As one of the most diverse and ecologically important clades of life, fungi are best known as pathogens, saprotrophs, mycorrhizae, and lichens. Yet an enormous amount of previously unknown diversity occurs among endophytic and endolichenic fungi--species-rich, horizontally transmitted fungi that live within asymptomatic photosynthetic structures such as leaves and lichens. Here, I explore the biodiversity of these understudied symbiotrophs and the ecological and biogeographic factors influencing their communities.To evaluate methods currently used in ecological studies of environmental samples of fungi, I assessed inter- and intraspecific divergence of a fast-evolving locus for four genera commonly found as endophytes, and compared analytical methods for identifying and delimiting OTUs. Then I used the most robust methods to show that after soil contact, seeds of a focal tree species contain diverse fungi that are closely related to endophytes and pathogens.To explore the ecological specificity of symbiotrophic fungi, I examined endophytic, endolichenic, and saprotrophic communities inhabiting physically proximate hosts in a biotically rich area of southeastern Arizona. I found that endolichenic fungi are largely distinct from plant-associated fungi, with the exception of a group of ecologically flexible symbionts that occur in lichens and mosses. Although numerous endophytes were found in non-living leaves, fungi that were highly abundant in leaf litter were seldom found as endophytes.To assess symbiotroph biodiversity and ecological specificity at a broad geographic and phylogenetic scale, I isolated>4100 endophytic and endolichenic fungi from diverse communities of plants and lichens across five climatic regions in North America. I found that the abundance, diversity, and composition of these nearly ubiquitous fungi differ as a function of climate, locality, and host. Differences among communities reflect environmental characteristics more strongly than geographic distance.Last, I addressed a series of hypotheses regarding the ecological specificity of fungi inhabiting living and non-living leaves. I show that like endophytes, saprotrophic communities are structured by environmental characteristics, and at small spatial scales by host and leaf status. Yet, differences in communities between living leaves and leaf litter suggest that most endophytes either rapidly complete their life-cycle or are out-competed by robust saprotrophs once leaves senesce.

La résistance aux antibiotiques ou la difficulté de plus en plus croissante à traiter les maladies actuelles avec les composés disponibles sur le marché ont contraint les chercheurs à trouver de nouvelles sources de molécules actives. Les lichens produisent divers composés biologiquement actifs en raison de la grande diversité de leur écosystème. Ils représentent ainsi une source prometteuse de composés bioactifs. Le profilage chimique de Nephroma laevigatum a été effectué. Une analyse LC-MS/MS avec des approches en réseaux moléculaires ont permis d’appréhender la diversité chimique de ce lichen et quatre composés différents ont été isolés et identifiés par RMN puis testés pour leur activité antiproliférative. Cependant, les ressources en lichens sont limitées, ce qui restreint leur utilisation. De plus, le thalle lichénique constitue une niche écologique de choix pour d’autres microorganismes, ce qui en fait une source potentielle de nouvelles molécules d’intérêts. La culture de champignons endolichéniques a été entreprise. Ainsi, 46 souches ont été isolées et identifiées par DNA barcoding (amorces ITS4 et ITS5). Les souches identifiées appartiennent au genre Nemania, Daldinia, Peziza et Coniochaeta. Une investigation biologique a été réalisée sur six souches sélectionnées appartenant à deux espèces (Nemania aenea var. aureolatum et N. serpens). Ainsi, deux souches se sont démarquées par leurs activités antiprolifératives et anti-biofilms. Des études chimiques et biologiques plus approfondies de ces dernières (Gir_20 N. aenea var. aureolatum et Cor_08 N. serpens) ont été par la suite effectuées et huit composés différents ont été isolés et identifiés par RMN 1D et 2D. L’étude de l’effet des extraits sur les lignées cancéreuses humaines HT- 29, HCT116, PC-3 et DU145 a permis de mettre en évidence des changements morphologiques au niveau cellulaire. L’analyse de l’expression de marqueurs protéiques pro- et anti-apoptotiques ainsi que la fragmentation de l’ADN mettent en évidence l’induction de l’apoptose. Le profilage chimique par LC-MS/MS de ces souches a ensuite été réalisé et comparé par des approches en réseaux moléculaires permettant ainsi de visualiser la diversité chimique entre les deux espèces de champignons endolichéniques. / Antibiotics resistance or increase of difficulty to treat for current diseases with commercially available compounds has obligated researchers to find new sources of active molecules. Lichens produce various biologically active compounds due to the great diversity of their ecosystem. Thus, they represent a promising source of bioactive compounds. Chemical profiling of Nephroma laevigatum was performed. LC-MS/MS analysis with molecular network approach allowed understanding chemical diversity of this lichen and four different compounds were isolated and identified by NMR and tested for their antiproliferative activity. However, lichen resources are limited, which limits their use. In addition, lichen thalli are an ecological niche for other microorganisms and a wide reservoir for access to bioactive molecules. Cultivation of endolichenic fungi was undertaken. Thus, 46 strains were isolated and identified by DNA barcoding (primers ITS4 and ITS5). The isolated fungi belong to genus Nemania, Daldinia, Peziza and Coniochaeta. Biological investigation was carried out on six selected strains belonging to two species (Nemania aenea var. aureolatum and N. serpens). So, two strains distinguished by their antiproliferative and anti-biofilm activities. Further chemical and biological studies of these strains (Gir_20 N. aenea var. aureolatum and Cor_08 N. serpens) were subsequently performed and eight different compounds were isolated and identified by 1D and 2D NMR. Study of effect of the extracts on the human cancer lines HT-29, HCT116, PC-3 and DU145 made it possible to highlight morphological changes at the cellular level. Analyses of the expression of pro- and anti-apoptotic protein markers as well as DNA fragmentation demonstrate the induction of apoptosis. LC-MS/MS chemical profiling of these strains was performed and compared with molecular network approach, to visualize chemical diversity between the two species of endolichenic fungi.