Department Aquatic Ecology

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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'.

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.

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.

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.

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.

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.

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.

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.

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.

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.