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International audience; Recent work has shown that evaluating functional trait distinctiveness, the average trait distance of a species to other species in a community offers promising insights into biodiversity dynamics and ecosystem functioning. However, the ecological mechanisms underlying the emergence and persistence of functionally distinct species are poorly understood. Here, we address the issue by considering a heterogeneous fitness landscape whereby functional dimensions encompass peaks representing trait combinations yielding positive population growth rates in a community. We identify four ecological cases contributing to the emergence and persistence of functionally distinct species. First, environmental heterogeneity or alternative phenotypic designs can drive positive population growth of functionally distinct species. Second, sink populations with negative population growth can deviate from local fitness peaks and be functionally distinct. Third, species found at the margin of the fitness landscape can persist but be functionally distinct. Fourth, biotic interactions (positive or negative) can dynamically alter the fitness landscape. We offer examples of these four cases and guidelines to distinguish between them. In addition to these deterministic processes, we explore how stochastic dispersal limitation can yield functional distinctiveness. Our framework offers a novel perspective on the relationship between fitness landscape heterogeneity and the functional composition of ecological assemblages.

International audience; Plant interactions play a key role in forest ecosystem dynamics. The tallest plants, namely the overstorey trees, are obvious major drivers, particularly in competition for light. This process has already been amply described. However, the role played by lower strata has often been underestimated. In this review, we first briefly recall the role of over- and understoreys in structuring forest microclimate, mostly through light sharing. We then focus on belowground interactions between over- and understorey, where knowledge is more piecemeal, partly because of measurement difficulties. Even so, some studies show that competition for water and nutrients by the overstorey controls the development of understorey vegetation much more than competition for light. The reverse (overstorey limitation by the understorey) has also been encountered, but has been much less well researched. We also address the involvement of mycorrhizae, specifically their role in alleviating overstorey drought stress and contributing to nutrient cycling. We go on to show how another example of key ecosystem engineers, large mammalian herbivores, shape above- and belowground resources and intervene in over- and understorey interactions. In conclusion, for a better understanding of forest dynamics and adapted management, particularly in the context of global climate change, we advocate taking account not only of trees but of all forest components. Belowground processes need more research. The roles of mycorrhizal networks, root exudates, microbiota, and chemical cues need to be further explored to gain a finer understanding of the interactions between over- and understorey.

An organism's body size plays an important role in ecological interactions such as predator-prey relationships. As predators are typically larger than their prey, this often leads to a strong positive relationship between body size and trophic position in aquatic ecosystems. The distribution of body sizes in a community can thus be an indicator of the strengths of predator-prey interactions. The aim of this study was to gain more insight into the relationship between fish body size distribution and trophic position in a wide range of European lakes. We used quantile regression to examine the relationship between fish species' trophic position and their log-transformed maximum body mass for 48 fish species found in 235 European lakes. Subsequently, we examined whether the slopes of the continuous community size distributions, estimated by maximum likelihood, were predicted by trophic position, predator-prey mass ratio (PPMR), or abundance (number per unit effort) of fish communities in these lakes. We found a positive linear relationship between species' maximum body mass and average trophic position in fishes only for the 75% quantile, contrasting our expectation that species' trophic position systematically increases with maximum body mass for fish species in European lakes. Consequently, the size spectrum slope was not related to the average community trophic position, but there were negative effects of community PPMR and total fish abundance on the size spectrum slope. We conclude that predator-prey interactions likely do not contribute strongly to shaping community size distributions in these lakes.

Above- and below-ground herbivory are key ecosystem processes that can be substantially altered by environmental changes. However, direct comparisons of the coupled variations of above- and below-ground herbivore communities along elevation gradients remain sparse. Here, we studied the variation in assemblages of two dominant groups of herbivores, namely, aboveground orthoptera and belowground nematodes, in grasslands along six elevation gradients in the Swiss Alps. By examining variations of community properties of herbivores and their food plants along montane clines, we sought to determine whether the structure and functional properties of these taxonomic groups change with elevation. We found that orthoptera decreased in both species richness and abundance with elevation. In contrast with aboveground herbivores, the taxonomic richness and the total abundance of nematode did not covary with elevation. We further found a stronger shift in above- than below-ground functional properties along elevation, where the mandibular strength of orthoptera matched a shift in leaf toughness. Nematodes showed a weaker pattern of declined sedentary behavior and increased mobility with elevation. In contrast to the direct exposal of aboveground organisms to the surface climate, conditions may be buffered belowground, which together with the influence of edaphic factors on the biodiversity of soil biota, may explain the differences between elevational patterns of above- and below-ground communities. Our study emphasizes the necessity to consider both the above- and below-ground compartments to understand the impact of current and future climatic variation on ecosystems, from a functional perspective of species interactions. Electronic supplementary material The online version of this article (10.1007/s00442-020-04778-7) contains supplementary material, which is available to authorized users.

Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote competitive and even parasitic behaviour. Based on three interesting case studies identified from the literature, we also highlight that such nonmutualistic interactions could be widespread and of particular significance for the survival of pathogens or the shaping of complex microbial communities.

International audience; There is growing interest in the potential for combining eDNA and artificial intelligence (machine learning) to detect and evaluate in real time changes in ecosystems at the global scale, in a more sensitive and cost-effective way than current biomonitoring methods. Machine learning might make better use of the eDNA census data that can currently be collected to evaluate the network of ecological interactions that are at the base of the services that ecosystems supply and that we wish to protect. To date, eDNA and machine learning developments have effectively progressed in parallel and in isolation in various spheres of ecosystem monitoring (disease, invasion, conservation, etc. in aerial, terrestrial, and aquatic systems).The goal of this Research Topic is to explore the range of ongoing activities to build the next generation of biomonitoring tools and in doing so to make researchers in the different spheres aware of the breadth of work being undertaken, and to set a unifying research agenda (the key questions) for the development of global biomonitoring using eDNA and machine learning.The scope of this Research Topic will be to explore:1. eDNA approaches currently being used in case study systems from all spheres of monitoring;2. Theoretical underpinnings of machine learning for biomonitoring;3. What type of networks do we need to reconstruct for effective monitoring (co-occurrence, trophic, etc);4. Examples of learning large scale, replicated networks from eDNA in the different spheres;5. Statistical and analytical approaches to analysing large-scale, highly replicated networks;6. Technological developments necessary to build a next-generation biomonitoring framework at the global scale;7. A research agenda paper that develops “10 key questions for eDNA and machine learning in biomonitoring”.Details for Authors: The Research Topic “A next-generation of global biomonitoring to detect ecosystem change” will publish conceptual, data, case study, technological and synthetic papers on eDNA and machine learning approaches for developing a unified next-generation biomonitoring framework. Paper length conforms to the guidelines of the journal Frontiers in Ecology and Evolution.

The attine ants are a monophyletic lineage that switched to fungus farming ca. 55–60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here, we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α‐ and γ‐Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia‐bearing cultivars, but before the origin of industrial‐scale farming based on leaf‐cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that almost the entire crown group of the higher attine ants, including the leaf‐cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic‐producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus farming symbioses and raise new questions for further in‐depth research., see also the Perspective by Pringle

Damage due to wind storms and droughts are increasing in many temperate forest, yet little is known about the long-term roles of these key climatic factors in forest dynamics and in the carbon budget. The objective of this study was to estimate individual and coupled effects of droughts and wind-storms on adult tree mortality across a 31-year period in 115 managed, mixed-coniferous forest stands from the Western Alps and the Jura mountains. For each stand, yearly mortality was inferred from management records, yearly drought from interpolated fields of monthly temperature, precipitation and soil water holding capacity, and wind-storms from interpolated fields of daily maximum wind-speed. We performed a thorough model selection based on a leave-one-out cross-validation of the time series. We compared different critical wind-speeds (CWSs) for damage, wind-storm and stand variables and statistical models. We found that a model including stand characteristics, drought and storm strength using a CWS of 25 ms−1 performed the best across most stands. Using this best model, we found that drought increased damage risk only in the most southerly forests, and its effect is generally maintained for up to two years. Storm strength increased damage risk in all forests in a relatively uniform way. In some stands, we found positive interaction between drought and storm strength most likely because drought weakens trees, and they became more prone to stem breakage under wind-loading. In other stands, we found negative interaction between drought and storm strength, where excessive rain likely leads to soil water saturation making trees more susceptible to overturning in a wind-storm. Our results stress that temporal data is essential to make valid inferences about ecological impacts of disturbance events, and that making inferences about disturbance agents separately can be of limited validity. Under projected future climatic conditions, the direction and strength of these ecological interactions could also change. This article is protected by copyright. All rights reserved.

We examine some unexpected epistemological conflicts that arise at the interfaces between ecological science, the ecosystem services framework, policy, and industry. We use an example from our own research to motivate and illustrate our main arguments, while also reviewing standard approaches to ecological science using the ecosystem services framework. While we agree that the ecosystem services framework has benefits in its industrial applications because it may force economic decision makers to consider a broader range of costs and benefits than they would do otherwise, we find that many alignments of ecology with the ecosystem services framework are asking questions that are irrelevant to real-world applications, and generating data that does not serve real-world applications. We attempt to clarify why these problems arise and how to avoid them. We urge fellow ecologists to reflect on the kind of research that can lead to both scientific advances and applied relevance to society. In our view, traditional empirical approaches at landscape scales or with place-based emphases are necessary to provide applied knowledge for problem solving, which is needed once decision makers identify risks to ecosystem services. We conclude that the ecosystem services framework is a good policy tool when applied to decision-making contexts, but not a good theory either of social valuation or ecological interactions, and should not be treated as one.

Mixed fruit-vegetable cropping systems (MFVCS) are a promising way of ensuringenvironmentally sustainable agricultural production systems in response to the challenge of beingable to fulfill local market requirements. Indeed, they combine productions and they also make abetter use of biodiversity. These agroforestry systems are based on a complex set of interactionsmodifying the utilization of light, water and nutrients. Thus, designing such a system must optimize theuse of these resources, by maximizing positive interactions (facilitation) and minimizing negative ones(competition). To attain these objectives, the system's design has to include the spatial and temporaldimensions of these interactions, taking into account the evolution of above- and belowgroundinteractions over a time horizon. However, a considerable amount of research has been conducted,on the one hand, to prove the interest of agroforestry, and on the other hand to propose modelssupporting cropping plan and crop rotation decisions, but to our knowledge, no model supports thespatial and temporal allocation of both vegetable crops and trees in agroforestry systems. Therefore,we initially built a first MFVCS prototype using the Weighted Constraint Satisfaction framework but theresolution was limited to small scale systems. In this paper, we explore larger MFVCS models using asolver based on Integer Quadratic Programming. The limits of exact methods in solving the MFVCSproblem are presented showing the need for approximation methods able to solve a large scalesystem with solutions of good quality in reasonable time, which could be used in interactive designwith farmers and advisers.

Biological diversity constitutes one of the major pattern of ecosystem functioning, and a potential for adaptation and evolution of life in the context of climate change. As species are in many ways tightly interconnected, biodiversity loss can trigger large cascade effects and might lead to largely unpredictable consequences, reaching far beyond the visible reduction in the number or distribution of species. The high complexity of ecological organization is often a nightmare for decision-making, starting from accurately measuring biodiversity. This is however a necessary step to take if we want to prioritize action in biodiversity management, in order to preserve as much diversity as possible under limited resources. Though this thesis does not pretend to provide complete answers to those quite complex issues, it provides some reflection points for biodiversity management. It is composed of four chapters. The first chapter raises the issue of dealing with a mixed biodiversity, in which invasive species can be guests. It highlights the interconnections between the severity of the impacts of biological invasions and the contexts in which this invasion occurs. Considering invasion impacts as inherently ''ambivalent'' - i.e. good, bad or neutral for the system in which it arrives - we propose a typology to assess ambivalence in impact, based on the identification of potential sources of impact variability. For the second chapter, we focus on the measurement of biodiversity when accounting for species interactions, which we incorporates into the Noah's Arch problem developed by Weitzman (1998). We then derive a general model for ranking in situ conservation projects. We show firstly that, when accounting for ecological interactions, the problem defined by Weitzman is still an extreme solution, and secondly, that a ranking reversal is possible and completely defined by the interaction categories. In the third chapter, we use the in situ cost-benefit framework developed in Chapter 2 to compare the outcomes of two biodiversity indices, Weitzman's and Rao's. Those two indexes combine information about species survival probability, ecological interaction and distinctiveness in a different way to measure biodiversity; We analyze simple biodiversity protection plans for each index, and disentangle the role played by the different data requirement in the rankings, in a three species ecosystem. We show that such pieces of information will come as a trade-off when considered simultaneously in the measure, and that the introduction of ecological interactions among more than two species lead to more complex conclusions. Ecological interactions thus give important additional information to determine conservation objectives. Our last chapter is an adaptation of the previously defined optimization framework for the prioritization of invasive species management. It elaborates a myopic rule to determine which invasions must be controlled in priority, taking into account relative management costs and trophic cascades impacts. We discuss the gradient of the objective function composed of a diversity function W and a utility function U, to see whether we should retain several or only a few species for management under a budget constraint.; La diversité biologique constitue l’un des piliers du fonctionnement des écosystèmes, et un potentiel pour l’adaptation et l’évolution de la vie dans le contexte du changement climatique. Les espèces constituant cette biodiversité sont étroitement connectées de différentes façons. Une diminution de cette biodiversité peut déclencher des effets de cascade et des conséquences largement imprévisibles, bien au delà de la seule réduction apparente du nombre ou de la distribution des espèces. La grande complexité de l’organisation écologique est très souvent un cauchemar pour la prise de décision. Les difficultés commencent avec le choix d’une mesure adéquate de la biodiversité. Une telle mesure est cependant une étape nécessaire si nous voulons prioriser nos actions de gestion de la biodiversité, afin de préserver le plus de diversité possible avec des ressources limitées. Bien que cette thèse ne prétende pas produire des réponses complètes à ces problèmes complexes, elle offre quelques points de réflexion pour la gestion de la biodiversité. Elle se compose de quatre chapitres. Le premier chapitre soulève la question de la gestion d’une biodiversité mélangée, au sein de laquelle des espèces invasives peuvent également s’inviter. Ce chapitre souligne les interconnections entre la sévérité des impacts des invasions biologiques et le contexte dans lequel cette invasion intervient. Considérant les impacts des invasions comme “ambivalents” — i.e. pouvant être positifs, négatifs, ou neutres pour le système dans lequel l’invasion s’installe — nous proposons une typologie afin d’évaluer l’ambivalence des impacts, sur la base de l’identification des sources potentielles de variabilité des impacts. Pour le second chapitre, nous nous concentrons sur la mesure de la biodiversité lorsque l’on tient compte des interactions entre espèces, de façon à produire une version de la métaphore de l’Arche de Noé (Weitzman, 1998) mieux adaptée aux problèmes de conservation in situ. Nous montrons tout d’abord que, lorsque l’on tient compte d’interactions écologiques, le problème défini par Weitzman demeure une solution extrême ; et deuxièmement, qu’un renversement de la hiérarchie des espèces préservées est possible et entièrement déterminée par la catégorie des interactions. Dans le troisième chapitre, nous utilisons le cadre de coût-bénéfice in-situ développé dans le chapitre 2 afin de comparer les résultats de priorisation de deux indices de biodiversité, Weitzman et Rao. Ces deux indices combinent différemment l’information sur les probabilités autonomes de survie des espèces, les interactions écologiques et la dissimilitude entre espèces afin de mesurer la biodiversité. Nous analysons des plans simples de protection de la biodiversité pour chaque indice, et démêlons le rôle joué par les différents éléments d’information nécessaires au calcul du ranking par l’indicateur, dans un écosystème à trois espèces. Nous montrons que chaque indice réalise un compromis qui lui est propre entre ces éléments d’information, et que l’introduction d’interactions écologiques entre plus de deux espèces mène à des conclusions plus complexes. Les interactions écologiques donnent ainsi une information additionnelle importante afin de déterminer les objectifs de conservation. Notre dernier chapitre est une adaptation du cadre d’optimisation défini précédemment. Il élabore une règle de décision myope afin de déterminer quelles invasions doivent être contrôlées en priorité, en tenant compte des coûts de gestion relatifs et les impacts trophiques en cascade. Nous discutons le gradient de la fonction d’objectif composé d’une fonction de diversité W et d’une fonction d’utilité U, afin de déterminer si nous devrions conserver plusieurs ou seulement quelques espèces sous une contrainte de budget.

Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus‐growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the same fungal diet, interact in varying intensities and are distantly related. We used tag‐encoded FLX 454 pyrosequencing and diagnostic PCR to map bacterial symbiont diversity across the Megalomyrmex phylogenetic tree, which also contains free‐living generalist predators. We show that social parasites and hosts share a subset of bacterial symbionts, primarily consisting of Entomoplasmatales, Bartonellaceae, Acinetobacter, Wolbachia and Pseudonocardia and that Entomoplasmatales and Bartonellaceae can co‐infect specifically associated combinations of hosts and social parasites with identical 16S rRNA genotypes. We reconstructed in more detail the population‐level infection dynamics for Entomoplasmatales and Bartonellaceae in Megalomyrmex symmetochus guest ants and their Sericomyrmex amabilis hosts. We further assessed the stability of the bacterial communities through a diet manipulation experiment and evaluated possible transmission modes in shared nests such as consumption of the same fungus garden food, eating of host brood by social parasites, trophallaxis and grooming interactions between the ants, or parallel acquisition from the same nest environment. Our results imply that cohabiting ant social parasites and hosts may obtain functional benefits from bacterial symbiont transfer even when they are not closely related.

Efficient management of biodiversity aims at allocating conservation efforts in order to maximize diversity. Defining a diversity criterion is however far to be trivial; there is not one but several indices that can be used as biodiversity measures. This paper elicits and compares two in situ criterions for biodiversity conservation, based on two biodiversity indices stemming from different disciplines: Weitzman’s index in economics and Rao’s index in ecology. Both indices combines differently pieces of information about (1) species survival probability, and (2) measures of dissimilarity between species. In order to truly have in situ protection criterions, we add another layer of information about (3) the ecological interactions between species. Considering a simple three species ecosystem, we show that choosing one criterion or the other has policy implications, for they sometimes deliver diverging protection recommendations. We unravel the role played by the elements (1), (2) and (3) in the ranking, which allows us to highlight some specificities of the in situ criterions. For example, other things equal, Weitzman’s in situ ranking tends to favor "robust" species, while Rao's in situ ranking gives priority to "fragile" species.

Efficient management of biodiversity aims at allocating conservation efforts in order to maximize diversity. Defining a diversity criterion is however far to be trivial; there is not one but several indices that can be used as biodiversity measures. This paper elicits and compares two in situ criterions for biodiversity conservation, based on two biodiversity indices stemming from different disciplines: Weitzman’s index in economics and Rao’s index in ecology. Both indices combines differently pieces of information about (1) species survival probability, and (2) measures of dissimilarity between species. In order to truly have in situ protection criterions, we add another layer of information about (3) the ecological interactions between species. Considering a simple three species ecosystem, we show that choosing one criterion or the other has policy implications, for they sometimes deliver diverging protection recommendations. We unravel the role played by the elements (1), (2) and (3) in the ranking, which allows us to highlight some specificities of the in situ criterions. For example, other things equal, Weitzman’s in situ ranking tends to favor "robust" species, while Rao's in situ ranking gives priority to "fragile" species.

Efficient management of biodiversity aims at allocating conservation efforts in order to maximize diversity. Defining a diversity criterion is however far to be trivial; there is not one but several indices that can be used as biodiversity measures. This paper elicits and compares two in situ criterions for biodiversity conservation, based on two biodiversity indices stemming from different disciplines: Weitzman’s index in economics and Rao’s index in ecology. Both indices combines differently pieces of information about (1) species survival probability, and (2) measures of dissimilarity between species. In order to truly have in situ protection criterions, we add another layer of information about (3) the ecological interactions between species. Considering a simple three species ecosystem, we show that choosing one criterion or the other has policy implications, for they sometimes deliver diverging protection recommendations. We unravel the role played by the elements (1), (2) and (3) in the ranking, which allows us to highlight some specificities of the in situ criterions. For example, other things equal, Weitzman’s in situ ranking tends to favor "robust" species, while Rao's in situ ranking gives priority to "fragile" species.

International audience; In microbial food webs, different types of interactions occur between microorganisms themselves and with meio- and macroorganisms. After an historical and general introduction, the biological components of the microbial food webs in the pelagic and benthic marine and lake ecosystems, as well as in the terrestrial ecosystems, are presented. The functioning of the microbial food webs in different ecosystems is illustrated and explained, including the trophic pathways and transfer of matter from microbial food webs toward meio- and macroorganisms of the superior trophic levels, the nutrient recycling in the aquatic environments, and the decomposition of organic matter in soils. Finally, the factors regulating microbial food webs, primarily “top-down” and “bottom-up” controls, are described with a special focus on the role of viruses in the aquatic microbial food webs.