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.

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.

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.

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.

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.

Rapid adaptation of herbivore consumers to nutrient limitation: eco-evolutionary feedbacks to population demography and resource control.

Humans alter biogeochemical cycles of essential elements such as phosphorus (P). Prediction of ecosystem consequences of altered elemental cycles requires integration of ecology, evolutionary biology and the framework of ecological stoichiometry. We studied micro-evolutionary responses of a herbivorous rotifer to P-limited food and the potential consequences for its population demography and for ecosystem properties. We subjected field-derived, replicate rotifer populations to P-deficient and P-replete algal food, and studied adaptation in common garden transplant experiments after 103 and 209 days of selection. When fed P-limited food, populations with a P-limitation selection history suffered 37% lower mortality, reached twice the steady state biomass, and reduced algae by 40% compared to populations with a P-replete selection history. Adaptation involved no change in rotifer elemental composition but reduced investment in sex. This study demonstrates potentially strong eco-evolutionary feedbacks from shifting elemental balances to ecosystem properties, including grazing pressure and the ratio of grazer:producer biomass.

Parasite and nutrient enrichment effects on Daphnia interspecific competition.

Increased productivity due to nutrient enrichment is hypothesized to affect density-dependent processes, such as transmission success of horizontally transmitting parasites. Changes in nutrient availability can also modify the stoichiometry and condition of individual hosts, which may affect their susceptibility for parasites as well as the growth conditions for parasites within the host. Consequently, if not balanced by increased host immuno-competence or life history responses, changes in the magnitude of parasite effects with increasing nutrient availability are expected. If these parasite effects are host-species specific, this may lead to shifts in the host community structure. We here used the Daphnia- parasite model system to study the effect of nutrient enrichment on parasite-mediated competition in experimental mesocosms. In the absence of parasites, D. magna was competitively dominant to D. pulex at both low and high nutrient levels. Introduction of parasites resulted in infections of D. magna, but not of D. pulex and, as such, reversed the competitive hierarchy between these two species. Nutrient addition resulted in an increased prevalence and infection intensity of some of the parasites on D. magna. However, there was no evidence that high nutrient levels enhanced negative effects of parasites on the hosts. Costs associated with parasite infections may have been compensated by better growth conditions for D. magna in the presence of high nutrient levels.

Stoichiometric regulation of phytoplankton toxins.

Ecological Stoichiometry theory predicts that the production, elemental structure and cellular content of biomolecules should depend on the relative availability of resources and the elemental composition of their producer organism. We review the extent to which carbon- and nitrogen-rich phytoplankton toxins are regulated by nutrient limitation and cellular stoichiometry. Consistent with theory, we show that nitrogen limitation causes a reduction in the cellular quota of nitrogen-rich toxins, while phosphorus limitation causes an increase in the most nitrogen-rich paralytic shellfish poisoning toxin. In addition, we show that the cellular content of nitrogen-rich toxins increases with increasing cellular N : P ratios. Also consistent with theory, limitation by either nitrogen or phosphorus promotes the C-rich toxin cell quota or toxicity of phytoplankton cells. These observed relationships may assist in predicting and managing toxin-producing phytoplankton blooms. Such a stoichiometric regulation of toxins is likely not restricted to phytoplankton, and may well apply to carbon- and nitrogen-rich secondary metabolites produced by bacteria, fungi and plants.

An ecosystem service approach to support integrated pond management: a case study using Bayesian belief networks--highlighting opportunities and risks.

Freshwater ponds deliver a broad range of ecosystem services (ESS). Taking into account this broad range of services to attain cost-effective ESS delivery is an important challenge facing integrated pond management. To assess the strengths and weaknesses of an ESS approach to support decisions in integrated pond management, we applied it on a small case study in Flanders, Belgium. A Bayesian belief network model was developed to assess ESS delivery under three alternative pond management scenarios: intensive fish farming (IFF), extensive fish farming (EFF) and nature conservation management (NCM). A probabilistic cost-benefit analysis was performed that includes both costs associated with pond management practices and benefits associated with ESS delivery. Whether or not a particular ESS is included in the analysis affects the identification of the most preferable management scenario by the model. Assessing the delivery of a more complete set of ecosystem services tends to shift the results away from intensive management to more biodiversity-oriented management scenarios. The proposed methodology illustrates the potential of Bayesian belief networks. BBNs facilitate knowledge integration and their modular nature encourages future model expansion to more encompassing sets of services. Yet, we also illustrate the key weaknesses of such exercises, being that the choice whether or not to include a particular ecosystem service may determine the suggested optimal management practice.

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.

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.

Dispersal-mediated trophic interactions can generate apparent patterns of dispersal limitation in aquatic metacommunities.

Dispersal is a major organising force in metacommunities, which may facilitate compositional responses of local communities to environmental change and affect ecosystem function. Organism groups differ widely in their dispersal abilities and their communities are therefore expected to have different adaptive abilities. In mesocosms, we studied the simultaneous compositional response of three plankton communities (zoo-, phyto- and bacterioplankton) to a primary productivity gradient and evaluated how this response was mediated by dispersal intensity. Dispersal enhanced responses in all three planktonic groups, which also affected ecosystem functioning. Yet, variation partitioning analyses indicated that responses in phytoplankton and bacterial communities were not only controlled by dispersal directly but also indirectly through complex trophic interactions. Our results indicate that metacommunity patterns emerging from dispersal can cascade through the food web and generate patterns of apparent dispersal limitation in organisms at other trophic levels.

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.

Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods.

The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community profiles were analyzed with canonical correspondence analysis. Our results clearly demonstrate that direct DNA extraction methods can significantly influence the DNA quantity, purity, and observed community patterns of microbiota in activated sludge. Fast and Mobio generated high amounts of good quality DNA compared to Bead and Qiagen. Mobio also resulted in the detection of the highest number of species while Fast scored the best in discriminating between the community patterns of different activated sludge types. With respect to the characterization of community profiles, our analyses demonstrated a strong sludge type dependent variability among methods. Taking into account our results, we recommend Fast as the most suitable DNA extraction method for activated sludge samples used for bacterial community studies.

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.

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.