Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community.

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.

Population genetic insights into establishment, adaptation, and dispersal of the invasive quagga mussel across perialpine lakes.

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.

Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds.

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.

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance.

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.

Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community.

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.

Non-additive effects of foundation species determine the response of aquatic ecosystems to nutrient perturbation.

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.

Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes.

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, 4998 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.

On biological evolution and environmental solutions.

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.

Interactive effects of foundation species on ecosystem functioning and stability in response to disturbance.

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.

Consumer-resource dynamics is an eco-evolutionary process in a natural plankton community.

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.

High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly in peri-Alpine lakes.

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.

Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism.

BACKGROUND: Regulatory circuits of infection in the emerging experimental model system, water flea Daphnia and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of Daphnia galeata to its highly virulent and common parasite Caullerya mesnili, an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from parasite-exposed (vs. control) Daphnia, at two time points (4 and 48 h) after parasite exposure. RESULTS: We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin). CONCLUSIONS: General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in Daphnia fecundity after Caullerya infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.

Long Term Diversity and Distribution of Non-photosynthetic Cyanobacteria in Peri-Alpine Lakes.

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.

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness.

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.

Parasites driving host diversity: Incidence of disease correlated with Daphnia clonal turnover.

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.

Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication.

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.

Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes.

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. IMPORTANCE: Cyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understanding of how these blooms form. We successfully reconstructed the past diversity of whole cyanobacterial communities over two hundred years by sequencing genes preserved in the sediments of two perialpine lakes in Switzerland. We identified changes in diversity over time and validated our results using existing data collected in the same two lakes over the past 40 years. This work shows the potential of our approach for addressing important ecological questions about the effects of a changing environment on lake ecology.

Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes.

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.

Cyanobacteria Affect Fitness and Genetic Structure of Experimental Daphnia Populations.

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.

Rapid evolutionary loss of metal resistance revealed by hatching decades-old eggs.

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.