase in phytoplankton abundance following nutrient additions. However, when both species were present, phytoplankton biomass increased substantially relative to other treatment combinations: non-additivity was evident for multiple ecosystem metrics following the nutrient perturbations in both years but was diminished in the intervening months between our perturbations. Overall, these results demonstrate how interactions between foundation species can cause surprisingly strong deviations from the expected responses of aquatic ecosystems to perturbations such as nutrient additions.

1. Submerged macrophytes are important foundation species that can strongly influence the structure and functioning of aquatic ecosystems, but only little is known about the temporal variation and the timescales of these effects (i.e. from hourly, daily, to monthly).
2. Here, we conducted an outdoor experiment in replicated mesocosms (1,000 L) where we manipulated the presence and absence of macrophytes to investigate the temporal variability of their ecosystem effects. We measured several parameters (chlorophyll-a, phycocyanin, dissolved organic matter [DOM], and oxygen) with high-resolution sensors (15-min intervals) over several months (94 days from spring to autumn), and modelled metabolic rates of each replicate ecosystem in a Bayesian framework. We also implemented a simple model to explore competitive interactions between phytoplankton and macrophytes as a driver of variability in chlorophyll-a.
3. Over the entire experiment, macrophytes had a positive effect on mean DOM concentration, a negative effect on phytoplankton biomass, and either a weak or no effect on mean metabolic rates, DOM composition, and conductivity. We also found that macrophytes increased the variance of dissolved organic carbon composition and metabolic rates, and, occasionally in the observed period, increased the variance of phytoplankton biomass and conductivity. The observation that macrophytes decreased the mean but increased the variance of phytoplankton biomass was consistent with the model that we implemented.
4. Our high-resolution time series embedded within a manipulative experiment reveal how a foundation species can affect ecosystem properties and processes that have characteristically different timescales of response to environmental variation. Specifically, our results show how macrophytes can affect short-term dynamics of algal biomass, while also affecting the seasonal build-up of DOM and the variance of ecosystem metabolism.

1. River regulation globally has reduced the riverine connectivity (longitudinal, lateral and vertically) with significant consequences for their abiotic and biotic components. To restore the ecological integrity of regulated rivers, artificial floods are increasingly being employed in large-scale flow restoration efforts. Despite considerable recognition regarding the ecological and geomorphological effects of artificial floods on benthic habitats, understanding the implications for the hyporheic zone is essentially absent. This void in our management knowledge base is considerable given that one of the most widely associated consequences of flow regulation is excessive deposition of fine sediment (sedimentation; particles <2 mm) that often disconnects the hyporheic zone from surface waters.
2. In this study, we examined the effects of an artificial flood on the hyporheic zone of the River Spöl in Switzerland. Fine sediment content of shallow benthic substrates (ca. 10 cm) was significantly reduced following the flood. The flushing of fine sediment was also apparent in hyporheic substrates (depths of 0.25 and 0.50 m), resulting in a reconnection of previously clogged interstitial pathways. The opening of interstitial pore space enhanced physicochemical conditions in the hyporheic zone, such as improved dissolved oxygen concentrations, and supported greater taxa richness.
3. Alterations in the composition of shallower hyporheic assemblages (0.25 m) were evident following the flood. These results indicated that benthic pore space became more connected to surface waters following the flood, thereby enhancing accessibility for interstitial organisms.
4. Our results suggest that artificial floods can be an effective management tool to restore spatial heterogeneity in sediment composition and pore space and improve vertical connectivity for macroinvertebrates. We anticipate that artificial floods would be required on a regular basis given the re-accumulation of fine sediment 10 months later in our study system. We encourage river managers and scientists to consider flow disturbance and restoration in a holistic manner that encompasses the multiple spatial dimensions of connectivity, including the hyporheic ecotone.

Sediment transport in mountain streams can be a major hazard to downstream infrastructure. Consequently, sediment traps are a common feature in many high gradient streams to retain large volumes of sediment and protect settlements from major sediment transport events. Despite the wide application of these instream structures, there is little knowledge regarding the environmental and ecological effects on streams. Here, we investigated the hydromorphological effects of sediment traps on instream habitats and associated macroinvertebrate communities in four impacted and three non-impacted streams in Switzerland. Sediment traps significantly disrupted the sediment regime homogenising grain size percentiles compared to the natural stepwise downstream fining in control streams. This disruption in the sediment regime resulted in finer grain size distributions upstream of the sediment trap, and reduced substrate diversity in the sediment retention basin and just downstream of the trap. The reductions in substrate diversity resulted in an altered macroinvertebrate community composition. Further, the disconnection in sediment transport led to a lack of longitudinal correlation in macroinvertebrate communities. Refugia provision downstream of the sediment trap, and resource availability within the retention basin, were diminished, potentially reducing resilience of macroinvertebrate assemblages to instream disturbances. The effects of sediment traps were most likely localised in three of the four streams with substrate diversity recovering to comparable control values within 8 wetted widths (ca. 50 m) downstream of the trap associated with natural longitudinal fining. In contrast, ecological and environmental effects propagated downstream in one impacted stream with no recovery being evident. Sediment retention basins in the impacted streams provided a local artificially unique habitat of dynamic-braided channels. Our results indicate that sediment traps can significantly disrupt the sediment regime with important consequences for instream ecology and environmental conditions, although these effects can be system specific. Further work is needed to fully understand the effects of sediment traps in mountain streams to assist resource managers in the mitigation and future construction of these structures.

In nature, populations can be affected by multiple chronic and short-term stressors simultaneously, which can interact with each other both by influencing phenotypic expression and as agents of natural selection. These interactions can shape adaptive processes at the level of populations and ultimately influence phenotypic and genetic variation in nature. Adaptive processes can be characterized by multiple selective forces acting on multidimensional phenotypes, which can lead to trade-offs in trait evolution. The integrative phenotype, characterized by all traits of an individual, can be split into genetic (G), environmental (E) and G x E interaction components. Hence, adaptation to environmental stressors can be driven simultaneously by genetic variation, phenotypic plasticity and a combination of both. Physiological traits, such as glucocorticoids, are often linked to many other traits of the composite phenotype. Their expression is influenced by abiotic as well as biotic environmental stressors and they can facilitate adaptive responses of organisms through plasticity or genetic variation. However, the exact role of physiological processes in adaptation of natural populations to stress is poorly understood. [...]

In der Natur können Populationen von mehreren lang- und kurzzeitigen Stressoren beeinflusst werden. Diese wiederum können miteinander interagieren und die phänotypische Ausprägung der Population und natürliche Selektion beeinflussen. Diese Interaktionen können adaptive Prozesse auf Populationsebene beeinflussen und schlussendlich die phänotypische und genetische Variation in der Population bestimmen. Dies heisst, dass adaptive Prozesse als multiple selektive Kräfte, die auf den multidimensionalen Phänotyp einwirken, beschrieben werden können, was zu Konflikten (Trade-off) während der Evolution von bestimmten Merkmalen führen kann. Der integrative Phänotyp, die Summe aller einzelnen Merkmalen eines Individuums, kann in eine genetische (G), umweltbedingte (E), und G x E interaktive Komponente aufgeteilt werden. Somit kann Adaptation an Umweltstressoren gleichzeitig durch genetische Variation, phänotypische Plastizität und die Kombination von beiden gesteuert werden. Physiologische Merkmale, wie Glukokortikoide, sind häufig mit vielen weiteren Merkmalen des integrativen Phänotyps vernetzt. Ihre Expression wird durch abiotische und biotische Umweltstressoren beeinflusst, und sie löst teils adaptive Prozesse in Organismen durch Plastizität oder genetischer Variation aus. Welche genaue Rolle physiologische Prozesse im Rahmen der Adaptation von natürlichen Populationen hinsichtlich Stressanpassungen spielen, ist jedoch wenig verstanden. [...]