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International audience; A healthy soil plant continuum is critical for maintaining agroecosystem functions and ensuring food security, which is thebasis of sustainable agricultural development. Diverse soil microorganisms form a complex assembly and play an importantrole in agroecosystems by regulating nutrient cycling, promoting plant growth, and alleviating biotic and abiotic stresses.Improving microbial coexistence may be an efective and practical solution for the promotion of soil–plant ecosystem healthin the face of the impacts of anthropogenic activities and global climate change. Modern coexistence theory is a usefultheoretical framework for studying the coexistence of species that are competing for resources. Here, we briefy introducethe basic framework of modern coexistence theory, including the theoretical defnitions and mathematical calculations forniche diference and ftness diference, as well as ways to test for these diferences empirically. The possible efects of severalmajor biotic and abiotic factors, such as biological interactions, climate change, environmental stress, and fertilization, onmicrobial niche and ftness diferences are discussed. From the perspective of stabilizing and equalizing mechanisms, thepotential roles of microbe–microbe interactions and plant–microbe interactions in promoting healthy soil–microbe–plantcontinuum are presented. We suggest that the use of the coexistence theory framework for the design and construction ofmicrobial communities in agricultural production can provide a solid basis for the biological improvement of agroecosystems

International audience; AbstractKey messageA better transfer to managers of studies examining the functional role of tree species diversity would be achieved by explicitly addressing two missing links: the effect of management interventions on coexistence mechanisms and the relationships between coexistence mechanisms and ecosystem functions.ContextPlant species diversity has been shown to promote a wide array of ecosystem functions and ecosystem services. However, scientific results concerning relationships between species diversity or species mixing and ecosystem functions have not been well transferred to management practices so far. Part of the problem lies in the difficulty of assessing whether interesting species mixtures can persist over the long term and how management influences ecosystem functions.AimsWe argue that a better transfer of knowledge to managers would be achieved by addressing two missing links: (i) the effect of management interventions on coexistence mechanisms and (ii) the relationships between coexistence mechanisms and ecosystem functions.MethodsTo do so, we first provide a brief overview of the recent scientific results on relations between tree diversity (or two-species mixing) and ecosystem functions, focusing on studies dealing with productivity and stability in forests. We further introduce the key question of whether mixed stands are transient or permanent. We then briefly present key elements of modern coexistence theory and illustrate them with three examples in forest ecosystems. We finish by discussing how management interventions in forests can affect coexistence mechanisms and by addressing some methodological perspectives.ResultsWe provide examples of management actions (e.g. gap-based silviculture, preferentialselection of the most frequent species, preferential selection of the most competitive species, plantingweakly competitive species) that may increase the strength of coexistence mechanisms.ConclusionAnalysing long-term management impacts on species coexistence and ecosystem functions with a combination of long-term monitoring of large permanent plots and mechanistic dynamic model simulations will be useful to develop relevant practices favouring mixed forests in the long term.

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVIN [ADD1_IRSTEA]Dynamique et fonctionnement des écosystèmes; International audience; How the patterns of niche occupancy vary from species-poor to species-rich communities is a fundamental question in ecology that has a central bearing on the processes that drive patterns of biodiversity. As species richness increases, habitat filtering should constrain the expansion of total niche volume, while limiting similarity should restrict the degree of niche overlap between species. Here, by explicitly incorporating intraspecific trait variability, we investigate the relationship between functional niche occupancy and species richness at the global scale. 2.We assembled 21 datasets worldwide, spanning tropical to temperate biomes and consisting of 313 plant communities representing different growth forms. We quantified three key niche occupancy components (the total functional volume, the functional overlap between species and the average functional volume per species) for each community, related each component to species richness, and compared each component to the null expectations. 3.As species richness increased, communities were more functionally diverse (an increase in total functional volume), and species overlapped more within the community (an increase in functional overlap) but did not more finely divide the functional space (no decline in average functional volume). Null model analyses provided evidence for habitat filtering (smaller total functional volume than expectation), but not for limiting similarity (larger functional overlap and larger average functional volume than expectation) as a process driving the pattern of functional niche occupancy. 4.Synthesis. Habitat filtering is a widespread process driving the pattern of functional niche occupancy across plant communities and coexisting species tend to be more functionally similar rather than more functionally specialized. Our results indicate that including intraspecific trait variability will contribute to a better understanding of the processes driving patterns of functional niche occupancy

International audience; Understanding the mechanisms of species coexistence is a key task for ecology. Recent theory predicts that both competition and predation (which causes apparent competition among prey) can either promote or limit species coexistence. Both mechanisms cause negative interactions between individuals, and each mechanism promotes stable coexistence if it causes negative interactions to be stronger between conspecifics than between heterospecifics. However, the relative importance of competition and predation for coexistence in natural communities is poorly known. Here, we study how competition and apparent competition via pre‐dispersal seed predators affect the long‐term fecundity of Protea shrubs in the fire‐prone Fynbos biome (South Africa). These shrubs store all viable seeds produced since the last fire in fire‐proof cones. Competitive effects on cone number and pre‐dispersal seed predation reduce their fecundity and can thus limit recruitment after the next fire. In 27 communities comprising 49 990 shrubs of 22 Protea species, we measured cone number and per‐cone seed predation rate of 2154 and 1755 focal individuals, respectively. Neighbourhood analyses related these measures to individual‐based community maps. We found that conspecific neighbours had stronger competitive effects on cone number than heterospecific neighbours. In contrast, apparent competition via seed predators was comparable between conspecifics and heterospecifics. This indicates that competition stabilizes coexistence of Protea species, whereas pre‐dispersal seed predation does not. Larger neighbours had stronger competitive effects and neighbours with large seed crops exerted stronger apparent competition. For 97% of the focal plants, competition reduced fecundity more than apparent competition. Our results show that even in communities of closely related and ecologically similar species, intraspecific competition can be stronger than interspecific competition. On the other hand, apparent competition through seed predators need not have such a stabilizing effect. These findings illustrate the potential of ‘community demography’, the demographic study of multiple interacting species, for understanding plant coexistence.

WOS:000393000500007; International audience; Individual diet variation (i.e. diet variation among individuals) impacts intra- and inter-specific interactions. Investigating its sources and relationship with species trophic niche organization is important for understanding community structure and dynamics. Individual diet variation may increase with intra-specific phenotypic (or "individual state") variation and habitat variability, according to Optimal Foraging Theory (OFF), and with species trophic niche width, according to the Niche Variation Hypothesis (NVH). OFT proposes "proximate sources" of individual diet variation such as variations in habitat or size whereas NVH relies on "ultimate sources" related to the competitive balance between intra- and inter-specific competitions. The latter implies as a corollary that species trophic niche overlap, taken as inter-specific competition measure, decreases as species niche width and individual niche variation increase. We tested the complementary predictions of OFT and NVH in a marine fish assemblage using stomach content data and associated trophic niche metrics. The NVH predictions were tested between species of the assemblage and decomposed into a between- and a within-functional group component to assess the potential influence of species' ecological function. For most species, individual diet variation and niche overlap were consistently larger than expected. Individual diet variation increased with intra-specific variability in individual state and habitat, as expected from OFT. It also increased with species niche width but in compliance with the null expectation, thus not supporting the NVH. In contrast, species niche overlap increased significantly less than null expectation with both species niche width and individual diet variation, supporting NVH corollary. The between- and within-functional group components of the NVH relationships were consistent with those between species at the assemblage level. Changing the number of prey categories used to describe diet (from 16 to 41) did not change the results qualitatively. These results suggest that, besides proximate sources, intra-specific competition favors higher individual diet variation than expected while inter-specific competition limits the increase of individual diet variation and of species niche overlap with species niche expansion. This reveals partial trophic resource partitioning between species. Various niche metrics used in combination allow inferring competition effects on trophic niches' organization within communities.

Summary Theories of species coexistence and invasion ecology are fundamentally connected and provide a common theoretical framework for studying the mechanisms underlying successful invasions and their ecological impacts. Temporal fluctuations in resource availability and differences in life-history traits between invasive and resident species are considered as likely drivers of the dynamics of invaded communities. Current critical issues in invasion ecology thus relate to the extent to which such mechanisms influence coexistence between invasive and resident species and to the ability of resident species to persist in an invasive-dominated ecosystem. We tested how a fluctuating resource, and species trait differences may explain and help predict long-term impacts of biological invasions in forest specialist insect communities. We used a simple invasion system comprising closely related invasive and resident seed-specialized wasps (Hymenoptera: Torymidae) competing for a well-known fluctuating resource and displaying divergent diapause, reproductive and phenological traits. Based on extensive long-term field observations (1977–2010), we developed a combination of mechanistic and statistical models aiming to (i) obtain a realistic description of the population dynamics of these interacting species over time, and (ii) clarify the respective contributions of fluctuation-dependent and fluctuation-independent mechanisms to long-term impact of invasion on the population dynamics of the resident wasp species. We showed that a fluctuation-dependent mechanism was unable to promote coexistence of the resident and invasive species. Earlier phenology of the invasive species was the main driver of invasion success, enabling the invader to exploit an empty niche. Phenology also had the greatest power to explain the long-term negative impact of the invasive on the resident species, through resource pre-emption. This study provides strong support for the critical role of species differences in interspecific competition outcomes within animal communities. Our mechanistic-statistical approach disentangles the critical drivers of novel species assemblages resulting from intentional and non-intentional introductions of non-native species.

Protective mutualisms, where a symbiont reduces the negative effects of another species on a shared host, represent a common type of species interaction in natural communities, yet it is still unclear what ecological conditions might favor their emergence. Studies suggest that the initial evolution of protective mutualists might involve closely related pathogenic variants with similar life histories, but different competitive abilities and impacts on host fitness. We derive a model to evaluate this hypothesis and show that, in general, a protective variant cannot spread from rarity or exclude a more pathogenic strain. While the conditions allowing mutualist invasion are more likely with increased environmental productivity, they still depend on initial densities in the invaded patch exceeding a threshold, highlighting the likely importance of spatial structure and demographic stochasticity. Using a numerical simulation approach, we show that regional coexistence is in fact possible in an explicitly spatial system and that, under some circumstances, the mutualist population can exclude the enemy. More broadly, the establishment of protective mutualists may be favored when there are other life-history differences from more pathogenic symbionts, such as vertical transmission or additional direct benefits to hosts.

International audience; Understanding the mechanisms drivingdiversity in nature is an important and ongoingchallenge in our changing world. To efficiently protectecosystem diversity it is crucial to explain why andhow species coexist. Over the last decades modelsexplaining species coexistence have increased incomplexity but usually don’t incorporate a detailedspatial context. However, spatial structure has beenshown to affect species coexistence and habitatdeterioration is one of the biggest threats to biodiver-sity. We therefore explore a spatially explicit two-species model and assess the effects of habitatstructure on species coexistence using a wide diversityof fractal landscapes. Each species is specialized in aparticular habitat type. We find that landscape struc-ture has a major influence on the stability andconstitution of a two species system and may besufficient to explain the coexistence of two species.Well connected and highly structured habitat config-urations allow spatial segregation of both species andthis decreases local interspecific competition; in ourmodel this is the most important process stabilizingcoexistence.

International audience; Intra-specific variability often produces an overlap between species distributions of individual performances which can influence competition relations and community dynamics. We analysed a two-species competitioncolonisation model of vegetation with intra-specific variability in juvenile growth. On each patch colonised by both species, the winner was the juvenile with higher individual growth. Intra-specific variability disproportionately favoured the more fecund species because the tail of its distribution represented more ndividuals. In some cases, this process could even lead to a reversal of competition hierarchy and exclusion of the species with higher mean juvenile performance. In the space of species 2 mean growth and fecundity traits, the combinations of traits allowing coexistence with species 1 appeared close to an ideal trade-off curve. Along this curve, species 2 and species 1 coexisted at similar abundance. The balance of relative abundances diminished with the distance of species 2 from this curve. For a given level of relative species performances, coexistence stability increased continuously as species differentiation increased. In contrast to classical models that exhibit abrupt changes of equilibrium community properties when species traits vary, our model displayed continuous changes of these properties in relation to the balance of life traits within and among species. Intra-specific variability allows flexible patterns of community dynamics and could explain discrepancies between observations and classical theories.

Ecologists have long been searching for mechanisms of species coexistence, particularly since G.E. Hutchinson raised the ‘paradox of the plankton’. A promising approach to solve this paradox and to explain the coexistence of many species with strong niche overlap is to consider over-compensatory density regulation with its ability to generate endogenous population fluctuations. Previous work has analysed the role of over-compensation in coexistence based on analytical approaches. Using a spatially explicit time-discrete simulation model, we systematically explore the dynamics and conditions for coexistence of two species. We go beyond the analytically accessible range of models by studying the whole range of density regulation from under- to very strong over-compensation and consider the impact of spatial structure and temporal disturbances. In particular, we investigate how coexistence can emerge in different types of population growth models. We show that two strong competitors are able to coexist if at least one species exhibits over-compensation. Analysing the time series of population dynamics reveals how the differential responses to density fluctuations of the two competitors lead to coexistence: The over-compensator generates density fluctuations but is the inferior competitor at strong amplitudes of those fluctuations; the competitor, therefore, becomes frequent and dampens the over-compensator's amplitudes, but it becomes inferior under dampened fluctuations. These species interactions cause a dynamic alternation of community states with long-term persistence of both species. We show that a variety of population growth models is able to reproduce this coexistence although the particular parameter ranges differ among the models. Spatial structure influences the probability of coexistence but coexistence is maintained for a broad range of dispersal parameters. The flexibility and robustness of coexistence through over-compensation emphasize the importance of nonlinear density dependence for species interactions, and they also highlight the potential of applying more flexible models than the classical Lotka–Volterra equations in community ecology.

International audience; The competition–colonization trade-off model is often used to explain the coexistence of species. Yet its applicability has been severely criticized, mainly because the original model assumed a strict competitive hierarchy of species and did not allow for any preemptive effect. We considered the impact of relaxing both of these limitations on coexistence. Relaxing trade-off intensity makes coexistence less likely and introduces a minimum colonization rate below which any coexistence is impossible. Allowing for preemption introduces a limit to dissimilarity between species. Surprisingly, preemption does not impede coexistence as one could presume from previous studies, but can actually increase the likelihood of coexistence. Its effect on coexistence depends on whether or not species in the regional pool are strongly limited in their colonization ability. Preemption is predicted to favour coexistence when: (i) species are not strongly limited in their colonization ability; and (ii) the competitive trade-off is not infinitely intense.