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Riparian vegetation along a stream regulates the flow of sediments and nutrients. It also provides stability to the riverbanks and controls the watershed microclimate that ultimately influences the primary production of lotic environments. The degradation of terrestrial vegetation can also have an impact on the biotic component of rivers. Periphyton communities are altered in their composition, abundance, and diversity when the natural conditions in the watershed are modified. While widely studied in Europe and North America, studies on changes in periphyton community structure in mountainous tropical ecosystems are rare. In this study, we investigated if and how alteration of the riparian vegetation results in changes in the diatom community composition of seven streams in southern Ecuador. Streams were sampled in one or 2 zones, with 5 sub-samples each. The sampled streams show different levels of degradation within their watersheds. Temperature was higher in open (i.e. deforested) areas within a stream and open areas, e.g. pastures, had higher abundance of cyanobacteria filaments. Total algal cell abundances increased from forested to open and more fully degraded zones. Species richness was lowest in the forested areas. Microbial diversity was low across all habitats, but the highest values were documented in the degraded habitats. Diatom communities dominated at all sites, followed by filamentous bacteria. Gomphonema minutum (Agardh) Agardh, G. parvulum (Kütz.) Kütz., and Achnanthidium minutissimum (Kütz.) Czarnacki were the most common and abundant species. Diatom communities from zones with different land use within a stream were as different from each other as communities from different watershed streams.

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short‐term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well‐developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short‐ and long‐term. We summarize the current understanding of storm‐induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions., Our understanding of ecosystem‐scale responses to storm events is fragmented, and terminological variability in defining a “storm” hinders resolution of generalizable impacts. We provide a comprehensive synthesis of the interactions between physical properties and biological responses in lakes that demonstrates the context‐dependency of storm impacts; lake/watershed attributes and their antecedent conditions mediate the extent to which storms impact lake ecosystems. We develop a framework which conceptualizes how abrupt, storm‐induced changes in the lake environment influence phytoplankton community dynamics through functional traits, identifies current limitations, and highlights several avenues of research to narrow knowledge gaps in synthetic and interdisciplinary ways.

The functioning of present ecosystems reflects deep evolutionary history of locally cooccurring species if their functional traits show high phylogenetic signal (PS). However, we do not understand what drives local PS. We hypothesize that local PS is high in undisturbed and stressful habitats, either due to ongoing local assembly of species that maintained ancestral traits, or to past evolutionary maintenance of ancestral traits within habitat species-pools, or to both., We quantified PS and diversity of 10 traits within 6704 local plant communities across 38 Dutch habitat types differing in disturbance or stress., Mean local PS varied 50-fold among habitat types, often independently of phylogenetic or trait diversity. Mean local PS decreased with disturbance but showed no consistent relationship to stress. Mean local PS exceeded species-pool PS, reflecting nonrandom subsampling from the pool. Disturbance or stress related more strongly to mean local than to species-pool PS., Disturbed habitats harbour species with evolutionary divergent trait values, probably driven by ongoing, local assembly of species: environmental fluctuations might maintain different trait values within lineages through an evolutionary storage effect. If functional traits do not reflect phylogeny, ecosystem functioning might not be contingent on the presence of particular lineages, and lineages might establish evolutionarily novel interactions.

Here we aim to incorporate trait-based information into the modern coexistence framework that comprises a balance between stabilizing (niche-based) and equalizing (fitness) mechanisms among interacting species. Taking the modern coexistence framework as our basis, we experimentally tested the effect of size differences among species on coexistence by using fifteen unique pairs of resident vs. invading cyanobacteria, resulting in thirty unique invasibility tests. The cyanobacteria covered two orders of magnitude differences in size. We found that both niche and fitness differences increased with size differences. Niche differences increased faster with size differences than relative fitness differences and whereas coexisting pairs showed larger size differences than non-coexisting pairs, ultimately species coexistence could not be predicted on basis of size differences only. Our findings suggest that size is more than a key trait controlling physiological and population-level aspects of phytoplankton, it is also relevant for community-level phenomena such as niche and fitness differences which influence coexistence and biodiversity.

Tropical high-altitude lakes are vital freshwater reservoirs in the Andean regions. They are heavily threatened by human activities that may alter their functioning and hamper the provisioning of key ecosystem services such as water supply. Despite their ecological and social relevance, we know little about these waterbodies, especially regarding the factors influencing their functioning. Here, we explored the links between several environmental variables and phytoplankton productivity, measured as chlorophyll-a concentration and total phytoplankton biovolume. For this, we sampled twenty-four tropical high-altitude lakes located over three-thousand meters above sea level in Southern Ecuador. We found that four abiotic factors combined explained 76% of the variation in chlorophyll-a concentration amongst lakes. Contrary to what studies from temperate regions suggest, taxa richness was not related to either chlorophyll-a concentrations or total phytoplankton biovolume. Moreover, phytoplankton biovolume diversity was negatively correlated to both chlorophyll-a concentrations and total phytoplankton biovolume. This was due to a very uneven distribution of productivity amongst taxa in the more productive lakes. To the best of our knowledge, this is the first attempt to explore the determinants of phytoplankton functioning in tropical high-altitude lakes. We hope that this study will help to establish a baseline for evaluating the consequences of human activities in the ecology and functioning of this vital but fragile ecosystem. Our results suggest that by modifying the abiotic and biotic parameters of tropical high-altitude lakes, human activities can indirectly impact their functioning and their capacity to provide vital ecosystem services.

Tropical high-altitude lakes are vital freshwater ecosystems for the functioning and dynamics of tropical high-altitude wetlands called páramos, found at over 3300 m above sea level. They play a major role in the hydrogeological cycle and provide important hydrological services such as water storage, and yet they are understudied. Describing the patterns and processes of community composition in these lakes is required to better understand the consequences of their degradation by human activities. In this study we tested the geographical and environmental components of distance–decay relationships in the phytoplankton structure across 24 tropical high-altitude lakes from Southern Ecuador. Phytoplankton composition at the phyla level showed high among-lake variation in the tropical high-altitude lakes from Tres Lagunas. We found no links, however, between the geographic distance and phytoplankton composition. On the contrary, we observed some environmentally related patterns of community structure like redox potential, altitude, water temperature, and total phosphorus. The absence of support for the distance–decay relationship observed here can result from a conjunction of local niche-based effects and dispersal limitations. Phytoplankton community composition in the Tres Lagunas system or any other ecosystem may be jointly regulated by niche-based and neutral forces that still need to be explored. Despite not proving a mechanistic explanation for the observed patterns of community structure, we hope our findings provide understanding of these vulnerable and vital ecosystems. More studies in tropical high-altitude lakes are urgently required.

When sunlight penetrates the ice layer covering lakes in winter, it warms the top water layer and sets up convection, with several potentially contrasting effects on phytoplankton. While convective mixing keeps cells in suspension and prevents sedimentation losses, it may also transport phytoplankton well below the euphotic zone. We investigated diurnal variations in the vertical distribution of phytoplankton under ice and just after ice-off in Lake Onego (Russia), a lake with moderate to high colored dissolved organic carbon (CDOM) levels. We showed that diurnal variation in convection under ice restricts phytoplankton access to light in the morning hours to a narrow euphotic zone, whereas cells are mixed through a deep aphotic layer in the afternoon. After ice-off, low chlorophyll a was found on the open-water side of the thermal bar as convection distributed cells throughout the water column. By contrast, the inshore side had significantly higher concentrations of chlorophyll a (p

Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether genetic diversity among species, often quantified as the degree of evolutionary divergence on a molecular phylogeny, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than species richness because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. Here, we re-analyze data from 16 experiments that have manipulated plant species richness in grassland ecosystems and examined the impact on aboveground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the phylogenetic diversity of plants impacts average community biomass production as well as the stability of community biomass production through time. Using four complementary analyses we show that, after statistically controlling for variation in species richness, phylogenetic diversity (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. After controlling for species richness, phylogenetic diversity was positively related to variation in community biomass over time via an increase in individual species variances but this relationship was not strong enough to influence community stability. In contrast to the non-significant relationships between phylogenetic diversity, biomass, and stability, after controlling for species richness, our analyses show that species richness tends to increase the mean biomass production of plant communities, after controlling for phylogenetic diversity. The relationship between species richness and temporal variation in community biomass was either non-significant or negative depending on which analysis was used. However, the increases in community biomass with species richness, independent of phylogenetic diversity, always led to increased stability. These results suggest that phylogenetic diversity is no better as a predictor of ecosystem functioning than species richness. Synthesis. Our study on grasslands offers a cautionary tale when trying to relate phylogenetic diversity to ecosystem functioning as there may be trait and functional variation among species that cannot be explained by their evolutionary relatedness. Management recommendations suggesting the conservation of evolutionarily distinct species will lead to more productive and more stable communities under changing environmental conditions are not well supported by the data explored in this study. Fil: Venail, Patrick. University of Michigan. School of Natural Resources and Environment; Estados Unidos. University of Geneva. Institute F.-A. Forel. Section of Earth and Environmental Sciences; Suiza Fil: Gross, Kevin. North Carolina State University. Statistics Department; Estados Unidos Fil: Oakley, Todd H.. University of California. Department of Ecology, Evolution and Marine Biology; Estados Unidos Fil: Narwani, Anita. University of Michigan. School of Natural Resources and Environment; Estados Unidos. Swiss Federal Institute of Aquatic Science and Technology. Aquatic Ecology; Suiza Fil: Allan, Eric. University of Bern. Institute of Plant Sciences; Estados Unidos Fil: Flombaum, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinacion Administrativa Ciudad Universitaria. Centro de Investigaciones del Mar y la Atmósfera; Argentina Fil: Isbell, Forest. University of Georgia. Department of Plant Biology; Estados Unidos Fil: Joshi, Jasmin. University of Potsdam. Biodiversity Research/Systematic Botany. Institute of Biochemistry and Biology; Alemania. Berlin-Brandenburg Institute of Advanced Biodiversity Research; Alemania Fil: Reich, Peter B.. University of Minnesota. Department of Forest Resources; Estados Unidos. University of Western Sydney. Hawkesbury Institute for the Environment; Australia Fil: Tilman, David. University of Minnesota. College of Biological Sciences; Estados Unidos. University of California. Bren School of Environmental Science and Management; Estados Unidos Fil: Van Ruijven, Jasper. Wageningen University. Department of Nature Conservation and Plant Ecology; Países Bajos Fil: Cardinale, Bradley J.. University of Michigan. School of Natural Resources and Environment; Estados Unidos

Summary 1. A long-standing hypothesis in ecology and evolutionary biology is that closely related species are more ecologically similar to each other and therefore compete more strongly than distant relatives do. A recent hypothesis posits that evolutionary relatedness may also explain the prevalence of mutualisms, with facilitative interactions being more common among distantly related species. Despite the importance of these hypotheses for understanding the structure and function of ecological communities, experimental tests to determine how evolutionary relatedness influences competition and facilitation are still somewhat rare. 2. Here, we report results of a laboratory experiment in which we assessed how competitive and facilitative interactions among eight species of freshwater green algae are influenced by their relatedness. We measured the prevalence of competition and facilitation among 28 pairs of freshwater green algal species that were chosen to span a large gradient of phylogenetic distances. For each species, we first measured its invasion success when introduced into a steady-state population of another resident species. Then, we compared its growth rate when grown alone in monoculture to its growth rate when introduced as an invader. The change in the species’ population growth rate as an invader (sensitivity) is used as a measure of the strength of its interaction with the resident species. A reduced growth rate in the presence of another species indicates competition, whereas an increased growth rate indicates facilitation. 3. Although competition between species was more frequent (75% of interactions), facilitation was common (the other 25% of interactions). We found no significant relationship between the phylogenetic distance separating two interacting species and the success of invasion, nor the prevalence or strength of either competition or facilitation. Interspecific interactions depended more on the identity of the species, with certain taxa consistently acting as good or bad competitors/facilitators. These species were not predictable a priori from their positions on a phylogeny. 4. Synthesis. The phylogenetic relatedness of the green algae species used here did not predict the prevalence of competitive and facilitative interactions, rejecting the hypothesis that close relatives compete strongly and contesting recent evidence that facilitation is likely to occur between distant relatives.

Bacterial infections are the second largest cause of mortality in shrimp hatcheries. Among them, bacteria from the genus Vibrio constitute a major threat. As the use of antibiotics may be ineffective and banned from the food sector, alternatives are required. Historically, phage therapy, which is the use of bacteriophages, is thought to be a promising option to fight against bacterial infections. However, as for antibiotics, resistance can be rapidly developed. Since the emergence of resistance is highly undesirable, a formal characterization of the dynamics of its acquisition is mandatory. Here, we explored the co-evolutionary dynamics of resistance between the bacteria Vibrio sp. CV1 and the phages V1G, V1P1, and V1P2. Single-phage treatments as well as a cocktail composed of the three phages were considered. We found that in the presence of a single phage, bacteria rapidly evolved resistance, and the phages decreased their infectivity, suggesting that monotherapy may be an inefficient treatment to fight against Vibrio infections in shrimp hatcheries. On the contrary, the use of a phage cocktail considerably delayed the evolution of resistance and sustained phage infectivity for periods in which shrimp larvae are most susceptible to bacterial infections, suggesting the simultaneous use of multiple phages as a serious strategy for the control of vibriosis. These findings are very promising in terms of their consequences to different industrial and medical scenarios where bacterial infections are present.

The hypotheses suggesting that the nature and strength of species interactions should be determined by phylogenetic relatedness have important implications for the understanding of community structure. However, to date, there is limited empirical evidence to support them. At least two basic conditions need to be met in order to expect species interactions to be determined by evolutionary relatedness: a phylogenetic signal in the traits involved in the interactions and changes in the interactions as species are more ecologically similar. Here, we report results of a removal experiment in the Chinese Tibetan plateau in which we directly assessed if the nature and/or strength of interactions among twelve alpine meadow plant species were influenced by their phylogenetic relatedness and/or their functional dissimilarity. For each plant species, we compared its biomass production when grown alone to its biomass in presence of another species and used it as a measure of species interactions. Competition between pairs of species was more frequent than facilitation, with 60% of interactions resulting in plants producing less biomass when a second species was present. We found no effect of phylogenetic relatedness on the prevalence or intensity of competition or facilitation, presumably as none of the studied traits showed phylogenetic signal. Functional dissimilarity based on maximum plant height alone was the best predictor of both the prevalence and strength of competition and facilitation, followed by functional dissimilarity using all five functional traits. Our results pinpoint the limited capacity of phylogenetic relatedness as predictor of species interactions; underlining the limitations of using phylogenetic dispersion patterns to infer mechanisms of community assembly. On the contrary, when the right functional traits are used, functional dissimilarity among species can predict both the nature and strength of their interactions; accentuating the relevance of trait-based approaches in community ecology research.

Although theory established the necessary conditions for diversification in temporally heterogeneous environments, empirical evidence remains controversial. One possible explanation is the difficulty of designing experiments including the relevant range of temporal grains and the appropriate environmental trade-offs. Here, we experimentally explore the impact of the grain on the diversification of the bacterium Pseudomonas fluorescens SBW25 in a temporally fluctuating environment by including 20 different pairs of environments and four temporal grains. In general, higher levels of diversity were observed at intermediate temporal grains. This resulted in part from the enhanced capacity of disruptive selection to generate negative genotypic correlations in performance at intermediate grains. However, the evolution of reciprocal specialization was an uncommon outcome. Although the temporal heterogeneity is in theory less powerful than the spatial heterogeneity to generate and maintain the diversity, our results show that diversification under temporal heterogeneity is possible provided appropriate environmental grains.

Species richness (SR) and phylogenetic diversity (PD) are highly correlated measures of plant diversity. Each, by itself, is significantly associated with plant community biomass in biodiversity experiments. As presented by Cadotte (2015) and as we present below, reasonable but alternative analyses that attempt to control for this correlation in different ways provide contradictory or inconclusive support for the hypothesis that PD is superior to SR as a predictor of community biomass. In Venail et al. (2015), we re-analysed data from 16 experimental manipulations of grassland SR to look at how SR and PD influence variation in plant community biomass through time. Using four types of analyses, we showed that, after statistically controlling for variation in SR, PD was not related to community biomass or to the temporal stability of biomass. We did, however, find that SR tends to increase the biomass production of plant communities after controlling for PD. In his comment, Cadotte expressed two concerns about our analyses. One is that we used non-random subsets of experiments, rather than the full data set, for some of our analyses (types 2, 3). We were clear in stating these analyses were based on non-random subsets that were specifically chosen to minimize the SR–PD correlation and avoid problems associated with multicollinearity. We acknowledge that our tests are conservative, a cost of which is that they sacrifice statistical power while, at the same time, minimizing the chance of drawing an incorrect conclusion. But we disagree with Cadotte’s suggestion that our use of non-random data subsets led to ‘biased’ conclusions, and demonstrate later in this response that his claim of bias is unsubstantiated. Cadotte’s second concern was that our analyses did not account for differences in biomass across studies. This is an important criticism to consider; we made a mistake by not controlling for variation in biomass. To address this issue, Cadotte used mixed models where study was included as a random effect, and ran analyses that standardized biomass among sites. Collectively, these led Cadotte to conclude ‘All analyses strongly support previous literature claims about the value of PD and I further show that: (i) PD provides a more powerful explanation of variation in biomass production than species richness; (ii) PD explains variation in biomass production after controlling for richness; and (iii) the use of data subsets inadvertently biased the conclusions’. We have two concerns with Cadotte’s re-analysis. First, Cadotte’s approach largely ignores the concerns we raised about multicollinearity. When two or more predictors

There is a long tradition in ecology of trying to understand community assembly processes by making inferences from patterns of community structure (Diamond 1975; Connor Simberloff 1979). Inferring process from pattern is appealing because the latter is more easily observed and quantified especially when manipulative controlled experiments are infeasible. In such cases our hope (albeit naïve at times) is that patterns of community structure bear some signature of the processes that generated them by assuming that a particular pattern is overwhelmingly the outcome of a single dominant process. However multiple processes can often generate the same pattern. A now well known example of the inference of processes from patterns is Joseph Connell's ‘Ghost of Competition Past’ (1980) which highlighted that although coexisting competitors may tend to be niche differentiated on average this pattern in and of itself is not proof that the observed niche differences are the result of divergent selection experienced by coevolving competitors. Connell emphasized that direct empirical support for the notion of character displacement enabling coexistence was virtually non existent. Another classic example of inferring process from pattern relates to the intermediate disturbance hypothesis (IDH) (Connell 1978) which suggests that intermediate levels of disturbance promote the highest levels of diversity (pattern) by preventing competitive exclusion by either good competitors in undisturbed environments or rapid growers in heavily disturbed environments (process). There have been very few attempts to directly test the process leading to this pattern and it has more recently been recognized that two alternative processes (i.e. competitive relative nonlinearity and storage effects) are capable of generating the same pattern (Chesson 2000; Shea Roxburgh Rauschert 2004). Such examples are important reminders that understanding community assembly requires careful understanding of how pattern and process are linked. Critical evaluation of existing research approaches an important role to play here by pointing the way towards more productive approaches and research agendas. For instance in response to the criticisms of Connell (1980) and others Schluter McPhail (1992) developed a checklist of criteria that must be satisfied in order to demonstrate character displacement. Recent reviews highlight which items on the checklist rarely are checked off thereby identifying productive directions for future work (Beans 2014; Stuart et al. 2014).

SUMMARY 1. Analysing and interpreting long-term phytoplankton time series present a number of challenges, arising from potential historical inconsistencies in data collection and taxonomic identification of organisms. In a previous paper, Pomati et al. (2012) found a remarkable increase in phytoplankton diversity that coincided with oligotrophication and warming of Lake Zurich over a 32-year period. These findings were recently challenged on the basis of potential biases in detection limits and taxonomic classification over the time series (Straile, Jochimsen & K€ 2013). We agree that being cautious with long-term phytoplankton data series is extremely important, but argue that the increase in richness detected in Lake Zurich cannot be due only to methodological bias. 2. Following additional analysis of the Lake Zurich phytoplankton dataset, we found that the shift in taxon detection limits reported by Straile et al. (2013) is not supported by the data and stems from a rounding error in the calculation of density in the dataset available to those authors. We found a decline in the proportional abundance for common taxa, an increase in the annual prevalence of taxa and reduced community turnover over the time series. Taken together, the data clearly indicate a trend of decreasing dominance, while more taxa coexist simultaneously. We also argue that the taxonomic classification has been robust (at least at the family level) and propose a diagnostic plot that can help detect an unbiased signal of change in plankton richness through time. 3. Straile et al. (2013) observed perfect synchrony in species occurrence between Lake Zurich and nearby Lake Walen. While we agree that such perfect synchrony in community composition can reflect a bias in the database compilation, it can also be an important ecological signal of changes in regional species pools that deserves further analysis. 4. We conclude that the results of Pomati et al. (2012) are robust and not substantially undermined by the criticisms of Straile et al. (2013). More generally, it is indeed possible to extract meaningful signals of biodiversity change from long-term phytoplankton monitoring datasets, provided there is a clear understanding of how the data have been sampled, recorded and analysed over the history of the time series.

Our understanding of how biodiversity influences ecosystem functioning is entering a new stage of its development through the incorporation of information about the evolutionary relatedness of species. Bacteria are prime providers of essential ecosystem services, representing an excellent model system to perform biodiversity-ecosystem function research. By using bacteria isolated from petroleum-contaminated sites, we show that communities composed of poorly related species were more productive than those containing highly related species. The nature of the forces controlling this positive effect of phylogenetic diversity on community productivity depended on the number of species in culture. In communities of two species the positive effect of phylogenetic diversity on productivity was driven by changes in the selection effect. Communities of two distantly related species were dominated by the most productive species in monoculture, whereas communities of two closely related species were dominated by the less productive species in monoculture. In communities of four species the positive effect of phylogenetic diversity on productivity was driven by changes in the complementarity effect. In communities composed of four distantly related species the influence of positive interactions such as facilitation, cross-feeding, and niche partitioning seemed to outweigh the influence of negative interactions such as interference. As a consequence the proportion of species favored by the presence of other species increased as they became less related. Multiple facets of biodiversity may influence ecosystem functioning. Here, we present evidence of an interaction between phylogenetic and taxonomic diversity on community productivity, underlining the importance of considering multiple aspects of biodiversity when studying its impact on ecosystem functioning.

The impact of biodiversity on the stability of ecological communities has been debated among biologists for more than a century. Recently summarized empirical evidence suggests that biodiversity tends to enhance the temporal stability of community-level properties such as biomass; however, the underlying mechanisms driving this relationship remain poorly understood. Here, we report the results of a microcosm study in which we used simplified systems of freshwater microalgae to explore how the phylogenetic relatedness of species influences the temporal stability of community biomass by altering the nature of their competitive interactions. We show that combinations of two species that are more evolutionarily divergent tend to have lower temporal stability of biomass. In part, this is due to negative ‘selection effects’ in which bicultures composed of distantly related species are more likely to contain strong competitors that achieve low biomass. In addition, bicultures of distantly related species had on average weaker competitive interactions, which reduced compensatory dynamics and decreased the stability of community biomass. Our results demonstrate that evolutionary history plays a key role in controlling the mechanisms, which give rise to diversity–stability relationships. As such, patterns of shared ancestry may help us predict the ecosystem-level consequences of biodiversity loss.

Despite their importance as ecosystem drivers, our understanding of the influence of bacterial diversity on ecosystem functioning is limited. After identifying twelve bacterial strains from two petroleum-contaminated sites, we experimentally explored the impact of biodiversity on total density by manipulating the number of strains in culture. Irrespective of the origin of the bacteria relative to the contaminant, biodiversity positively influenced total density. However, bacteria cultured in the crude oil of their origin (autochthonous) reached higher densities than bacteria from another origin (allochthonous) and the relationship between diversity and density was stronger for autochthonous bacteria. By measuring the relative contribution of each strain to total density we showed that the observed positive effect of increasing diversity on total density was mainly due to positive interactions among species and not the presence of a particular species. Our findings can be explained by the complex chemical composition of crude oil and the necessity of a diverse array of organisms with complementary enzymatic capacities to achieve its degradation. The long term exposure to a contaminant may have allowed different bacteria to become adapted to the use of different fractions of the crude, resulting in higher complementarity in resource use in autochthonous bacteria compared to allochthonous ones. Our results could help improve the success of bioaugmentation as a bioremediation technique by suggesting the use of a diversified set of autochthonous organisms.

The most unique feature of Earth is the existence of life, and the most extraordinary feature of life is its diversity. Approximately 9 million types of plants, animals, protists and fungi inhabit the Earth. So, too, do 7 billion people. Two decades ago, at the first Earth Summit, the vast majority of the world's nations declared that human actions were dismantling the Earth's ecosystems, eliminating genes, species and biological traits at an alarming rate. This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper.

International audience; The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.

Summary 1. Ecological specialization is one of the main concepts in ecology and conservation. However, this concept has become highly context-dependent and is now obscured by the great variability of existing definitions and methods used to characterize ecological specialization. 2. In this study, we clarify this concept by reviewing the strengths and limitations of different approaches commonly used to define and measure ecological specialization. We first show that ecological specialization can either be considered as reflecting species’ requirements or species’ impacts. We then explain how specialization depends on species-specific characteristics and on local and contingent environmental constraints. We further show why and how ecological specialization should be scaled across spatial and temporal scales, and from individuals to communities. 3. We then illustrate how this review can be used as a practical toolbox to classify widely used metrics of ecological specialization in applied ecology, depending on the question being addressed, the method used, and the data available. 4. Synthesis and applications. Clarifying ecological specialization is useful to make explicit connections between several fields of ecology using the niche concept. Defining this concept and its practical metrics is also a crucial step to better formulate predictions of scientific interest in ecology and conservation. Finally, understanding the different facets of ecological specialization should facilitate to investigate the causes and consequences of biotic homogenization and to derive relevant indicators of biodiversity responses to land-use changes.

International audience; The relationship between biodiversity and ecosystem functioning (BEF) has become a cornerstone of community and ecosystem ecology(1-3) and an essential criterion for making decisions in conservation biology and policy planning(4,5). It has recently been proposed that evolutionary history should influence the BEF relationship because it determines species traits and, thus, species' ability to exploit resources(6,7). Here we test this hypothesis by combining experimental evolution with a BEF experiment. We isolated 20 bacterial strains from a marine environment and evolved each to be generalists or specialists(8). We then tested the effect of evolutionary history on the strength of the BEF relationship with assemblages of 1 to 20 species constructed from the specialists, generalists and ancestors(9). Assemblages of generalists were more productive on average because of their superior ability to exploit the environmental heterogeneity(10). The slope of the BEF relationship was, however, stronger for the specialist assemblages because of enhanced niche complementarity. These results show how the BEF relationship depends critically on the legacy of past evolutionary events.

The influence of biodiversity on ecosystem functioning is a major concern of ecological research. However, the biodiversity–ecosystem functioning relationship has very often been studied independently from the mechanisms allowing coexistence. By considering the effects of dispersal and niche partitioning on diversity, the metacommunity perspective predicts a spatial scale-dependence of the shape of the relationship. Here, we present experimental evidence of such scale-dependent patterns. After approximately 500 generations of diversification in a spatially heterogeneous environment, we measured functional diversity (FD) and productivity at both local and regional scales in experimental source-sink metacommunities of the bacterium Pseudomonas fluorescens SBW25. At the regional scale, environmental heterogeneity yielded high levels of FD and we observed a positive correlation between diversity and productivity. At the local scale, intermediate dispersal increased local FD through a mass effect but there was no correlation between diversity and productivity. These experimental results underline the importance of considering the mechanisms maintaining biodiversity and the appropriate spatial scales in understanding its relationship with ecosystem functioning.

A number of studies have demonstrated a positive relationship between species diversity and ecosystem productivity over short periods, but little is known about how they relate over evolutionary time. The use of bacteria as a model is one way of cracking the timescale problem. In an experiment in Pseudomonas fluorescens microcosms evolving for around 500 generations, adaptive radiation driven by environmental heterogeneity and dispersal resulted in the de novo evolution of a positive relationship between functional diversity and productivity, which both peak at intermediate dispersal rates. This suggests that evolutionary diversification plays a central role in generating community and ecosystem properties related to those observed in nature. An investigation into the role of dispersal in determining diversity and productivity over evolutionary time scales using the bacterium Pseudomonas fluorescens shows that adaptive radiation driven by environmental heterogeneity and dispersal leads to the de novo evolution of a positive relationship between functional diversity and productivity, which both peak at intermediate dispersal rates. Positive relationships between species diversity and productivity have been reported for a number of ecosystems1,2. Theoretical and experimental studies have attempted to determine the mechanisms that generate this pattern over short timescales1,2, but little attention has been given to the problem of understanding how diversity and productivity are linked over evolutionary timescales. Here, we investigate the role of dispersal in determining both diversity and productivity over evolutionary timescales, using experimental metacommunities of the bacterium Pseudomonas fluorescens assembled by divergent natural selection. We show that both regional diversity and productivity peak at an intermediate dispersal rate. Moreover, we demonstrate that these two patterns are linked: selection at intermediate rates of dispersal leads to high niche differentiation between genotypes, allowing greater coverage of the heterogeneous environment and a higher regional productivity. We argue that processes that operate over both ecological and evolutionary timescales should be jointly considered when attempting to understand the emergence of ecosystem-level properties such as diversity–function relationships.

Nature 486, 59–67 (2012); doi:10.1038/nature11148 In Table 1 and Supplementary Table 2 of this Review, under the ‘Category of service’ called ‘Regulating’, the first two ‘Measures of service provision’ related to ‘Biocontrol’ should read ‘Abundance of herbivorous pests’ instead of ‘Control of herbivorous pests’.