Amphibians harbor beneficial skin bacteria that can contribute to host defense against chytridiomycosis, an infectious disease caused by the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd). However, while skin-associated microbial communities may alter host infection risk, the structure of these complex microbial communities can be impacted by both biotic and abiotic factors. In a series of three studies, I investigated the natural temporal and spatial variation in bacterial communities on the skin of wild and captive-born amphibians using 16S rRNA gene amplicon sequencing to characterize bacterial community diversity. First, in a study examining the skin bacterial communities of two sympatric treefrog species (Agalychnis callidryas and Dendropsophus ebraccatus) at a single pond over multiple seasons and years, I found that annual, seasonal, and even daily fluctuations in temperature and rainfall changed the skin bacterial communities on these species. Second, I further investigated the impact of seasonality and rainfall on amphibian skin bacterial communities with a study of the bacterial communities on Craugastor fitzingeri, a common terrestrial species, along a rainfall gradient, and five co-occurring amphibian species at a single site. The strong wet and dry seasonality in the tropical lowland forest impacted the bacterial communities of multiple stream-dwelling co-occurring species, but the nature of the changes differed among the frog species. For C. fitzingeri sampled along the rainfall gradient, I found there was variation in bacterial community structure among sites, although this was not correlated with the latitudinal rainfall gradient. Finally, I investigated the challenges faced by captive-reared Atelopus limosus, an endangered amphibian species, after soft-release into natural habitat with the use of mesocosms. I found that the skin bacterial communities reverted to wild-type fairly quickly, body condition decreased to come closer to wild conspecifics, and 15% of the frogs became infected with Bd during the 27 day trial in mesocosms. Overall, I found that skin bacterial communities of lowland amphibians change across time and space, that variation sometimes correlates with environmental conditions at the time and the site of sampling, and that skin bacterial communities on captive-born frogs revert to wild-frog's state soon after soft-release to natural habitat. / Doctor of Philosophy / Beneficial bacteria found on amphibian skin can provide protection against an infectious disease caused by the lethal amphibian chytrid fungus (Batrachochytrium dendrobatidis), that has been linked with the decline and extinction of amphibian species worldwide. However, while skin bacterial communities may play a key role in determining disease outcome, these complex microbial communities can be impacted by biological and environmental factors. In a series of three studies, I investigated the natural variation in skin bacterial communities on wild and captive-born amphibians through time and space using modern DNA sequencing technologies to characterize bacterial community diversity. First, in a study examining the skin bacterial communities of two treefrog species at a single pond over multiple years and seasons, I found that annual, seasonal, and even daily fluctuations in temperature and rainfall changed the skin bacterial communities on these species. Second, I further investigated the impact of seasonality and rainfall with a study sampling the skin of one common frog species along a rainfall gradient, and five amphibian species at a single site across seasons. The strong wet and dry seasonality in the tropical lowland forest impacted the bacterial communities of multiple species found near streams, but the nature of the changes differed among the different frogs. For the common species sampled along the rainfall gradient, I found there was variation in bacterial community structure among sites, although this was not correlated with the rainfall gradient. Finally, I investigated the challenges faced by captive-reared Atelopus limosus, an endangered amphibian species from Panama, after release into field enclosures in the natural habitat. I found that the skin bacterial communities reverted to wild-type fairly quickly, body mass decreased to come closer to wild frogs of the same species, and 15% of the frogs became infected with the chytrid fungus during the 27 day trial in the field enclosures. Overall, I found that skin bacterial communities of lowland amphibians change across time and space, that variation is sometimes linked with environmental conditions at the time and site of sampling, and that captive-born frogs revert to wild states soon after release to natural habitat.

Throughout history species has gone extinct due to anthropogenic activities. During the last century efforts have been done to reintroduce species back into the wild. Zoos that originally were created as amusement parks for people have today a new purpose; to keep and breed species in captivity for later reintroductions in the wild. However a relaxed environment such as a zoo leads to a general fitness decline of up to 40% per generation in captivity. The probability of a successful reintroduction of a species that has been bred in a zoo will be lower the longer time it has been kept in captivity. The reintroduction of a captive bred species can also cause secondary extinctions and other negative effects on the food-web. Both changes in the community caused by the loss of a species and changes in the species itself caused by captivity can be expected to affect the outcome of a reintroduction attempt. Using a modeling approach I here investigate how the reintroduction of a captive bred species (at three different trophic levels; basal, intermediate and top predator species) affects a food-web and what risks there are in reintroducing it. A Lokta-Volterra model with type II functional response is used. I investigate three scenarios: the reintroduction of a species with 0% change in its attributes, 40% change in its attributes and 75% change in its attributes. It was found that the most important factor for reintroduction success when reintroducing a species is whether it is a producer species (basal species) or a consumer species (intermediate and top predator species). The producer species were most sensitive to the changes in their attributes, whilst consumer species were more sensitive to change in the food-web (Euclidian distance). The producer species were found to cause most secondary extinctions in all scenarios, hence indicating that it is a bottom-up controlled food-web. The present study suggests that the success of a reintroduction attempt is affected both by the degree of changes in the food web caused by the initial loss of the species and the degree of change in the species itself caused by captivity.

Ce mémoire visait à déterminer les pratiques et les facteurs favorables au succès des réintroductions du carex faux-lupulina (Carex lupuliformis), une espèce vivace menacée poussant dans divers types de milieux humides ouverts du nord-est de l’Amérique du Nord. Pour répondre à cet objectif, des expériences de germination en serres ont été réalisées, et la survie, la vigueur et le microhabitat de chaque plant de carex faux-lupulina connu au Québec (sauvage ou réintroduit) ont été mesurés. Nos résultats montrent que le carex faux-lupulina est une espèce facile à propager ex situ. Une stratification froide (4°C) des semences dans du sable humide pendant un mois induit des taux de germination élevés. Nos résultats montrent également que des pucerons exotiques, ainsi qu’une transplantation dans des habitats inadaptés aux besoins de l’espèce en termes d’humidité du sol et de lumière disponible, ont causé la mort prématurée d’un grand nombre de transplants. Notre programme de réintroduction a permis d’établir une nouvelle population de l’espèce au Québec, et a potentiellement permis de sextupler la taille des populations de la province. Globalement, cette étude a permis de mieux comprendre l’écologie du carex faux-lupulina, et ainsi de faciliter la restauration de ses populations. / This study aimed to determine the practices and factors influencing the success of the reintroductions of false hop sedge, an endangered perennial species growing in North American open wetlands. To do so, germination experiments were performed, and the survival, vigour and microhabitat of each false hop sedge plant known in Québec (wild or reintroduced) were measured. Our results show that false hop sedge is easy to propagate ex situ. A cold stratification (4°C) of seeds in wet sand for one month induced higher germination rates. Our results also show that exotic aphids, as well as a transplantation in habitats that did not meet the false hop sedge requirements in terms of soil moisture and available light, caused the premature death of many transplants. Our reintroduction program allowed the establishment of at least one new false hop sedge population in Québec, and potentially contributed to sextupling the size of the provincial population. Overall, this study allowed us to better understand the ecology of false hop sedge, and thus facilitate the restoration of its populations.