Les écosystèmes côtiers sont des milieux complexes au sein desquels les communautés microbiennes, jouant un rôle majeur dans leur fonctionnement et leur maintien, s’adaptent et sont tolérantes à des conditions environnementales fluctuantes. En effet, au rythme des marées et de l'activité de la macrofaune, des oscillations oxie/anoxie influencent la composition et la dynamique des communautés microbiennes et par conséquent leur implication métabolique. Afin d’appréhender le devenir du pétrole dans ces écosystèmes, il est donc indispensable d’apporter des connaissances sur l’écologie des microorganismes intervenant dans son élimination, notamment dans des conditions oscillantes anoxie/oxie. Ainsi, ce travail de thèse a eu pour objectif de décrypter l’assemblage de communautés microbiennes hydrocarbonoclastesde sédiments intertidaux soumises à des oscillations anoxie/oxie en présence de pétrole lors d’une expérience en bioréacteurs. Les réponses écologiques des communautés bactériennes globales et de micro-organismes sulfato-réducteurs en conditions oscillantes ont pu être décrites en comparaison avec celles obtenues en conditions d’oxie ou d’anoxie permanentes, par l’analyse des données obtenues par séquençage haut-débit des gènes de l’ARN 16S et dsrB au niveau transcriptionnel. Ces études comparatives ont mis en évidence des profils écologiques en réponseaux conditions oscillantes, pouvant être répandus dans différents environnements marins côtiers. En réponse à ces conditions particulières, de nombreux microorganismes semblent avoir le potentiel à tolérer et/ou s’adapter aux différentes conditions d'oxygénation. Cette capacité d’acclimatation rapide des communautés bactériennes aux conditions oscillantes se sont accompagnées de capacités de dégradation équivalentes ou supérieures dans ces conditions par rapport à la condition d’oxie permanente montrant l’influence des oscillations anoxie/oxie sur le devenir du polluant dans les environnements pollués soumis à ces conditions. / Coastal ecosystems are complex environments in which microbial communities, playing a major role in their functioning and maintain, are tolerant and adapt to changing environmental conditions. Indeed, the tides and the macrofauna’s activity generate oxic/anoxic oscillations which influence the composition and dynamics of microbial communities and consequently their metabolic in volvement. To understand the fate of oil in these ecosystems, it is essential to provide knowledge on the ecology of microorganisms involved in these systems, taking into account anoxic/oxicoscillating conditions. Thus, this thesis aimed to decipher the organization of hydrocarbonoclastic microbial communities inhabiting intertidal sediments, when they are subjected to anoxic/oxic oscillations in an experiment in bioreactors with oil addition. Ecological responses of bacterial communities and sulfate-reducing microorganisms in oscillating conditions have been described comparing with those obtained with permanent oxic or anoxic conditions, using high-throughputsequencing analyses of the 16S rRNA and dsrB genes at the transcriptional level. These comparatives studies have highlighted ecological profiles in response to the oscillating conditions, which can be prevalent in different coastal marine environments. In response to these particular conditions, many organisms seem to have the potential to tolerate and / or adapt to the different conditions of oxygenation. This rapid acclimation capacity of bacterial communities tothese changing conditions have been accompanied by equivalent or greater degradation capacity under these conditions compared to the permanent oxic condition, showing the influence of the anoxic/oxic oscillations on the fate of pollutant in environments subjected tothese conditions.

[Truncated abstract] Removal of consumers through fishing has been shown to influence ecosystem structure and function by changing the biomass and composition of organisms occupying lower trophic levels. The western rock lobster (Panurilus cygnus), an abundant consumer along the temperate west coast of Australia, forms the basis of Australia's largest single species fishery, with catches frequently exceeding 11000 tonnes annually. Despite their high abundance and commercial importance, the diet and trophic role of adult lobster populations in deep-coastal-ecosystems (35-60 m) remains unknown. An understanding of the diet and trophic role of lobsters in these ecosystems is a key component of the assessment of ecosystem effects of the western rock lobster fishery. This study uses gut content and stable isotope analyses to determine the diet and trophic role of lobsters in deep-coastal ecosystems. Dietary analysis indicated adult lobsters in deep-coastal ecosystems were primarily carnivorous with diet reflecting food available on the benthos. Gut content analyses indicate crabs (62 %) and amphipods/isopods (~10 %) are the most important lobster dietary sources. Stable isotope analysis indicates natural diet of lobsters in deep coastal ecosystems is dominated by amphipods/isopods (contributing up to ~50 %) and crabs (to ~75 %), with bivalves/gastropods, red algae and sponges of lesser importance (<10 % of diet each). Diet of lobsters in deep-coastal ecosystems differed from that reported for lobsters inhabiting shallow water ecosystems in this region, reflecting differences in food availability and food choice between these ecosystems. Bait from the fishery was also determined (by stable isotope analyses) to be a significant dietary component of lobsters in deep-coastal ecosystems, contributing between 10 and 80 % of lobster food requirements at some study locations. '...' Given observed effects of organic matter addition in trawl fisheries, and also associated with aquaculture, bait addition is likely to have implications for processes occurring within deep-coastal ecosystems in this region, particularly given its oligotrophic status, most likely by increasing the food available to scavenging species. Removal of lobsters from deep-coastal ecosystems may affect the composition and abundance of lobster prey communities through a reduction in predation pressure. Such effects have been demonstrated for other spiny lobster species. These effects are typically most observable amongst common prey taxa which in other studies have been commonly herbivores. In deep-coastal ecosystems, crabs and amphipods/isopods are the most common prey taxa and most likely to be effected. The ecosystem-impacts of top-down control of non-herbivorous prey species is unknown and constrains the inferences possible from this study. However, the establishment of 'no-take' areas in deep-coastal ecosystems would allow the ecosystem effects of lobster removal to be further assessed in these deep-coastal ecosystems. While data from the current study did not allow the ecosystem effects of lobster removal to be properly assessed, this study provided information regarding the ecology of western rock lobsters in previously unstudied ecosystems.

Les écosystèmes marins côtiers sont constament soumis à des pollutions, notamment aux hydrocarbures, du fait de leur localisation et de leurs caractéristiques environnementales. Le rôle clé des microorganismes dans la dégradation de ces polluants est aujourd’hui très bien décrit. Toutefois, les conditions d’oxygénation fluctuantes dans ces environnements côtiers, dues aux marées et aux activités de bioturbation de la macrofaune, influencent les communautés microbiennes.Ainsi, ce travail de thèse a eu pour objectif de caractériser, l’assemblage de communautés microbiennes hydrocarbonoclastes de sédiments marins côtiers soumises à des oscillations oxie/anoxie en présence de pétrole lors d’une expérience en bioréacteurs. L’adaptation des bactéries marines hydrocarbonoclastes notamment des genres Alcanivorax et Cycloclasticus vis-à-vis de ces variations d’oxygène a pu être investiguée par oligotypage. Des écotypes ont été identifiés en fonction des conditions d’oxygénation démontrant ainsi les capacités d’adaptation aux conditions oscillantes d’oxygène de ces deux genres. La structure des communautés archéennes (séquençage des transcrits du gène de l’ARNr 16S) n’a pas montré de modification évidente liée aux conditions d’oxygénation démontrant ainsi des capacités d’adaptation et/ou de résistance plus importantes chez ces microorganismes comparées aux communautés bactériennes. Enfin, les analyses métagénomiques ont mis en évidence une réponse fonctionnelle spécifique aux oscillations oxie/anoxie. Ainsi, ces travaux de thèse apportent de nouvelles connaissances sur l’influence des variations d’oxygénation sur les communautés microbiennes et par conséquent sur la dégradation des hydrocarbures au sein des écosystèmes marins côtiers. / Coastal marine ecosystems are constantly subject to pollution, particularly hydrocarbons, because of their location and their environmental characteristics. The key role of microorganisms in the degradation of these pollutants is now well described. However, fluctuating oxygenation conditions in these coastal environments, due to tides and macrofauna bioturbation activities influence microbial communities.Thus, this thesis work aimed to characterize the assembly of microbial hydrocarbonoclastic communities of coastal marine sediments subjected to oxic/anoxic oscillations in the presence of oil during a bioreactor experiment. The adaptation of MOHCB, particularly of Alcanivorax and Cycloclasticus genera, to these oxygen variations has been investigated by oligotyping. Ecotypes were identified according to the oxygenation conditions demonstrating adaptation capacities of these two genera to the oscillating oxygen conditions. The structure of archaeal communities (16S rRNA transcript sequencing) did not show any modification related to the oxygenation conditions thus demonstrating greater adaptation and/or resistance capacities in these microorganisms compared to the bacterial communities. Finally, metagenomics analyses revealed a specific functional response to oxic/anoxic oscillations. Thus, this thesis provides new insights into the influence of oxygenation variations on microbial communities and consequently on the degradation of hydrocarbons in coastal marine ecosystems.

What makes a community sustainable? Is it the effective management of local environmental resources? Or meeting the social, economic and health needs of its population? For the five UBC researchers in the following pages, the answer is unequivocally both. From tackling water scarcity to environmental health and planning, these researchers are individually working to ensure local communities are equipped with the necessary knowledge to remain sustainable for generations to come.