SEED: A framework for integrating ecological stoichiometry and eco-evolutionary dynamics.

Characterising the extent and sources of intraspecific variation and their ecological consequences is a central challenge in the study of eco-evolutionary dynamics. Ecological stoichiometry, which uses elemental variation of organisms and their environment to understand ecosystem patterns and processes, can be a powerful framework for characterising eco-evolutionary dynamics. However, the current emphasis on the relative content of elements in the body (i.e. organismal stoichiometry) has constrained its application. Intraspecific variation in the rates at which elements are acquired, assimilated, allocated or lost is often greater than the variation in organismal stoichiometry. There is much to gain from studying these traits together as components of an 'elemental phenotype'. Furthermore, each of these traits can have distinct ecological effects that are underappreciated in the current literature. We propose a conceptual framework that explores how microevolutionary change in the elemental phenotype occurs, how its components interact with each other and with other traits, and how its changes can affect a wide range of ecological processes. We demonstrate how the framework can be used to generate novel hypotheses and outline pathways for future research that enhance our ability to explain, analyse and predict eco-evolutionary dynamics.

Restoring gradual land-water transitions in a shallow lake improved phytoplankton quantity and quality with cascading effects on zooplankton production.

Land-water transition areas play a significant role in the functioning of aquatic ecosystems. However, anthropogenic pressures are posing severe threats on land-water transition areas, which leads to degradation of the ecological integrity of many lakes worldwide. Enhancing habitat complexity and heterogeneity by restoring land-water transition areas in lake systems is deemed a suitable method to restore lakes bottom-up by stimulating lower trophic levels. Stimulating productivity of lower trophic levels (phytoplankton, zooplankton) generates important food sources for declining higher trophic levels (fish, birds). Here, we study ecosystem restoration project Marker Wadden in Lake Markermeer, The Netherlands. This project involved the construction of a 700-ha archipelago of five islands in a degrading shallow lake, aiming to create additional sheltered land-water transition areas to stimulate food web development from its base by improving phytoplankton quantity and quality. We found that phytoplankton quantity (chlorophyll-a concentration) and quality (inversed carbon:nutrient ratio) in the shallow waters inside the Marker Wadden archipelago were significantly improved, likely due to higher nutrient availabilities, while light availability remained sufficient, compared to the surrounding lake. Higher phytoplankton quantity and quality was positively correlated with zooplankton biomass, which was higher inside the archipelago than in the surrounding lake due to improved trophic transfer efficiency between phytoplankton and zooplankton. We conclude that creating new land-water transition areas can be used to increase light and nutrient availabilities and thereby enhancing primary productivity, which in turn can stimulate higher trophic levels in degrading aquatic ecosystems.

An experimental test of the growth rate hypothesis as a predictive framework for microevolutionary adaptation.

The growth rate hypothesis (GRH) posits that the relative body phosphorus content of an organism is positively related to somatic growth rate, as protein synthesis, which is necessary for growth, requires P-rich rRNA. This hypothesis has strong support at the interspecific level. Here, we explore the use of the GRH to predict microevolutionary responses in consumer body stoichiometry. For this, we subjected populations of the rotifer Brachionus calyciflorus to selection for fast population growth rate (PGR) in P-rich (HPF) and P-poor (LPF) food environments. With common garden transplant experiments, we demonstrate that in HP populations evolution toward increased PGR was concomitant with an increase in relative phosphorus content. In contrast, LP populations evolved higher PGR without an increase in relative phosphorus content. We conclude that the GRH has the potential to predict microevolutionary change, but that its application is contingent on the environmental context. Our results highlight the potential of cryptic evolution in determining the performance response of populations to elemental limitation of their food resources.

The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure.

Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.

Herbivore consumers face different challenges along opposite sides of the stoichiometric knife-edge.

Anthropogenic activities have reshaped the relative supply rates of essential elements to organisms. Recent studies suggested that consumer performance is strongly reduced by food that is either very high or very low in relative phosphorus content. However, the generality of such 'stoichiometric knife-edge' and its underlying mechanisms are poorly understood. We studied the response of a planktonic rotifer to a 10-fold food carbon : phosphorus (C : P) gradient and confirmed the existence of the stoichiometric knife-edge. Interestingly, we observed a complete homeostatic breakdown associated with strong growth reductions at high food C : P. In contrast, at low food C : P, animals maintained homeostasis despite pronounced performance reductions. Our results suggest that the mechanisms underlying adverse effects of stoichiometric imbalance are determined by both the identity of elements that are limiting and those that are present in excess. Negative effects of excess P reveal an additional way of how eutrophication may affect consumers.

Phytoplankton growth and stoichiometric responses to warming, nutrient addition and grazing depend on lake productivity and cell size.

Global change involves shifts in multiple environmental factors that act in concert to shape ecological systems in ways that depend on local biotic and abiotic conditions. Little is known about the effects of combined global change stressors on phytoplankton communities, and particularly how these are mediated by distinct community properties such as productivity, grazing pressure and size distribution. Here, we tested for the effects of warming and eutrophication on phytoplankton net growth rate and C:N:P stoichiometry in two phytoplankton cell size fractions (<30 µm and >30 µm) in the presence and absence of grazing in microcosm experiments. Because effects may also depend on lake productivity, we used phytoplankton communities from three Dutch lakes spanning a trophic gradient. We measured the response of each community to multifactorial combinations of temperature, nutrient, and grazing treatments and found that nutrients elevated net growth rates and reduced carbon:nutrient ratios of all three phytoplankton communities. Warming effects on growth and stoichiometry depended on nutrient supply and lake productivity, with enhanced growth in the most productive community dominated by cyanobacteria, and strongest stoichiometric responses in the most oligotrophic community at ambient nutrient levels. Grazing effects were also most evident in the most oligotrophic community, with reduced net growth rates and phytoplankton C:P stoichiometry that suggests consumer-driven nutrient recycling. Our experiments indicate that stoichiometric responses to warming and interactions with nutrient addition and grazing are not universal but depend on lake productivity and cell size distribution.

Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.

Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.

Reverse taxonomy applied to the Brachionus calyciflorus cryptic species complex: Morphometric analysis confirms species delimitations revealed by molecular phylogenetic analysis and allows the (re)description of four species.

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key.

Managing Successional Stage Heterogeneity to Maximize Landscape-Wide Biodiversity of Aquatic Vegetation in Ditch Networks.

The presence of a high diversity of different successional stages in a landscape may help to conserve and promote landscape-wide biodiversity. A strategy to achieve this is using Cyclic Rejuvenation through Management (CRM), an approach employed in a variety of different ecosystems. CRM periodically resets the successional stages in a landscape. For aquatic systems this constitutes vegetation removal and dredging. For this approach to be useful (a) successional stages are required to be different in community composition and (b) these differences need to be caused by true replacement of species between stages. While potentially valid, these assumptions are not generally tested prior to application of CMR. In this study we test these assumptions to explore the usefulness of managing on successional stage heterogeneity for maximizing landscape-wide aquatic plant diversity. We carried out vegetation surveys in the ditch networks of 21 polder landscapes in Netherlands, each containing 24 ditch reaches. Using a clustering approach combined with insight from literature on vegetation succession in these systems we assigned our sampled communities to defined successional stages. After partitioning landscape diversity into its alpha and beta components, we quantified the relative importance of replacement among successional stages. Next, through scenario analyses based on simulations we studied the effects of reducing successional stage heterogeneity on landscape-wide biodiversity. Results showed that differences in community composition among successional stages were a potentially important factor contributing to landscape diversity. Early successional stages were characterized by higher replacement of species compared to late successional stages. In a scenario of gradual decrease of heterogeneity through the systematic loss of the earliest successional stages we found 20% of the species richness in a polder was lost, pointing toward the importance of maintaining early successional stages in a polder. This makes a compelling case for application of CRM within agricultural drainage ditch landscapes to maximize regional aquatic plant diversity. While applied to drainage ditch systems, our data-driven approach is broadly applicable to other systems and may help in providing first indications of the potential of the CRM approach. We argue that CRM may maintain and promote regional biodiversity without compromising the hydrological function of the systems.

The genome of the freshwater monogonont rotifer Brachionus calyciflorus.

Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.

Direct and Indirect Effects of Resource P-Limitation Differentially Impact Population Growth, Life History and Body Elemental Composition of a Zooplankton Consumer.

One of the central tenets of ecological stoichiometry is that consumer growth rate is strongly determined by food phosphorus (P) content. In planktonic organisms population growth rates of zooplankton have repeatedly been shown to be reduced when fed with P-limited algal food sources. However, P-limitation may also affect other quality-related aspects of algae, such as biochemical composition or palatability. We studied the population growth, detailed life history and body elemental composition of the herbivorous rotifer, Brachionus calyciflorus, in response to three different food quality treatments: algae cultured in high phosphorus conditions (average algal molar C:P ≈ 112, 'HP'), algae cultured in low P conditions (molar C:P ≈ 631, 'LP') and low-P cultured algae spiked with P just before feeding (molar C:P ≈ 113, 'LP+P'). LP+P algae thus combined high P content with a history of growth under P-limited conditions. Total P content and the C:P ratio of rotifers in the LP+P treatment equaled those of rotifers in the HP treatment. Rotifer population growth rates were higher in HP than in LP and intermediate in the LP+P treatment. Similarly, many life history traits observed for animals in the LP+P treatment, such as somatic growth rate, age at maturity, and egg production rate were also intermediate to those observed in the LP and HP treatments. However, there were important deviations from this pattern: size at first reproduction and egg mortality in the LP+P treatment equaled the HP treatment, whereas size and development time of the first eggs equaled those of the LP treatment. Our results indicate that elemental limitation cannot fully explain reduced performance of consumers fed with P-limited algae and strongly suggest that indirect, non-stoichiometric effects of P-limitation, e.g., via changes in biochemical composition or morphology of the algae also play a major role. Furthermore, our study highlights that such indirect effects have a differential impact on major fitness components and may as such also determine the population dynamics and demographic structure of consumer populations.

Integrating community assembly and biodiversity to better understand ecosystem function: the Community Assembly and the Functioning of Ecosystems (CAFE) approach.

The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function.

Genome-wide identification of 31 cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and analysis of their benzo[α]pyrene-induced expression patterns.

While marine invertebrate cytochrome P450 (CYP) genes and their roles in detoxification mechanisms have been studied, little information is available regarding freshwater rotifer CYPs and their functions. Here, we used genomic sequences and RNA-seq databases to identify 31 CYP genes in the freshwater rotifer Brachionus calyciflorus. The 31 Bc-CYP genes with a few tandem duplications were clustered into CYP 2, 3, 4, mitochondrial, and 46 clans with two marine rotifers Brachionus plicatilis and Brachionus koreanus. To understand the molecular responses of these 31 Bc-CYP genes, we also examined their expression patterns in response to benzo[α]pyrene (B[α]P). Three Bc-CYP genes (Bc-CYP3044B3, Bc-CYP3049B4, Bc-CYP3049B6) were significantly upregulated (P<0.05) in response to B[α]P, suggesting that these CYP genes can be involved in detoxification in response to B[α]P exposure. These genes might be useful as biomarkers of B[α]P exposure in B. calyciflorus. Overall, our findings expand the repertoire of known CYPs and shed light on their potential roles in xenobiotic detoxification in rotifers.

Species sorting and stoichiometric plasticity control community C:P ratio of first-order aquatic consumers.

Ecological stoichiometry has proven to be invaluable for understanding consumer response to changes in resource quality. Although interactions between trophic levels occur at the community level, most studies focus on single consumer species. In contrast to individual species, communities may deal with trophic mismatch not only through elemental plasticity but also through changes in species composition. Here, we show that a community of first-order consumers (e.g. zooplankton) is able to adjust its stoichiometry (C:P) in response to experimentally induced changes in resource quality, but only to a limited extent. Furthermore, using the Price equation framework we show the importance of both elemental plasticity and species sorting. These results illustrate the need for a community perspective in ecological stoichiometry, requiring consideration of species-specific elemental composition, intraspecific elemental plasticity and species turnover.

Effects of dispersal and environmental heterogeneity on the replacement and nestedness components of ß-diversity.

Traditionally metacommunity studies have quantified the relative importance of dispersal and environmental processes on observed ß-diversity. Separating ß-diversity into its replacement and nestedness components and linking such patterns to metacommunity drivers can provide richer insights into biodiversity organization across spatial scales. It is often very difficult to measure actual dispersal rates in the field and to define the boundaries of natural metacommunities. To overcome those limitations, we revisited an experimental metacommunity dataset to test the independent and interacting effects of environmental heterogeneity and dispersal on each component of ß-diversity. We show that the balance between the replacement and nestedness components of ß-diversity resulting from eutrophication changes completely depending on dispersal rates. Nutrient enrichment negatively affected local zooplankton diversity and generated a pattern of ß-diversity derived from nestedness in unconnected, environmentally heterogeneous landscapes. Increasing dispersal erased the pattern of nestedness, whereas the replacement component gained importance. In environmentally homogeneous metacommunities, dispersal limitation created community dissimilarity via species replacement whereas the nestedness component remained low and unchanged across dispersal levels. Our study provides novel insights into how environmental heterogeneity and dispersal interact and shape metacommunity structure.

The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems.

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex.

Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and 4 nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.

A naturally heterogeneous landscape can effectively slow down the dispersal of aquatic microcrustaceans.

Several studies have suggested that aquatic microcrustaceans are relatively efficient dispersers in a variety of landscapes, whereas others have indicated dispersal limitation at large spatial scales or under specific circumstances. Based on a survey of a set of recently created ponds in an area of approximately 18 × 25 km, we found multiple indications of dispersal limitation affecting the community assembly of microcrustacean communities. Spatial patterns in the community composition were better explained by the geomorphological structure of the landscape than by mere geographic distances. This suggests that ridges separating the network of valleys act as dispersal barriers, and as such may channel the dispersal routes of the studied taxa and, likely, also of their animal vectors. Dispersal limitation was further supported by a strong positive relationship between species richness and the abundance of neighboring water bodies, suggesting that isolation affects colonization rates. Finally, the apparent dispersal limitation of microcrustaceans is further corroborated by the observation of low colonization rates in newly dug experimental ponds in the study area.

The Impact of Conservation Management on the Community Composition of Multiple Organism Groups in Eutrophic Interconnected Man-Made Ponds.

Ponds throughout the world are subjected to a variety of management measures for purposes of biodiversity conservation. Current conservation efforts typically comprise a combination of multiple measures that directly and indirectly impact a wide range of organism groups. Knowledge of the relative impact of individual measures on different taxonomic groups is important for the development of effective conservation programs. We conducted a field study of 28 man-made ponds, representing four management types differing in the frequency of periodic pond drainage and the intensity of fish stock management. We disentangled the relative importance of direct and indirect effects of pond management measures on the community composition of phytoplankton, zooplankton, aquatic macro-invertebrates, submerged and emergent vascular plants. With the exception of phytoplankton, pond management had strong effects on the community composition of all investigated biota. Whether management affected communities directly or indirectly through its impact on fish communities or local environmental conditions in the pond varied between organism groups. Overall, the impact of pond drainage regime and fish community characteristics on the community composition of target organism groups were more important than local environmental conditions. The majority of taxa were negatively associated with fish density, whereas multiple emergent plant species and several taxa of aquatic macro-invertebrates were positively affected by increased drainage frequency. The effects of fish community and drainage tended to be largely independent. The present study indicates that pond drainage is an important element for biodiversity conservation in eutrophicated shallow and interconnected man-made ponds.