Taxonomic diversity, biology and ecology of leaf endophytes were studied from some evergreen plants including Arbutus unedo, Buxus sempervirens, flex aquifolium, Laurus nobilis, Ligustrum vulgare, Prunus lusitanica, Rhododendron ponticum, Rhododendron sp., and Skimmia sp. from England, and some others from China. It was found: 1. A great number of fungal species, including several new species and new British records, have been isolated. Distribution patterns of endophyte assemblages and their variations between plant species and geographical locations are described. 2. Comparisons of leaf endophytes and saprobes of R. ponlicum at the same locality showed they belonged to two different ecological groups. This was further confirmed by study on endophytes and saprobes from a number of plant species growing in the same locality. 3. Host specificity of endophytic fungi at the species level was rare and this was supported by comparisons of endophyte assemblages from both taxonomically related (same family) and unrelated (different families) plant species. Molecular characterisations of Phyllosticta species confirmed this. 4. Infection and colonisation studies during a two year period showed that leaf endophytes of R. ponlicum were horizontally transmitted. Internal bud material was sterile and became infected by aerial spores. The infection and colonisation level of endophytes were strongly affected by environmental conditions. 5. Phylogenetic studies of Phyllosticta based on ITS 1-5.8s rDNA-ITS2 sequences concluded there was no evidence to show that the evolution of host plants of Phyllosticta species and ITS were related. Most Phyllosticta species from the same locality were found to have a broad host range and occurred on many taxonomically unrelated plants in the same locality. P. concentrica was separated into 4 species including P. concentrica on Hedera, P. arxii on Ilex, P. maxima on Rhododendron and P. taxi on Taxus.

A herbivoria em pastagens naturais apresenta papel de destaque no direcionamento das dinâmicas vegetacionais, determinando modificações na estrutura da vegetação, nos padrões de biodiversidade e na produtividade do sistema. Essas alterações, que de modo geral contribuem para a sustentabilidade dos ecossistemas em níveis moderados de intensidade de pastejo, podem dar origem a processos de degradação ambiental quando a lotação animal utilizada é superior à capacidade de suporte das pastagens. O objetivo do presente trabalho foi avaliar a capacidade de recuperação dos padrões de diversidade, composição botânica, biomassa de forragem, altura do pasto, interceptação luminosa e do banco de sementes de uma pastagem natural degradada por sobrepastejo, por meio do diferimento, tomando como base uma área de referência. Três tratamentos baseados em exclusões estacionais do pastejo (Diferimento de Primavera, Diferimento de Outono e Pastoreio Contínuo) com três repetições foram aplicados simultaneamente em áreas manejadas por um longo período com duas intensidades de pastejo: severa e moderada (utilizada como área de referência). A pastagem manejada com pastejo severo apresentou rápida alteração na composição botânica e nos padrões de diversidade em resposta ao diferimento. Depois de dois anos de exclusões temporárias do pastejo, a composição botânica da vegetação estabelecida e do banco de sementes dessa área sofreu alterações nos grupos funcionais de gramíneas na direção das espécies características da comunidade vegetal sob pastejo moderado. Também foram verificados importantes incrementos na biomassa de forragem, altura e interceptação luminosa. A comunidade vegetal sob pastejo moderado apresentou maior equilíbrio entre diferentes grupos funcionais de plantas, especialmente entre espécies com hábitos de crescimento prostrado e cespitoso. Essa condição favoreceu o aparecimento de estrutura espacial na distribuição das espécies de plantas, maior diversidade, riqueza e melhores condições estruturais do pasto. O diferimento realizado na moderada intensidade de pastejo proporcionou dominância de espécies cespitosas, determinando decréscimo na diversidade e riqueza de plantas. As épocas de diferimento apresentaram padrões de resposta semelhantes dentro de cada intensidade de pastejo, com magnitude superior para o diferimento de primavera. Os resultados revelam a importância do diferimento do pastejo como uma ferramenta para a recuperação de pastagens degradadas por sobrepastejo. / The herbivory on natural grasslands has a prominent role in driving vegetation dynamics, determining changes in vegetation structure, biodiversity patterns and primary and secondary productivity. These changes, which generally contribute to the ecosystems sustainability at moderate grazing intensities, can cause environmental degradation when the stocking rate used is higher than the pasture carrying capacity. The objective of this study was to evaluate the efficiency of temporary grazing exclusion to restore diversity, botanical composition, forage biomass, sward height, light interception and soil seed bank from a natural grassland degraded by overgrazing based on a reference area. Three treatments based on seasonal grazing exclusions (spring deferment, autumn deferment and continuous stocking) with three replications were applied simultaneously in areas managed for a long period with two grazing intensities: severe and moderate (used as reference area). The pasture managed under severe grazing showed a rapid change in botanical composition and diversity patterns in response to grazing exclusions. After two years of temporary grazing exclusions, grass functional groups of the established vegetation and soil seed bank from overgrazed pasture changed toward the characteristic species of plant community under moderate grazing. We also verified significant increases in forage biomass, sward height and light interception. The plant community under moderate grazing intensity showed better balance between different functional groups of plants, especially among species with prostrate and cespitose growth habits. This condition favored the spatial structure of appearance in the distribution of plant species, greater diversity, species richness and better structural pasture conditions. The grazing exclusion in moderate intensity grazing provided dominance tussock species, determining decrease in the diversity and richness of plants. The deferment periods showed similar response patterns within each grazing intensity with higher magnitude for spring deferment. These results reveal the importance of grazing exclusion as a tool for the recovery of degraded pastures by overgrazing.

A herbivoria em pastagens naturais apresenta papel de destaque no direcionamento das dinâmicas vegetacionais, determinando modificações na estrutura da vegetação, nos padrões de biodiversidade e na produtividade do sistema. Essas alterações, que de modo geral contribuem para a sustentabilidade dos ecossistemas em níveis moderados de intensidade de pastejo, podem dar origem a processos de degradação ambiental quando a lotação animal utilizada é superior à capacidade de suporte das pastagens. O objetivo do presente trabalho foi avaliar a capacidade de recuperação dos padrões de diversidade, composição botânica, biomassa de forragem, altura do pasto, interceptação luminosa e do banco de sementes de uma pastagem natural degradada por sobrepastejo, por meio do diferimento, tomando como base uma área de referência. Três tratamentos baseados em exclusões estacionais do pastejo (Diferimento de Primavera, Diferimento de Outono e Pastoreio Contínuo) com três repetições foram aplicados simultaneamente em áreas manejadas por um longo período com duas intensidades de pastejo: severa e moderada (utilizada como área de referência). A pastagem manejada com pastejo severo apresentou rápida alteração na composição botânica e nos padrões de diversidade em resposta ao diferimento. Depois de dois anos de exclusões temporárias do pastejo, a composição botânica da vegetação estabelecida e do banco de sementes dessa área sofreu alterações nos grupos funcionais de gramíneas na direção das espécies características da comunidade vegetal sob pastejo moderado. Também foram verificados importantes incrementos na biomassa de forragem, altura e interceptação luminosa. A comunidade vegetal sob pastejo moderado apresentou maior equilíbrio entre diferentes grupos funcionais de plantas, especialmente entre espécies com hábitos de crescimento prostrado e cespitoso. Essa condição favoreceu o aparecimento de estrutura espacial na distribuição das espécies de plantas, maior diversidade, riqueza e melhores condições estruturais do pasto. O diferimento realizado na moderada intensidade de pastejo proporcionou dominância de espécies cespitosas, determinando decréscimo na diversidade e riqueza de plantas. As épocas de diferimento apresentaram padrões de resposta semelhantes dentro de cada intensidade de pastejo, com magnitude superior para o diferimento de primavera. Os resultados revelam a importância do diferimento do pastejo como uma ferramenta para a recuperação de pastagens degradadas por sobrepastejo. / The herbivory on natural grasslands has a prominent role in driving vegetation dynamics, determining changes in vegetation structure, biodiversity patterns and primary and secondary productivity. These changes, which generally contribute to the ecosystems sustainability at moderate grazing intensities, can cause environmental degradation when the stocking rate used is higher than the pasture carrying capacity. The objective of this study was to evaluate the efficiency of temporary grazing exclusion to restore diversity, botanical composition, forage biomass, sward height, light interception and soil seed bank from a natural grassland degraded by overgrazing based on a reference area. Three treatments based on seasonal grazing exclusions (spring deferment, autumn deferment and continuous stocking) with three replications were applied simultaneously in areas managed for a long period with two grazing intensities: severe and moderate (used as reference area). The pasture managed under severe grazing showed a rapid change in botanical composition and diversity patterns in response to grazing exclusions. After two years of temporary grazing exclusions, grass functional groups of the established vegetation and soil seed bank from overgrazed pasture changed toward the characteristic species of plant community under moderate grazing. We also verified significant increases in forage biomass, sward height and light interception. The plant community under moderate grazing intensity showed better balance between different functional groups of plants, especially among species with prostrate and cespitose growth habits. This condition favored the spatial structure of appearance in the distribution of plant species, greater diversity, species richness and better structural pasture conditions. The grazing exclusion in moderate intensity grazing provided dominance tussock species, determining decrease in the diversity and richness of plants. The deferment periods showed similar response patterns within each grazing intensity with higher magnitude for spring deferment. These results reveal the importance of grazing exclusion as a tool for the recovery of degraded pastures by overgrazing.

A herbivoria em pastagens naturais apresenta papel de destaque no direcionamento das dinâmicas vegetacionais, determinando modificações na estrutura da vegetação, nos padrões de biodiversidade e na produtividade do sistema. Essas alterações, que de modo geral contribuem para a sustentabilidade dos ecossistemas em níveis moderados de intensidade de pastejo, podem dar origem a processos de degradação ambiental quando a lotação animal utilizada é superior à capacidade de suporte das pastagens. O objetivo do presente trabalho foi avaliar a capacidade de recuperação dos padrões de diversidade, composição botânica, biomassa de forragem, altura do pasto, interceptação luminosa e do banco de sementes de uma pastagem natural degradada por sobrepastejo, por meio do diferimento, tomando como base uma área de referência. Três tratamentos baseados em exclusões estacionais do pastejo (Diferimento de Primavera, Diferimento de Outono e Pastoreio Contínuo) com três repetições foram aplicados simultaneamente em áreas manejadas por um longo período com duas intensidades de pastejo: severa e moderada (utilizada como área de referência). A pastagem manejada com pastejo severo apresentou rápida alteração na composição botânica e nos padrões de diversidade em resposta ao diferimento. Depois de dois anos de exclusões temporárias do pastejo, a composição botânica da vegetação estabelecida e do banco de sementes dessa área sofreu alterações nos grupos funcionais de gramíneas na direção das espécies características da comunidade vegetal sob pastejo moderado. Também foram verificados importantes incrementos na biomassa de forragem, altura e interceptação luminosa. A comunidade vegetal sob pastejo moderado apresentou maior equilíbrio entre diferentes grupos funcionais de plantas, especialmente entre espécies com hábitos de crescimento prostrado e cespitoso. Essa condição favoreceu o aparecimento de estrutura espacial na distribuição das espécies de plantas, maior diversidade, riqueza e melhores condições estruturais do pasto. O diferimento realizado na moderada intensidade de pastejo proporcionou dominância de espécies cespitosas, determinando decréscimo na diversidade e riqueza de plantas. As épocas de diferimento apresentaram padrões de resposta semelhantes dentro de cada intensidade de pastejo, com magnitude superior para o diferimento de primavera. Os resultados revelam a importância do diferimento do pastejo como uma ferramenta para a recuperação de pastagens degradadas por sobrepastejo. / The herbivory on natural grasslands has a prominent role in driving vegetation dynamics, determining changes in vegetation structure, biodiversity patterns and primary and secondary productivity. These changes, which generally contribute to the ecosystems sustainability at moderate grazing intensities, can cause environmental degradation when the stocking rate used is higher than the pasture carrying capacity. The objective of this study was to evaluate the efficiency of temporary grazing exclusion to restore diversity, botanical composition, forage biomass, sward height, light interception and soil seed bank from a natural grassland degraded by overgrazing based on a reference area. Three treatments based on seasonal grazing exclusions (spring deferment, autumn deferment and continuous stocking) with three replications were applied simultaneously in areas managed for a long period with two grazing intensities: severe and moderate (used as reference area). The pasture managed under severe grazing showed a rapid change in botanical composition and diversity patterns in response to grazing exclusions. After two years of temporary grazing exclusions, grass functional groups of the established vegetation and soil seed bank from overgrazed pasture changed toward the characteristic species of plant community under moderate grazing. We also verified significant increases in forage biomass, sward height and light interception. The plant community under moderate grazing intensity showed better balance between different functional groups of plants, especially among species with prostrate and cespitose growth habits. This condition favored the spatial structure of appearance in the distribution of plant species, greater diversity, species richness and better structural pasture conditions. The grazing exclusion in moderate intensity grazing provided dominance tussock species, determining decrease in the diversity and richness of plants. The deferment periods showed similar response patterns within each grazing intensity with higher magnitude for spring deferment. These results reveal the importance of grazing exclusion as a tool for the recovery of degraded pastures by overgrazing.

Orientador: Raoul Henry / Resumo: As lagoas marginais são habitats lênticos, laterais ao rio, que podem manter comunicação permanente ou não com o rio. Nesses ecossistemas é encontrada elevada biodiversidade aquática, inclusive de zooplâncton. O objetivo deste estudo foi verificar diferenças na estrutura da comunidade zooplanctônica em lagoas marginais com diferentes níveis de conectividade hidrológica, por meio dos atributos ecológicos (riqueza, abundância, diversidade beta e funcional). Foi analisada a influência da conectividade hidrológica na comunidade de Cladocera e Rotifera em seis lagoas marginais antes e após um pulso de inundação do rio Paranapanema. Os resultados mostram que a estrutura da comunidade de Cladocera e Rotifera tende a ser mais distinta após o pulso de inundação. A diversidade beta foi mais elevada nas lagoas isoladas e na lagoa conectada que possui alta compartimentalização. Outro tema abordado diz respeito à analise da distribuição de Rotifera em um gradiente longitudinal da zona litorânea e envolvendo também a zona pelágica de uma lagoa marginal colonizada por macrófitas, por meio da diversidade taxonômica e funcional. A diversidade taxonômica foi maior na região de ecótono (transição da zona pelágica e litorânea) enquanto a diversidade funcional foi mais elevada na zona litorânea da lagoa. Neste estudo, também foi descrito como os microcrustáceos estão distribuídos em um transecto horizontal da zona litorânea e pelágica de uma lagoa marginal. A comunidade de microcrustáceos foi div... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The marginal lakes are lentic habitats, lateral to the river, that can maintain permanent communication or not with the river. High aquatic biodiversity is found in these ecosystems, including zooplankton. The aim of this study was to o verify differences in the structure of the zooplankton community in marginal lakes with different levels of hydrological connectivity, through ecological attributes (richness, abundance, beta and functional diversity). The influence of hydrological connectivity in the community of Cladocera and Rotifera in six marginal lakes was analyzed before and after the Paranapanema River pulse flood. The beta diversity was higher in isolated lakes and in connected lakes, which has high compartmentalization. Another topic addressed concerns the analysis of the distribution of Rotifera in a longitudinal gradient of the littoral zone and also involving the pelagic zone of a marginal lake colonized by macrophytes, through taxonomic and functional diversity. Taxonomic diversity was greater in the ecotone region (transition from the pelagic and littoral zone) while the functional diversity was higher in the littoral zone of the lake. In this study, it was also described how microcrustaceans are distributed in a horizontal transect of the littoral and pelagic zone of a marginal lake. The microcrustacean community was divided into six functional groups, with a predominance of the G2 group (bosminids) in the lake. Macrophytes had a strong influence on variations ... (Complete abstract click electronic access below) / Doutor

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.

Travail réalisé en cotutelle avec l'université du Littoral côte d'opale, France / Afin de réduire l’usage des fertilisants chimiques et leurs empreintes environnementales, la production de bioinoculants à base de bactéries rhizosphériques solubilisatrices de Phosphore (PSB) est une biotechnologie prometteuse. Lorsque celle-ci est associée à l’apport de phosphate de roche (RP), elle pourrait constituer une alternative écoresponsable d’amélioration de la fertilité des sols rhizosphériques, notamment à travers l’augmentation du phosphore (P) biodisponible. Pour répondre à cet enjeu environnemental majeur, il est indispensable d’étudier la biodiversité microbienne des sols en interaction avec le RP. Ainsi, ce travail de thèse a pour objectif de caractériser, d’un point de vue taxonomique, les communautés bactériennes et fongiques associées aux compartiments racinaires et rhizosphériques de plantes natives d’environnements singuliers, peu explorés, que sont d’anciens sites miniers riches en RP. Le séquençage Illumina MiSeq d’amplicons de gènes ribosomiques des différents groupes microbiens et l’assignation taxonomique des séquences regroupées en ASV, nous ont permis de mettre en évidence des valeurs de richesse et de diversité microbiennes comparables malgré la différence des teneurs en RP et en P des sols étudiés. De même, une grande similarité entre les profils des communautés a été identifiée à haut niveau taxonomique, avec une prévalence marquée des phyla Actinobacteriota et Ascomycota, et de l’ordre Glomerales pour les communautés de champignons mycorhiziens arbusculaires (CMA). À un niveau taxonomique plus bas, un core microbien de 26 ASV mycorhiziennes, persistantes à travers le gradient de RP et de P, a également été mis en évidence. Toutefois, l’analyse statistique des données environnementales nous a permis d’identifier des ASV indicatrices des habitats enrichis versus non enrichis en RP, pour chaque communauté microbienne étudiée. La synthèse de ces résultats originaux montre une influence mineure des teneurs en RP et en P sur le profil des communautés microbiennes des sites étudiés et questionne la signification écologique de la prévalence de certains taxa en lien avec l’histoire minière du site, sa restauration écologique et sa résilience, ainsi que les stratégies de vie et les attributs fonctionnels des taxa dominants. Par ailleurs, une collection de PSB a été réalisée à partir d’isolats racinaires issus des sites miniers étudiés, ou à partir d’isolats issus de spores et d’hyphes mycorhiziens piégés au contact d’apports en RP déposés dans la rhizosphère de plantes d’intérêt agronomique. Ces PSB racinaires ou hyphosphériques, testés par ailleurs pour plusieurs traits additionnels promoteurs de la croissance des plantes, ont été assignés à trois phyla : Proteobacteria, Firmicutes et, dans une moindre mesure, Actinobacteria ; Bacillus et Pseudomonas étaient les genres prédominants. Enfin, à partir de ces isolats, deux consortia bactériens avec différent traits promoteurs de la croissance des plantes (PGP), ont été constitués et testés seuls ou en combinaison avec l’apport de RP et/ou l’ajout d’un inoculum mycorhizien à base de Rhizophagus irregularis, sur la croissance de la tomate, espèce d’intérêt agronomique. Une augmentation du taux de germination, un accroissement de la hauteur des jeunes plantules et des modifications au niveau du système racinaire des plants adultes, en particulier des variations de la densité du tissu racinaire, ont été observés en réponse à l’inoculation simple par les consortia ou à leur interaction double ou tripartite avec le RP et/ou le CMA. Le profil taxonomique du microbiote natif avant et après apport des inoculants et du RP a été caractérisé. En conclusion, l’ensemble de nos travaux s’appuyant sur l’analyse des données environnementales, combinées aux données de laboratoire sur l’inoculation de plantes par des isolats bactériens, notamment d’origine minière, soulignent l’intérêt mais aussi la complexité de l’élaboration d’inoculants microbiens promoteurs de la croissance des plantes, solubilisateurs de P. / In order to reduce the use of chemical fertilizers and their environmental footprint, the production of bioinoculants based on phosphorus solubilizing rhizospheric bacteria (PSB) is a promising biotechnology. When combined with rock phosphate (RP), it could be an eco-responsible alternative to improve rhizospheric soil fertility, especially by increasing bioavailable phosphorus (P). To address this major environmental issue, studying soil microbial biodiversity and its interactions with RP is required. Thus, the objective of this thesis is to characterize, from a taxonomic point of view, the bacterial and fungal communities associated with the root and rhizospheric compartments of native plants in singular, little explored environments, located in former mining sites rich in RP. Illumina MiSeq sequencing of ribosomal gene amplicons of the different microbial groups, then taxonomic assignment of the sequences grouped in ASV, allowed us to highlight comparable microbial richness and diversity indexes of soils despite their differences in RP and P contents. As well, a high degree of similarity between the community profiles was identified at a high taxonomic level, with a marked prevalence of the phyla Actinobacteriota and Ascomycota, and of the order Glomerales for the arbuscular mycorrhizal fungi (AMF) community. At a lower taxonomic level, a microbial core of 26 mycorrhizal ASV, persistent across the RP and P gradient, was also documented. However, statistical analysis of the environmental data allowed us to identify indicator ASV for PR-enriched versus non-rich habitats for each microbial community studied. All together, these original results contributed to rule on a minor influence of RP and P levels on the microbial community’s profiles across the studied sites, and raised the questions of the ecological significance of the prevalence of certain taxa regarding the site’s mining history, its ecological restoration, as well as the life strategies and functional attributes of the dominant taxa. In addition, a collection of PSB was made from mine site root isolates, or from isolates associated with spores and mycorrhizal hyphae trapped in contact with PR inputs deposited in the rhizosphere of agronomic plants. These root or hyphospheric PSB, tested elsewhere for several additional plant growth-promoting traits, were assigned to three phyla: Proteobacteria, Firmicutes, and, to a lesser extent, Actinobacteria; Bacillus and Pseudomonas were the predominant genera. Finally, from these isolates, two bacterial consortia with different plant growth promoting (PGP) traits were constituted and tested, alone or in combination with RP inputs and/or a mycorrhizal inoculum based on Rhizophagus irregularis, on the growth of tomato, a species with an agronomic interest. An increase in germination rate or height of young seedlings, and changes in the root system of adult plants, particularly changes in root tissue density, were observed in response to single inoculation by the consortia or to their dual or tripartite interaction with RP and/or AMF. The taxonomic profile of the native microbiota before and after inoculants and RP input was characterized. In conclusion, our work based on the analysis of environmental data, combined with laboratory data from plant inoculation experiments by bacterial isolates, especially of mining origin, underlines the interest but also the complexity of the development of microbial inoculants promoting plant growth, solubilizers of P.

Les sols pollués par des métaux lourds sont colonisés par des communautés de microorganismes qui ont développé différentes adaptations leur permettant de résister à ces contaminants. Afin d'analyser au niveau moléculaire la diversité de ces adaptations, une approche expérimentale innovante basée sur l'étude du méta transcriptome eucaryote des sols a été utilisée pour comparer les fonctions exprimées au sein d'une communauté de microorganismes eucaryotes colonisant un sol contaminé, anciennement contaminé et non contaminé par des métaux lourds. Les banques d’ADNc eucaryotes construites à partir des ARNm extraits directement de ces sols ont été criblées par séquençage aléatoire de leurs inserts et par complémentation fonctionnelle de mutants de levures sensibles au cadmium.Cette étude a permis d’identifier de nouveaux gènes et de nouveaux mécanismes impliqués dans la résistance au cadmium ainsi qu’un nombre important de nouvelles protéines hypothétiques. Ceci démontre l’intérêt appliqué de cette approche pour la recherche de nouveaux bio catalyseurs et molécules bio actives.En parallèle, la diversité microbienne eucaryote a été révélée et comparée entre les sols par le clonage-séquençage du gène codant la petite sous-unité ribosomique 18S. Cette étude a mis en évidence une diversité inattendue de microorganismes eucaryotes dans ces sols et une analyse phylogénétique a permis de découvrir un nouveau clade de protistes (Rhizaria,Cercozoa). / Heavy metal-polluted soils are colonised by microbial communities which have developed different adaptations that allow them to resist to these pollutants. The objectives of this study were to reveal at the molecular level the diversity of these adaptations. To this aim,we implemented an innovative approach based upon the analysis of soil eukaryotic metatranscriptome to compare resistance mechanisms expressed by eukaryotic microorganisms living in heavy metal contaminated and control non contaminated or formerly-contaminated soils. Eukaryotic cDNA libraries were prepared using mRNA directly extracted from these soils and screened by either systematic sequencing of their inserts or functional complementation of yeast mutants sensitive to cadmium. This study allowed us to characterise novel genes and mechanisms implicated in Cd resistance as well as numerousnovel hypothetical proteins. This study also demonstrates the potential of this experimental approach to look for novel biocatalysts as well as novel bio-active molecules.In addition, eukaryotic molecular diversity was studied by the cloning-sequencing of the gene encoding the 18S ribosomal RNA. This study revealed an unexpected diversity of eukaryotic diversity in the studied soils and allowed us to discover a novel clade of protists(Rhizaria, Cercozoa).

Atividades humanas podem causar degradação e impedir que serviços ambientais cheguem á sociedade. Evitá-la demanda constante monitoramento, que pode ser realizado com indicadores ambientais. Buscamos selecionar indicadores da exploração de petróleo nas comunidades microbianas de riachos da Amazônia, Mata Atlântica, Cerrado e Caatinga. Avaliamos as diversidades taxonômica (Sequenciamento 16S) e funcional (GeoChip 5.0M) e comparamos os resultados de amostras de água, sedimento, biofilme e solo das margens de riachos influenciados por campos de petróleo com áreas de referência. Todas as estações apresentaram alta riqueza, baixa similaridade taxonômica e alta similaridade funcional. Impactos da atividade de exploração de petróleo foram relacionados ao uso do solo e não à contaminação por hidrocarbonetos, já que as estações não tinham histórico de vazamentos. Os indicadores identificados não foram atreldos a grupos taxonômicos ou atividades metabólicas específicas, sendo mais promissora a utilização de um conceito baseado em sequencias genéticas indicadoras. / Human activities can cause degradation and prevent environmental services from reaching society. Avoid it demand constant monitoring, which can be carried out with environmental indicators. We sought to select indicators of oil exploration in the microbial communities of streams in the Amazon, Atlantic Forest, Cerrado and Caatinga morphoclimatic domains. We evaluated taxonomic (16S Sequencing) and functional (GeoChip 5.0M) diversity and compared the results from water, sediment, biofilm and soil (from the margins of streams) samples influenced by oil fields with reference areas. All of them presented high richness, low taxonomic similarity and high functional similarity. Impacts of the oil exploration activity are related to the use of soil and not to hydrocarbon contamination, since the sampling stations we choose are historically not affected by oil spills. The indicators we identified are not related to taxonomic groups or specific metabolic activities, and the use of a concept based on indicator sequences is more promising.

Les changements globaux, du fait de l’empreinte humaine, sont associés à de nombreux déclins de populations et de disparitions d'espèces, et ce, notamment au sein des systèmes insulaires. L'importante biodiversité abritée par de tels écosystèmes est particulièrement vulnérable aux pressions anthropiques en raison de diverses caractéristiques (p. ex. syndrome d’insularité, faible redondance fonctionnelle, isolement géographique des îles). En dépit de cette vulnérabilité accrue, peu d’études se sont jusqu'à lors intéressées à ces systèmes comme modèle d’étude pour évaluer les patrons de menaces sur les différentes facettes de la diversité (taxonomique, fonctionnelle, et phylogénétique). Pourtant, un tel travail permettrait d’améliorer notre compréhension des menaces qui pèsent au sein des îles. Dans ce sens, l’objectif de cette thèse est de décrire les patrons de diversité endémique insulaire dans le contexte actuel des changements globaux et dans un contexte futur de changements climatiques, en explorant les différentes facettes de la diversité. Une finalité de ce travail est de mettre en évidence des priorités éventuelles de conservation pour ces écosystèmes particulièrement vulnérables. Nous avons abordé l'ensemble de ce travail de thèse à une grande échelle à l’aide de deux bases données recensant les îles mondiales et les espèces qui y sont endémiques. Dans une première partie, nous avons caractérisé les menaces pesant sur les écosystèmes insulaires à l'échelle globale, et prospecté également leurs distributions au sein de différents groupes taxonomiques et régions insulaires. Dans une deuxième partie, nous avons analysé l'incidence des menaces sur la biodiversité endémique insulaire et en particulier sur la composante fonctionnelle. Dans une troisième partie, nous avons identifié les régions insulaires à forte représentativité de la biodiversité endémique menacée au travers de différentes facettes et prospecté leurs niveaux de protection via les aires protégées et les menaces les affectant. Dans une dernière partie, nous avons étudié la vulnérabilité future des îles et de la biodiversité endémique face au changement climatique à l’échéance 2050. À la lumière de nos résultats (identification de menaces majeures dont l'importance varie suivant les groupes taxonomiques, les régions insulaires et également les dimensions de biodiversité considérées), nous avons discuté de l’implication des changements globaux pour la biodiversité endémique insulaire dans un contexte de conservation. Cette thèse révèle l’importance d’intégrer de multiples menaces (et leurs associations) et dimensions de diversité pour les approches de changements globaux et de conservation. / Global changes, because of human activities, are associated with numerous population declines and species extinctions, which are especially pronounced in island systems. The important biodiversity of such ecosystems is particularly vulnerable to anthropogenic pressures because of several characteristics (e.g. island syndrome, low functional redundancy, island geographical isolation). Despite this increased vulnerability, few studies have so far looked at these systems as a study model for assessing patterns of threats to the different facets of diversity (taxonomic, functional, and phylogenetic). However, such work would improve our understanding of islands threats. In this sense, the aim of this PhD thesis is to describe patterns of insular endemic diversity in the current context of global changes and in a future climate change context, by exploring different facets of diversity. The purpose of this work is to highlight potential conservation priorities for these particularly vulnerable ecosystems. We have addressed all of this thesis work on a large scale using two databases of worldwide islands and endemic species. In a first part, we characterized threats to island ecosystems at a global scale and also explored their distributions within different taxonomic groups and island regions. In a second part, we analyzed the impact of threats on the functional component of island endemic biodiversity. In a third part, we have identified priority areas for insular endemic biodiversity representativeness and conservation across different dimensions of biodiversity and explored their levels of protection through protected areas and threats affecting them. In a last part, we studied the future vulnerability of islands and endemic biodiversity to climate change by 2050 based on endemic mammals. In the light of our results (identification of major threats whose importance varies according to the taxonomic groups, the island regions and also the dimensions of biodiversity considered), we discussed the implications of global changes for island endemic biodiversity in a conservation context. This PhD thesis reveals the importance of integrating multiple threats and diversity dimensions for global changes and conservation approaches.