Abteilung Aquatische Ökologie

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.

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.

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.

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?

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Danube Delta shallow lakes experience cyanobacteria blooms that can negatively affect the aquatic ecosystem. Although there are several studies on Danube Delta cyanobacteria, little is known about their spatial–temporal patterns and the potential predictive role they can offer. We therefore analyzed the distribution of cyanobacteria in 19 lakes belonging to three lake complexes and tested whether their seasonal dynamics are in line with the predictions of the PEG model. Furthermore, we investigated to which extent cyanobacteria diversity and abundance were related to lake hydrogeomorphological characteristics such as surface, water level, connectivity, water retention, flood risk, and transparency. Although lakes had different seasonal cyanobacterial assemblages, the biovolume and genus richness had a geographical pattern, decreasing from south-east (lakes forming the fluvial delta) towards north-west (lakes forming the maritime delta). Cyanobacteria biovolume reflected largely the PEG model peaking in summer (the fluvial delta) and autumn (the maritime delta). Genus richness followed the same pattern. Cyanobacteria distribution was predicted by various abiotic (e.g., risk of flooding, connectivity) and biotic factors (e.g., submersed macrophytes, phytoplankton diversity, peat deposits). Our study contributes to the understanding of cyanobacteria diversity and distribution in shallow interconnected lakes by revealing the complexity of predictors for geographical and seasonal patterns.

Changing reproductive strategy from investment in current (asexual eggs) to future (sexual ephippia) reproduction depending on environmental cues is an important fitness trait in zooplankton species like water fleas, Daphnia. Different cues are reported for ephippia production, for example food limitation, changes in photoperiod and temperature, the presence of predators, nutrient depletion or signals of crowding. However, the reliability of these cues strongly depends on the local habitat. In Daphnia galeata, ephippia production might not be subject to any of the environmental cues outlined. Here, we directly test whether changes in crowding alone provides a reliable cue for D. galeata to switch reproductive mode. We conducted life history assays using 10 genotypes of D. galeata from a Swiss Lake to investigate density dependent reproduction and production of ephippia. We started populations at different densities and eliminated competition for food by systematically increasing food availability with population size. Our results suggest that population density depresses population growth rate via a change in energy allocation from current into future reproduction in D. galeata. Thus, signals of crowding produced at high population density constitute a reliable and sufficient cue for D. galeata to switch from asexual to sexual reproduction.

Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4,998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.

Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.

Eutrophication of shallow lakes often triggers a series of cascading ecological effects. Among these are shifts in the zooplankton community structure due to phytoplankton changes, or shifts in the fish community reducing size-selective feeding of planktivorous fish. In such conditions, larger zooplankton (e.g. Daphnia) can have a selective advantage. Re-oligotrophication can reverse such food-web interactions. Europe’s largest wetland system (the Danube Delta) went through a period of eutrophication and is now slowly recovering again. However, changes in the Daphnia populations triggered by eutrophication in this system have remained unstudied. We used different sampling strategies to screen 24 lakes (which differ in their ecological state) for the presence of Daphnia as well as for biotic and abiotic parameters potentially explaining Daphnia abundance. Daphnia densities were surprisingly low. We found D. magna ephippia in the sediment, but no D. magna in the water column. Microsatellite analyses on pelagic Daphnia populations confirmed the presence of the D. longispina complex and provided evidence for significant hybridisation events. FluoroProbe data showed that Daphnia was mainly present in lakes with a higher phytoplankton production. Our study provides insights into the spatial and temporal distribution of Daphnia in a very dynamic wetland system.

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies about community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and over environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We detected a weak influence of phosphorus, but no significant effect of nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the past century.

The phylum Cyanobacteria comprises a non-photosynthetic lineage. The diversity and distribution of non-photosynthetic cyanobacteria (NCY) across aquatic environments are currently unknown, including their ecology. Here, we report about composition and phylogenetic diversity of two clades of NCY in ten lakes of the European peri-Alpine region, over the past ~100 years. Using 16S rDNA sequences obtained from dated sediment cores, we found almost equal proportion of taxa assigned to Melainabacteria and the deepest-branching group Sericytochromatia (ML635J-21) (63 total detected taxa). The topology of our reconstructed phylogenies reflected evolutionary relationships expected from previous work, that is, a clear separation between the deepest branching Sericytochromatia, the Melainabacteria, and the photosynthetic cyanobacteria clades. While different lakes harbored distinct NCY communities, the diversity of NCY assemblages within and between lakes (alpha and beta diversity) did not significantly change over the last century. This is in contrast with what was previously reported for photosynthetic cyanobacteria. Unchanged community phylogenetic similarity over geographic distance indicated no dispersal limitation of NCY at the regional scale. Our results solicit studies linking in-lake environmental factors to the composition of these microorganisms’ communities, whose assembly appeared not to have been influenced by large-scale anthropogenic environmental changes. This is the first attempt to study the diversity and distribution of NCY taxa across temperate lakes. It provides a first step towards understanding their distribution and ecological function in pelagic aquatic habitats, where these organisms seem to be prevalent.

A major challenge in ecology is to understand determinants of ecosystem functioning and stability in the face of disturbance. Some important species can strongly shape community structure and ecosystem functioning, but their impacts and interactions on ecosystem-level responses to disturbance are less well known. Shallow ponds provide a model system in which to study the effects of such species because some taxa mitigate transitions between alternative ecosystem states caused by eutrophication. We performed pond experiments to test how two foundation species (a macrophyte and a mussel) affected the biomass of planktonic primary producers and its stability in response to nutrient additions. Individually, each species reduced phytoplankton biomass and tended to increase rates of recovery from disturbance, but together the species reversed these effects, particularly with larger nutrient additions. This reversal was mediated by high cyanobacterial dominance of the community and a resulting loss of trait evenness. Effects of the foundation species on primary producer biomass were associated with effects on other ecosystem properties, including turbidity and dissolved oxygen. Our work highlights the important role of foundation species and their interactive effects in determining responses of ecosystem functioning to disturbance.

When traits affecting species interactions evolve rapidly, ecological dynamics can be altered while they occur. These eco-evolutionary dynamics have been documented repeatedly in laboratory and mesocosm experiments. We show here that they are also important for understanding community functioning in a natural ecosystem. Daphnia is a major planktonic consumer influencing seasonal plankton dynamics in many lakes. It is also sensitive to succession in its phytoplankton food, from edible algae in spring to relatively inedible cyanobacteria in summer. We show for Daphnia mendotae in Oneida Lake, New York, United States, that within-year ecological change in phytoplankton (from spring diatoms, cryptophytes and greens to summer cyanobacteria) resulted in consumers evolving increasing tolerance to cyanobacteria over time. This evolution fed back on ecological seasonal changes in population abundance of this major phytoplankton consumer. Oneida Lake is typical of mesotrophic lakes broadly, suggesting that eco-evolutionary consumer-resource dynamics is probably common.

We compared taxon composition of the Daphnia longispina hybrid community, as reconstructed from dormant eggs (retrieved from sediment samples) and the pelagic population (retrieved from formaldehyde-preserved zooplankton samples), from the same lake and of the same time period. As microsatellite markers do not work on largely fragmented DNA, such as of formaldehyde-preserved samples, both types of samples (dormant eggs and pelagic Daphnia) were screened with single-nucleotide polymorphism (SNP) markers. Here, we designed a genotyping panel of short SNP-bearing amplicons and, to facilitate screening, we developed a multiplex genotyping protocol. The results of this comparison confirmed differences between dormant and pelagic samples. Specifically, D. galeata was overrepresented in the sedimentary egg bank in comparison to the pelagic population, indicating that this taxon is more involved in sexual reproduction than other taxa. In addition to being successfully applied on formaldehyde-preserved samples, SNP-genotyping was more efficient than microsatellites on sedimentary eggs, and was more sensitive for hybrid detection. In conclusion, the SNP-based genotyping panel presented here enables to study the genetic structure of past populations from common formaldehyde-preserved collections. It is also promising for genotyping old dormant eggs, which can extend the temporal range of Daphnia community reconstructions.
 

Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits – which determine responses to the abiotic and biotic environment – may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been limited. Here we compared the predictive power of trait richness (trait space coverage), evenness (regularity in trait distribution) and divergence (prevalence of extreme phenotypes) derived from individual-based measurements with two species-level metrics (taxonomic richness and evenness) when modelling the productivity of natural phytoplankton communities. Using phytoplankton data obtained from 28 lakes sampled at different spatial and temporal scales, we found that the diversity in individual-level morphophysiological traits strongly improved our ability to predict community resource-use and biomass yield. Trait evenness – the regularity in distribution of individual cells/colonies within the trait space – was the strongest predictor, exhibiting a robust negative relationship across scales. Our study suggests that quantifying individual microbial phenotypes in trait space may help us understand how to link physiology to ecosystem-scale processes. Elucidating the mechanisms scaling individual-level trait variation to microbial community dynamics could there improve our ability to forecast changes in ecosystem properties across environmental gradients.

The measurement and assessment of life history traits, such as fecundity and survival, typically rely on life tables generated from individual-based assays, where growth, maturation and reproductive rates are measured in isolated individuals. In reality, individuals often live in populations, which together form communities. For many species, it is possible to distinguish single individuals and measure their individual life history traits acting in populations, in wolves for example. However, for other species individuals are indistinguishable, for example in zooplankton, so it is impossible to mark and track a single animal. In these indistinguishable and non-markable animals, the problem with traditional life history assessment is that it is based on traits measured in individuals and these trait values are then extrapolated to population level without measuring life history traits of individuals in the populations. To overcome the limitations of individual life history trait assessments, other parameters are necessary to describe populations, for example the rate of change of population size using population growth rate or Edmondson egg ratio. Extrapolating from individuals to populations is suitable for estimating population level effects as long as individuals in the population do not interact. However, if individuals do interact, which is common, then effects of those interactions between individuals, must also be considered.
The main aim of my research was to determine life history trait parameters of individuals and simultaneously assess population growth rate variation directly in Daphnia populations grown at different population densities. By using several genotypes potentially adapted to different environmental conditions, I was also able to test whether life history traits and population growth rates differed between single and mixed genotype populations.
For this I conducted two life history assays using 10 resurrected Daphnia galeata clones ineither different initial densities or populations starting with 2 individuals of mixed or singlegenotypes. Both experiments were conducted without food limitation, to disentangle the effect of density from competition for food.
In all clones, population growth rate decreased with higher initial density, even though food availability was increased too. Of all life history traits I examined, only one, investment in reproduction, changed with increasing initial density, while neither age nor size at maturity, nor Edmondson egg ratio differed between initial densities. Instead Edmonson egg ratio decreased with rising ephippia production. In every life history trait, there were large differences between clones. Additionally, populations grown in single genotype populations showed no difference in population growth rate compared to mixed genotype populations.
It appears that initial population density depresses population growth rate most likely through fecundity reduction in populations, even when food is not limiting, and is independent of genotypic diversity. I could point that in D. galeata decreasing investment in current reproduction is linked to increasing investment in future reproduction. This study shows that in Daphnia experiments considering life history traits, it is important to regard density-dependence. Furthermore because genotypes differed greatly in the strength of the association with density, and in individual life history parameters, this study highlights that experiments using Daphnia, or any other clonal organism need to be based on multiple genotypes to allow more generalizable results.

Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacterial assemblages over one century of eutrophication and climate change by sequencing DNA preserved in the sediments of ten European peri-Alpine lakes. We found species losses and gains at the lake scale, while species richness increased at the regional scale over approximately the past 100 years. Our data show a clear signal for beta diversity loss, with the composition and phylogenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and around the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and, as a consequence, nutrient fluctuations, which favoured cyanobacterial taxa able to regulate buoyancy. Our results reinforce previous reports of human-induced homogenization of natural communities and reveal how potentially toxic and bloom-forming cyanobacteria have widened their geographic distribution in the European temperate region.

According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency-dependant selection by coevolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia–Caullerya host–parasite system. The clonal make-up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme and later microsatellite markers. Significant differences in the clonal composition between random and infected subsamples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host–parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite-based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis.

In wild populations natural selection is a constant companion and adaptation the only way of surviving, and in the long-term that adaptation must be heritable. Daphnia represent an ideal system to test for heritable adaptation as they are a widespread freshwater zooplankton. Even though different species are found all over the world, individual populations have limited dispersal ability and are mostly confined to their lake and compelled to adapt to that lake’s properties and its fluctuations. Daphnia reproduce mainly asexually, but when presented with adverse environments they produce resting eggs which can be recovered from lake sediments. These eggs can be hatched in the laboratory and provide snapshots of past phenotypes and genotypes.
Switzerland’s lake Greifensee has been intensively studied over the past decades during which time the environment within the lake changed a lot. In the second half of the 20th century human-caused eutrophication of the lake took place, peaking in the 1950-1970s and a subsequent clearing of the lake water when waste water treatment plants were put into operation. By using the resurrection method, it has previously been shown that Daphnia from times of eutrophication are better adapted to pollution in water than their counterparts originating from times of clear water. In this Thesis, I combine whole genome resequencing and population genetic methods to find genetic evidence of this adaptation in 43 Daphnia galeata clones hatched from ephippia taken from dated core samples of Greifensee originating from 1958 to 2012.
The population genomic methods I used revealed genetic differentiation and isolation over time, temporal population structure and evidence of strong diversifying selection. Comparison of allele frequencies with long term environmental data collected from Greifensee, suggests a strong association between allele frequency and environmental parameters particularly phosphorous and temperature. My results identify a number of variable sites in the Daphnia galeata genome that are correlated with changing environments, and these candidates can be used in future studies to test functional significance. In the final section of my thesis I also discuss the many technical advances in Daphnia growing and harvesting that was made during this research.

Anthropogenic global changes have affected almost all ecosystems on Earth and threatened biodiversity worldwide, but the extent of the impact of this pervasive influence is not fully understood. In aquatic ecosystems, eutrophication of lakes has led to the periodic dominance of cyanobacteria, which affects the services that lake ecosystems provide to human society (e.g., tourism, drinking water, fisheries), and sometimes directly threatens the health of animals, including humans. Many lakes in the European peri-Alpine region are regularly affected by the presence of cyanobacteria, but how rapid changes in local and regional lake conditions have contributed to determine their diversity and distribution, for example favouring toxic and bloom-forming taxa, is not well known. Peri-Alpine lakes, with their well-studied eutrophication and climate history, represent excellent study sites for reconstructing past assemblages of planktonic organisms and for investigating their diversity over long time scales of anthropogenic influence by applying molecular techniques to the sedimentary archive.
The general aim of this thesis project was to investigate the effects of environmental change, especially climate warming and alteration of nutrient regimes, over the distribution, the biodiversity, and the phylogenetic structure of lacustrine cyanobacterial communities. We used high-throughput sequencing on DNA extracted from dated sediment cores and performed phylogenetic and diversity analyses of the cyanobacterial communities over two centuries to cover the periods of pre-, mid- and post eutrophication of lakes. The first project (Chapter II) was to validate the sedimentary DNA-based reconstruction method by comparing the long-term diversity of cyanobacterial communities recovered from the sediments of two lakes (Greifensee and Lake Zurich) with the diversity assessed by microscopy in water samples collected over four decades as part of lake monitoring programmes. This study confirms the feasibility of the sedimentary DNA approach for assessing the richness and phylogenetic diversity of past communities of cyanobacteria.
The second project (Chapter III) was to investigate the biogeography of cyanobacteria and compare their community composition and phylogenetic structure across lakes. For that, the study region was expended to ten lakes across the peri-Alpine area. The results of this project show evidence for the homogenisation of lakes abiotic conditions due to climate warming and eutrophication, and reveal that over the past 150 years, the richness and similarity of cyanobacterial communities has generally increased, particularly gaining buoyant and colonial taxa.
The presence of cyanobacteria do not only impair water quality and ecosystem services, but they also have negative effects on other levels of lake food-webs. Chapter IV aims at linking the diversity of Daphnia and cyanobacteria in lakes impacted by anthropogenic eutrophication. This study using the sedimentary Daphnia egg bank and cyanobacterial DNA from two peri-alpine lakes (Switzerland) and a shallow lake in the Danube Biosphere Reserve (Romania) confirms the invasion of D. galeata and the subsequent replacement of native Daphnia lineages by D. galeata taxa in the two Swiss lakes. The results further suggest that D. galeata, D. cucullata, and their sexual descendants appear to have been favoured by the presence of filamentous cyanobacteria at all sites. These results provide novel insights into long-term community interactions between two important plankton groups.
During our investigation of cyanobacterial diversity in the sedimentary archive (chapters II & III), we detected two newly described clades of ancestral cyanobacteria called Melainabacteria and MLE635J-21. Chapter V presents a short literature review describing these nonphotosynthetic cyanobacteria, and explores their diversity within and across the same ten lakes investigated in chapter II, with the aim to compare their dynamics to the trends observed in cyanobacteria. This study reveals that, unlike cyanobacteria, the richness and composition of nonphotosynthetic cyanobacteria did not vary significantly over the past ~150 years, suggesting that the ladder are not governed by the same environmental factors as the photosynthetic clades.
Taken together, the results of these four studies reveal previously unreported patterns in the composition and structure of cyanobacterial communities over broad temporal and spatial scales, and highlight the effects of human-induced environmental changes on cyanobacterial assemblages in freshwater lakes that provide important ecosystem services to humans. Our results support the hypothesis that shifts in the diversity and distribution of taxa might not be reversible even after applying stringent remediation measures for the reduction of water eutrophication, and highlight the importance of increasing our understanding of the underlying mechanisms that regulate community structure to gain predictive ability for future lake management purposes.

Eutrophication generally favours the growth of cyanobacteria over eukaryotic green algae in freshwater lakes. Cyanobacteria constitute a poor food source for the waterflea Daphnia, an important primary consumer of phytoplankton in lakes. While it is known that some Daphnia species are adapted to eutrophic conditions and can cope with cyanobacteria in their diet, it is less known whether cyanobacterial community composition can influence Daphnia population structure in lakes. We studied the variation in genetic diversity of Daphnia resting eggs and cyanobacterial DNA preserved in sediment cores from three European lakes impacted by eutrophication. Our retrospective analysis confirms that D. galeata invaded the two pre-alpine lakes around the middle of the twentieth century, hybridized with and became dominant over D. longispina. This coincides with the presence in all lakes and the increase in the proportion of colonial and filamentous cyanobacteria in the pre-alpine lakes. The recent re-oligotrophication of the lakes did not reverse the cyanobacterial and Daphnia assemblages to their pre-eutrophication composition and genetic structure, suggesting that both changed irreversibly due to anthropogenic influence on the ecosystems. Genetic analyses applied to lake sedimentary archives have the potential to unveil how different compartments of the food web covary in a changing environment.

Daphnia perform diel vertical migration (DVM), a predator-avoidance strategy to migrate towards deeper and colder layers in the water column in the morning and movement to the algae-rich surface layers in the evening. However, individuals performing DVM incur several trade-offs since they might suffer from resource limitation and a slower instantaneous birth rate in deeper depths. DVM patterns may be modified by abiotic factors such as temperature, food concentration, or pH and vary among different Daphnia species and genotypes. Furthermore, Daphnia host a variety of microparasites that might pose an additional factor influencing DVM behaviour. For infected individuals, migration into cooler temperature layers might slow down parasite growth. Moreover, parasites can increase opacity of their hosts. Non-migrating individuals might then be selectively purged from the upper layers by visually hunting predators. With these premises we asked, whether epidemics of the ichthyosporean parasite Caullerya mesnili affect or are affected by the DVM behaviour of Daphnia in Lake Greifensee, Switzerland by analysing the vertical distribution of Daphnia during day and night on two dates. Furthermore, we were interested whether a potential interaction depends on host genotype. We therefore studied the genotypic composition of the integrated population in regular sampling intervals over the course of one year and on a fine-grained vertical resolution during the Caullerya epidemic in late summer. Since Caullerya-infected Daphnia migrated equally well as uninfected ones, the findings of this study suggest that Caullerya epidemics neither affected nor were affected by the DVM behaviour of Daphnia. We observed clonal succession in the lake but could not link this succession to the Caullerya epidemic; all except one of the common multilocus genotypes were under-infected. In addition, outbreak and course of this Caullerya epidemic seemed to rely mainly on environmental cues. Because this first study only provides a snapshot of time, we hope that further studies will be done to verify our results.

Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members of the Daphnia longispina species complex were reconstructed over the last 100 years for three large temperate lakes under strong anthropogenic pressures via palaeogenetic analyses of resting egg banks. Drastic changes in the genetic structure of the Daphnia community, associated with hybridization events between D. longispina and D. galeata and subsequent introgression, were detected in Lakes Geneva and Bourget. In Lake Bourget, these changes were induced by the successful establishment of D. galeata with rising phosphorus levels and reinforced by the sensitivity of D. longispina to fish predation pressure. In Lake Geneva, the pattern of hybridization during eutrophication is more likely a function of the original taxonomic composition of the species complex in this lake. Lakes seem to require at least a meso-oligotrophic status to allow D. galeata populations to establish and accordingly no D. galeata genotypes were found in the egg bank of oligotrophic Lake Annecy. In contrast to the generally assumed pattern of unidirectional hybridization in this species complex, bidirectional hybridization was recorded in Lakes Geneva and Bourget. Our results also demonstrate complex genetic trajectories within this species complex and highlight the irreversibility of changes in the genotypic architecture of populations driven by local human pressures. Finally, we show that extensive hybridization and introgression do not necessarily result in a large and homogenous hybrid swarm.

Zooplankton communities can be strongly affected by cyanobacterial blooms, especially species of genus Daphnia, which are key-species in lake ecosystems. Here, we explored the effect of microcystin/nonmicrocystin (MC/non-MC) producing cyanobacteria in the diet of experimental Daphnia galeata populations composed of eight genotypes. We used D. galeata clones hatched from ephippia 10 to 60 years old, which were first tested in monocultures, and then exposed for 10 weeks as mixed populations to three food treatments consisting of green algae combined with cyanobacteria able/unable of producing MC. We measured the expression of nine genes potentially involved in Daphnia acclimation to cyanobacteria: six protease genes, one ubiquitin-conjugating enzyme gene, and two rRNA genes, and then we tracked the dynamics of the genotypes in mixed populations. The expression pattern of one protease and the ubiquitin-conjugating enzyme genes was positively correlated with the increased fitness of competing clones in the presence of cyanobacteria, suggesting physiological plasticity. The genotype dynamics in mixed populations was only partially related to the growth rates of clones in monocultures and varied strongly with the food. Our results revealed strong intraspecific differences in the tolerance of D. galeata clones to MC/non-MC-producing cyanobacteria in their diet, suggesting microevolutionary effects.

Studies of parasite population dynamics in natural systems are crucial for our understanding of host–parasite coevolutionary processes. Some field studies have reported that host genotype frequencies in natural populations change over time according to parasite-driven negative frequency-dependent selection. However, the temporal patterns of parasite genotypes have rarely been investigated. Moreover, parasite-driven negative frequency-dependent selection is contingent on the existence of genetic specificity between hosts and parasites. In the present study, the population dynamics and host-genotype specificity of the ichthyosporean Caullerya mesnili, a common endoparasite of Daphnia water fleas, were analysed based on the observed sequence variation in the first internal transcribed spacer (ITS1) of the ribosomal DNA. The Daphnia population of lake Greifensee (Switzerland) was sampled and subjected to parasite screening and host genotyping during C. mesnili epidemics of four consecutive years. The ITS1 of wild-caught C. mesnili-infected Daphnia was sequenced using the 454 pyrosequencing platform. The relative frequencies of C. mesnili ITS1 sequences differed significantly among years: the most abundant C. mesnili ITS1 sequence decreased and rare sequences increased over the course of the study, a pattern consistent with negative frequency-dependent selection. However, only a weak signal of host-genotype specificity between C. mesnili and Daphnia genotypes was detected. Use of cutting edge genomic techniques will allow further investigation of the underlying micro-evolutionary relationships within the Daphnia–C. mesnili system.

We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R² = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.

The seasonal dominance of cyanobacteria in the phytoplankton community of lake ecosystems can have severe implications for higher trophic levels. For herbivorous zooplankton such as Daphnia, cyanobacteria have poor nutritional value and some species can produce toxins affecting zooplankton survival and reproduction. Here we present another, hitherto largely unexplored aspect of cyanobacteria, namely that they can increase Daphnia susceptibility to parasites. In a 12-yr monthly time-series analysis of the Daphnia community in Greifensee (Switzerland), we observed that cyanobacteria density correlated significantly with the epidemics of a common gut parasite of Daphnia, Caullerya mesnili, regardless of what cyanobacteria species was present or whether it was colonial or filamentous. The temperature from the previous month also affected the occurrence of Caullerya epidemics, either directly or indirectly by the promotion of cyanobacterial growth. A laboratory experiment confirmed that cyanobacteria increase the susceptibility of Daphnia to Caullerya, and suggested a possible involvement of cyanotoxins or other chemical traits of cyanobacteria in this process. These findings expand our understanding of the consequences of toxic cyanobacterial blooms for lake ecosystems and might be relevant for epidemics experienced by other aquatic species.

Evolution occurs on time scales ranging from a few generations to millions of years. The traditional view of evolution taking geologic ages was relatively recently overturned. It was only in the 1980s and 1990s that we realized the glacial evolutionary rates inferred by paleontology may mask rapid evolutionary dynamics that lead to little net change over time. Nevertheless, these rapid changes are what allows populations to adapt and survive in rapidly changing environments, and we now have a greater appreciation for their importance. After a strong interest in "rapid evolution" in the 1990s, we now know that these rates are in fact normal, and researchers have begun to appreciate that ecological change and evolutionary change may occur on the same time scales, and indeed influence each other.
Despite these realizations, the temporal range of evolutionary studies is limited. Researchers may be only able to measure wild populations for a few years, or conversely may rely on preserved remains that give little insight to (e.g.) physiology or behavior. In my doctoral research, I addressed evolutionary questions on the decade scale, using a variety of strategies and the model organism Daphnia, an ecologically important freshwater crustacean.
In Chapters 2 and 3, we took the first steps towards opening a rich genetic archive spanning over decades. Samples of plankton and other organisms are preserved in formaldehyde in many institutions, but the conditions of preservation were thought to destroy DNA. However, we developed novel methods for the extraction of DNA from formaldehyde-preserved Daphnia, and developed new genetic markers for use on this degraded material. Together, these tools may enable high resolution study of evolution over decades in several lakes.
In Chapter 4, we "resurrected" animals from decades past and brought them together with modern genotypes to directly address evolution for resistance to an important pollutant. Atmospheric pollution of lead (Pb) released by automobiles contaminated the entire biosphere from the 1920s to a peak in the 1970s, declining to near background levels only today. Despite this global contamination, there has been little or no investigation of the evolutionary consequences. We took a first step towards understanding the impact of Pb pollution by hatching Daphnia eggs from periods of high pollution in two lakes. We compared their laboratory resistance to Pb to that by modern genotypes, and found that the animals from decades ago were much more resistant. We infer that Daphnia may have developed this resistance over time, and conclude that it was lost as the selective pressure relaxed.
In Chapter 5, we combined data from several projects to accumulate a decade-scale time series of Daphnia genetic diversity, and used this to address a major outstanding evolutionary question. According to the Red Queen theory, the clonal diversity of asexual animals such as Daphnia may be driven by negative frequency-dependent selection by coevolving parasites. Despite broad theoretic support, this hypothesis has very little empirical evidence due to the difficulty of collecting the requisite data. We assembled Daphnia genetic data at hundreds of time points, representing thousands of individuals, and compared their rate of clonal turnover to a variety of physical and ecological parameters. The best correlate of turnover was parasitism, providing empirical support for Red Queen theory with unprecedented temporal resolution.

We investigated the evolutionary response of an ecologically important freshwater crustacean, Daphnia, to a rapidly changing toxin environment. From the 1920s until the 1960s, the use of leaded gasoline caused the aquatic concentration of Pb to increase at least fivefold, presumably exerting rapid selective pressure on organisms for resistance. We predicted that Daphnia from this time of intense pollution would display greater resistance than those hatched from times of lower pollution. This question was addressed directly using the resurrection ecology approach, whereby dormant propagules from focal time periods were hatched and compared. We hatched several Daphnia genotypes from each of two Swiss lakes, during times of higher (1960s /1980s) and lower (2000s) lead stress, and compared their life histories under different laboratory levels of this stressor. Modern Daphnia had significantly reduced fitness, measured as the population growth rate (λ), when exposed to lead, whereas those genotypes hatched from times of high lead pollution did not display this reduction. These phenotypic differences contrast with only slight differences measured at neutral loci. We infer that Daphnia in these lakes were able to rapidly adapt to increasing lead concentrations, and just as rapidly lost this adaptation when the stressor was removed.

Despite the relevance of resting eggs for ecology and evolution of many aquatic organisms and their exposure to contaminants accumulating in sediments, ecotoxicological studies using resting eggs are vastly underrepresented. The authors established a method to perform exposure assays with resting eggs produced by the Daphnia longispina species complex, key species in large lake ecosystems. A mixture of organic contaminants previously detected in sediments of Lake Greifensee was selected to test the potential effect of organic contaminants present in sediments on the hatching process. Resting eggs were exposed to a mix of 10 chemicals, which included corrosion inhibitors, biocides, pesticides, and personal care products, for a period of 15 d. Using an automated counting software, the authors found a significant increase in hatching success in the exposed resting eggs compared with controls. Such an effect has not yet been reported from ecotoxicological assays with resting eggs. Possible mechanistic explanations as well as the potential implications on the ecology and evolution of aquatic species that rely on a resting egg banks are discussed. Observed increased mortality and developmental abnormalities for hatchlings in the exposure treatments can be explained by toxic contaminant concentrations. The results of the present study highlight the need for additional studies assessing the effects of organic contaminants on resting egg banks and aquatic ecosystems.

Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as ‘European D. pulicaria’ originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.

Forecasts of ecological dynamics in changing environments are increasingly important, and are available for a plethora of variables, such as species abundance and distribution, community structure and ecosystem processes. There is, however, a general absence of knowledge about how far into the future, or other dimensions (space, temperature, phylogenetic distance), useful ecological forecasts can be made, and about how features of ecological systems relate to these distances. The ecological forecast horizon is the dimensional distance for which useful forecasts can be made. Five case studies illustrate the influence of various sources of uncertainty (e.g. parameter uncertainty, environmental variation, demographic stochasticity and evolution), level of ecological organisation (e.g. population or community), and organismal properties (e.g. body size or number of trophic links) on temporal, spatial and phylogenetic forecast horizons. Insights from these case studies demonstrate that the ecological forecast horizon is a flexible and powerful tool for researching and communicating ecological predictability. It also has potential for motivating and guiding agenda setting for ecological forecasting research and development.

In order to trace community dynamics and reticulate evolution in hybrid species complexes, long-term comparative studies of natural populations are necessary. Such studies require the development of tools for fine-scale genetic analyses. In the present study, we developed species-diagnostic SNP-based markers for hybridizing freshwater crustaceans: the multispecies Daphnia longispina complex. Specifically, we took advantage of transcriptome data from a key species of this hybrid complex, the annotated genome of a related Daphnia species and well-defined reference genotypes from three parental species. Altogether eleven nuclear loci with several species-specific SNP sites were identified in sequence alignments of these reference genotypes from three parental species and their interspecific hybrids. A PCR-RFLP assay was developed for cost-efficient large population screening by SNP-based genotyping. Taxon assignment by RFLP patterns was nearly perfectly concordant with microsatellite genotyping across several screened populations from Europe. Finally, we were able to amplify two short regions of these loci in formaldehyde-preserved samples dating back to the year 1960. The species-specific SNP-based markers developed here provide valuable tools to study hybridization over time, including the long-term impact of various environmental factors on hybridization and biodiversity changes. SNP-based genotyping will finally allow eco-evolutionary dynamics to be revealed at different time scales.

The stable isotopic composition of fossil resting eggs (ephippia) of Daphnia spp. is being used to reconstruct past environmental conditions in lake ecosystems. However, the underlying assumption that the stable isotopic composition of the ephippia reflects the stable isotopic composition of the parent Daphnia, of their diet and of the environmental water have yet to be confirmed in a controlled experimental setting. We performed experiments with Daphnia pulicaria cultures, which included a control treatment conducted at 12 °C in filtered lake water and with a diet of fresh algae and three treatments in which we manipulated the stable carbon isotopic composition (δ¹³C value) of the algae, stable oxygen isotopic composition (δ¹⁸O value) of the water and the water temperature, respectively. The stable nitrogen isotopic composition (δ¹⁵N value) of the algae was similar for all treatments. At 12 °C, differences in algal δ¹³C values and in δ¹⁸O values of water were reflected in those of Daphnia. The differences between ephippia and Daphnia stable isotope ratios were similar in the different treatments (δ¹³C: +0.2 ± 0.4 ‰ (standard deviation); δ¹⁵N: −1.6 ± 0.4 ‰; δ¹⁸O: −0.9 ± 0.4 ‰), indicating that changes in dietary δ¹³C values and in δ¹⁸O values of water are passed on to these fossilizing structures. A higher water temperature (20 °C) resulted in lower δ¹³C values in Daphnia and ephippia than in the other treatments with the same food source and in a minor change in the difference between δ¹³C values of ephippia and Daphnia (to −1.3 ± 0.3 ‰). This may have been due to microbial processes or increased algal respiration rates in the experimental containers, which may not affect Daphnia in natural environments. There was no significant difference in the offset between δ¹⁸O and δ¹⁵N values of ephippia and Daphnia between the 12 and 20 °C treatments, but the δ¹⁸O values of Daphnia and ephippia were on average 1.2 ‰ lower at 20 °C than at 12 °C. We conclude that the stable isotopic composition of Daphnia ephippia provides information on that of the parent Daphnia and of the food and water they were exposed to, with small offsets between Daphnia and ephippia relative to variations in Daphnia stable isotopic composition reported from downcore studies. However, our experiments also indicate that temperature may have a minor influence on the δ¹³C, δ¹⁵N and δ¹⁸O values of Daphnia body tissue and ephippia. This aspect deserves attention in further controlled experiments.

Many freshwater and marine algal species are described as having cosmopolitan distributions. Whether these widely distributed morphologically similar algae also share a similar gene pool remains often unclear. In the context of island biogeography theory, stronger spatial isolation deemed typical of freshwater lakes should restrict gene flow and lead to higher genetic differentiation among lakes. Using nine microsatellite loci, we investigate the genetic diversity of a widely distributed freshwater planktonic diatom, Asterionella formosa, across different lakes in Switzerland and the Netherlands. We applied a hierarchical spatial sampling design to determine the geographical scale at which populations are structured. A subset of the isolates was additionally analysed using amplified fragment length polymorphism (AFLP) markers. Our results revealed complex and unexpected population structure in A. formosa with evidence for both restricted and moderate to high gene flow at the same time. Different genetic markers (microsatellites and AFLPs) analysed with a variety of multivariate methods consistently revealed that genetic differentiation within lakes was much stronger than among lakes, indicating the presence of cryptic species within A. formosa. We conclude that the hidden diversity found in this study is expected to have implications for the further use of A. formosa in biogeographical, conservation and ecological studies. Further research using species-level phylogenetic markers is necessary to place the observed differentiation in an evolutionary context of speciation.

During the last few decades, biological invasions have become a main threat to numerous species. Depending on human action and environmental characteristics, introduced species from any trophic level may be able to transform community composition as well as ecosystem properties, change nutrient-cycling and even affect ecosystem services. Daphnia are among the most important freshwater planktonic grazers responding to environmental changes, and exert strong effects on the ecosystem. Coinciding with intense eutrophication of most European Lakes in the 1970s European, Daphnia pulicaria successfully invaded lower Lake Constance. In November 2012, European D. pulicaria also entered and successfully established in Lake Greifen. Here we show all changes, trends and patterns in genetic diversity, differentiation and vertical distribution that took place during the first year of the aquatic invasion of European D. pulicaria in Lake Greifen. Our results demonstrate a drastic decrease in diversity parameters and a rapid allelic change, indicating an immediate selective response to new environmental conditions. These outcomes are contrary to those of the long-term study in Lake Constance, which highlights the importance to consider short-term observations following an introduction event, in order to gather detailed information on selective mechanisms taking place in the initial phase. Furthermore, spatial analysis revealed diel vertical migrations among layers of metalimnic and hypolimnic layers. These observations are associated with various possible trade-offs regarding food availability, fish predation and oxygen concentration. As our assay depicts new discoveries regarding genetic and spatial mechanisms, we anticipate our assay to be a starting point for further detailed research on traits of European D. pulicaria which is a key organism in many aquatic food webs. Generally, this study gives an insight into mechanisms and interactions occurring during the first year of a biological invasion.

Emerging contaminants are important since they can have complex effects on ecosystems. However, the fate and occurrence of many organic contaminants could not be assessed in the past due to the lack of technology available. Measurements of emerging contaminants such as pharmaceutical and personal care products started in the 1990s, thus the exposure before this time is not well studied.
Sediment cores have been shown to be useful to reconstruct environmental changes over time, providing historic records of natural events, changes in ecosystems, and climate. Therefore, sediments could be suitable to reconstruct the environmental contamination to provide records of anthropogenic impact. [...]

Verunreinigungen durch neuartige chemische Stoffe haben vielfältige Einflüss auf Ökosysteme. In der Vergangenheit konnte das Auftreten von vielen organischen Verunreinigungen jedoch nicht analysiert werden, da keine analytischen Messmethoden zur Verfügung standen. Die Messung von neuartigen Substanzen wie beispielsweise von Arzneimitteln oder von Körperpflegeprodukten begann erst in den 90er Jahren. Daher ist über die Verbreitung dieser Chemikalien in Ökosystemen vor dieser Zeit nur wenig bekannt.
Die Analyse von Sedimentbohrkernen hat sich als nützlich erwiesen, um Umweltereignisse der Vergangenheit sowie Veränderungen in Ökosystemen oder des Klimas zu rekonstruieren. Insbesondere sind Sedimentbohrkerne geeignet, chemische Umweltbelastungen der Vergangenheit sowie anthropogene Einflüsse zu beschreiben. [...]

Host density can increase infection rates and reduce host fitness as increasing population density enhances the risk of becoming infected either through increased encounter rate or because host condition may decline. Conceivably, potential hosts could take high host density as a cue to up-regulate their defence systems. However, as host density usually covaries with food availability, it is difficult to examine the importance of host density in isolation. Thus, we performed two full-factorial experiments that varied juvenile densities of Daphnia magna (a freshwater crustacean) and food availability independently. We also included a simulated high-density treatment, where juvenile experimental animals were kept in filtered media that previously maintained Daphnia at high-density. Upon reaching adulthood, we exposed the Daphnia to their sterilizing bacterial parasite, Pasteuria ramosa, and examined how the juvenile treatments influenced the likelihood and severity of infection (Experiment I) and host immune investment (Experiment II). Neither juvenile density nor food treatments affected the likelihood of infection; however, well-fed hosts that were well-fed as juveniles produced more offspring prior to sterilization than their less well-fed counterparts. By contrast, parasite growth was independent of host juvenile resources or host density. Parasite-exposed hosts had a greater number of circulating haemocytes than controls (i.e., there was a cellular immune response), but the magnitude of immune response was not mediated by food availability or host density. These results suggest that density dependent effects on disease arise primarily through correlated changes in food availability: low food could limit parasitism and potentially curtail epidemics by reducing both the host's and parasite's reproduction as both depend on the same food.

Cyanobacteria blooms occur frequently in eutrophic lakes and can highly impair the well-being of zooplankton communities. It is generally assumed that cyanobacteria are a bad food resource for zooplankton. They lack certain fatty acids which are essential for growth, reproduction and immune system functioning, their morphology (colonies, filaments) is often difficult to handle for small zooplankton (e.g. Daphnia sp.) and some genera are known to produce secondary metabolites (e.g. microcystins) which are toxic to many species, including Daphnia sp. In Lake Greifensee, a highly eutrophic peri alpine lake in Switzerland, cyanobacteria abundance was observed to highly correlate with epidemics of the Daphnia gut parasite Caullerya mesnili. However, the connection between parasite epidemics and cyanobacteria occurrence are unknown. Here I could show how a cyanobacteria strain isolated from a recent epidemic could drastically increase infection success of C. mesnili in Daphnia longispina and Daphnia longispina × galeata. Moreover, an involvement of microcystins in Caullerya infections is likely. Animals that were offered the microcystin producing Microcystis aeruginosa PCC7806 as a food resource were observed to die much earlier in the presence of C. mesnili spores. However, high mortality rates in this food × parasite combination after 14 days made it impossible to see if C. mesnili infection success was enhanced or not. Furthermore, a general cyanobacteria influence is unlikely, since a microcystin – deficient M. aeruginosa strain did not increase infection success. Furthermore, the vertical distribution of C. mesnili infected and uninfected Daphnia and the genotype pattern of infected versus uninfected animals were assessed in a field survey. The different multilocus genotypes (MLG) showed distinct infection proportions where certain MLGs were over- or underinfected. However, C. mesnili does not seem to affect depth selection or migration patterns of Daphnia sp. in Lake Greifensee. Whether cyanobacteria in Lake Greifensee temporally co-occur with Daphnia sp. in the water column– a premise for a potential influence – could not be assessed.

Parasite environments are heterogeneous at different levels. The first level of variability is the host itself. The second level represents the external environment for the hosts, to which parasites may be exposed during part of their life cycle. Both levels are expected to affect parasite fitness traits. We disentangle the main and interaction effects of variation in the immediate host environment, here the diatom Asterionella formosa (variables host cell volume and host condition through herbicide pre-exposure) and variation in the external environment (variables host density and acute herbicide exposure) on three fitness traits (infection success, development time and reproductive output) of a chytrid parasite. Herbicide exposure only decreased infection success in a low host density environment. This result reinforces the hypothesis that chytrid zoospores use photosynthesis-dependent chemical cues to locate its host. At high host densities, chemotaxis becomes less relevant due to increasing chance contact rates between host and parasite, thereby following the mass-action principle in epidemiology. Theoretical support for this finding is provided by an agent-based simulation model. The immediate host environment (cell volume) substantially affected parasite reproductive output and also interacted with the external herbicide exposed environment. On the contrary, changes in the immediate host environment through herbicide pre-exposure did not increase infection success, though it had subtle effects on zoospore development time and reproductive output. This study shows that both immediate host and external environment as well as their interaction have significant effects on parasite fitness. Disentangling these effects improves our understanding of the processes underlying parasite spread and disease dynamics.

Organic contaminants detected in sediments from Lake Greifensee and other compounds falling in the log Dow range from 1 to 7 were selected to study the bioconcentration of organic contaminants in sediments in Daphnia resting eggs (ephippia). Our results show that octocrylene, tonalide, triclocarban, and other personal care products, along with pesticides and biocides can accumulate in ephippia with log BCF values up to 3. Data on the uptake and depuration kinetics show a better fit toward a two compartment organism model over a single compartment model due to the differences in ephippial egg content in the environment. The obtained BCFs correlate with hydrophobicity for neutral compounds. Independence between BCF and hydrophobicity was observed for partially ionized compounds with log D_ow values around 1. Internal concentrations in ephippia in the environment were predicted based on sediment concentrations using the equilibrium partitioning model and calculated BCFs. Estimated internal concentration values ranged between 1 and 68,000 µg/kg_lip with triclocarban having the highest internal concentrations followed by tonalide and triclosan. The outcomes indicate that contaminants can be taken up by ephippia from the water column or the pore water in the sediment and might influence fitness and sexual reproduction in the aquatic key species of the genus Daphnia.

The occurrence of members of the highly diverse Daphnia longispina complex in Southern and Central Asian high-mountain lakes has been recognized for more than a century. Until now, however, no molecular data have been available for these populations inhabiting the "Roof of the World". Here, we present the first identification for D. gr. longispina from that region based on a molecular phylogeny. Our findings show that alpine lakes in the Pamir and Himalaya mountains host populations of widespread species of the complex, for which these are the highest known localities. A spineless morph from the Himalaya region, previously labeled as D. longispina var. aspina, was clustering tightly with D. dentifera, while a population from the Pamir mountain range was grouped with D. longispina. In addition, we analyzed ecological data available for lakes in the Khumbu region (Himalaya) to investigate ecological preferences of non-pigmented D. gr. longispina. The identified factors can at least partly be related to avoidance of high UV conditions by this species. We conclude that the widespread species D. dentifera and D. longispina also colonized the Asian high-mountain lakes, and identify the need for further research to trace the possible effect of rapid environmental changes in this region on the diversity and ecology of high-altitude Daphnia populations.

Parasites play an important role in the regulation of host population growth. How these ubiquitous stressors interact with anthropogenic stressors is less often studied. In a full factorial experiment we explored the independent and combined effects of the widely used herbicide diuron and a chytrid parasite on the fitness of genetically different monoclonal diatom populations. Furthermore, we evaluated how herbicide exposure influenced infection dynamics, parasite fitness and the impact of infectious disease on host populations. We found no evidence of host genetic variation for diuron sensitivity and parasite resistance. Instead, host population phenotype was a decisive factor in controlling parasite growth. Although herbicide exposure initially posed a constraint on disease transmission, it enhanced the spread of disease over time. Consequently, the nature of the parasite–toxicant stressor interaction shifted from antagonistic (on exponential host growth) towards additive (on final uninfected host density). We conclude that herbicide exposure can modify infection dynamics and impact of disease on host populations through the complex interplay between host and parasite growth dynamics and host population phenotype.

Organisms are exposed to multiple biotic and abiotic environmental stressors, which can influence the dynamics of individual populations and communities. Populations may also genetically adapt to both natural (e.g. disease) and anthropogenic (e.g. chemical pollution) stress. In the present study, we studied fitness consequences of exposure to both a parasite (i.e. biotic) and a pesticide (i.e. abiotic) for the water flea Daphnia. In addition, we investigated whether these fitness consequences change through time as a population evolves. Thus, we exposed Daphnia magna clones, hatched from dormant eggs isolated from different time layers of a natural dormant egg bank, to the parasite Pasteuria ramosa and the insecticide diazinon in a multifactorial experiment. While our experimental treatments for unknown reasons failed to induce disease symptoms in the Daphnia, we did observe a reduced survival of D. magna when simultaneously exposed to both the parasite and the pesticide. No increased mortality upon exposure to individual stressors was observed. We did not observe an evolutionary change in fitness response of the Daphnia clones hatched from different time horizons upon exposure to stressors.

1. Environmental stressors can influence population and community structure. However, the majority of experimental work on multiple environmental stressors has been done at the individual level only.
2. In this work, we followed changes in experimental assemblages of Daphnia (waterfleas; consisting of two taxa and three clones per taxon) after exposure to the fungal parasite Metschnikowia sp. and/or the pesticide diazinon.3. We found a significant shift in taxonomic and clonal composition under both stressors. Strikingly, in the parasite and parasite+pesticide treatments, one taxon went extinct. While the pesticide had no effect on total parasite prevalence, the taxon that was more susceptible to extinction was, at the same time, more infected when additionally exposed to the pesticide. Furthermore, the density of all adult females was significantly reduced in the parasite treatment, but not in the pesticide treatment.
4. Our results demonstrate that the dynamics of Daphnia assemblages are altered by parasites and pesticide exposure. Given the key role of Daphnia in aquatic food webs in transferring primary production into fish food, this could be of wide significance in aquatic ecosystems.