The endangered northern long-eared bat (<i>Myotis septentrionalis</i>) has experienced severe population declines since the 2007 introduction of <i>Pseudogymnoascus destructans</i>, the fungal pathogen that causes white-nose syndrome (WNS). Due to continued mortality, failed recruitment, and range fragmentation, effective species conservation would benefit from local and regional research related to habitat selection and suitability, seasonal activity, and large-scale estimates of continued occupancy across the post-WNS landscape. In this dissertation, I explored maternity colony home range size and habitat selection, both coastal and interior seasonal activity patterns, habitat suitability, and species occupancy trends in the Mid-Atlantic and Northeastern United States. Research from the Coastal Plain of North Carolina, based on diurnal roost locations, revealed that core and peripheral home range estimates were large but comparable to areas of contiguous forest cover in other regions of the species' range. Prior to juvenile volancy, female northern long-eared bats selected red maple (<i>Acer rubrum</i>), water ash (<i>Fraxinus caroliniana</i>), and loblolly pine (<i>Pinus taeda</i>) as day-roosts, but then used sweetgum (<i>Liquidambar styraciflua</i>), swamp bay (<i>Persea palustris</i>), and water tupelo (<i>Nyssa aquatica</i>) after juvenile volancy. At the second-order spatial scale (i.e., home range within a region), roosting home ranges were associated with woody wetlands farther from anthropogenic development and open water. However, within the third-order scale (i.e., core home range within a periphery), northern long-eared bats selected woody wetlands adjacent to intact upland forests, areas containing shorter trees and occurring proximal to open water. Research utilizing passive acoustic monitoring on the Coastal Plain of both Virginia and North Carolina found that northern long-eared bat relative activity was highest in areas containing greater proportions of woody wetlands and upland pine-dominated evergreen forests. Conversely, the likelihood to record northern long-eared bats was associated with smaller proportions of woody wetlands and open water resources, emphasizing the importance of upland forests adjacent to these features. I also observed a higher probability of recording northern long-eared bats during non-winter seasons and when temperatures were between 10 and 25 °C, potentially highlighting an optimal thermoneutral zone for the species regionally. Research using presence data from the Monongahela National Forest (MNF) in the Central Appalachians of West Virginia found that northern long-eared bat habitat, whether occupied or not, was abundant (43.1% of the MNF) and widely dispersed. Northern long-eared bat habitat on the MNF was often characterized as mature, interior mixed mesophytic forests. Research using passive acoustic surveys associated with hibernacula in western Virginia found that northern long-eared bats were most active near hibernacula during warmer weeks of the fall swarm and spring emergence, when rainfall was low. Similarly, the probability of northern long-eared bat activity was highest near hibernacula during the spring/summer season. However, unlike relative activity, the likelihood of recording northern long-eared bats was associated with more heterogeneous, interior forests. Finally, research using a combination of long-term repeated and single-season clearance survey data from New England found that northern long-eared bat occupancy was highest on steep hillsides in contiguous forested landscapes with minimal anthropogenic development. My results also indicated higher occupancy of northern long-eared bats in warmer regions, particularly along the New England coastline and offshore islands. These findings collectively stress the importance of managing areas of large core forest to promote sustainable roost formation and productive foraging areas, often associated with dynamic ecotones, to support the survival and recovery of northern long-eared bats in the post-WNS Mid-Atlantic and Northeast. / Doctor of Philosophy / The northern long-eared bat was once one of the most common bat species in North America. However, due to population impacts caused by white-nose syndrome (WNS) the species is now recognized as endangered by the United States Fish and Wildlife Service. In this dissertation, I explore habitat selection and suitability, seasonal activity, and occupancy trends of remnant populations of northern long-eared bats in the Mid-Atlantic and Northeast of the United States, representing approximately 25% of the species' historical range. Specifically, I examined home range size and habitat selection of a reproductively successful maternity colony on the Mid-Atlantic Coastal Plain, overwintering activity at both interior and coastal sites, habitat suitability in the Central Appalachians, and spatial occupancy trends across New England. My research found that reproductive northern long-eared bats actively selected for specific cover features and displayed notable shifts in roost tree selection throughout the maternity season on the Coastal Plain of North Carolina. My research also indicated that northern long-eared bats were more active during non-winter seasons, favoring moderate temperatures and areas of forested wetlands adjacent to evergreen forests in coastal North Carolina and Virginia. In Virginia, northern long-eared bat activity near mountain hibernacula was highest in areas of greater landscape richness prior to and after hibernation. Finally, my research from New England found that northern long-eared bat occupancy was highest in steeper, forested landscapes in the absence of human development. Overall, this research highlights the need to conserve and manage forest ecosystems to promote recovery of the endangered northern long-eared bat. Conservation and management efforts informed by population status, activity trends, and habitat associations will be invaluable in guiding species recovery efforts.

Le syndrome du museau blanc (SMB), causé par le champignon Pseudogymnoascus destructans (Pd), a mis en péril les populations de chauves-souris hibernantes en Amérique du Nord. Certaines espèces sont hautement vulnérables à la maladie alors que d’autres espèces semblent être résistantes ou tolérantes à l’infection. Plusieurs facteurs physiologiques et environnementaux peuvent expliquer ces différences. Or avant 2015, peu d’études avaient porté sur le microbiome de la peau en relation avec cette maladie. La présente thèse vise à caractériser le microbiome cutané de chiroptères affectés par le SMB afin d’identifier les facteurs de vulnérabilité ou de résistance à la maladie. L’objectif principal est de déterminer comment le microbiome est affecté par la maladie ainsi que de déterminer si celui-ci à un rôle dans la protection face à l’infection fongique. Au Chapitre 1, nous avons tout d’abord exploré et comparé le microbiote cutané de petites chauves-souris brunes (Myotis lucifugus) non affectées par le SMB avec celui de chauves-souris survivantes au SMB pour tester l’hypothèse selon laquelle le microbiote cutané est modifié par la maladie. Nos résultats montrent que le site d’hibernation influence fortement la composition et la diversité du microbiote cutané. Les sites d’hibernations Pd positifs et négatifs diffèrent significativement en termes de diversité, ainsi qu’en termes de composition du microbiote. La diversité est réduite au sein du microbiote des chauves-souris survivantes au SMB et enrichi en taxons tels que Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia et Rhodococcus. Certains de ces taxons sont reconnus pour leur potentiel antifongique et des souches spécifiques de Rhodococcus et de Pseudomonas peuvent inhiber la croissance de Pd. Nos résultats sont cohérents avec l’hypothèse selon laquelle l’infection par Pd modifie le microbiote cutané des chauves-souris survivantes et suggèrent que le microbiote peut jouer un rôle de protection face au SMB. Au Chapitre 2, nous avons étudié le microbiote d’une espèce résistante au champignon Pd en milieu contrôlé avant et après infection afin d’établir la réponse potentielle à la maladie. L’espèce étudiée est la grande chauve-souris brune (Eptesicus fuscus) dont le microbiote cutané pourrait jouer un rôle de protection contre l’infection. Nos résultats montrent que la diversité du microbiote de la grande chauve-souris brune inoculée avec Pd est plus variable dans le temps, tandis que la diversité du microbiote des chauves-souris du groupe contrôle demeure stable. Parmi les taxons les plus abondants, Pseudomonas et Rhodococcus, deux taxons connus pour leur potentiel antifongique contre Pd et d’autres champignons, sont restés stables durant l’expérience. Ainsi, bien que l’inoculation par le champignon Pd ait déstabilisé le microbiote cutané, les bactéries aux propriétés antifongiques n’ont pas été affectées. Cette étude est la première à démontrer le potentiel du microbiote cutané d’une espèce de chauves-souris pour la résistance au SMB. Au Chapitre 3, le microbiome cutané de la petite chauve-souris brune a été évalué en milieu naturel dans le contexte du SMB, à l’aide de la métagénomique, une approche haute résolution pour observer le potentiel fonctionnel du microbiome (métagénome fonctionnel). Nos résultats ont permis d’établir que le temps depuis l’infection a un effet significatif sur le métagénome fonctionnel. En effet, les chauves-souris dans la première année suivant l’infection ont un métagénome fonctionnel perturbé qui subit une perte de diversité fonctionnelle importante. Toutefois, le métagénome fonctionnel revient à une structure et composition similaire d’avant infection après 10 ans. Certaines fonctions détectées suite à l’infection sont associées à des gènes reliés au transport et à l’assimilation de métaux, des facteurs limitants pour la croissance du champignon. Ces gènes pourraient donc avoir un rôle à jouer dans la résistance ou la vulnérabilité à la maladie. Globalement, l’étude du métagénome chez la petite chauve-souris brune indique une vulnérabilité du métagénome fonctionnel au champignon, mais que celui-ci semble se rétablir après 10 ans. Une telle réponse pourrait avoir un impact sur la résilience de M. lucifugus. Cette thèse a permis d’acquérir des connaissances fondamentales sur le microbiome cutané des chauves-souris en hibernation pour mieux comprendre les communautés microbiennes de la peau dans le contexte du SMB. Le microbiome pourrait en effet jouer un rôle dans la vulnérabilité et la résistance des chauves-souris à la maladie, et il est essentiel d’adapter notre façon d’aborder la protection de ces espèces et de leur microbiome. Nous souhaitons que les travaux de cette thèse permettent de sensibiliser les acteurs de la conservation à l’existence et à l’importance potentielle du microbiome pour la santé de son hôte. Cette thèse fait également état de l’avancement des méthodes d’analyses qui permettront d’être de plus en plus précis et d’appliquer les connaissances du microbiome en biologie de la conservation. / White-nose syndrome (WNS) caused by the fungus Pseudogymnoascus destructans (Pd) has put hibernating bat populations at risk in North America. Some species are highly vulnerable to the disease while other species appear to be resistant or tolerant. Several physiological and environmental factors can explain these differences. However, before 2015, few studies have focused on the skin microbiome in relation to this disease. The present thesis aims to characterize the cutaneous microbiome of bats affected by WNS in order to identify the factors of vulnerability or resistance to the disease. The main objective is to determine how the microbiome can protect against the Pd fungus, or conversely how the microbiome is altered by the fungal infection. In Chapter 1, we first explored and compared the skin microbiota of little brown bats (Myotis lucifugus) unaffected by WNS with that of WNS survivors to test the hypothesis that the skin microbiota is modified by the disease. Our results show that the hibernation site strongly influences the composition and diversity of the skin microbiota. The Pd positive and negative sites differ significantly in terms of diversity, as well as in terms of the composition of the microbiota. Diversity is reduced within the microbiota of bats surviving WNS and enriched in taxa such as Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia, and Rhodococcus. Some of these taxa are recognized for their antifungal potential and specific strains of Rhodococcus and Pseudomonas may inhibit the growth of Pd. Our results are consistent with the hypothesis that Pd infection modifies the skin microbiota of surviving bats and suggest that the microbiota may play a protective role against WNS. In Chapter 2, we studied in a controlled environment the microbiota of a species that exhibits evidence of resistance with mild WNS symptoms, before and after infection, to establish the potential response to the disease. The species studied is the big brown bat (Eptesicus fuscus), whose skin microbiota could play a protective role against infection. Our results show that the diversity of the microbiota of big brown bats inoculated with Pd is more variable over time, while the diversity of the microbiota of the control bats remains stable. Among the most abundant taxa, Pseudomonas and Rhodococcus, two taxa known for their antifungal potential against Pd and other fungi, remained stable during the experiment. Thus, although inoculation with the Pd fungus destabilized the skin microbiota, bacteria with antifungal properties were not affected. This study is the first to demonstrate the potential of the skin microbiota of a bat species for resistance to WNS. In Chapter 3, the skin microbiome of the little brown bat was evaluated in the natural environment in the context of WNS, using metagenomics, a higher-resolution approach to observe the functional potential of the microbiome (functional metagenome). Our results established that the time since infection has a significant effect on the functional metagenome. Indeed, bats in the first year after infection have a disrupted functional metagenome that undergoes a significant loss of functional diversity. However, the functional metagenome returns to a similar structure and composition to that observed before infection after 10 years. Certain functions detected following infection are associated with genes linked to the transport and assimilation of metals, known limiting factors for the growth of the fungus. These genes could therefore have a role to play in resistance or vulnerability to the disease. Overall, this metagenomics study indicates functional metagenome vulnerability to the fungus, although the original functional metagenome is reestablished after 10 years. Such diversified response could impact M. lucifugus resilence. This thesis provides fundamental knowledge on the skin microbiome of hibernating bats to better understand the microbial communities of the skin in the context of WNS. The microbiome could indeed play a role in the vulnerability and resistance of bats to disease and it is essential to adapt our way of approaching the protection of these species and their microbiomes. We hope that the results of this thesis will raise awareness among conservation stakeholders about the existence and potential importance of the microbiome for the health of its host. This thesis also reports on the advancement of analytical methods that will make it possible to be more and more precise and to apply knowledge of the microbiome in conservation biology.