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The Mediterranean Sea is renowned for its heterogeneity of habitats and endemism, to the point that it is considered a miniature ocean and a hotspot of biodiversity. Since the last century, the human pressure in this basin has increased drastically with serious consequences to the different ecosystems and species occurring within it. The study of microbial communities, including those living freely and those associated with hosts, can provide support for monitoring and preserving ecosystem and organism health. The microbial communities associated with the intestinal mucosa of fishes are described to influence greatly host’s homeostasis and metabolism. Yet, limited information is available for wild fish species, and in the Mediterranean Sea only a handful of studies have explored this subject.We investigated the gut microbiota of wild Mediterranean demersal fishes to determine if its variability across the Mediterranean Sea is related to the habitat heterogeneity in this basin. Demersal fishes are a good model to evaluate this relationship since they strongly rely on the type of sea bottom during their life. Hence, we have selected multiple populations of four demersal species (Scorpaena notata, Scorpaena porcus, Scorpaena scrofa, Diplodus vulgaris) living across the Mediterranean Sea to address our question.The gut mucosa microbiota of fishes is described in the literature to be rather homogenous taxonomically, with host species being one of the factors predicting its taxonomic composition. Although we observed a significant influence of the host species on the taxonomical composition of the gut microbiota, we mostly highlighted a spatial variability of the taxonomical and functional features of the microbial communities at both small and large geographical scales. Furthermore, we relied on a single population of D. vulgaris to define the correlation between the features of the gut microbiota and those of the benthic substratum occurring in the home range of the fis, Doctorat en Sciences agronomiques et ingénierie biologique, info:eu-repo/semantics/nonPublished

Antipatharians or black corals are non-calcified colonial marine hexacorals that do not rely on algal symbionts for energy acquisition. For these reasons, they are present above and below the photic layer, with a high number of species described at mesophotic depths. They can form high-density aggregations referred to as black coral forests, serving as habitat, nursery or feeding area for a myriad of associated species, thereby creating biodiversity hotspots throughout the world oceans. Because black corals are threatened by anthropogenic activities (overharvesting, bottom trawling), they are listed under the CITES appendix II. Yet, the effects of another major threat, ocean warming, remained uninvestigated on this ectotherm taxon. Therefore, this thesis aimed at assessing the effects of increased seawater temperatures on antipatharians under laboratory-controlled conditions. As this was the first study of its kind, a global and comparative approach was used by considering species of various morphologies (branched and unbranched) and from different families (Antipathidae and Myriopathidae), climatic regions (Atlantic, Pacific and Indian Oceans, Mediterranean Sea) and depths (25 to 80m). Local bottom temperatures were recorded in each site and antipatharians were submitted in the laboratory to short/mid-term heat stress. Thermal performance curve for oxygen consumption were established for each studied species and their shapes (optimum temperature, width of the thermal window) were compared across species and sites. Other studied endpoints included tissue necrosis, healing capacity, release of bailout propagules as well as mucus and total antioxidant productions. Results showed that tolerance of antipatharians vary between species and sites. A large local annual temperature range was linked with a higher thermal tolerance evidenced by a wide thermal window and low or no impact on measured endpoints. On the contrary, a small annual temperature range went together with, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Global food animal production systems are experiencing rapid transformation, driven by expanding demand for animal source nutrition. Aquaculture is amongst the fastest growing food animal sectors globally and generates half of all aquatic animals for human consumption. As part of this global expansion, antimicrobials are used to treat and control disease in aquatic food animal production, exerting selective pressures driving antimicrobial resistance. Antimicrobial resistance—the capacity of microbes to withstand antimicrobial therapy—represents an urgent and growing threat to human and animal health, sustainable development, and the long-term viability of food production industries. Yet trends in antimicrobial use and antimicrobial resistance in aquatic food animals are seldom documented, despite their potential to inform global action.This work pursues three primary objectives. First, to generate quantitative estimates of antimicrobial use in the global aquaculture industry. Second, to synthesize current evidence on antimicrobial resistance from aquatic food animals over two decades in Asia – the world’s most productive aquaculture and fisheries region. And third, to examine dispersal pathways for antimicrobial resistant pathogens and their resistance determinants.In Chapter 2, species-specific antimicrobial use coefficients from point prevalence surveys are combined with aquaculture production volumes to model global aquaculture antimicrobial use, pointing to a projected 33% increase between 2017 and 2030 with Asia contributing the largest share of use. In Chapter 3, a dataset of antimicrobial resistance rates is generated and used to map resistance at 10 km resolution in freshwater and marine systems, revealing resistance hotspots corresponding to areas experiencing rapid aquaculture and fisheries growth and identifying priority freshwater locations for future surveillance effort. Elevated multi-drug resistance is found in cultured aquatic animals intended for hu, Les systèmes mondiaux de production d'animaux destinés à l'alimentation connaissent une transformation rapide, motivée par la demande croissante de nutrition d'origine animale. L'aquaculture est l'un des secteurs des animaux destinés à l’alimentation qui connaît la croissance la plus rapide au niveau mondial; ce secteur génère la moitié des animaux aquatiques destinés à la consommation humaine. Dans le cadre de cette expansion mondiale, des antimicrobiens sont utilisés pour traiter et contrôler les maladies dans la production d'animaux aquatiques destinés à l'alimentation, ce qui exerce des pressions sélectives favorisant la résistance aux antimicrobiens. La résistance aux antimicrobiens, c'est-à-dire la capacité des microbes à résister aux traitements antimicrobiens, représente une menace urgente et croissante pour la santé humaine et animale, le développement durable et la viabilité à long terme des industries de production alimentaire. Pourtant, les tendances en matière d'utilisation d'antimicrobiens et de résistance aux antimicrobiens chez les animaux aquatiques destinés à l'alimentation sont rarement documentées, malgré leur potentiel à éclairer l'action mondiale.Ce travail poursuit trois objectifs principaux. Tout d’abord, générer des estimations quantitatives de l'utilisation des antimicrobiens dans l'industrie aquacole mondiale. Deuxièmement, synthétiser les données actuelles sur l'antibiorésistance des animaux aquatiques destinés à l'alimentation sur deux décennies en Asie, la région la plus productive au monde en matière d'aquaculture et de pêche. Et troisièmement, examiner les voies de dispersion des pathogènes résistants aux antimicrobiens et leurs déterminants de résistance.Dans le chapitre 2, les coefficients d'utilisation d'antimicrobiens spécifiques aux espèces, issus d'enquêtes de prévalence ponctuelle, sont combinés aux volumes de production aquacole afin de modéliser l'utilisation mondiale des antimicrobiens en aquaculture. Il en ressort une augme, Doctorat en Sciences agronomiques et ingénierie biologique, info:eu-repo/semantics/nonPublished

The underexplored intertidal ecosystems of Antarctica are facing rapid changes in important environmental factors. Associated with temperature increase, reduction in coastal ice will soon expose new ice-free areas that will be colonized by local or distant biota. To enable detection of future changes in faunal composition, a biodiversity baseline is urgently required. Here, we evaluated intertidal faunal diversity at 13 locations around the Gerlache Strait (western Antarctic Peninsula), using a combination of a quadrat approach, morphological identification and genetic characterization. Our data highlight a community structure comprising four generally distributed and highly abundant species (the flatworm Obrimoposthia wandeli, the bivalve Kidderia subquadrata, and the gastropods Laevilitorina umbilicata and Laevilitorina caliginosa) as well as 79 rarer and less widely encountered species. The most abundant species thrive in the intertidal zone due to their ability to either survive overwinter in situ or to rapidly colonize this zone when conditions allow. In addition, we confirmed the presence of multiple trophic levels at nearly all locations, suggesting that complex inter-specific interactions occur within these communities. Diversity indices contrasted between sampling locations (from 3 to 32 species) and multivariate approaches identified three main groups. This confirms the importance of environmental heterogeneity in shaping diversity patterns within the investigated area. Finally, we provide the first genetic and photographic baseline of the Antarctic intertidal fauna (106 sequences, 137 macrophotographs), as well as preliminary insights on the biogeography of several species. Taken together, these results provide a timely catalyst to assess the diversity and to inform studies of the potential resilience of these intertidal communities

Sea stars are a diverse and important component of the Southern Ocean benthos. However, scarce information is available regarding their diversity, distribution, evolution, and taxonomic uncertainties persist for multiple taxa. The Magellanic Region (south of Chile) remains under-sampled despite its pivotal location for species distribution and diversity, being located at the crossroad of three ocean basins. In this study, we assessed the biodiversity of coastal Magellanic sea stars and their affinities with other oceanic bioregions. An integrative approach combining morphological identification with DNA barcoding was implemented to highlight taxonomic discrepancies such as suspected synonymy and unrecognised diversity. Firstly, we identified a total of 15 species from the coastal Magellanic Region and reported the occurrence of Cycethra frigida Koehler, 1917 for the first time in this region. The distribution of these 15 species ranged from only in South America to circumpolar, bipolar, or possibly cosmopolitan. Secondly, we highlighted possible synonymy in two species pairs within the genera Anasterias and Odontaster. This preliminary biodiversity assessment forms an important baseline for monitoring and conservation purposes, especially in the face of distribution shifts as a response to climate change and the increased presence of invasive species. Developmental mode has previously been suggested to be important in shaping biogeographical patterns. However, developmental mode was insufficient to explain the observed patterns, and other factors (e.g. physiological constraints, competition, bathymetrical range, and the possibility of passively rafting on kelp) are suggested to be at least equally important. Finally, an increase in barcoding effort is needed to better capture phylogeographic patterns for each species, both by increasing the number of specimens investigated and by covering a broader geographical range., SCOPUS: ar.j, info:eu-repo/semantics/published

Multiple initiatives have called for large-scale representative networks of marine protected areas (MPAs). MPAs should be ecologically representative to be effective, but in large, remote regions this can be difficult to quantify and assess. We present a novel bioregionalization for the Southern Ocean, which uses the modelled circumpolar habitat importance of 17 marine bird and mammal species. The habitat-use of these predators indicates biodiversity patterns that require representation in Southern Ocean conservation and management planning. In the predator habitat importance predictions, we identified 17 statistical clusters, falling into four larger groups. We characterized and contrasted these clusters based on their predator, prey and oceanographic characteristics. Under the existing Southern Ocean MPA network, some clusters fall short of 10 % representation, yet others meet or exceed these targets. Implementation of currently proposed MPAs can in some cases contribute to meeting even 30 % spatial coverage conservation targets. However, the effectiveness of mixed-use versus no-take MPAs should be taken into consideration, since some clusters are not adequately represented by no-take MPAs. These results, combined with previous studies in the Southern Ocean, can help inform the continued design, implementation, and evaluation of a representative system of MPAs for Southern Ocean conservation and management.

Multiple initiatives have called for large-scale representative networks of marine protected areas (MPAs). MPAs should be ecologically representative to be effective, but in large, remote regions this can be difficult to quantify and assess. We present a novel bioregionalization for the Southern Ocean, which uses the modelled circumpolar habitat importance of 17 marine bird and mammal species. The habitat-use of these predators indicates biodiversity patterns that require representation in Southern Ocean conservation and management planning. In the predator habitat importance predictions, we identified 17 statistical clusters, falling into four larger groups. We characterized and contrasted these clusters based on their predator, prey and oceanographic characteristics. Under the existing Southern Ocean MPA network, some clusters fall short of 10 % representation, yet others meet or exceed these targets. Implementation of currently proposed MPAs can in some cases contribute to meeting even 30 % spatial coverage conservation targets. However, the effectiveness of mixed-use versus no-take MPAs should be taken into consideration, since some clusters are not adequately represented by no-take MPAs. These results, combined with previous studies in the Southern Ocean, can help inform the continued design, implementation, and evaluation of a representative system of MPAs for Southern Ocean conservation and management., SCOPUS: ar.j, info:eu-repo/semantics/published

The western Antarctic Peninsula is facing rapid environmental changes and many recent publications stress the need to gain new knowledge regarding ecosystems responses to these changes. In the framework of the Belgica 121 expedition, we tested the use of a nimble vessel with a moderate environmental footprint as an approach to tackle the urgent needs of the Southern Ocean research community in terms of knowledge regarding the levels of marine biodiversity in shallow areas and the potential impacts of retreating glaciers on this biodiversity in combination with increasing tourism pressure. We discuss the strengths and drawbacks of using a 75’ (23 m) sailboat in this research framework, as well as its sampling and environmental efficiency. We propose that the scientific community considers this approach to 1) fill specific knowledge gaps and 2) improve the general coherence of the research objectives of the Antarctic scientific community in terms of biodiversity conservation and the image that such conservation conveys to the general public., SCOPUS: re.j, info:eu-repo/semantics/published

info:eu-repo/semantics/published

The fate and toxicity of ingested marine microplastics (MPs) have been of major concern in aquatic ecotoxicology for the last decade. Although their ingestion by a wide range of marine organisms has been proven, the uptake of MPs within organs is not yet fully understood and relies on the ability of ingested microplastics to transfer from the gut to tissues beyond the digestive wall (i.e. translocation). The present study investigates the in vitro transfer of fluorescent high-density polyethylene particles of different sizes classes (1–5 µm; 10–29 µm; 38–45 µm) across the intestinal wall of the sea urchin Paracentrotus lividus using Ussing chambers. Small microplastics (1–5 µm) were proven to be able to cross the intestinal wall of P. lividus and reach the coelomic fluid, while larger microplastics (≥ 10 µm) were not observed to cross the intestinal wall. Results demonstrate a size-dependent passage of polyethylene microparticles across the intestinal walls of P. lividus for the first time, highlighting the suitability of Ussing chamber systems to study the transfer of MPs across the intestinal wall of animals., SCOPUS: ar.j, info:eu-repo/semantics/published

Antipatharians (black corals) are major components of mesophotic ecosystems in the Mediterranean Sea. The arborescent species Antipathella subpinnata has received particular attention as it is the most abundant and forms dense forests harbouring high levels of biodiversity. This species is currently categorized as “Near Threatened” in the IUCN Red List, due to increasing fishing pressure and bottom-trawling activities. Yet, the effects of ocean warming have never been investigated for this species, nor for any other antipatharians from temperate regions. Our study aimed at evaluating the effects of increasing seawater temperatures on A. subpinnata, by combining predictive distribution modelling with a physiological tolerance experiment. During the latter, we exposed A. subpinnata for 15 days to different temperature conditions spanning the current seasonal range to forecasted temperatures for 2100, while measuring biological endpoints such as oxygen consumption rates and different signs of stress (tissue necrosis, total antioxidant capacity). Unexpectedly, no stress was found at organism nor cellular level (wide thermal breadth) suggesting low susceptibility of this species to mid-term temperature increase. If the response to the 15-days heat stress is representative of the response to longer-term warming, ocean warming is unlikely to affect A. subpinnata. The species distribution model predicted the presence of A. subpinnata at depths that correspond to temperatures colder than its maximum thermal tolerance (as determined by the physiology experiment). This suggests that the presence of A. subpinnata at shallower depths is not limited by physiological constraints but by other ecological factors including interspecific competition., Godefroid M. and Zeimes T. contributed equally., SCOPUS: ar.j, info:eu-repo/semantics/published