Genome evolution and host-microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom-forming Microcystis aeruginosa.

Intraspecific niche divergence is an important driver of species range, population abundance and impacts on ecosystem functions. Genetic changes are the primary focus when studying intraspecific divergence; however, the role of ecological interactions, particularly host-microbiome symbioses, is receiving increased attention. The relative importance of these evolutionary and ecological mechanisms has seen only limited evaluation. To address this question, we used Microcystis aeruginosa, the globally distributed cyanobacterium that dominates freshwater harmful algal blooms. These blooms have been increasing in occurrence and intensity worldwide, causing major economic and ecological damages. We evaluated 46 isolates of M. aeruginosa and their microbiomes, collected from 14 lakes in Michigan, USA, that vary over 20-fold in phosphorus levels, the primary limiting nutrient in freshwater systems. Genomes of M. aeruginosa diverged along this phosphorus gradient in genomic architecture and protein functions. Fitness in low-phosphorus lakes corresponded with additional shifts within M. aeruginosa including genome-wide reductions in nitrogen use, an expansion of phosphorus assimilation genes and an alternative life history strategy of nonclonal colony formation. In addition to host shifts, despite culturing in common-garden conditions, host-microbiomes diverged along the gradient in taxonomy, but converged in function with evidence of metabolic interdependence between the host and its microbiome. Divergence corresponded with a physiological trade-off between fitness in low-phosphorus environments and growth rate in phosphorus-rich conditions. Co-occurrence of genotypes adapted to different nutrient environments in phosphorus-rich lakes may have critical implications for understanding how M. aeruginosa blooms persist after initial nutrient depletion. Ultimately, we demonstrate that the intertwined effects of genome evolution, host life history strategy and ecological interactions between a host and its microbiome correspond with an intraspecific niche shift with important implications for whole ecosystem function.

Consumer adaptation mediates top-down regulation across a productivity gradient.

Humans have artificially enhanced the productivity of terrestrial and aquatic ecosystems on a global scale by increasing nutrient loading. While the consequences of eutrophication are well known (e.g., harmful algal blooms and toxic cyanobacteria), most studies tend to examine short-term responses relative to the time scales of heritable adaptive change. Thus, the potential role of adaptation by organisms in stabilizing the response of ecological systems to such perturbations is largely unknown. We tested the hypothesis that adaptation by a generalist consumer (Daphnia pulicaria) to toxic prey (cyanobacteria) mediates the response of plankton communities to nutrient enrichment. Overall, the strength of Daphnia's top-down effect on primary producer biomass increased with productivity. However, these effects were contingent on prey traits (e.g., rare vs. common toxic cyanobacteria) and consumer genotype (i.e., tolerant vs sensitive to toxic cyanobacteria). Tolerant Daphnia strongly suppressed toxic cyanobacteria in nutrient-rich ponds, but sensitive Daphnia did not. In contrast, both tolerant and sensitive Daphnia genotypes had comparable effects on producer biomass when toxic cyanobacteria were absent. Our results demonstrate that organismal adaptation is critical for understanding and predicting ecosystem-level consequences of anthropogenic environmental perturbations.

Unexpected population response to increasing temperature in the context of a strong species interaction.

Climate change is driving large changes in the spatial and temporal distributions of species, with significant consequences for individual populations. Community- and ecosystem-level implications of altered species distributions may be complex and challenging to anticipate due to the cascading effects of disrupted interactions among species, which may exhibit threshold responses to extreme climatic events. Toxic, bloom-forming cyanobacteria like Microcystis are expected to increase worldwide with climate change, due in part to their high temperature optima for growth. In addition, invasive zebra mussels (Dreissena polymorpha) have caused an increase in Microcystis aeruginosa, a species typically associated with eutrophication, in low-nutrient lakes. We conducted a 13-yr study of a M. aeruginosa population in a low-nutrient lake invaded by zebra mussels. In 10 of the 13 years, there was a significant positive relationship between M. aeruginosa biomass and accumulated degree days, which are projected to increase with climate change. In contrast, Microcystis biomass was up to an order of magnitude lower than predicted by the above relationship during the other three years, including the warmest in the data set, following repeated heat-induced mass mortality of D. polymorpha. Thus, the positive relationship between Microcystis biomass and temperature was negated when its facilitating species was suppressed during a series of exceptionally warm summers. Predicting the net response of a species to climate change may therefore require, at minimum, quantification of responses of both the focal species and species that strongly interact with it over sufficiently long time periods to encompass the full range of climatic variability. Our results could not have been predicted from existing data on the short-term responses of these two interacting species to increased temperature.

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes.

Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method's constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystis cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystis oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystis oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystis oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.

The interaction between cyanobacteria and zooplankton in a more eutrophic world.

As blooms of cyanobacteria expand and intensify in freshwater systems globally, there is increasing interest in their ecological effects. In addition to being public health hazards, cyanobacteria have long been considered a poor quality food for key zooplankton grazers that link phytoplankton to higher trophic levels. While past laboratory studies have found negative effects of nutritional constraints and defensive traits (i.e., toxicity and colonial or filamentous morphology) on the fitness of large generalist grazers (i.e., Daphnia), cyanobacterial blooms often co-exist with high biomass of small-bodied zooplankton in nature. Indeed, recent studies highlight the remarkable diversity and flexibility in zooplankton responses to cyanobacterial prey. Reviewed here are results from a wide range of laboratory and field experiments examining the interaction of cyanobacteria and a diverse zooplankton taxa including cladocerans, copepods, and heterotrophic protists from temperate to tropical freshwater systems. This synthesis shows that longer exposure to cyanobacteria can shift zooplankton communities toward better-adapted species, select for more tolerant genotypes within a species, and induce traits within the lifetime of individual zooplankton. In turn, the function of bloom-dominated plankton ecosystems, the coupling between primary producers and grazers, the stability of blooms, and the potential to use top down biomanipulation for controlling cyanobacteria depend largely on the species, abundance, and traits of interacting cyanobacteria and zooplankton. Understanding the drivers and consequences of zooplankton traits, such as physiological detoxification and selective vs. generalist grazing behavior, are therefore of major importance for future studies. Ultimately, co-evolutionary dynamics between cyanobacteria and their grazers may emerge as a critical regulator of blooms.

Nitrogen availability increases the toxin quota of a harmful cyanobacterium, Microcystis aeruginosa.

An important objective in understanding harmful phytoplankton blooms is determining how environmental factors influence the toxicity of bloom-forming species. We examined how nutrients and grazers (dreissenid mussels) affect the production of microcystin (a liver toxin) by the cyanobacterium Microcystis aeruginosa, via a combination of field and laboratory experiments, and field observations in Lake Erie. The field experiment revealed no effect of mussel density on microcystin quota (particulate microcystin per unit Microcystis biomass). In contrast, in both field and laboratory experiments, nitrogen-limited conditions led to substantially reduced microcystin quota relative to phosphorus-limited or nutrient-saturated conditions. In the field experiment, microcystin per unit of mcyB gene was strongly reduced under nitrogen-limited conditions, indicating a phenotypic response. Results from a seasonal survey in the western basin of Lake Erie revealed a similar negative influence of nitrogen limitation (as indexed by nitrate concentration) on microcystin quota. Our results are consistent with stoichiometric considerations in that the cell quota of a nitrogen-rich secondary metabolite, microcystin, was reduced disproportionately under nitrogen limitation.

Do high concentrations of microcystin prevent Daphnia control of phytoplankton?

Toxin-producing cyanobacteria have frequently been hypothesized to limit the ability of herbivorous zooplankton (such as Daphnia) to control phytoplankton biomass by inhibiting feeding, and in extreme cases, causing zooplankton mortality. Using limnocorral experiments in hyper-eutrophic ponds located in Alabama and Michigan (U.S.A.), we tested the hypothesis that high levels of cyanobacteria and microcystin, a class of hepatotoxins produced by several cyanobacterial genera, prevent Daphnia from strongly reducing phytoplankton abundance. At the start of the first experiment (Michigan), phytoplankton communities were dominated by toxic Microcystis and Anabaena (∼96% of total phytoplankton biomass), and concentrations of microcystin were ∼3 µg L⁻¹. Two weeks after adding Daphnia pulicaria from a nearby eutrophic lake, microcystin levels increased to ∼6.5 µg L⁻¹, yet Daphnia populations increased exponentially (r = 0.24 day⁻¹). By the third week, Daphnia had suppressed phytoplankton biomass by ∼74% relative to the no Daphnia controls and maintained reduced phytoplankton biomass until the conclusion of the five-week experiment. In the second experiment (Alabama), microcystin concentrations were greater than 100 µg L⁻¹, yet a mixture of three D. pulicaria clones from eutrophic lakes in southern MI increased and again reduced phytoplankton biomass, in this case by over 80%. The ability of Daphnia to increase in abundance and suppress phytoplankton biomass, despite high initial levels of cyanobacteria and microcystin, indicates that the latter does not prevent strong control of phytoplankton biomass by Daphnia genotypes that are adapted to environments with abundant cyanobacteria and associated cyanotoxins.

Large effects of consumer offense on ecosystem structure and function.

Study of the role of within-species adaptation in ecological dynamics has focused largely on prey adaptations that reduce consumption risk (prey defense). Few, if any, studies have examined how consumer adaptations to overcome prey defenses (consumer offense) affect ecosystem structure and function. We manipulated two sets of genotypes of a planktonic herbivore (Daphnia pulicaria) in a highly productive ecosystem with abundant toxic prey (cyanobacteria). The two sets of consumer genotypes varied widely in their tolerance of toxic cyanobacteria in the diet (i.e., sensitive vs. tolerant). We found a large effect of tolerant D. pulicaria on phytoplankton biomass and gross primary productivity but no effect of sensitive genotypes, this result stemming from genotype-specific differences in population growth in the presence of toxic prey. The former effect was as large as effects seen in previous Daphnia manipulations at similar productivity levels. Thus, we demonstrated that the effect of consumer genotypes with contrasting offensive adaptations was as large as the effect of consumer presence/absence.

Phosphorus addition reverses the positive effect of zebra mussels (Dreissena polymorpha) on the toxic cyanobacterium, Microcystis aeruginosa.

We tested the hypothesis that zebra mussels (Dreissena polymorpha) have positive effects on the toxin-producing cyanobacterium, Microcystis aeruginosa, at low phosphorus (P) concentrations, but negative effects on M. aeruginosa at high P, with a large-scale enclosure experiment in an oligotrophic lake. After three weeks, mussels had a significantly positive effect on M. aeruginosa at ambient P (total phosphorus, TP ∼10 µg L⁻¹), and a significantly negative effect at high P (simulating a TP of ∼40 µg L⁻¹ in lakes). Positive and negative effects were strong and very similar in magnitude. Thus, we were able to ameliorate a negative effect of Dreissena invasion on water quality (i.e., promotion of Microcystis) by adding P to water from an oligotrophic lake. Our results are congruent with many field observations of Microcystis response to Dreissena invasion across ecosystems of varying P availability.

Growth rate consequences of coloniality in a harmful phytoplankter.

BACKGROUND: Allometric studies have shown that individual growth rate is inversely related to body size across a broad spectrum of organisms that vary greatly in size. Fewer studies have documented such patterns within species. No data exist directly documenting the influence of colony size on growth rate for microscopic, colonial organisms. METHODOLOGY/PRINCIPAL FINDINGS: To determine if similar negative relationships between growth rate and size hold for colonial organisms, we developed a technique for measuring the growth of individual colonies of a bloom-forming, toxic cyanobacterium, Microcystis aeruginosa using microscopy and digital image analysis. For five out of six genotypes of M. aeruginosa isolated from lakes in Michigan and Alabama, we found significant negative relationships between colony size and growth rate. We found large intraspecific variation in both the slope of these relationships and in the growth rate of colonies at a standard size. In addition, growth rate estimates for individual colonies were generally consistent with population growth rates measured using standard batch culture. CONCLUSIONS/SIGNIFICANCE: Given that colony size varies widely within populations, our results imply that natural populations of colonial phytoplankton exist as a mosaic of individuals with widely varying ecological attributes (since size strongly affects growth rate, grazing mortality, and migration speed). Quantifying the influence of colony size on growth rate will permit development of more accurate, predictive models of ecological interactions (e.g., competition, herbivory) and their role in the proliferation of harmful algal blooms, in addition to increasing our understanding about why these interactions vary in strength within and across environments.

Citizen monitoring: Testing hypotheses about the interactive influences of eutrophication and mussel invasion on a cyanobacterial toxin in lakes.

An existing volunteer monitoring network in the state of Michigan was exploited to conduct a statewide survey of the cyanobacterial toxin, microcystin, and to test hypotheses about the interactive influences of eutrophication and dreissenid mussel invasion. A total of 77 lakes were sampled by citizen volunteers for microcystin, total phosphorus (TP) and chlorophyll a. Microcystin was measured in depth-integrated samples collected from the euphotic zone as well as in surface-water samples collected along the shoreline. Average microcystin in samples collected by volunteers was not different from samples collected side-by-side by professionals. Euphotic-zone microcystin was positively related to TP in lakes without dreissenids (uninvaded) but not in lakes with dreissenids (invaded). Regression-tree analysis indicated that euphotic-zone microcystin was eight times higher in the presence of dreissenids for lakes with TP between 5 and 10microgL(-1). In contrast, euphotic-zone microcystin was almost identical in invaded and uninvaded lakes with TP between 10 and 26microgL(-1). Across all lakes, microcystin concentrations at the surface were on average more than double, and in some cases an order-of-magnitude greater than, concentrations in the euphotic-zone. Given these results, it seems prudent to include dreissenid invasion status in forecasting models for microcystin, and to include shoreline sampling in monitoring programs aimed at assessing recreational exposure to cyanobacterial toxins.

Allee effect limits colonization success of sexually reproducing zooplankton.

Understanding the dynamics of populations at low density and the role of Allee effects is a priority due to concern about the decline of rare species and interest in colonization/invasion dynamics. Despite well-developed theory and observational support, experimental examinations of the Allee effect in natural systems are rare, partly because of logistical difficulties associated with experiments at low population density. We took advantage of fish introduction and removal in alpine lakes to experimentally test for the Allee effect at the whole-ecosystem scale. The large copepod Hesperodiaptomus shoshone is often extirpated from the water column by fish and sometimes fails to recover following fish disappearance, despite the presence of a long-lived egg bank. Population growth rate of this dioecious species may be limited by mate encounter rate, such that below some critical density a colonizing population will fail to establish. We conducted a multi-lake experiment in which H. shoshone was stocked at densities that bracketed our hypothesized critical density of 0.5-5 copoepods/m3. Successful recovery by the copepod was observed only in the lake with the highest initial density (3 copepods/m3). Copepods stocked into small cages at 3000 copepods/m3 survived and reproduced at rates comparable to natural populations, confirming that the lakes were suitable habitat for this species. In support of mate limitation as the mechanism underlying recovery failure, we found a significant positive relationship between mating success and density across experimental and natural H. shoshone populations. Furthermore, a mesocosm experiment provided evidence of increased per capita population growth rate with increasing population density in another diaptomid species, Skistodiaptomus pallidus. Together, these lines of evidence support the importance of the Allee effect to population recovery of H. shoshone in the Sierra Nevada, and to diaptomid copepods in general.

Limits to genetic bottlenecks and founder events imposed by the Allee effect.

The Allee effect can result in a negative population growth rate at low population density. Consequently, populations below a minimum (critical) density are unlikely to persist. A lower limit on population size should constrain the loss of genetic variability due to genetic drift during population bottlenecks or founder events. We explored this phenomenon by modeling changes in genetic variability and differentiation during simulated bottlenecks of the alpine copepod, Hesperodiaptomus shoshone. Lake surveys, whole-lake re-introduction experiments and model calculations all indicate that H. shoshone should be unlikely to establish or persist at densities less than 0.5-5 individuals m(-3). We estimated the corresponding range in minimum effective population size using the distribution of habitat (lake) sizes in nature and used these values to model the expected heterozygosity, allelic richness and genetic differentiation resulting from population bottlenecks. We found that during realistic bottlenecks or founder events, >90% of H. shoshone populations in the Sierra Nevada may be resistant to significant changes in heterozygosity or genetic distance, and 70-75% of populations may lose <10% of allelic richness. We suggest that ecological constraints on minimum population size be considered when using genetic markers to estimate historical population dynamics.

Type III functional response in Daphnia.

The functional response of Daphnia, a common pelagic herbivore in lakes, was assessed with a combination of secondary and meta-analyses of published data and new data from an experiment conducted using very low food levels. Secondary analyses of literature data (28 studies, n = 239-393) revealed a significant positive influence of food concentration on Daphnia clearance rate at low food levels, i.e., evidence of an overall Type III functional response. This result was not an artifact of including data from Daphnia that were exhausted from prolonged food deprivation (more than three hours at very low food). Meta-analysis of Daphnia clearance rate vs. food concentration across a range of low food concentrations (eight studies) showed a significantly positive slope across studies, which also supports the presence of a Type III response. Congruent with these analyses of published data, the feeding experiment showed clear evidence of a Type III functional response for D. pulicaria feeding on Ankistrodesmus falcatus. Food levels at which Daphnia clearance rate declined with decreasing food were near the minimum resource requirement for Daphnia population maintenance at steady state (R*). We suggest that Type III responses are more common than previously believed, perhaps because of the relative paucity of observations at low food levels, and that reduced prey mortality at low phytoplankton densities could be a stabilizing mechanism for Daphnia-phytoplankton systems under resource scarcity.

Recovery after local extinction: factors affecting re-establishment of alpine lake zooplankton.

The introduction of fishes into naturally fishless mountain lakes often results in the extirpation of large-bodied zooplankton species. The ability to predict whether or not particular species will recover following fish removal is critically important for the design and implementation of lake restoration efforts but is currently not possible because of a lack of information on what factors affect recovery. The objective of this study was to identify the factors influencing recovery probability in two large-bodied zooplankton species following fish removal. We predicted that (1) Daphnia melanica would have a higher probability of recovery than Hesperodiaptomus shoshone due to differences in reproductive mode (D. melanica is parthenogenetic, H. shoshone is obligately sexual), (2) recovery probability would be a decreasing function of fish residence time due to the negative relationship between fish residence time and size of the egg bank, and (3) recovery probability would be an increasing function of lake depth as a consequence of a positive relationship between lake depth and egg bank size. To test these predictions, we sampled contemporary zooplankton populations and collected paleolimnological data from 44 naturally fishless lakes that were stocked with trout for varying lengths of time before reverting to a fishless condition. D. melanica had a significantly higher probability of recovery than did H. shoshone (0.82 vs. 0.54, respectively). The probability of recovery for H. shoshone was also significantly influenced by lake depth, fish residence time, and elevation, but only elevation influenced the probability of recovery in D. melanica. These results are consistent with between-species differences in reproductive mode combined with the much greater longevity of diapausing eggs in D. melanica than in H. shoshone. Our data also suggest that H. shoshone will often fail to recover in lakes with fish residence times exceeding 50 years.

Genetic variation of the bloom-forming Cyanobacterium Microcystis aeruginosa within and among lakes: implications for harmful algal blooms.

To measure genetic variation within and among populations of the bloom-forming cyanobacterium Microcystis aeruginosa, we surveyed a suite of lakes in the southern peninsula of Michigan that vary in productivity (total phosphorus concentrations of approximately 10 to 100 microg liter(-1)). Survival of M. aeruginosa isolates from lakes was relatively low (i.e., mean of 7% and maximum of 30%) and positively related to lake total phosphorus concentration (P = 0.014, r2 = 0.407, n = 14). In another study (D. F. Raikow, O. Sarnelle, A. E. Wilson, and S. K. Hamilton, Limnol. Oceanogr. 49:482-487, 2004), survival rates of M. aeruginosa isolates collected from an oligotrophic lake (total phosphorus of approximately 10 mug liter(-1) and dissolved inorganic nitrogen:total phosphorus ratio of 12.75) differed among five different medium types (G test, P of <0.001), with higher survival (P = 0.003) in low-nutrient media (28 to 37% survival) than in high-nutrient media. Even with the relatively low isolate survivorship that could select against detecting the full range of genetic variation, populations of M. aeruginosa were genetically diverse within and among lakes (by analysis of molecular variance, Phi(sc) = 0.412 [Phi(sc) is an F-statistic derivative which evaluates the correlation of haplotypic diversity within populations relative to the haplotypic diversity among all sampled populations], P = 0.001), with most clones being distantly related to clones collected from lakes directly attached to Lake Michigan (a Laurentian Great Lake) and culture collection strains collected from Canada, Scotland, and South Africa. Ninety-one percent of the 53 genetically unique M. aeruginosa clones contained the microcystin toxin gene (mcyA). Genotypes with the toxin gene were found in all lakes, while four lakes harbored both genotypes possessing and genotypes lacking the toxin gene.

Nonlinear effects of an aquatic consumer: causes and consequences.

The assumption that per capita consumer effects on prey density are independent of consumer and prey density is examined with a large-scale manipulation of an aquatic herbivore (Daphnia). A gradient of consumer removal was maintained long enough to allow the abundances of both consumer and prey (phytoplankton) to equilibrate to the manipulation. Strong and unequivocal nonlinearities were found in the effect of Daphnia on total phytoplankton abundance and the abundance of most of the common phytoplankton species. Daphnia's suppression of phytoplankton was strong between 0 and approximately 400 microg Daphnia L(-1) but essentially nil from approximately 400 to 900 microg Daphnia L(-1). The sharp deceleration in Daphnia's effect was not caused by a shift within the phytoplankton community toward consumption-resistant forms. The most likely explanation for the deceleration was a reduction in Daphnia's filtering effort at low phytoplankton abundance, that is, a Type III functional response. A review of experimental literature suggested that decelerating effects of consumers are the norm in aquatic systems. Nonlinear effects present problems for the estimation of interaction strength and the building of community interaction models from the results of predator manipulations. It is suggested that the role of field experiments in community ecology should be to test rather than to parameterize models.

Effects of an invertebrate grazer on the spatial arrangement of a benthic microhabitat.

We demonstrated the effect of an aquatic herbivore on the spatial arrangement of benthic algal biomass within artificial stream channels. Transects of ceramic tiles were exposed to a gradient of snail (Physella) densities in a 30 d experiment. We observed positive effects of snails on the mean abundance of "overstory" algae (the filamentous chlorophyte Cladophora and associated epiphytes), an important benthic microhabitat in streams. Snails altered several aspects of the spatial arrangement of overstory algae. Snails reduced the strength of downstream gradients in overstory biomass, as well as residual variability around these gradients. Geostatistical analysis revealed that snails also reduced the strength of spatial dependence, and so reduced spatial heterogeneity of the overstory, at small scales (<40 cm). As a result, organisms inhabiting the overstory might experience a more fragmented habitat landscape at high snail densities. In addition, snails increased the scale of spatial dependence in understory algal biomass (algae remaining on tiles after overstory was removed) from 10 cm to 40 cm. Consumer effects on the spatial arrangement of a microhabitat argue for the inclusion of feedbacks between the biota and the environment in spatially-explicit models.