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International audience; Life history strategies of most organisms are constrained by resource allocation patterns that follow a 'slow-fast continuum'. It opposes slow growing and long-lived organisms with late investment in reproduction to those that grow faster, have earlier and larger reproductive effort and a short longevity. In plants, the Leaf Economics Spectrum (LES) depicts a leaf-level trade-off between the rate of carbon assimilation and leaf lifespan, as stressed in functional ecology from interspecific comparative studies. However, it is still unclear how the LES is connected to the slow-fast syndrome. Interspecific comparisons also impede a deep exploration of the linkage between Les variation and adaptation to climate. Here, we measured growth, morpho-physiological and life-history traits, at both the leaf and whole-plant levels, in 378 natural accessions of Arabidopsis thaliana. We found that the Les is tightly linked to variation in whole-plant functioning, and aligns with the slow-fast continuum. A genetic analysis further suggested that phenotypic differentiation results from the selection of different slow-fast strategies in contrasted climates. slow growing and long-lived plants were preferentially found in cold and arid habitats while fast growing and short-lived ones in more favorable habitats. Our findings shed light on the role of the slow-fast continuum for plant adaptation to climate. More broadly, they encourage future studies to bridge functional ecology, genetics and evolutionary biology to improve our understanding of plant adaptation to environmental changes. Investigations of the genetic and phenotypic differentiation of plant lineages along environmental gradients is crucial for the understanding of plant evolutionary responses to current and future climate variations. As plants cannot simultaneously optimize competing eco-physiological functions, an important question is how plant adaptation occurs under the influence of major trade-offs between traits. The slow-fast continuum is a pervasive trade-off between resource allocation to growth, reproduction and survival , spread across the tree of life 1. The slow end of this continuum is characterized by slow growing, long-lived species and low reproductive output, while species at the fast end reach reproductive maturity faster and produce more offsprings. In plants, the leaf economics spectrum (LES hereafter) 2-4 is thought to reflect the physiological basis of the slow-fast continuum 4. The LES arrays plant species along a continuum of leaf trait syndromes going from short-lived leaves with fast metabolism to the reverse syndrome 3. Core LES traits include leaf dry mass per area (LMA), leaf lifespan (LLS) and net photosynthetic rate per mass unit (A mass) 3,5-7. LES traits are widely used in comparative ecology to infer whole-plant ecological strategies 4,8-12. However, the extent to which leaf-level resource economics reflects whole-plant physiology, performance, and ultimately fitness, is still under debate 13. Many processes can lead to a mismatch between LES and whole-plant functioning 14 , including the impact of self-shading among leaves and resource allocation patterns, such as carbon investment in non-photosynthetic tissues 15,16. To gain insights into the robustness of the slow-fast continuum at different organizational levels, we need

Worldwide, changing nutrient concentrations pose main stressors in many ecosystems, which is likely to continue in the future. Consumer communities are often not directly affected but changes in resource quantity and quality have led to shifts in taxonomic as well as functional composition. For example, under phosphorous-rich conditions, some studies showed that small and fast-growing taxa were favored and also some shifts towards P-rich taxa were reported. Ecological stoichiometry theory (=EST) offers a framework to investigate the equilibrium and fluxes of elements (i.e. nutrients) between organisms one another and the environment. Stoichiometric traits, that is the elemental composition of an organism’s body tissue, has been successfully linked to resource quality or functional traits, especially growth rate and feeding groups. However, so far, most studies did not go beyond taxon or population level and explicit links towards nutrient availabilities are rare. It was thus the aim of my PhD to investigate whether – and to what extent – the integration of stoichiometric traits into community analyses can improve our understanding of a community response towards global stressors, i.e. changes in nutrient concentration and their ratios Using stream macroinvertebrates as model organisms, I tested assumptions from EST on community level relying to three databases comprising (i) stoichiometric traits (which I constructed based on field samplings campaigns and a literature research), (ii) functional traits and (iii) community datasets (abundances & environmental parameters). I found significant links between stoichiometric traits and (other) functional traits, as well as between water nutrient concentration and community stoichiometry. These results could complementarily be explained by EST and phylogeny. Phylogeny was found to largely control a taxon’s body stoichiometry leading to partly distinct responses among major taxonomic groups. Also confounding factors affecting community stoichiometry via shifts among those groups seemed to have weaken the global trends over a spatial nutrient gradient. On a temporal scale however the community stoichiometry and functional response followed our expectations based on EST: Under decreasing phosphorous concentrations, the community shifted towards P-poor taxa which decreased community %P. Further, high phosphorous conditions favoured traits related to fast development (e.g. small body sizes, short life duration) and detritus feeding; whereas low phosphorus conditions favoured slow-developing and predatory taxa. Stoichiometric traits were largely involved in this link, underlining their potential to explain ecological responses towards nutrient changes. It remains to be investigated how such a changed consumer nutrient pool affect nutrient cycling towards higher/lower trophic levels or adjacent terrestrial ecosystems. It might also be interesting to study its application towards – and interaction with – other global stressors, notably global warming, which already was shown to affect stoichiometry and/or traits related to body stoichiometry (i.e. growth, development). The extension of the stoichiometric trait data base could further help broadening the application of this approach and testing our findings also for other systems/regions., Dans de nombreux écosystèmes à travers le monde, les changements de concentrations et d’abondance relative des nutriments constituent un facteur de stress majeur. Les communautés de consommateurs ne sont souvent pas directement affectées par ces changements, mais plutôt indirectement par les modifications induites dans la quantité et la qualité des ressources de base. Par exemple, dans des conditions de forte disponibilité en phosphore, les taxons de petite taille et à croissance rapide sont favorisés tous comme ceux étant naturellement riches en phosphore. La théorie de la Stœchiométrie Ecologique (EST, Ecological Stoichiometry Theory) offre un cadre conceptuel pour étudier l'équilibre et les flux d'éléments (c.a.d. de nutriments) entre les organismes et l'environnement. Les traits stœchiométriques, ici considérés sous l’angle de la composition élémentaire des tissus corporels d'un organisme, ont pu être liés avec succès à la qualité des ressources ou à des traits fonctionnels des taxons, notamment le taux de croissance et le groupe trophique des organismes. Néanmoins, jusqu'à présent, la plupart des études n'ont pas dépassé le niveau du taxon ou de la population et les liens explicites entre la structure des communautés de consommateurs et la disponibilité en nutriments restent rares. L'objectif de mon doctorat était d'étudier si - et dans quelle mesure - l'intégration de traits stœchiométriques dans les analyses de communautés pouvait améliorer notre compréhension de leur réponse aux changements de concentrations en nutriments. En prenant pour communautés modèles les macroinvertébrés des cours d'eau, j'ai testé les hypothèses de l'EST en m'appuyant sur trois bases de données comprenant (i) des traits stœchiométriques (base de données construite dans le cadre de cette thèse), (ii) des traits fonctionnels et (iii) la structure des communautés de macroinvertébrés en France (abondances et paramètres environnementaux). J'ai ainsi pu mettre en évidence des liens entre les traits stœchiométriques et les autres traits fonctionnels des taxons, ainsi qu'entre la concentration des nutriments de l'eau et la stœchiométrie des communautés. Ces résultats pourraient être expliqués de manière complémentaire par l’EST et la phylogénie. La phylogénie contrôle largement la stœchiométrie des taxons, entraînant des réponses distinctes parmi les principaux groupes taxonomiques. De même, les variations d’abondance relative des différents taxons selon la disponibilité des nutriments tendent à réduire l’importance des traits stœchiométriques comme facteur explicatif. Cependant, en considérant un seul cours d’eau subissant une réduction progressive des concentrations en phosphore, la stœchiométrie de la communauté et sa réponse fonctionnelle ont suivi nos attentes basées sur l'EST : Une réduction du phosphore sélectionne des taxons pauvres en P et réduit le %P de la communauté. En outre, des conditions de phosphore élevées ont favorisé les traits liés au développement rapide (par ex. petites tailles de corps, courte durée de vie) et à la détritivorie, tandis que des conditions de phosphore faibles ont favorisé les taxons à développement lent et à dominance prédateurs. Les traits stœchiométriques étaient largement impliqués dans ce lien, soulignant leur potentiel pour expliquer les réponses écologiques aux changements de concentrations en nutriments. Il reste maintenant à étudier comment les changements de stocks de nutriments constitués par les consommateurs affecte in fine le cycle des nutriments, et le transfert de ces nutriments vers les niveaux trophiques supérieurs et les écosystèmes adjacents. Il pourrait également être intéressant d'étudier l’applicabilité de ces approches à d'autres facteurs de stress globaux, notamment le réchauffement climatique. L'extension de la base de données de traits stœchiométriques pourrait ainsi contribuer à élargir l'application de cette approche et à tester nos résultats sur d'autres types d’écosystèmes.

Trees interact with diverse microbial communities that influence their fitness and the functioning of terrestrial ecosystems. Unlike microorganisms associated with roots and soil, microorganisms that colonize the forest canopy are still poorly understood. The objective of this thesis is to better understand the functions of microorganisms associated with the aerial parts of trees (leaves, stems, seeds) as well as their vertical (from the plant to its offspring) and horizontal (emission from the plant to the atmosphere) transmission dynamics, by combining molecular ecology and plant ecophysiology analyses. The first chapter [P1] shows a vertical stratification of fungal and foliar bacterial communities within the beech canopy (Fagus sylvatica). This stratification is more pronounced for epiphytic microorganisms than for endophytes. It also decreases during the growing season in bacteria and appears to be related to morphology rather than foliar physiology. Vertical stratification of microbial functions is being analyzed. The second chapter [P2] highlights the presence of fungi in the internal tissues of the acorns of sessile oak (Quercus petraea), including the embryo, suggesting that the microbiota can be transmitted vertically from the mother tree to its offsprings and influence forest regeneration. Acorns contain in particular several fungal pathogens, in association with their mycoparasites. These fungal communities vary significantly depending on the mother tree and the oak population. Finally, the third chapter [P3] tests a prototype for measuring bacterial emission fluxes over plant cover. It shows that half of the species captured in the atmosphere are present on the leaf surface and suggests that the composition of bioaerosols is strongly influenced by the locally dominant cultivated plant, the grapevine (Vitis vinifera). Complementary measures, including a wider range of forest and non-forestry habitats, will have to be carried out to better understand the origin of emissions, which are known to influence the water cycle. This thesis therefore provides elements for modelling the dynamics and evolution of the tree-microbiota-atmosphere system, which will need to be strengthened and integrated into knowledge of the soil system in order to respond to the challenges raised by climate change; Les arbres interagissent avec des communautés microbiennes diversifiées qui influencent leur fitness et le fonctionnement des écosystèmes terrestres. Contrairement aux micro-organismes associés aux racines et au sol, les micro-organismes qui colonisent la canopée forestière sont encore mal connus. L’objectif de cette thèse est de mieux comprendre les fonctions des micro-organismes associés aux parties aériennes des arbres (feuilles, tiges, graines) ainsi que leur dynamique de transmission verticale (de l’arbre à ses descendants) et horizontale (émission de l’arbre vers l’atmosphère), en combinant des analyses d’écologie moléculaire et d’écophysiologie végétale. Le premier chapitre [P1] montre une stratification verticale des communautés fongiques et bactériennes foliaires au sein de la canopée du hêtre (Fagus sylvatica). Cette stratification est plus marquée chez les micro-organismes épiphytes que chez les endophytes, elle s’atténue au cours de la saison végétative chez les bactéries et semble être liée à la morphologie plutôt qu’à la physiologie foliaire. La stratification verticale des fonctions microbiennes est en cours d’analyse. Le deuxième chapitre [P2] met en évidence la présence de champignons dans les tissus internes des glands du chêne sessile (Quercus petraea), y compris l’embryon, suggérant que le microbiote peut être transmis verticalement de l’arbre mère à ses descendants et influencer la régénération forestière. Les glands contiennent en particulier plusieurs espèces de champignons pathogènes, en association avec leurs mycoparasites. Ces communautés fongiques varient significativement en fonction de l’arbre mère et de la population de chêne. Enfin, le troisième chapitre [P3] teste un prototype de mesure des flux d’émissions bactériennes au-dessus des couverts végétaux. Il montre que la moitié des espèces capturées dans l’atmosphère est présente sur la surface des feuilles et suggère que la composition des bioaérosols est fortement influencée par la plante cultivée dominante localement, la vigne (Vitis Vinifera). Des mesures complémentaires, incluant une plus large gamme d’habitats forestiers et non-forestiers, devront être réalisées pour mieux cerner l’origine des émissions, qui sont connues pour influencer le cycle de l’eau. Cette thèse apporte donc des éléments pour modéliser la dynamique et l’évolution du système arbre-microbiote-atmosphère, qu’il conviendra de renforcer et d’intégrer aux connaissances sur le système sol afin de répondre aux défis posés par le changement climatique

The ensemble of biological, geochemical, and physical processes that occur within ecosystems is driven by the interplay between biological communities and the abiotic environment. Explaining the spatial and temporal dynamics of biological communities in relation to environmental conditions is therefore essential for understanding ecosystem functioning, and ultimately for achieving sustainable development. In marine ecosystems, fish communities are key to ecosystem functioning, and fisheries provide livelihoods for over 10% of the world’s population. However, understanding the processes structuring fish communities remains difficult because community structure varies with both natural environmental fluctuations and, increasingly, human pressures. Effectively managing fisheries and marine ecosystems under global change therefore requires better characterizing fish community dynamics over time and space and disentangling the underlying drivers and mechanisms. While fish ecologists have traditionally relied on species-based approaches (i.e., taxonomic approaches) to study community structure, trait-based approaches (i.e., functional approaches) are increasingly used because they can provide better insight into community assembly and the mechanisms driving community responses. To meet this need for a better understanding of biodiversity dynamics, the present thesis took advantage of long-term scientific monitoring data to characterize the functional responses of fish communities to environmental gradients in the North Sea, Eastern English Channel, and Bay of Somme. All three ecosystems experienced temperature rises and oceanographic changes associated with a warming phase of the Atlantic Multidecadal Oscillation (AMO), which rapidly impacted fish community structure. Consistent biological responses were observed across the three ecosystems despite their different spatial scales, demonstrating that fish communities were affected by environmental change through bio-ecological traits associated with habitat preference and life history. In the North Sea and Eastern Channel, pelagic species were the most responsive and contributed largely to community dynamics, which is likely explained by their greater mobility, higher dispersal rates, and fewer habitat requirements. However, beyond habitat preference, species with r-selected life histories (e.g., low size and age at maturity, low parental investment, small offspring) had the fastest environmental responses whether or not they were pelagic, likely due to their rapid population turnover and generation time. Importantly, the way these species’ responses shaped community structure depended on environmental context. R-selected, pelagic species rapidly declined in the Bay of Somme and Eastern Channel, but rapidly increased in the North Sea. This likely reflects environmental suitability, indicating that after the phase change of the AMO, the Eastern Channel became a less favorable environment for these species, while the North Sea became more favorable. Thus, species with high mobility and fast life history cycles appear capable of rapidly tracking environmental conditions, shifting in abundance in response to environmental suitability. Additionally, as these ecosystems have warmed over the last 30 years, community responses were characterized by increases in mean thermal preference. Importantly, the amplitude of community changes was partially determined by communities’ initial structure and redundancy of bio-ecological traits, showing that community responses depended not only on environmental changes but also on biodiversity itself. Lastly, while fish community responses were consistently associated with climatic changes, historical fishing pressure on large-bodied, demersal species appeared to render fish communities more sensitive to environmental changes by increasing the relative of abundance of pelagic and r-selected species., Il est essentiel de décrire la dynamique spatiale et temporelle des communautés de poissons pour comprendre le fonctionnement et les services des écosystèmes marins. Cette thèse a utilisé des données de surveillance scientifique à long terme pour caractériser les réponses fonctionnelles des communautés de poissons aux gradients environnementaux en baie de Somme, Manche orientale et mer du Nord. Les trois écosystèmes ont connu des hausses de température associées à une phase de réchauffement de l'oscillation multidécennale de l'Atlantique, ce qui a eu des impacts rapides sur la structure des communautés. Dans les trois écosystèmes, les réponses des communautés ont été médiées par des traits associés à l’habitat et à l’histoire de vie. Dans la mer du Nord et la Manche Est, les espèces pélagiques étaient les plus sensibles, ce qui s'explique probablement par leur mobilité et leur dispersion plus élevés. Cependant, au-delà de l'habitat, les espèces à stratégie démographique r (faible taille et âge à maturité, faible investissement parental, etc.) ont eu des réponses environnementales plus rapides. La pression historique de la pêche semble d’avoir rendu les communautés plus sensibles aux changements environnementaux en augmentant l'abondance relative des espèces pélagiques et à stratégie r. De plus, comme ces écosystèmes se sont réchauffés au cours des 30 dernières années, les réponses des communautés ont été caractérisées par une augmentation de la préférence thermique moyenne, ce qui suggère que le réchauffement climatique favorisera des espèces mieux adaptées aux conditions chaudes et que les espèces ayant des cycles de vie rapides seront les premières à répondre.

Plant adaptation to drought has been extensively studied at many scales from ecology to molecular biology across a large range of model species. However, the conceptual frameworks underpinning the definition of plant strategies, and the terminology used across the different disciplines and scales are not analogous. 'Drought resistance' for instance refers to plant responses as different as the maintenance of growth and productivity in crops, to the survival and recovery in perennial woody or grassland species. Therefore, this paper aims to propose a unified conceptual framework of plant adaptive strategies to drought based on a revised terminology in order to enhance comparative studies. Ecological strategies encapsulate plant adaptation to multidimensional variation in resource variability but cannot account for the dynamic and short-term responses to fluctuations in water availability. Conversely, several plant physiological strategies have been identified along the mono-dimensional gradient of water availability in a given environment. According to a revised terminology, dehydration escape, dehydration avoidance, dehydration tolerance, dormancy, and desiccation tolerance are clearly distinguishable. Their sequential expression is expressed as water deficit increases while cavitation tolerance is proposed here to be a major hydraulic strategy underpinning adaptive responses to drought of vascular plants. This continuum of physiological strategies can be interpreted in the context of the ecological trade-off between water-acquisition vs. water-conservation, since growth maintenance is associated with fast water use under moderate drought while plant survival after growth cessation is associated with slow water use under severe drought. Consequently, the distinction between 'drought resistance' and 'drought survival', is emphasized as crucial to ensure a correct interpretation of plant strategies since 'knowing when not to grow' does not confer 'drought resistance' but may well enhance 'drought survival'. This framework proposal should improve cross-fertilization between disciplines to help tackle the increasing worldwide challenges that drought poses to plant adaptation.

In this study, the SMPs from four commercially important and divergent bivalve species crassostrea gigas (pacific oyster), Mya truncata (soft shell clam), Mytilus edulis (blue mussel) and Pecten maximus (king scallop) were extracted and analysed using standardized extraction protocol and proteomic pipeline. This enables us to identify critical elements of basic biomineralization tool kit for calcification process irrespective of their shell morphology, mineralogy and microstructure. In addition, it enables the identification of SMPs that are specific to calcite and aragonite mineralogies. The signifiant numbers of SMPs found species-specific were hypothesized as adaptation to their modus vivendi. In fact, the latter proteins possess immunity-related functions and fit into specific pathway, phenoloxidase, suggesting their role in defense against pathogen. The comparative study of shell proteome of mussels living in full marine condition, North Sea and the Iow saline Baltic Sea showed the modulation of the SMPs that constitute the basic biomineralization tool kit. Higher modulation of chitin related proteins and non-modulated protein such as carbonic anhydrase, EGF and fibronectin domain containing proteins points out the impaired scaffold and mineral nucleation process in Baltic mussel. The modulation of immunity related proteins denote the influence of biotic components. These investigations show the functional diversity of SMPs and their roles beyond shell formation in the bivalvesand put forth the idea that shell is dynamic, endowed with both biochemical and mechanical protection.; Le processus de biominéralisation confère aux organismes qui le développent une valeur adaptative. La coquille carbonatée des mollusques intègre les fonctions de protection biomécanique à différentes échelles. La coquille résulte de l'association de composés inorganiques et d'une matrice organique protéique, médiatrice du contrôle biologique de la minéralisation. L'analyse du protéome de la coquille chez 4 espèces de bivalves met en évidence deux patrons fonctionnels et leur degré de conservation phylogénétique : l'un lié au contrôle de la minéralisation stricto sensu ; l'autre à la protection immune. L'étude de populations vivant à l'état naturel en mer Baltique, dont les eaux présentent localement de fortes variations ioniques montre que le protéome intègre également l'impact de conditions environnementales limitantes. L'anthropocène impose un rythme adaptatif pressant aux organismes et la modification acido-basique des eaux océaniques est susceptible d'impacter sensiblement les organismes calcifiants. La signature de mécanismes adaptatifs du contrôle biologique de la biominéralisation se traduit dans le protéome de la coquille. Les implications sont particulièrement signifiantes dans un contexte d'intérêt de développement aquacole grandissant.

Interoperability and discovery of AnaEE distributed resources through semantic annotations. Ontology & Semantic Web for Research. LifeWatch-ITA & EUDAT Workshop

Ecological studies are increasingly moving towards trait-based approaches, as the evidence mounts that functions, as opposed to taxonomy, drive ecosystem service delivery. Among ecosystem services, biological control has been somewhat overlooked in functional ecological studies. This is surprising given that, over recent decades, much of biological control research has been focused on identifying the multiple characteristics (traits) of species that influence trophic interactions. These traits are especially well developed for interactions between arthropods and flowers - important for biological control, as floral resources can provide natural enemies with nutritional supplements, which can dramatically increase biological control efficiency. Traits that underpin the biological control potential of a community and that drive the response of arthropods to environmental filters, from local to landscape-level conditions, are also emerging from recent empirical studies. We present an overview of the traits that have been identified to (i) drive trophic interactions, especially between plants and biological control agents through determining access to floral resources and enhancing longevity and fecundity of natural enemies, (ii) affect the biological control services provided by arthropods, and (iii) limit the response of arthropods to environmental filters, ranging from local management practices to landscape-level simplification. We use this review as a platform to outline opportunities and guidelines for future trait-based studies focused on the enhancement of biological control services.

One of the remarkable characteristics of the New Caledonian flora is the presence of numerousangiosperm lineages recognized as the earliest divergences of the flowering plants, due to their phylogeneticpositions. Within these lineages, some species are likely to bear ancestral morpho-anatomical features.Therefore, under a comparative perspective, the study of these species can provide compelling information forunderstanding the early evolutionary stages of angiosperms. The first part of this thesis aims to study thestructural and functional characteristics of representative groups of basal angiosperms. The study of Amborellatrichopoda, sister species to the remaining flowering plants, shows a covariation of functional traits (stem-leaf)and a morphological plasticity in response to changes in the light environment. This suggests that these plasticresponses were already present in the common ancestor of angiosperms. In parallel, the study of the anatomicalevolution of Piperales, the most diversified basal angiosperm order, suggests that their common ancestor had anactive cambium. These results support the hypothesis that early angiosperms had a woody habit and thatsympodial growth may have been acquired early during angiosperms evolution.Basal angiosperms are among the over-represented angiosperm lineages of New Caledonia. However,the mechanisms underlying this disharmony remain unexplored. A second component of this thesis analyzes theenvironmental distribution of New Caledonian basal angiosperms to know their habitat preferences and theirenvironmental requirements. Further, we assess the influence of their drought tolerance on their environmentaldistribution. We show that most species have a preference for rain forest habitats with small variations intemperature. Drought-induced hydraulic vulnerability stands as a major trait that restricts the distribution of thesespecies to humid habitats. These stable conditions seem to have persisted in refugial areas in the archipelagoduring the last glacial maximum, allowing the persistence of basal angiosperm species. Therefore, a past climaticstability could explain the over-representation of some groups of forest species that may have disappeared inneighboring regions. The distribution of basal angiosperms in New Caledonia, as well as their droughtsensitivity, support the hypothesis suggesting that early angiosperms lived in humid and stable environments.; L’une des remarquables originalités de la flore néo-calédonienne repose sur la présence de nombreuseslignées correspondant aux premières divergences des plantes à fleurs, compte tenu de leurs positionsphylogénétiques. Au sein de ces lignées, certaines espèces sont susceptibles de porter des traits morphoanatomiquesancestraux. Par conséquent, dans un contexte comparatif, l'étude de ces espèces peut fournir desinformations cruciales pour comprendre les premières étapes évolutives des angiospermes. Un premier volet decette thèse vise à étudier des caractéristiques structurelles et fonctionnelles des groupes représentatifsd’angiospermes basales. L'étude d'Amborella trichopoda, espèce sœur de toutes les angiospermes, nous a montréune covariation des traits fonctionnels (tige-feuille) et une plasticité morphologique en réponse à des variationsde l'environnement lumineux. Cela suggère que ces réponses plastiques étaient déjà présentes chez l'ancêtrecommun de toutes les plantes à fleurs. En parallèle, l’étude de l'évolution anatomique des Piperales, ordre le plusriche parmi les angiospermes basales, suggère que leur ancêtre commun aurait possédé un cambium actif. Cesrésultats supportent que les premières angiospermes avaient une forme de vie ligneuse et une probable structuresympodiale.Les angiospermes basales comptent parmi les lignées d'angiospermes surreprésentées en Nouvelle-Calédonie. Cependant, les mécanismes à l’origine de cette dysharmonie demeurent inexplorés. Un deuxièmevolet de cette thèse analyse la répartition environnementale des angiospermes basales de l'archipel afin deconnaitre leurs préférences en termes d’habitats, ainsi que leurs exigences environnementales. Cette distributionenvironnementale a également été analysée au regard de leur résistance à la sécheresse. Nous montrons que laplupart des espèces présentent une préférence marquée pour des habitats de forêt humide avec des faiblesvariations en température. La vulnérabilité hydraulique face à la sécheresse apparaît comme un trait majeur quiconfine la distribution de ces espèces dans des habitats humides. Ces conditions auraient persisté dans des zonesrefuges dans l'archipel lors de la dernière période glaciaire, permettant ainsi le maintien de certaines lignéesd’angiospermes basales. Une stabilité climatique passée pourrait donc être à l'origine de la surreprésentation decertains groupes d'espèces forestières qui ont disparu dans les régions voisines. La distribution des angiospermesbasales néo-calédoniennes, ainsi que leur sensibilité à la sécheresse, supportent l'hypothèse suggérant que lespremières angiospermes habitaient des milieux humides et stables.

International audience; AbstractGrassland covers about one quarter of the Earth’s land area and is currently estimated to contribute to the livelihoods of over 800 million people. Grassland provides ecosystem goods and services, mainly through the provisioning of milk and meat. Therefore, the proper use of grasslands will be essential for feeding the nine billion people that will inhabit planet Earth by 2050. In the context of a changing climate, we should better understand the interactions of environment, management and grass crop at individual, community and ecosystem levels. Functional ecology focuses on the roles and functions that species play in the community or ecosystem in which they occur. Functional ecology thus aims to understand how plant species adapt to environmental conditions and how management can alter this adaptation. Here, we review the latest advances in plant functional traits research and on species strategies to the main environmental factors occurring in grassland ecosystems: nutrient availability, grazing, cutting and shading. Functional ecology also provides a framework to better understand how species strategies interact with the species composition at the community level. Therefore, the literature on community assembling theories in relation to ecosystem processes most relevant to grassland management and services is also reviewed. Finally, future research questions and some new orientations for grassland experts are offered in order to meet the challenge of maintaining productivity and preservation of these semi-natural environments in the face of global change.

Questions: One central assumption of trait screening approaches in comparative plant ecology, i.e. simultaneous measurement of traits on a large number of species or populations, is that the species level captures a major part of trait variation. The current development of large databases has led to a new screening approach that relies on the extraction of trait values from databases, rather than on measurement of traits in the field. We tested this assumption with the following questions: (1) is the magnitude of intra-specific variability of co-occurring species lower than inter-specific variability for a given trait, in comparisons at different spatial scales; (2) is species hierarchy based on trait values conserved across different spatial scales and data sets (stable species hierarchy hypothesis); and (3) when we compare different traits, what is the more stable trait that is conserved across different spatial scales and data sets? Methods: We combined approaches commonly used in functional ecology, i.e. experimental data, field observations and extraction of data from a global database, and analysed the magnitude of intra-specific and inter-specific trait variations for a large number of traits across contrasting environmental conditions for 18-39 (mostly) herbaceous species, according to the data set used. Results: For most traits, inter-specific variability was higher than intra-specific variability, and species ranking was conserved across different data sets and spatial scales. However, we also detected important differential responses in terms of intra-specific trait variability, depending on the trait examined: SLA, LDMC, SM, seed N concentration and onset of flowering were more stable, whereas leaf chemical traits and RH were more flexible traits. Conclusions: Our study validated, for the species studied, the stable species hierarchy hypothesis in the case of several, but not all, widely used traits. The main conclusion is that the strength of the species signal is strong enough for some traits to allow values to be used from different data sets (experiments, databases) to characterize local populations of species: for SM, seed N concentration, RH, SLA and LDMC.

Understanding the relationships between ecohydrology and functional structure of plant communities is a timely issue in plant ecology. From ecosystem to species levels, this works investigated the effects of a resource availability gradient on the structure and functioning of Mediterranean rangelands in Southern France. Using a water-balance modeling approach, differences in water-use at the ecosystem level were quantified across five contrasting years, accounting for the variability in both soil characteristics and vegetation functioning. Plant water-use and productivity scaled with soil water storage capacity and its filling rate, suggesting a functional equilibrium between plant communities and local water availability. Using a trait-based approach, we then showed that the ratio of total leaf area of the community on total root area determined an allometric relationship between potential evapotranspiration and water uptake capacity. The “coordination” between above- and belowground compartment of the vegetation was achieved by a suite of architectural and morphological adaptations. Modifications of species relative abundances and species turn-over explained morphological and functioning adaptations to cope with limiting resources. Finally at species level, a removal experiment allowed to quantify the relative importance of water limitations and effects of plant-plant interaction on individual plant productivity of three target species of graminoïds. The importance of competition increased with soil resource availability and depended more on trait-trait hierarchical distances among species than standing biomass. Competition among plants affects the axes of the functional niche of species independently, leading to the convergence of leaf dry matter content towards low values but to greater functional divergence for plant height. Overall, this functional approach provided an integrative understanding of the role of plant diversity in the response of ecological systems to changes in water availability. Furthermore, these results on ecohydrological properties of natural communities can contribute to the design of complex agro-ecosystem better adapted to intense droughts predicted under climate change.; Comprendre les relations entre écohydrologie et structure fonctionnelle des communautés végétales est une problématique croissante en écologie. Cette thèse a pour objectif d'analyser les effets d'un gradient de ressource édaphique sur la structure et le fonctionnement de parcours herbacés dans le sud de la France, en intégrant les niveaux de l'écosystème à la plante. Par modélisation du bilan hydrique, les différences d'utilisation de l'eau au niveau de l'écosystème ont été quantifiées pour cinq années contrastées révélatrices de la variabilité des propriétés des sols et du fonctionnement végétal. Utilisation de l'eau et productivité des plantes sont proportionnelles à la réserve utile des sols et à son taux de remplissage, suggérant un équilibre fonctionnel entre les communautés végétales et la disponibilité de l'eau locale. Par une approche ‘traits', nous avons ensuite montré que le ratio entre surface foliaire et surface racinaire totales de la communauté est le facteur déterminant une relation 'allométrique' entre évapotranspiration potentielle et capacité de prélèvements hydriques. La coordination entre les compartiments racinaire et aérien de la végétation dépend d'une suite d'adaptations architecturales et morphologiques. Des modifications d'abondances relatives spécifiques et le turn-over d'espèces génèrent une variabilité de morphologie et de fonctionnement des communautés permettant leur adaptation à des ressources limitées. Au niveau plante, une expérimentation de transplantation a permis de quantifier l'importance relative de la disponibilité hydrique et des interactions entre plantes sur la productivité individuelle de trois espèces-cibles. L'importance de la compétition s'est révélée plus élevée sous fort niveau de ressource et dépendait plus des relations hiérarchiques entre traits que de la biomasse. La compétition entre plantes affecte les axes de niche fonctionnelle des espèces de façon indépendante, avec une convergence de la ‘teneur en matière sèche des feuilles' pour des faibles valeurs mais une plus forte divergence fonctionnelle pour la ‘hauteur des plantes'. Cette approche fonctionnelle a permis d'éclairer le rôle de la diversité végétale dans la réponse des systèmes écologiques à des ressources hydriques variables. De plus, ces résultats sur les propriétés écohydrologiques des communautés naturelles peuvent contribuer à la conception d'agro-écosytèmes complexes mieux adaptés aux sécheresses intenses prévues dans le contexte actuel de changement climatique.

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVIN; International audience; The rhizosphere is a key zone for pollutant removal in treatment wetlands; therefore, studies on microbial activity may provide helpful information for a better understanding of purification processes. We studied microbial activity in a vertical-downflow constructed wetland system treating waste activated sludge with high organic matter concentrations, under Mediterranean climate. The aims of the work were to study the influence of (i) the presence of plants, (ii) the plant species (Phragmites australis Cav., Typha latifolia L., Iris pseudacorus L.), and (iii) the plant growth stage (plant senescence and plant fast growing stage) on total respiration rate and phosphatase activity in the substrate (intented here as the solid support on which the plants grow). The presence of plants had a positive influence on microbial activity, since substrate respiration and both acid and alkaline phosphatase activity were always higher in planted than in unplanted mesocosms. Among the three tested species, Phragmites was the one that most stimulated both substrate respiration rate and phosphatase activity, followed by Typha and Iris. These differences of microbial activity between mesocosms were corresponding to differences of removal efficiency. Substrate respiration and phosphatase activity were of similar magnitude at the two growth stages, while the stimulating effect of plants seemed to have been delayed and microbial activity showed higher fluctuations at plant fast growing stage than at plant senescence.

Establishing the link between microbial diversity and ecosystem functioning constitutes one of the fundamental questions in microbial ecology. However, microbial biodiversity cannot be resolved in a single manner and the question arises about which of the genetic and/or taxonomic and/or functional components of biodiversity are the most relevant in such a problematic. To date, most researches in this field has focused on genetic diversity and few investigations have examined functional diversity, resulting in a poor understanding of the manner in which genetic and taxonomic diversity affect functional diversity or ecosystem properties. This can be explained by paucity of methods allowing an in situ and without a priori functional analysis of indigenous microbial communities. This statement recently stimulated the development of new approaches allowing the characterization of microbial metaproteome (i.e. all the proteins synthesized at the scale of the community at a given moment) extracted from environmental samples. Since proteins, and more precisely enzymes, are involved in biotransformation processes, metaproteome analysis constitutes a suitable way to characterize the dynamics of microbial functions in a holistic way. Our presentation deals with interest and expected outcomes of the development of the metaproteomic approach for the functional analysis of microbial communities in their habitat. Different applications will be presented, highlighting the specificity and the sensitivity of the approach to characterize modifications of the functional structure and of the physiology of indigenous bacterial communities in response to metallic pollutions or organic matter inputs. Results presented show that, depending on soil characteristics, bacterial communities with similar genetic structures can harbour different functional structures and thus be potentially of different ecological significance for soil functioning. However, since they do not necessarily evolve in the same way, the simultaneous characterisation of genetic and the functional structures appears warranted to highlight fine and qualitative modifications in bacterial communities induced by variations in surrounding environmental conditions.

International audience; The aim of this paper is to illustrate how some extreme events could affect forest ecosystems. Forest tree response can be analysed using dendroecological methods, as tree-ring widths are strongly controlled by climatic or biotic events. Years with such events induce similar tree responses and are called pointer years. They can result from extreme climatic events like frost, a heat wave, spring water logging, drought or insect damage... Forest tree species showed contrasting responses to climatic hazards, depending on their sensitivity to water shortage or temperature hardening, as illustrated from our dendrochronological database. For foresters, a drought or a pest disease is an extreme event if visible and durable symptoms are induced (leaf discolouration, leaf loss, perennial organs mortality, tree dieback and mortality). These symptoms here are shown, lagging one or several years behind a climatic or biotic event, from forest decline cases in progress since the 2003 drought or attributed to previous severe droughts or defoliations in France. Tree growth or vitality recovery is illustrated, and the functional interpretation of the long lasting memory of trees is discussed. A coupled approach linking dendrochronology and ecophysiology helps in discussing vulnerability of forest stands, and suggests management advices in order to mitigate extreme drought and cope with selective mortality.; Cet article illustre comment des événements extrêmes peuvent affecter les écosystèmes forestiers. La réponse des arbres peut être étudiée par des méthodes dendroécologiques, les largeurs de cernes étant étroitement contrôlées par les contraintes climatiques ou biotiques. Ces contraintes induisent des réponses similaires des arbres, lors d’années dites « années caractéristiques ». Elles traduisent les réponses de la croissance à un événement climatique ou biotique extrême : gel intense,canicule, excès d’eau printanier, sécheresse, ravageur. . . comme l’illustre notre base de données dendrochronologiques. Pour le forestier, une sécheresse ou un aléa biotique sont considérés comme extrêmes s’ils induisent des dysfonctionnements visibles et durables (coloration anormale du feuillage, perte foliaire, mortalité de branches, dépérissement, mortalités anormales). De tels impacts, souvent différés de quelques années après l’aléa, sont illustrés à partir d’études de dépérissements forestiers avérés depuis 2003, ou attribués à des sécheresses ou des défoliations plus anciennes en France. La récupération de la croissance ou la vitalité des arbres est illustrée et des éléments fonctionnels d’interprétation des effets différés sont discutés. Enfin, en couplant dendroécologie et écophysiologie, nous abordons la vulnérabilité des peuplements forestiers et suggérons des recommandations de gestion forestière permettant d’atténuer l’intensité des sécheresses extrêmes et d’anticiper les mortalités sélectives des espèces ou des individus les moins résistants.

Trees interact with diverse microbial communities that influence their fitness and the functioning of terrestrial ecosystems. Unlike microorganisms associated with roots and soil, microorganisms that colonize the forest canopy are still poorly understood. The objective of this thesis is to better understand the functions of microorganisms associated with the aerial parts of trees (leaves, stems, seeds) as well as their vertical (from the plant to its offspring) and horizontal (emission from the plant to the atmosphere) transmission dynamics, by combining molecular ecology and plant ecophysiology analyses. The first chapter [P1] shows a vertical stratification of fungal and foliar bacterial communities within the beech canopy (Fagus sylvatica). This stratification is more pronounced for epiphytic microorganisms than for endophytes. It also decreases during the growing season in bacteria and appears to be related to morphology rather than foliar physiology. Vertical stratification of microbial functions is being analyzed. The second chapter [P2] highlights the presence of fungi in the internal tissues of the acorns of sessile oak (Quercus petraea), including the embryo, suggesting that the microbiota can be transmitted vertically from the mother tree to its offsprings and influence forest regeneration. Acorns contain in particular several fungal pathogens, in association with their mycoparasites. These fungal communities vary significantly depending on the mother tree and the oak population. Finally, the third chapter [P3] tests a prototype for measuring bacterial emission fluxes over plant cover. It shows that half of the species captured in the atmosphere are present on the leaf surface and suggests that the composition of bioaerosols is strongly influenced by the locally dominant cultivated plant, the grapevine (Vitis vinifera). Complementary measures, including a wider range of forest and non-forestry habitats, will have to be carried out to better understand the origin of emissions, which are known to influence the water cycle. This thesis therefore provides elements for modelling the dynamics and evolution of the tree-microbiota-atmosphere system, which will need to be strengthened and integrated into knowledge of the soil system in order to respond to the challenges raised by climate change, Les arbres interagissent avec des communautés microbiennes diversifiées qui influencent leur fitness et le fonctionnement des écosystèmes terrestres. Contrairement aux micro-organismes associés aux racines et au sol, les micro-organismes qui colonisent la canopée forestière sont encore mal connus. L’objectif de cette thèse est de mieux comprendre les fonctions des micro-organismes associés aux parties aériennes des arbres (feuilles, tiges, graines) ainsi que leur dynamique de transmission verticale (de l’arbre à ses descendants) et horizontale (émission de l’arbre vers l’atmosphère), en combinant des analyses d’écologie moléculaire et d’écophysiologie végétale. Le premier chapitre [P1] montre une stratification verticale des communautés fongiques et bactériennes foliaires au sein de la canopée du hêtre (Fagus sylvatica). Cette stratification est plus marquée chez les micro-organismes épiphytes que chez les endophytes, elle s’atténue au cours de la saison végétative chez les bactéries et semble être liée à la morphologie plutôt qu’à la physiologie foliaire. La stratification verticale des fonctions microbiennes est en cours d’analyse. Le deuxième chapitre [P2] met en évidence la présence de champignons dans les tissus internes des glands du chêne sessile (Quercus petraea), y compris l’embryon, suggérant que le microbiote peut être transmis verticalement de l’arbre mère à ses descendants et influencer la régénération forestière. Les glands contiennent en particulier plusieurs espèces de champignons pathogènes, en association avec leurs mycoparasites. Ces communautés fongiques varient significativement en fonction de l’arbre mère et de la population de chêne. Enfin, le troisième chapitre [P3] teste un prototype de mesure des flux d’émissions bactériennes au-dessus des couverts végétaux. Il montre que la moitié des espèces capturées dans l’atmosphère est présente sur la surface des feuilles et suggère que la composition des bioaérosols est fortement influencée par la plante cultivée dominante localement, la vigne (Vitis Vinifera). Des mesures complémentaires, incluant une plus large gamme d’habitats forestiers et non-forestiers, devront être réalisées pour mieux cerner l’origine des émissions, qui sont connues pour influencer le cycle de l’eau. Cette thèse apporte donc des éléments pour modéliser la dynamique et l’évolution du système arbre-microbiote-atmosphère, qu’il conviendra de renforcer et d’intégrer aux connaissances sur le système sol afin de répondre aux défis posés par le changement climatique