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Previous research has shown that a range of physical and biological drivers can influence the composition of faunal assemblages occupying localities within streams. There is much debate in the literature about which of these is more important. Descriptive and experimental field studies were conducted in two relatively undisturbed, second order rainforest streams in southeast Queensland, Australia. The principal objectives were to describe spatial and temporal patterns in pool fauna and explore relationships between these patterns and physical attributes of habitat, disturbance and biotic interactions. The macroinvertebrate and vertebrate fauna of 12 small stream pools were sampled approximately monthly over a period of 15 months. Samples were collected from all major within-pool habitat types and concurrent measurements of potentially important environmental parameters were made at landscape scales of stream, pool and habitat patch. Faunal assemblages were consistently different between the two streams and between the various within-pool habitat types, although the latter may partially be explained by differences in sampling protocols applied in the different habitat types. However, spatial and temporal variation in faunal assemblages within habitat types was large at the scales of whole pools and within-pool habitats, and this variation occurred apparently independently of variation in physical habitat attributes. These results indicated that very little of the local scale faunal variation could be explained by abiotic drivers and that some other factors must be responsible for the observed faunal patterns. Previous research had indicated that atyid shrimps can play a significant ecological role in rainforest streams, where they act as 'ecosystem engineers' by removing fine sediment from hard surfaces. This subsequently alters algal dynamics and faunal composition in streams. A pool-scale manipulative experiment was conducted to investigate the role of the atyid Paratya australiensis, which is an abundant and conspicuous component of the fauna. Removal of shrimp from pools had no effect on sediment accrual on hard surfaces and consequently did not affect algal biomass or faunal assemblages. The lack of effect on sediment accumulation was attributed to the low rate of deposition in these streams, which was an order of magnitude lower than in streams where atyids have been demonstrated to play a keystone role. The fish Mogurnda adspersa was found to be the primary predator of pool fauna in the study streams, where it preyed on a wide variety of taxa. Dietary analyses revealed that an ontogenetic shift occurred in both diet and the within-pool habitat where fish fed. Within this general framework, individual fish had strong individual prey preferences. Significant correlations were found between the natural abundance of Mogurnda in pools and faunal assemblage patterns in both gravel habitat and pools in general, indicating that predation had an effect on pool fauna. The nature of this effect varied between habitats. A direct density dependent response was observed in gravel habitat. In contrast, the response in pools varied considerably between individual pools, perhaps reflecting the differing prey preferences of individual fish. Despite these correlations, an experimental manipulation of the density of Mogurnda at a whole-pool scale did not conclusively identify a predation effect. This may have been due to problems with fish moving between treatments, despite attempts to constrain them, and low experimental power due to the inherent high variability of pool fauna. Overall, the results of the study indicated that there was considerable spatial and temporal variation in pool fauna despite similarities in the physical attributes of pools and their close proximity. This variation appeared to occur at random and could not be explained by abiotic or biotic factors. Predation had a small effect, but could not explain the overall patterns, whereas disturbance by spates had very little effect at all. Stochastic processes associated with low level random recruitment were identified as a possible and plausible explanation for observed patterns. These conclusions are discussed in terms of their implications for our understanding of the ecology and management of streams.

Researchers have learned much about the biological assemblages that form around hydrothermal vents. However, identities of species in these assemblages and their basic ecological features are often lacking. In 2015, the first leg of the Hydrothermal Hunt expedition identified likely new vent sites in the Mariana Back-arc Spreading Center (BASC). In 2016, the second leg of the expedition used a remotely operated vehicle (ROV) to confirm and sample two new sites and two previously known sites. My first objective is to identify the animals collected from these four vent sites. In these samples, I identify 42 animal taxa, including the discovery of four new vent-associated species, five potentially new species and six taxa not previously reported in the Mariana BASC vents. My second objective is to combine these new data with previous studies and examine the species distributions among all known vent sites in the Mariana BASC using the α-, β-, and γ-diversity framework. I present updated species absence-presence lists for all eight Mariana BASC vent sites, which begin to resolve some of the issues with species identification. In this thesis, my approach to assessing β-diversity is novel in the field of hydrothermal vent ecology. My work also provides the first intra-regional scale assessments of β-diversity that include all sites known in a vent system. My third objective is to explore environmental factors driving these species distribution patterns. The α-diversity of BASC vent sites gradually increases with latitude, and the β-diversity calculated using the Raup-Crick index correlates with distance to nearby vent sites. Stochastic assembly processes likely shape the diversity patterns throughout the Mariana BASC as few environmental variables are known to correlate with these patterns. My fourth objective is to compare the β-diversity patterns between the Mariana BASC vent sites and those in two other vent systems: the Mariana Arc and the Juan de Fuca Ridge. The γ- and average α-diversity values for the BASC vents are relatively low compared to the other two systems. The Jaccard index revealed that the average number of shared species among the Arc vent sites is much lower than those of the BASC and the Juan de Fuca Ridge. The Raup-Crick index indicates that stochastic processes explain the average β-diversity of the Mariana BASC vents better than those of the Mariana Arc and Juan de Fuca Ridge. / Graduate / 2021-04-17

Au niveau des fonds océaniques, souvent considérés comme des déserts aux conditions de vie extrêmes, des oasis luxuriants de vie existent pourtant. Les sources hydrothermales et les suintements froids, principalement localisés au niveau des dorsales océaniques et des marges continentales, vont permettre le développement de communautés microbiennes et animales très particulières. Le Bassin de Guaymas, situé dans le Golfe de Californie (Mexique) présente la particularité de regrouper à la fois une zone de sources hydrothermales et une zone de suintements froids, situées à une soixantaine de kilomètres l’une de l’autre, et toutes deux recouvertes par une épaisse couche sédimentaire. Ces deux zones sont également colonisées par des étendues de bivalves, des buissons de vers tubicoles ainsi que de tapis microbiens blancs ou colorés comparables. Afin de mieux comprendre le fonctionnement global de ces deux types d’écosystèmes et notamment le rôle structurant des communautés microbiennes sédimentaires sur la répartition des différents assemblages de surface, les travaux entrepris dans cette thèse se proposaient d’étudier les communautés microbiennes sédimentaires associés à la zone de suintements froids (Marge de Sonora) et la zone de sources hydrothermales (Southern Trough) du Bassin de Guaymas. Pour cela, la diversité des communautés microbiennes (Bacteria et Archaea) de différents habitats caractérisés par une faune et des profils géochimiques particuliers, a été étudiée grâce à l’utilisation d’une technique de séquençage haut-débit, le pyroséquençage par la technique du 454, combinée à d’autres techniques comme le FISH ou la PCR quantitative. Cette étude a permis de déterminer que la structure et la diversité des communautés microbiennes dans ces sédiments étaient très spécifiques de ces environnements. Par ailleurs, les colonisateurs présents en surface des sédiments reflétaient des profils géochimiques et des communautés microbiennes très différentes au sein des sédiments. Dans les sédiments colonisés par les tapis microbiens, riches en méthane, les communautés microbiennes dominantes (ANME, Deltaproteobacteria…) utiliseraient notamment les émissions de méthane des couches sédimentaires profondes et produiraient d'importantes concentrations de sulfures, nécessaires à l’installation des communautés microbiennes thiotrophes de surface formant les tapis. Ces fortes concentrations en sulfure excluraient en revanche les communautés animales de ce périmètre. A contrario, dans les sédiments présentant de faibles concentrations en méthane et en sulfure, permettant l'installation d’assemblages faunistiques variés, les communautés microbiennes méthanotrophes anaérobies et productrices de sulfure étaient minoritaires. L'activité et le métabolisme de ces colonisateurs de surface pourraient par ailleurs permettre le développement des lignées microbiennes détectées dans ces habitats (MBG-D, Chloroflexi…). L'analyse des larges jeux de données obtenus au cours de cette étude nous a donc permis de mettre en évidence un système dynamique complexe fonctionnant en équilibre entre les communautés microbiennes sédimentaires, les organismes colonisant la surface du sédiment et la composition géochimique des eaux interstitielles. / Whereas the deep-sea environment is often considered to be a desert, hydrothermal vents andcold seeps provide “oases” of biological activity on the ocean floor. Vent and seep ecosystems support complex food webs based on microbial chemoautotrophic primary production. These hydrothermal vent and cold seeps ecosystems both release hydrocarbon- and sulfide-rich fluids,fueling various surface assemblages such as mat-forming giant bacteria or symbiont-bearinginvertebrates (e.g. bivalves, tubeworms). In the Guaymas Basin, the nearby presence at a few tens of kilometers of cold seeps and hydrothermal vents coupled with comparable sedimentary settings and depths offer a unique opportunity to assess and compare the microbial community composition of these ecosystems. Tobetter understand their overall functioning, we studied sedimentary microbial communities associated with cold seep and hydrothermal vent areas in the Guaymas Basin. The diversity of microbial communities inhabiting sediments was studied using high throughput sequencing (454pyrosequencing), combined with complementary approaches, such as FISH and quantitative PCR. This study reveals that sediments found in the Guaymas Basin were colonized by microbial communities typically found in these types of ecosystems. Our results revealed a high similarity between microbial communities composition associated with the cold seep and hydrothermal vent areas as a probable consequence of the sedimentary context. Nonetheless, thermophilic and hyperthermophilic lineages (e.g.: Thermodesulfobacteria, Desulfurococcales, etc) were exclusively identified in hydrothermally influenced sediments highlighting the strong influence of temperature gradients and other hydrothermally-related factors on microbial community composition. Furthermore, sediments populated by different surface assemblages show distinct porewater geochemistry features and are associated with distinct microbial communities. Indeed, in the sediments underlying microbial mats characterized by high methane porewater concentrations,microbial communities were dominated by anaerobic methane oxidizers (ANME), known to produce sulfide which provides high fluxes of sulfide to the seafloor. In contrast, sediment associated microbial communities underlying faunal assemblages were characterized by a lower biomass and lower methane porewater concentrations in sediments, limiting porewater sulfide concentrations. Without elevated and toxic sulfide concentrations, faunal assemblages can colonize the surface. Together, geochemical and microbial surveys indicate that porewater methane concentrations play an important role in the microbial community structure and subsequently in the establishment of the surface colonizers. Furthermore, presence and activity of the surface colonizers influence the underlying microbial communities probably because of modification of energy source availabilities. Finally, the existence of similar microbial populations between the two ecosystems also raises the question of their dispersal mechanisms. Our results support the hypothesis of a potential continuity among deep-sea ecosystems. In absence of physical borders, environmental conditions (temperature, specific compounds associated withhydrothermal fluids) might select specific and highly adapted microorganisms from the pool of microorganisms dispersed globally across the seafloor.

Culture types in Pacific Northwest archaeology are characteristic artifact assemblages distinguishing different prehistoric periods. Assemblages indicate a culture type transition during the 2,630 BP–270 BP occupation of Willows Beach (DcRt-10), southeastern Vancouver Island. Faunal remains could reveal links to subsistence patterns, following Croes’s theory that culture type change reflects subsistence intensification. Five dated DcRt-10 faunal assemblages underwent taxonomic and size classification, weighing and MNI calculation. Vertebrate weight and NISP percentages were compared between stratigraphic units associated with the later Gulf of Georgia and earlier Locarno Beach culture types. The youngest assemblage contains a smaller proportion of land mammal bone, suggesting increased sea mammal, fish, and bird procurement. Faunal remains also suggest a greater variety of taxa exploited over time. Faunal assemblages suggest that culture type change at DcRt-10 is the product of subsistence change, increasing knowledge of the culture historic sequence of this region.