Les picocyanobactéries marines Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants sur la planète et sont présentes dans presque tous les océans. Au cours de cette thèse, j'ai cherché à mieux comprendre les liens entre diversité génétique et adaptation à la niche écologique chez ces deux genres. Tout d'abord, l'étude de la répartition des populations de picocyanobactéries à l'échelle mondiale à l'aide d'un marqueur taxonomique très résolutif m'a permis de définir des unités taxonomiques écologiquement significatives, et d'identifier les principaux facteurs abiotiques influençant leur répartition. La deuxième partie de ce travail a visé à identifier les bases génétiques de l'adaptation des picocyanobactéries marines à des niches écologiques distinctes. L'étude comparative de 81 génomes non-redondants de ces organismes a révélé le rôle combiné des gains et pertes de gènes et des substitutions d'acides aminés dans la diversification des deux genres, et l'analyse de la répartition des gènes de picocyanobactéries marines dans l'océan mondial m'a permis de montrer que chaque communauté, adaptée à un environnement donné, possède un répertoire de gènes distinct. Enfin, le dernier volet de cette thèse a consisté en la caractérisation physiologique et transcriptomique de cinq souches de Synechococcus soumises à des stress lumineux et thermique afin d'analyser la variabilité écotypique de la réponse au stress. Les résultats obtenus au cours de cette thèse ont donc permis d'améliorer notre connaissance des niches écologiques occupées par les picocyanobactéries marines, et de mieux comprendre les mécanismes leur ayant permis de s'y adapter. / The marine picocyanobacteria Synechococcus and Prochlorococcus are the two most abundant photosynthetic organisms on earth and are present in almost all oceans. During this PhD thesis, I explored the links between genetic diversity and niche adaptation in these two genera. First, the analysis of the distribution of picocyanobacterial populations at the global scale using a high-resolution taxonomic marker allowed me to define ecologically significant taxonomic units, to improve the delineation of their ecological niches and to identify the main abiotic factors influencing their in situ distribution. The second part of this work aimed at identifying the genetic bases of adaptation of marine picocyanobacteria to distinct niches. The comparative analysis of 81 non-redundant genomes of these organisms revealed the combined role of gene gains and losses and of substitutions in protein sequences in the diversification of both genera, and the analysis of the distribution of all known picocyanobacterial genes in the global ocean allowed me to show that each community, adapted to specific environmental conditions, possesses a distinct gene repertoire. Finally, the last part of this work has consisted in the physiological and transcriptomic characterization of five Synechococcus strains, which were submitted to light and thermal stresses in order to better understand the ecotypic variability of the stress response in this genus. Altogether, results obtained during this PhD provided many new insights into the ecological niches occupied by marine picocyanobacteria and the mechanisms allowing them to adapt to these various niches.

Environmental filters play an important role in plant community assembly. Evaluating spatial variation in functional traits across environmental gradients may help determine the environmental filters that play a role in community assembly and how plant communities respond to prevailing environmental conditions. In this study, we evaluated spatial variation in leaf traits (size, thickness, specific area and dry matter content) of coastal sand dune plant communities across 16 sites along a precipitation gradient in the Yucatan Peninsula. We described community-wide trait variation in terms of dispersion and dominant values across the gradient in order to answer the following questions: Which environmental filters explain variation in leaf traits? What ecological strategies, in terms of leaf economics, do these environmental filters favour? Mean specific leaf area and dispersion in leaf thickness tended to be lower in drier sites, suggesting that plants invest more biomass per leaf (a conservative strategy) and become more succulent as aridity increases. Contrary to expectation, leaf size increased with proximity to the coastline and dry matter content was significantly greater in the wettest region. Therefore, variation in these leaf traits content cannot be explained by the precipitation gradient. We have shown that predictable variation in some functional leaf traits can be found, even at small scales within the same vegetation zone in coastal sand dunes. Our study supports the notion that variation in water availability can be an important driver of functional trait distribution in the plant communities of some arid environments.

The number of co-flowering species, floral density and floral trait diversity can be major determinants of pollinator-mediated plant–plant interactions in a community. However, evaluation of how each one of these co-flowering components affects the pollination success of a single focal plant species, and how these effects vary at different spatial scales, is lacking. Here, we evaluated the effects of functional diversity (flower morphology and colour), taxonomic diversity (reflecting potential sampling effects) and flower density (conspecific and heterospecific), on the pollinator environment (i.e. visitation rate and pollinator diversity) and pollination success (i.e. pollen load size and number of pollen tubes per style) of Cakile edentula (Brassicaceae). We applied structural equation models (SEMs) at the floral-neighbourhood (plot level) and community-wide scales to uncover the factors that mediate co-flowering community effects on C. edentula pollination success. We found that co-flowering community effects at the community level are more important than fine-scale floral-neighbourhood differences in mediating plant pollination success in our study species. Increasing plant functional diversity decreased pollinator visitation rate but increased the diversity of pollinator functional groups visiting C. edentula flowers. Taxonomic diversity negatively affected pollinator diversity suggesting that other unmeasured floral traits may be relevant or that single-species effects (sampling effects) may be important. Overall, our results suggest that functional floral trait diversity in a community may be the most important factor influencing pollination success of species in a community. We also found evidence for intra- and interspecific pollinator competition mediated by flower density, but none of these effects seemed to have a significant impact on pollination success. This study is an important step towards understanding the complexity of co-flowering community effects on the pollination success of individual plant species at multiple spatial scales. This study further reveals the potential importance of plant functional diversity in a community in helping predict competitive and facilitative interactions in co-flowering communities. Synthesis. Floral density and taxonomic and functional co-flowering diversity are important drivers of pollination success in flowering plants. The effects of the co-flowering diversity on the pollination success of plant species can largely depend on the spatial scale being studied. Only evaluating the outcomes of pollinator-mediated plant–plant interactions at multiple stages of the pollination process can lead to a complete understanding of their ecological consequences in nature.

One of the central questions of ecology aims to understand the mechanisms that maintain patterns of species coexistence. Community assembly, the process of structuring communities, occurs in ecological time, is influenced by biotic interactions at local scales, and is thought to help maintain diversity patterns. Species invasions, however, as a result of globalization and intense marine trade, are common in coastal ecosystems, and have the potential to change the outcome of biotic interactions and community structure. Human-induced disturbance also disrupts community structure and coastal habitats are at greater risk due to encroachment of human populations near coasts. Changes in community structure are usually quantified as the number and distribution of species, however, the processes that shape communities act on the traits that allow and optimize species survival. Recently, ecological questions aiming to understand changes in community structure, invasion dynamics, and responses to disturbance are using measures that reflect species’ ecological functions (i.e., traits) and describe the trait composition of communities (i.e., functional structure and diversity).The objectives of my dissertation are to use functional diversity and structure to 1) determine trait responses from predation across latitude while considering interaction histories between native and introduced species with local predators, 2) use functional diversity patterns and changes in functional structure to infer the relative influence of predation and competition on community assembly through time and across latitude, and 3) assess trait responses to physical disturbance, also, through time and across latitude while considering the trait diversity of the system. To achieve these objectives, I used field experiments to grow coastal sessile marine invertebrate communities in treatments that test the influence of biotic interactions or disturbance. Experiments ran for three or twelve months at 12 sites in four regions of the Pacific Coast: Alaska, California, Mexico, and Panama. For my first objective, I found predation driven trait responses mainly occurred at lower latitudes where biotic interactions are expected to be stronger. Additionally, the native and introduced species of focal communities showed opposite trait responses to predation at lower latitudes with traits related to palatability and parental investment being primarily influenced. For my second objective, I found strong competition influenced late-stage assembly across the latitudinal gradient, while predation had a greater influence during early assembly in the tropics. Thus, the relative strength of biotic interactions changes with time and latitude and either predation or competition may serve as primary filters of community assembly. For my third objective, I found fast colonization and regeneration abilities help communities recover from intense disturbance, but only at lower latitudes where communities were most impacted by disturbance. In plant communities, functional traits have been studied quite extensively for several years and have set the stage for exploration in other ecosystems. In marine systems, the link between traits and ecological processes that influence community structure are mostly understudied, and my dissertation is contributing to close this knowledge gap about nearshore communities from across 47 degrees of latitude. / Biology

Microbial community functional diversity enhances the degradation of organic matter and pollutants in the environment, but there is a growing concern that these ecosystem services may be altered by the introduction of emerging environmental contaminants including silver nanoparticles (AgNPs) into aquatic systems. We added 0, 25, 50, 75, 100, and 125 mg L−1 (nominal concentrations) of citrate-AgNP and polyvinylpyrrolidone-AgNP (PVP-AgNP) each to freshwater sediment and examined their antimicrobial effects on microbial communities using community-level physiological profiling. The results showed that citrate-AgNP decreased the overall microbial catabolic activity by 80% from 1.16 ± 0.02 to 0.23 ± 08 while PVP-AgNP decreased the catabolic activity by 51% from 1.25 ± 0.07 to 0.61 ± 0.19 at 125 mg L−1. Citrate-AgNP and PVP-AgNP caused a statistically significant reduction in substrate richness and substrate diversity that decreased microbial functional diversity. AgNPs decreased microbial catabolic capability and functional diversity at concentrations ranging from 0.12 ± 0.04 to 0.43 ± 0.07 mg Ag kg-1 which are lower than the predicted concentrations in freshwater sediment. To our knowledge, this is the first study to demonstrate inhibition of microbial functional diversity by citrate-AgNP and PVP-AgNP in a pathogen impaired stream. Citrate-AgNP caused greater inhibition of carbon substrate utilization but amino acids, carbohydrates, and carboxylic acids were the most affected carbon groups which led to a shift in the metabolic fingerprint pattern of the microbial community. AgNPs decreased the catabolic capability and the ability of the microbial community to degrade organic matter and a variety of pollutants in the environment.

This study tested an experimental approach to use in teaching the concept of functional diversity. The project culminated in a laboratory exercise for use in high schools. Experimental design consisted of representatives of three functional groups of plants, (legumes, grasses, and forbs), planted singly, and in two, or three species combinations. Legumes were represented by Trifolium repens and Medicago lupulina, grasses were represented by Cynodon dactylon and Festuca rubra, and forbs were represented by Helianthus annus and Raphanus sativa. Plants were grown inside a controlled growth chamber. During the growth phase, measurements were taken to highlight temporal differences in development. After two months, wet and dry weights of aboveground and belowground portions were measured as indicators of productivity. Research showed unique developmental patterns related to functional groups. Secondly, functional combination, not functional group number, produced a significant difference in biomass. Laboratory use involves group discussion, active-learning, and higher understanding of conservation.

Los coleópteros saproxílicos son aquellos que, al menos en una parte de su ciclo vital, dependen directamente o indirectamente de la madera muerta o moribunda y de otros organismos saproxílicos, como hongos habitantes de la madera. La madera muerta o moribunda posee una gran diversidad de formas y orígenes (árboles muertos, caídos o en pie, árboles moribundos, ramas muertas, caídas o no, oquedades o heridas en árboles sanos o no, o restos de troncos como tocones y cortezas), por lo que los organismos saproxílicos, son de gran importancia en los ecosistemas, sobre todo en los forestales. Sin embargo, y a pesar de ello están gravemente amenazados por cambios en sus hábitats y microhábitats, principalmente causados por el ser humano. Aunque tradicionalmente la biodiversidad de los ecosistemas ha sido medida a través de la identidad y abundancia de especies, en las últimas décadas se ha desarrollado otro modo medir la biodiversidad basándose en los rasgos funcionales de las especies, que ha sido conocido como diversidad funcional. El objetivo general de esta tesis es profundizar en el conocimiento de las comunidades de escarabajos saproxílicos en áreas protegidas y bien conservadas de la Península Ibérica a través del estudio de su diversidad taxonómica y funcional, con el fin de comprender qué variables y mecanismos pueden estar detrás de su biodiversidad. Con el fin de lograr este objetivo se realizó un muestreo sistemático de las comunidades de escarabajos saproxílicos en tres áreas protegidas de España (parque nacional de Cabañeros, parque natural de Font Roja y parque natural de Sierra Espadán) usando para ello tres tipos de trampas (trampas de intersección en vuelo o trampas de ventana, trampas de emergencia en oquedades, y trampas de emergencia en troncos en suelo). La incorporación funcional al estudio de estas comunidades ha permitido aseverar que el número de especies o la abundancia de estas no provee suficiente información sobre dichas comunidades, por lo que ambos aspectos de la biodiversidad deberían tenerse en cuenta a la hora de proponer estrategias de conservación, tanto a nivel temporal como espacial. Asimismo, la presente tesis ha demostrado que aunque dependen de variables distintas, tanto la diversidad taxonómica como la diversidad funcional de escarabajos saproxílicos son altamente dependientes del área de muestreo, por lo que en cada área protegida se deberían poner en marcha medidas de conservación y manejo adaptadas a sus características.

No description available.

Understanding mechanisms regulating the assembly of ecological communities is a major goal of community ecology. I combined experimental and theoretical approaches to investigate the influences of various ecological factors on the assembly of protist communities. My research included three experimental studies and one theoretical study. Two experimental studies used freshwater heterotrophic ciliated protists as model organisms to examine how species dispersal across local communities and functional and phylogenetic diversity of the species pool influence historical contingency of the assembled communities, respectively. The results of the first experiment showed that the differences in species colonization history led to alternative community states that substantially differed in species composition and abundances, regardless of the level of species dispersal. The results of the second experiment showed that historical contingency, measured by beta diversity and the strength of inhibitive priority effects decreased as phylogenetic and functional diversity of the species pool increased. In the third experimental study, I used the same model system and observed positive relationships between phylogenetic diversity and temporal stability of community biomass. These positive relationships are likely due to the reduced competition among species and increased asynchronous species responses to environmental changes under higher phylogenetic diversity. The theoretical study explored how phytoplankton and zooplankton coevolution drives species diversity patterns along productivity gradients in a mathematical model system. I explored the conditions for evolutionary divergence in phytoplankton and zooplankton and the consequent productivity-diversity relationships (PDR) using the theory of adaptive dynamics and numerical simulations. The results of numerical simulations showed that the coevolutionary dynamics of phytoplankton and zooplankton can generate transient unimodal or positive PDRs, and positive PDRs when the systems reach steady states. The findings of my research suggest an important role of traits and species ecological difference in understanding causes and consequences of biodiversity in community ecology.

It is increasingly being recognized that the soil microbes can mineralize recalcitrant soil organic matter (SOM) by using the fresh carbon (C) as a source of energy, a process called priming effect (PE). It has been shown mostly in lab incubations that PE can have important consequences for sequestration of organic C in soils. However, the importance of PE in C and N dynamics of ecosystems remains little known. The soil-plant interactions and rhizospheric processes can modulate the rates of PE and its consequences on C and N dynamics in an ecosystem. The objective of this thesis was to determine the role of PE in the C and N dynamics of permanent grasslands and the modulation of this role in response to management (plant clipping, fertilization) and global warming. Moreover, it was aimed to identify the microbial groups involved in PE and to unravel the way, e.g. absorption of N, root exudations and litter deposition, by which plant can induce PE. The thesis was based on a new approach allowing continuous dual labelling of multiple grassland plants with 13C- and 14C-CO2. The dual labelling permitted the separation of soil-derived CO2 from plant-derived CO2, the calculation of PE and the determination of mean age of soil-derived CO2-C. Moreover, phospholipids fatty-acids analysis (PLFA) permitted to correlate the variation of PE with changes in microbial community composition. Our work showed that the increased SOM mineralization under grasses was consistently two to three times more than that in bare soils (i.e. PE) over long term (511 days). This reveals that the PE plays key role in ecosystem CO2-C flux and indicates that a very large pool of SOM is under the control of PE. Moreover, we report that 15,000 years old organic C from an undisturbed deep soil can be mineralized after the supply of fresh C by living plants to soil microbes. This result supports the idea that the SOM in deep soils is stable due to the energy-limitation of microbes and the ‘inert' pool of organic C defined in current models is not so ‘inert' finally. The supply of N in soil-plant system through the use of fertilizer or legume decreased the PE suggesting that the C storage in soils is limited by nutrient supply. Similarly, plant clipping reduced the plant N uptake thereby PE. Collectively these results suggest synchronization between plant N uptake and SOM mineralization supporting the idea that soils under permanent plant cover function as a bank of nutrients for the plant, maximizing plant productivity and nutrient retention. An innovative method clearly showed that the root exudation is the major way by which grassland plants induce PE. Moreover, saprophytic fungi are suggested as the key actors in the mineralization of recalcitrant SOM & PE. Lastly, we developed a new theory on temperature response of SOM mineralization by taking into account the energy-limitation of microbes and the temperature-dependent inactivation of enzymes. This theory predicts a negative relationship between temperature and mineralization of recalcitrant SOM, which was supported by experimental results. This finding challenges the classical paradigm of positive relationship between temperature and recalcitrant SOM mineralization. Overall, these investigations on plant-soil systems reinforce the idea that PE and underlying mechanisms play a key role in ecosystem C and N dynamics and even suggest that this role was underestimated in lab experiments. / It is increasingly being recognized that the soil microbes can mineralize recalcitrant soil organic matter (SOM) by using the fresh carbon (C) as a source of energy, a process called priming effect (PE). It has been shown mostly in lab incubations that PE can have important consequences for sequestration of organic C in soils. However, the importance of PE in C and N dynamics of ecosystems remains little known. The soil-plant interactions and rhizospheric processes can modulate the rates of PE and its consequences on C and N dynamics in an ecosystem. The objective of this thesis was to determine the role of PE in the C and N dynamics of permanent grasslands and the modulation of this role in response to management (plant clipping, fertilization) and global warming. Moreover, it was aimed to identify the microbial groups involved in PE and to unravel the way, e.g. absorption of N, root exudations and litter deposition, by which plant can induce PE. The thesis was based on a new approach allowing continuous dual labelling of multiple grassland plants with 13C- and 14C-CO2. The dual labelling permitted the separation of soil-derived CO2 from plant-derived CO2, the calculation of PE and the determination of mean age of soil-derived CO2-C. Moreover, phospholipids fatty-acids analysis (PLFA) permitted to correlate the variation of PE with changes in microbial community composition. Our work showed that the increased SOM mineralization under grasses was consistently two to three times more than that in bare soils (i.e. PE) over long term (511 days). This reveals that the PE plays key role in ecosystem CO2-C flux and indicates that a very large pool of SOM is under the control of PE. Moreover, we report that 15,000 years old organic C from an undisturbed deep soil can be mineralized after the supply of fresh C by living plants to soil microbes. This result supports the idea that the SOM in deep soils is stable due to the energy-limitation of microbes and the ‘inert' pool of organic C defined in current models is not so ‘inert' finally. The supply of N in soil-plant system through the use of fertilizer or legume decreased the PE suggesting that the C storage in soils is limited by nutrient supply. Similarly, plant clipping reduced the plant N uptake thereby PE. Collectively these results suggest synchronization between plant N uptake and SOM mineralization supporting the idea that soils under permanent plant cover function as a bank of nutrients for the plant, maximizing plant productivity and nutrient retention. An innovative method clearly showed that the root exudation is the major way by which grassland plants induce PE. Moreover, saprophytic fungi are suggested as the key actors in the mineralization of recalcitrant SOM & PE. Lastly, we developed a new theory on temperature response of SOM mineralization by taking into account the energy-limitation of microbes and the temperature-dependent inactivation of enzymes. This theory predicts a negative relationship between temperature and mineralization of recalcitrant SOM, which was supported by experimental results. This finding challenges the classical paradigm of positive relationship between temperature and recalcitrant SOM mineralization. Overall, these investigations on plant-soil systems reinforce the idea that PE and underlying mechanisms play a key role in ecosystem C and N dynamics and even suggest that this role was underestimated in lab experiments.