Prey evolution on the time scale of predator-prey dynamics revealed by allele-specific quantitative PCR

Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics

Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.

Local adaptation through countergradient selection in northern populations of Skeletonema marinoi

Marine microorganisms have the potential to disperse widely with few obvious barriers to gene flow. However, among microalgae, several studies have demonstrated that species can be highly genetically structured with limited gene flow among populations, despite hydrographic connectivity. Ecological differentiation and local adaptation have been suggested as drivers of such population structure. Here we tested whether multiple strains from two genetically distinct Baltic Sea populations of the diatom Skeletonema marinoi showed evidence of local adaptation to their local environments: the estuarine Bothnian Sea and the marine Kattegat Sea. We performed reciprocal transplants of multiple strains between culture media based on water from the respective environments, and we also allowed competition between strains of estuarine and marine origin in both salinities. When grown alone, both marine and estuarine strains performed best in the high-salinity environment, and estuarine strains always grew faster than marine strains. This result suggests local adaptation through countergradient selection, that is, genetic effects counteract environmental effects. However, the higher growth rate of the estuarine strains appears to have a cost in the marine environment and when strains were allowed to compete, marine strains performed better than estuarine strains in the marine environment. Thus, other traits are likely to also affect fitness. We provide evidence that tolerance to pH could be involved and that estuarine strains that are adapted to a more fluctuating pH continue growing at higher pH than marine strains.

Evolution of population dynamics following invasion by a non-native predator

Invasive predatory species are frequently observed to cause evolutionary responses in prey phenotypes, which in turn may lead to evolutionary shifts in the population dynamics of prey. Research has provided a link between rates of predation and the evolution of prey population growth in the lab, but studies from natural populations are rare. Here, we tested for evolutionary changes in population dynamics parameters of zooplankton Daphnia pulicaria following invasion by the predator Bythotrephes longimanus into Lake Kegonsa, Wisconsin, US. We used a resurrection ecological approach, whereby clones from pre- and post-invasive periods were hatched from eggs obtained in sediment cores and were used in a 3-month growth experiment. Based on these data, we estimated intrinsic population growth rates (r), the shape of density dependence (θ) and carrying capacities (K) using theta-logistic models. We found that post-invasion Daphnia maintained a higher r and K under these controlled, predation-free laboratory conditions. Evidence for changes in θ was weaker. Whereas previous experimental evolution studies of predator-prey interactions have demonstrated that genotypes that have evolved under predation have inferior competitive ability when the predator is absent, this was not the case for the Daphnia. Given that our study was conducted in a laboratory environment and the possibility for genotype-by-environment interactions, extrapolating these apparent counterintuitive results to the wild should be done with caution. However, barring such complications, we discuss how selection for reduced predator exposure, either temporally or spatially, may have led to the observed changes. This scenario suggests that complexities in ecological interactions represents a challenge when predicting the evolutionary responses of population dynamics to changes in predation pressure in natural systems.

Advantages of laboratory natural selection in the applied sciences

In the past three decades, laboratory natural selection has become a widely used technique in biological research. Most studies which have utilized this technique are in the realm of basic science, often testing hypotheses related to mechanisms of evolutionary change or ecological dynamics. While laboratory natural selection is currently utilized heavily in this setting, there is a significant gap with its usage in applied studies, especially when compared to the other selection experiment methodologies like artificial selection and directed evolution. This is despite avenues of research in the applied sciences which seem well suited to laboratory natural selection. In this review, we place laboratory natural selection in context with other selection experiments, identify the characteristics which make it well suited for particular kinds of applied research and briefly cover key examples of the usefulness of selection experiments within applied science. Finally, we identify three promising areas of inquiry for laboratory natural selection in the applied sciences: bioremediation technology, identifying mechanisms of drug resistance and optimizing biofuel production. Although laboratory natural selection is currently less utilized in applied science when compared to basic research, the method has immense promise in the field moving forward.

The evolution of convex trade-offs enables the transition towards multicellularity

The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach

Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.

Cell-growth gene expression reveals a direct fitness cost of grazer-induced toxin production in red tide dinoflagellate prey

Induced prey defences against consumers are conspicuous in microbes, plants and animals. In toxigenic prey, a defence fitness cost should result in a trade-off between defence expression and individual growth. Yet, previous experimental work has failed to detect such induced defence cost in toxigenic phytoplankton. We measured a potential direct fitness cost of grazer-induced toxin production in a red tide dinoflagellate prey using relative gene expression (RGE) of a mitotic cyclin gene (cyc), a marker that correlates to cell growth. This approach disentangles the reduction in cell growth from the defence cost from the mortality by consumers. Treatments where the dinoflagellate Alexandrium catenella were exposed to copepod grazers significantly increased toxin production while decreasing RGE of cyc, indicating a defence-growth trade-off. The defence fitness cost represents a mean decrease of the cell growth rate of 32%. Simultaneously, we estimate that the traditional method to measure mortality loss by consumers is overestimated by 29%. The defence appears adaptive as the prey population persists in quasi steady state after the defence is induced. Our approach provides a novel framework to incorporate the fitness cost of defence in toxigenic prey-consumer interaction models.

Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities

Predator-prey interactions heavily influence the dynamics of many ecosystems. An increasing body of evidence suggests that rapid evolution and coevolution can alter these interactions, with important ecological implications, by acting on traits determining fitness, including reproduction, anti-predatory defence and foraging efficiency. However, most studies to date have focused only on evolution in the prey species, and the predator traits in (co)evolving systems remain poorly understood. Here, we investigated changes in predator traits after approximately 600 generations in a predator-prey (ciliate-bacteria) evolutionary experiment. Predators independently evolved on seven different prey species, allowing generalization of the predator's evolutionary response. We used highly resolved automated image analysis to quantify changes in predator life history, morphology and behaviour. Consistent with previous studies, we found that prey evolution impaired growth of the predator, although the effect depended on the prey species. By contrast, predator evolution did not cause a clear increase in predator growth when feeding on ancestral prey. However, predator evolution affected morphology and behaviour, increasing size, speed and directionality of movement, which have all been linked to higher prey search efficiency. These results show that in (co)evolving systems, predator adaptation can occur in traits relevant to foraging efficiency without translating into an increased ability of the predator to grow on the ancestral prey type.

Why Do Phytoplankton Evolve Large Size in Response to Grazing?

Phytoplankton are among the smallest primary producers on Earth, yet they display a wide range of cell sizes. Typically, small phytoplankton species are stronger nutrient competitors than large phytoplankton species, but they are also more easily grazed. In contrast, evolution of large phytoplankton is often explained as a physical defense against grazing. Conceptually, this explanation is problematic, however, because zooplankton can coevolve larger size to counter this size-dependent escape from grazing. Here, we hypothesize that there is another advantage for the evolution of large phytoplankton size not so readily overcome: larger phytoplankton often provide lower nutritional quality for zooplankton. We investigate this hypothesis by analyzing an eco-evolutionary model that combines the ecological stoichiometry of phytoplankton-zooplankton interactions with coevolution of phytoplankton and zooplankton size. In our model, evolution of cell size modifies the nutrient uptake kinetics of phytoplankton according to known allometric relationships, which in turn affect the nutritional quality of phytoplankton. With this size-based mechanism, the model predicts that low grazing pressure or nonselective grazing by zooplankton favors evolution of small phytoplankton cells of high nutritional quality. In contrast, selective grazing for nutritious food favors evolution of large phytoplankton of low nutritional quality, which are preyed on by medium- to large-sized zooplankton. This size-dependent change in food quality may explain the commonly observed shift from dominance by small picophytoplankton in oligotrophic waters with low grazing pressure to large phytoplankton species in nutrient-rich waters with high grazing pressure.

Maladapted Prey Subsidize Predators and Facilitate Range Expansion

Dispersal of prey from predator-free patches frequently supplies a trophic subsidy to predators by providing more prey than are produced locally. Prey arriving from predator-free patches might also have evolved weaker defenses against predators and thus enhance trophic subsidies by providing easily captured prey. Using local models assuming a linear or accelerating trade-off between defense and population growth rate, we demonstrate that immigration of undefended prey increased predator abundances and decreased defended prey through eco-evolutionary apparent competition. In individual-based models with spatial structure, explicit genetics, and gene flow along an environmental gradient, prey became maladapted to predators at the predator's range edge, and greater gene flow enhanced this maladaptation. The predator gained a subsidy from these easily captured prey, which enhanced its abundance, facilitated its persistence in marginal habitats, extended its range extent, and enhanced range shifts during environmental changes, such as climate change. Once the predator expanded, prey adapted to it and the advantage disappeared, resulting in an elastic predator range margin driven by eco-evolutionary dynamics. Overall, the results indicate a need to consider gene flow-induced maladaptation and species interactions as mutual forces that frequently determine ecological and evolutionary dynamics and patterns in nature.

Company matters: The presence of other genotypes alters traits and intraspecific selection in an Arctic diatom under climate change

Arctic phytoplankton and their response to future conditions shape one of the most rapidly changing ecosystems on the planet. We tested how much the phenotypic responses of strains from the same Arctic diatom population diverge and whether the physiology and intraspecific composition of multistrain populations differs from expectations based on single strain traits. To this end, we conducted incubation experiments with the diatom Thalassiosira hyalina under present-day and future temperature and pCO2 treatments. Six fresh isolates from the same Svalbard population were incubated as mono- and multistrain cultures. For the first time, we were able to closely follow intraspecific selection within an artificial population using microsatellites and allele-specific quantitative PCR. Our results showed not only that there is substantial variation in how strains of the same species cope with the tested environments but also that changes in genotype composition, production rates, and cellular quotas in the multistrain cultures are not predictable from monoculture performance. Nevertheless, the physiological responses as well as strain composition of the artificial populations were highly reproducible within each environment. Interestingly, we only detected significant strain sorting in those populations exposed to the future treatment. This study illustrates that the genetic composition of populations can change on very short timescales through selection from the intraspecific standing stock, indicating the potential for rapid population level adaptation to climate change. We further show that individuals adjust their phenotype not only in response to their physicochemical but also to their biological surroundings. Such intraspecific interactions need to be understood in order to realistically predict ecosystem responses to global change.

Eco-evolutionary feedbacks between prey densities and linkage disequilibrium in the predator maintain diversity

Diversity occurs at multiple scales. Within a single population, there is diversity in genotypes and phenotypes. At a larger scale, within ecological communities, there is diversity in species. A number of studies have investigated how diversity at these two scales influence each other through what has been termed eco-evolutionary feedbacks. Here we study a three-species ecological module called apparent competition, in which the predator is evolving in a trait that determines its interaction with two prey species. Unlike previous studies on apparent competition, which employed evolutionary frameworks with very simple genetics, we study an eco-evolutionary model in which the predator's trait is determined by two recombining diallelic loci, so that its mean and variance can evolve, as well as associations (linkage disequilibrium) between the loci. We ask how eco-evolutionary feedbacks with these two loci affect the coexistence of the prey species and the maintenance of polymorphisms within the predator species. We uncover a novel eco-evolutionary feedback between the prey densities and the linkage disequilibrium between the predator's loci. Through a stability analysis, we demonstrate how these feedbacks affect polymorphisms at both loci and, among others, may generate stable cycling.

Not attackable or not crackable-How pre- and post-attack defenses with different competition costs affect prey coexistence and population dynamics

It is well-known that prey species often face trade-offs between defense against predation and competitiveness, enabling predator-mediated coexistence. However, we lack an understanding of how the large variety of different defense traits with different competition costs affects coexistence and population dynamics. Our study focusses on two general defense mechanisms, that is, pre-attack (e.g., camouflage) and post-attack defenses (e.g., weaponry) that act at different phases of the predator-prey interaction. We consider a food web model with one predator, two prey types and one resource. One prey type is undefended, while the other one is pre- or post-attack defended paying costs either by a higher half-saturation constant for resource uptake or a lower maximum growth rate. We show that post-attack defenses promote prey coexistence and stabilize the population dynamics more strongly than pre-attack defenses by interfering with the predator's functional response: Because the predator spends time handling "noncrackable" prey, the undefended prey is indirectly facilitated. A high half-saturation constant as defense costs promotes coexistence more and stabilizes the dynamics less than a low maximum growth rate. The former imposes high costs at low resource concentrations but allows for temporally high growth rates at predator-induced resource peaks preventing the extinction of the defended prey. We evaluate the effects of the different defense mechanisms and costs on coexistence under different enrichment levels in order to vary the importance of bottom-up and top-down control of the prey community.

Reversed predator-prey cycles are driven by the amplitude of prey oscillations

Ecoevolutionary feedbacks in predator-prey systems have been shown to qualitatively alter predator-prey dynamics. As a striking example, defense-offense coevolution can reverse predator-prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic ¼-phase lag. From this key insight, it follows that in reversed cycles (i.e., ¾-lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator-prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small-amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems.

Rapid adaptation of harmful cyanobacteria to rising CO2

Rising atmospheric CO2 concentrations are likely to affect many ecosystems worldwide. However, to what extent elevated CO2 will induce evolutionary changes in photosynthetic organisms is still a major open question. Here, we show rapid microevolutionary adaptation of a harmful cyanobacterium to changes in inorganic carbon (Ci) availability. We studied the cyanobacterium Microcystis, a notorious genus that can develop toxic cyanobacterial blooms in many eutrophic lakes and reservoirs worldwide. Microcystis displays genetic variation in the Ci uptake systems BicA and SbtA, where BicA has a low affinity for bicarbonate but high flux rate, and SbtA has a high affinity but low flux rate. Our laboratory competition experiments show that bicA + sbtA genotypes were favored by natural selection at low CO2 levels, but were partially replaced by the bicA genotype at elevated CO2 Similarly, in a eutrophic lake, bicA + sbtA strains were dominant when Ci concentrations were depleted during a dense cyanobacterial bloom, but were replaced by strains with only the high-flux bicA gene when Ci concentrations increased later in the season. Hence, our results provide both laboratory and field evidence that increasing carbon concentrations induce rapid adaptive changes in the genotype composition of harmful cyanobacterial blooms.

Competitive advantage and higher fitness in native populations of genetically structured planktonic diatoms

It has been shown that the planktonic diatom Skeletonema from neighbouring areas are genetically differentiated despite absence of physical dispersal barriers. We revisited two sites, Mariager Fjord and Kattegat, NE Atlantic, and isolated new strains. Microsatellite genotyping and F-statistics revealed that the populations were genetically differentiated. An experiment was designed to investigate if populations are locally adapted and have a native competitive advantage. Ten strains from each location were grown individually in native and foreign water to investigate differences in produced biomass. Additionally, we mixed six pairs, one strain from each site, and let them grow together in native and foreign water. Strains from Mariager Fjord and Kattegat produced higher biomass in native water. In the competition experiment, strains from both sites displayed higher relative abundance and demonstrated competitive advantage in their native water. The cause of the differentiated growth is unknown, but could possibly be attributed to differences in silica concentration or viruses in the two water types. Our data show that dispersal potential does not influence the genetic structure of the populations. We conclude that genetic adaptation has not been overruled by gene flow, but instead the responses to different selection conditions are enforcing the observed genetic structure.

Priority effects in a planktonic bloom-forming marine diatom

Priority effects occur when a species or genotype with earlier arrival has an advantage such that its relative abundance in the community or population is increased compared with later-arriving species. Few studies have dealt with this concept in the context of within-species competition. Skeletonema marinoi is a marine diatom that shows a high degree of genetic differentiation between populations over small geographical distances. To test whether historical events such as priority effects may have been important in inducing these patterns of population differentiation, we performed microcosm experiments with successive inoculation of different S. marinoi strains. Our results show that even in the absence of a numerical advantage, significant priority effects were evident. We propose that priority effects may be an important mechanism in initiating population genetic differentiation.

Intraspecific facilitation by allelochemical mediated grazing protection within a toxigenic dinoflagellate population

Dinoflagellates are a major cause of harmful algal blooms (HABs), with consequences for coastal marine ecosystem functioning and services. Alexandrium fundyense (previously Alexandrium tamarense) is one of the most abundant and widespread toxigenic species in the temperate Northern and Southern Hemisphere and produces paralytic shellfish poisoning toxins as well as lytic allelochemical substances. These bioactive compounds may support the success of A. fundyense and its ability to form blooms. Here we investigate the impact of grazing on monoclonal and mixed set-ups of highly (Alex2) and moderately (Alex4) allelochemically active A. fundyense strains and a non-allelochemically active conspecific (Alex5) by the heterotrophic dinoflagellate Polykrikos kofoidii. While Alex4 and particularly Alex5 were strongly grazed by P. kofoidii when offered alone, both strains grew well in the mixed assemblages (Alex4 + Alex5 and Alex2 + Alex5). Hence, the allelochemical active strains facilitated growth of the non-active strain by protecting the population as a whole against grazing. Based on our results, we argue that facilitation among clonal lineages within a species may partly explain the high genotypic and phenotypic diversity of Alexandrium populations. Populations of Alexandrium may comprise multiple cooperative traits that act in concert with intraspecific facilitation, and hence promote the success of this notorious HAB species.

Stochastic eco-evolutionary model of a prey-predator community

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.

Ecological effects of aphid abundance, genotypic variation, and contemporary evolution on plants

Genetic variation and contemporary evolution within populations can shape the strength and nature of species interactions, but the relative importance of these forces compared to other ecological factors is unclear. We conducted a field experiment testing the effects of genotypic variation, abundance, and presence/absence of green peach aphids (Myzus persicae) on the growth, leaf nitrogen, and carbon of two plant species (Brassica napus and Solanum nigrum). Aphid genotype affected B. napus but not S. nigrum biomass explaining 20 and 7% of the total variation, respectively. Averaging across both plant species, the presence/absence of aphids had a 1.6× larger effect size (Cohen's d) than aphid genotype, and aphid abundance had the strongest negative effects on plant biomass explaining 29% of the total variation. On B. napus, aphid genotypes had different effects on leaf nitrogen depending on their abundance. Aphids did not influence leaf nitrogen in S. nigrum nor leaf carbon in either species. We conducted a second experiment in the field to test whether contemporary evolution could affect plant performance. Aphid populations evolved in as little as five generations, but the rate and direction of this evolution did not consistently vary between plant species. On one host species (B. napus), faster evolving populations had greater negative effects on host plant biomass, with aphid evolutionary rate explaining 23% of the variation in host plant biomass. Together, these results show that genetic variation and evolution in an insect herbivore can play important roles in shaping host plant ecology.

Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium

Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼ 17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼ 20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm.

Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system

Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

Biological control of toxic cyanobacteria by mixotrophic predators: an experimental test of intraguild predation theory

Intraguild predators both feed on and compete with their intraguild prey. In theory, intraguild predators can therefore be very effective as biological control agents of intraguild prey species, especially in productive environments. We investigated this hypothesis using the mixotrophic chrysophyte Ochromonas as intraguild predator and the harmful cyanobacterium Microcystis aeruginosa as its prey. Ochromonas can grow photoautotrophically, but can also graze efficiently on Microcystis. Hence, it competes with its prey for inorganic resources. We developed a mathematical model and parameterized it for our experimental food web. The model predicts dominance of Microcystis at low nutrient loads, coexistence of both species at intermediate nutrient loads, and dominance of Ochromonas but a strong decrease of Microcystis at high nutrient loads. We tested these theoretical predictions in chemostat experiments supplied with three different nitrogen concentrations. Ochromonas initially suppressed the Microcystis abundance by > 97% compared to the Microcystis monocultures. Thereafter, however, Microcystis gradually recovered to -20% of its monoculture abundance at low nitrogen loads, but to 50-60% at high nitrogen loads. Hence, Ochromonas largely lost control over the Microcystis population at high nitrogen loads. We explored several mechanisms that might explain this deviation from theoretical predictions, and found that intraspecific interference at high Ochromonas densities reduced their grazing rates on Microcystis. These results illustrate the potential of intraguild predation to control pest species, but also show that the effectiveness of their biological control can be reduced in productive environments.

Comparative analyses of three Chlorella species in response to light and sugar reveal distinctive lipid accumulation patterns in the Microalga C. sorokiniana

While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM) and heterotrophy in BBM supplemented with glucose (10 g L⁻¹). Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18∶1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18∶2 relative to 18∶1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L⁻¹ d⁻¹ to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L⁻¹ d⁻¹. This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis.

Eco-evolutionary feedbacks drive species interactions

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host-microbe interactions.

Challenges for complex microbial ecosystems: combination of experimental approaches with mathematical modeling

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature.

Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature

In proposing his genetic feedback mechanism, David Pimentel was one of the first biologists to argue that the reciprocal interplay of ecological and evolutionary dynamics is an important process regulating population dynamics and ultimately affecting community composition. Although the past decade has seen an increase in research activity on these so-called eco-evolutionary dynamics, there remains a conspicuous lack of compelling natural examples of such feedback. Here we argue that this lack may be due to an inherent difficulty in detecting eco-evolutionary dynamics in nature. By examining models of virulence evolution, host resistance evolution, and antigenic evolution, we show that the influence of evolution on ecological dynamics can often be obscured by other ecological processes that yield similar dynamics. We then show, however, that mechanistic models can be used to navigate this, in Pimentel's words, "devious" course of evolution when effectively combined with empirical data. We argue that these models, improving upon Pimentel's original mathematical models, will therefore play an increasingly important role in identifying more subtle, but possibly ubiquitous, eco-evolutionary dynamics in nature. To highlight the importance of identifying these potentially subtle dynamics in nature, we end by considering our ability to anticipate the effect of population control strategies in the presence of these eco-evolutionary feedbacks.

Multiple stressor effects of predation by rotifers and herbicide pollution on different Chlamydomonas strains and potential impacts on population dynamics

Environmental factors can interact with the effects of chemical pollutants on natural systems by inducing multiple stressor effects in individual organisms as well as by altering selection pressure on tolerant strains in heterogeneous populations. Predation is a stressful environmental factor relevant for many species. Therefore, the impact of predation by the rotifer Brachionus calyciflorus on tolerance of eight genetically different strains of the green alga Chlamydomonas reinhardtii to simultaneous exposure to each of the three herbicides (diuron, paraquat, and S-metolachlor) was tested. Interactions of combined stressors were analyzed based on the independent action model; additive, synergistic, and antagonistic effects of the combined exposure could be detected depending on the herbicide and strain tested. If cultures were acclimated (pre-exposed) to one stressor, tolerance to the second stressor could be increased. This indicates that physiological changes can induce cotolerance of predation-exposed algae to herbicides and of herbicide-treated algae to predation depending on the combination of stressors. The strain-specific differences in multiple stressor effects also changed the correlation of strains' tolerances to individual stressors determined during combined and single-stressor exposure. Changes in cotolerance to stressors affect selection pressure and population dynamics during long-term exposure. This shows that predation stress can have adverse effects on the toxicity of chemical pollutants to microalgae on the organism and population levels.

Experimental evolution

Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vaccine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed understanding of the genomic and molecular basis of experimental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limitations, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.

The functional genomics of an eco-evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics

Feedbacks between ecological and evolutionary change may play important roles in community and ecosystem functioning, but a complete eco-evolutionary feedback loop has not been demonstrated at the community level, and we know little about molecular mechanisms underlying this kind of eco-evolutionary dynamics. In predator-prey (rotifer-alga) microcosms, cyclical changes in predator abundance generated fluctuating selection for a heritable prey defence trait, cell clumping. Predator population growth was affected more by prey evolution than by changes in prey abundance, and changes in predator abundance drove further prey evolution, completing the feedback loop. Within a predator-prey cycle, genes up-regulated as clumping declined were down-regulated as clumping increased, and vice-versa. Genes changing most in expression tended to be associated with defence or its cost. Expression patterns of individual genes differed greatly between consecutive cycles (often reversing direction), suggesting that a particular phenotype may be produced by several (perhaps many) different gene transcription pathways.