abstract: The ocean is vital to the health of our planet but remains virtually unexplored. Many researchers seek to understand a wide range of geological and biological phenomena by developing technologies which enable exploration of the deep-sea. The task of developing a technology which can withstand extreme pressure and temperature gradients in the deep ocean is not trivial. Of these technologies, underwater vehicles were developed to study the deep ocean, but remain large and expensive to manufacture. I am proposing the development of cost efficient miniaturized underwater vehicle (mUV) with propulsion systems to carry small measurement devices and enable deep-sea exploration. These mUV's overall size is optimized based on the vehicle parameters such as energy density, desired velocity, swimming time and propulsion performance. However, there are limitations associated with the size of the mUV which leads to certain challenges. For example, 2000 m below the sea level, the pressure is as high as 3000 psi. Therefore, certain underwater vehicle modules, such as the propulsion system, will require pressure housing to ensure the functionality of the thrust generation. In the case of a mUV swimming against the deep-sea current, a thrust magnitude is required to enable the vehicle to overcome the ocean current speed and move forward. Therefore, the size of the mUV is limited by the energy density and the propeller size. An equation is derived to miniaturize underwater vehicle while performing with a certain specifications. An inrunner three-phase permanent magnet brushless DC motor is designed and fabricated with a specific size to fit inside the mUV's core. The motor is composed of stator winding in a pressure housing and an open to water ring-propeller rotor magnet. Several ring-propellers are 3D printed and tested experimentally to determine their performances and efficiencies. A planer motion optimal trajectory for the mUV is determined to minimize the energy usage. Those studies enable the design of size optimized underwater vehicle with propulsion to carry small measurement sensors and enable underwater exploration. Developing mUV's will enable ocean exploration that can lead to significant scientific discoveries and breakthroughs that will solve current world health and environmental problems. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2014

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-02-20T13:27:08Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Moura 2016 - Taxonomia e ditribuição de holoturias (Echinodermata Holothuroidea) do mar profundo brasileiro.pdf: 6982689 bytes, checksum: 8b2fe1855238da965159b25b0fec9d36 (MD5) / Made available in DSpace on 2017-02-20T13:27:08Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Moura 2016 - Taxonomia e ditribuição de holoturias (Echinodermata Holothuroidea) do mar profundo brasileiro.pdf: 6982689 bytes, checksum: 8b2fe1855238da965159b25b0fec9d36 (MD5) Previous issue date: 2016-02-23 / CAPES / A classe Holothuroidea (Echinodermata) possui cerca de 1400 espécies válidas recentes, encontradas desde a zona costeira rasa até as fossas hadais. O conhecimento acerca desses organismos no Atlântico Sudoeste é considerado bastante limitado. Este trabalho tem como objetivo principal ampliar o conhecimento sobre a riqueza dos holoturoides de oceano profundo no Brasil por meio de um estudo taxonômico e da distribuição das espécies encontradas no contexto da expedição MD55/Brasil, realizada em parceria entre a Universidade Santa Úrsula e o Muséum National d’Histoire Naturelle – Paris, e nos projetos “Heterogeneidade Ambiental da Bacia de Campos” (HABITATS) e “Avaliação das comunidades bentônicas nas Bacias Potiguar e do Ceará” (BPOT), coordenados pelo CENPES/PETROBRAS. O material estudado provém de três áreas principais: a Cadeia Vitória-Trindade e as Bacias de Campos e Potiguar. Foram examinados 430 exemplares da macro e megafauna com ocorrência entre 150 e 5092 m de profundidade e, destes, foram identificadas 24 espécies e 1 subespécie, pertencentes a 10 famílias. Foram reconhecidas quatro novas espécies da ordem Apodida pertencentes aos gêneros Labidoplax e Protankyra, além de Taeniogyrus yvonnae Moura, Campos & Esteves, 2015. Dez espécies constituem primeiros registros para águas brasileiras: Peniagone cf. islandica Deichmann, 1930; Psychroplanes obsoleta (Hérouard, 1889); Benthodytes typica Théel, 1882; Psychropotes semperiana Théel, 1882; Amphigymnas bahamensis Deichmann; 1930; Mesothuria gargantua Deichmann, 1930; Mesothuria maroccana Perrier, 1898; Zygothuria lactea (Théel, 1886); Euapta lappa (Müller, 1850) e Prototrochus aff. taniae O´Loughlin & VandenSpiegel, 2007. Molpadia musculus (Risso, 1826) e Molpadia parva (Clark, 1908), antes registradas apenas em listas taxonômicas, foram descritas e ilustradas aqui pela primeira vez. A biologia e ecologia das espécies foram abordadas, sempre que possível, incluindo observações de aspectos reprodutivos e comportamentais, também com base em observações de ROV. A riqueza variou de 8 a 15 espécies nas áreas de estudo, sendo mais alta na Bacia de Campos provavelmente devido à variedade de equipamentos utilizados na amostragem. Considerando-se apenas os holoturoides da megafauna, a riqueza nas áreas da Bacia de Campos e Potiguar foi similar (12 e 11 spp., respectivamente). Houve um aumento da riqueza com o aumento da profundidade na zona batial. Os táxons com distribuição mais ampla no Oceano Atlântico foram Deima validum validum Théel, 1879, Mesothuria verrilli (Théel, 1886) e Molpadia blakei (Théel, 1886). A fauna de holoturoides aqui avaliada possui afinidade com aquela de áreas bem conhecidas do Caribe. Os resultados obtidos refletem um acréscimo de 28% no total de espécies de holoturoides registrados no país (64), em relação ao número anterior (54). Reconhecendo que cerca de 70% da zona econômica exclusiva brasileira corresponde a águas profundas inexploradas, existe a necessidade de maximizar o esforço amostral nas zonas batial e abissal para ampliar o conhecimento de sua fauna e os padrões de distribuição dessa fauna. / The class Holothuroidea (Echinodermata) has about 1,400 recent valid species, found from the shallow coastal zone to hadal trenches. The knowledge on these South Atlantic organisms was considered very limited. The main objective of this work is to increase our knowledge on deep-sea holothuroid species richness from Brazil. This taking into account a detailed taxonomic and distribution study relative to the expedition MD55/Brasil, partnership between Universidade Santa Úrsula and Muséum National d’Histoire Naturelle – Paris, and the projects "Campos Basin Environmental Heterogeneity" (HABITATS); and "Assessment of benthic communities from the Potiguar and Ceará Basins" (BPOT), coordinated by CENPES/PETROBRAS. The sampled material came from three main areas: the Vitória-Trindade Seamount Chain; and Campos and Potiguar basins. A total of 430 macro and megafaunal specimens was examined. These occurred between 150 and 5092 m depth. A total of 24 species and 1 subspecies was identified, belonging to 10 families. Four new species of apodids were described from the genera Labidoplax and Protankyra, besides Taeniogyrus yvonnae Moura, Campos & Esteves, 2015. Ten species are first records for the Brazilian 8rgent: Peniagone cf. islandica Deichmann, 1930; Psychroplanes obsoleta (Hérouard, 1889); Benthodytes typica Théel, 1882; Psychropotes semperiana Théel, 1882; Amphigymnas bahamensis Deichmann; 1930; Mesothuria gargantua Deichmann, 1930; Mesothuria maroccana Perrier, 1898; Zygothuria lactea (Théel, 1886); Euapta lappa (Müller, 1850); Prototrochus aff. taniae O’Loughlin, 2007. Molpadia musculus (Risso, 1826) and Molpadia parva (Clark, 1908), previsouly recorded from taxonomic lists, were described and ilustrated here for the fist time. The species biology and ecology were addressed whenever possible, including reproductive and behavioral observations based on ROV imaging. Species richness ranged from 8 to 15 in the study área, being higher at Campos Basin, probably because of the use of a variety of sampling gears. Species richness at Campos and Potiguar and basins was similar (12 and 11 spp., respectively) taking into account only the megafaunal holothuroids. There was species richness increase in relation to increasing depth at the batial zone. Deima validum validum Théel, 1879, Mesothuria verrilli (Théel, 1886) and Molpadia blakei (Theel, 1886) have wide distribution in the Atlantic Ocean. The holothuroid fauna evaluated here showed affinity with that of well-known localities in the Caribbean. This study contributed to a 28% increase in holothuroid species number (69) in relation to those previously known for the country (54). About 70% of the Brazilian economic exclusive zone are deep sea biologically unexplored. Therefore, there is an urgent need to maximize the sampling effort of the bathyal and abyssal zones if we are to increase our knowledge on diversity and distribution patterns.

There is currently worldwide pressure to establish Marine Protected Area (MPA) networks which are self-sustaining and will persistently protect habitats and species. In order for MPA networks to be effective, the species targeted for conservation must be able to disperse between protected areas and maintain a gene-flow necessary for population sustainability and persistence. This warrants new research on how to quantify and map faunal dispersal to ensure that protection will be effective and sustainable. Population genetic methods have merit, with the ability to track parentage and gene flow between areas directly. However the costs, quantity of samples, and time required to genetically quantify dispersal for multiple species make these approaches prohibitive as the only method of assessment, especially in relatively inaccessible offshore waters. Dispersal modelling is now becoming more accessible and may fulfil immediate needs in this field (although ground truthing will be necessary in the future). There have been very few dispersal modelling studies focussed on deep sea or offshore areas, predominantly due to the lack of high resolution hydrodynamic models with sufficient geographic extent away from shore. Current conclusions have been drawn based on shallow water coastal studies, informing offshore MPA network size and spacing. However the differences between these two environments may mean that dispersal abilities are not comparable. Deep water receives less influence from wind and weather, and the scales are vastly different in terms of a) the depth ranges covered, b) the planktonic larval durations (PLDs) of animals, and c) the geographic areas concerned as a consequence. Global hydrodynamic models with reasonable resolution are now becoming more accessible. With the outputs from these models, and freely available particle simulators, it is becoming more practical to undertake offshore deep water dispersal studies. This thesis aims to undertake an analysis of these accessible modelling tools within a deep sea context. The guidelines which are currently available to dispersal modellers are yet to encompass the needs of deep water modellers which may require some additional considerations given the extended depth range covered and the different hydrodynamic drivers away from the air/sea interface. Chapter 1 reviews the larval dispersal process, the factors which may affect dispersal success, and those which should be incorporated into future predictions of dispersal. The current methods for assessing larval dispersal are explored covering genetics, elemental tagging and modelling approaches with an extended look at modelling considerations. Existing marine conservation policy is also touched on in the context of connectivity and larval dispersal. Chapter 2 is designed to inform future deep sea modellers on how to parameterise and understand a dispersal model. As models appear as a ‘black box’ to the majority of users, sensitivity tests can offer a way of scaling model inputs and tempering expectations from model outputs. A commonly used model pairing (the HYCOM hydrodynamic model and the Connectivity Modeling System) is assessed, using parameters which link to the temporal and spatial scales of mixing in the modelled system: timestep of particle tracer, horizontal and vertical positioning of release points, release frequency of larvae, and temporal range of simulation. All parameters were shown to have a decreased sensitivity with depth, with patterns reflecting local watermass structure. Future studies observing similar hydrodynamic conditions seeking to optimise their model set up would be advised to stratify their model release locations with depth. A means to incorporate all sensitivity test results into optimal input parameters for future studies is demonstrated. Chapter 3 investigates whether dispersal models provide any advantage over a “sphere of influence” estimate based on average current speeds and PLDs: there is no use pursuing dispersal modelling if the outputs are too erroneous to provide any advantage over a back-of-the-envelope calculation. This chapter examines the outputs of two dispersal models driven by two different hydrodynamic models in order to observe the variability in prediction between models. This model comparison revealed a greater disparity between hydrodynamic model predictions than has been previously understood by ecologists. The two models compared (POLCOMS and HYCOM) may equally be considered as suitable to promote realism in the study region, but slight differences in resolution and numerical error handling resulted in dispersal predictions from which opposing conclusions can be drawn. This chapter therefore emphasises the necessity for model ground truthing before predictions can be trusted. Chapter 4 assimilates the findings of the previous chapters and applies their advice to a study of MPA network dispersal connectivity. Using the hydrodynamic model which performed best in chapter 3 (HYCOM), a simulation was undertaken for cold water coral (Lophelia pertusa (Linnaeus 1758)) larval dispersal between already established MPAs in the NE Atlantic. As larval characters have only been observed ex situ, dispersal was simulated using two null models (passive and active vertical migration) and averaged to provide an intermediate prediction. A method for assessing dispersal within MPAs and MPA networks is offered based on the intermediate prediction, as well as a network wide assessment of the difference in dispersal patterns for passive and active larvae. It was found that the existing network performs well at supplying larvae to non-networked sites, but performs poorly at supplying other MPAs. The ‘best’ MPAs were central to the network and facilitated the traverse of regional gaps in suitable habitat. The ‘worst’ MPAs were peripheral to the network and small in size. Network-wide passive and active dispersal matrices had no significant difference between them. However site specific variability in the effect of vertical migration was detected subject to variability in local topographic barriers to dispersal, only some of which could be surmounted with vertical migration. All chapters aim to inform future deep sea dispersal modellers, and encourage exploration of this tool in other contexts, as well as marine conservation. The thesis cautions against the transplantation of shallow water assumptions to deep water environments, and advocates region specific studies and mandatory ground truthing of predictions. An upcoming study will ground truth the findings of this thesis with both genetic and oceanographic data, allowing the accuracy of study results to be quantified.

Bear Seamount (39° 55’ N; 67° 30’ W) is the westernmost peak of extinct undersea volcanoes in the New England Seamount Chain (Moore et al., 2003). It is located on the continental slope off Georges Bank, and is governed by unique environmental factors and currents that may be unlike those of the other seamounts (Moore et al., 2003). Previous cruises to this seamount have been successful in capturing abundant fishes, cephalopods and invertebrates (Moore et al., 2003; Moore et al., 2004; Moore et al., 2008), but only the distribution patterns of the fishes and cephalopods have been examined, leaving a lack of information on the deep-sea crustaceans. The diversity, catch per unit effort (CPUE) and biogeography of trawl-vulnerable micronekton in the vicinity of Bear Seamount were investigated, with primary focus on baseline data collection. Sixty-six species of pelagic Crustacea (Decapoda, Lophogastrida, and Euphausiacea) were collected at 35 trawl stations in the spring of 2003 and 2004 and fall of 2014 with the International Young Gadoid Pelagic Trawl (IYGPT) and a Polytron Midwater Rope Trawl (PMRT). Depths sampled ranged from the surface to 1700 m, with most trawls sampling primarily below 1000 m. When comparing relative biogeography of the nekton in IYGPT samples, the assemblage on the south side of the seamount was the most diverse, while the summit assemblage was the most abundant and species rich. In the PMRT samples, the summit assemblage was the most diverse and species rich while the assemblage on the west side had the greatest abundance. Overall CPUE was dominated by cold temperate species, typical of mid- to higher latitudes in the North Atlantic. Eusergestes arcticus and Meganyctiphanes norvegica were particularly dominant in both the IYGPT and PMRT samples. At least two species were new records for Northwest Atlantic waters and may have traveled by means of currents and/or from nearby seamounts.

This thesis presents the first description of the geographic and depth distributions of pelagic decapod shrimps in the area located around the Deepwater Horizon oil spill, based on the NOAA (National Oceanic and Atmospheric Administration) NRDA (National Resource Damage Assessment) trawl samples collected from April – June, 2011. This information is important in ecosystem models investigating trophic effects of the spill because pelagic decapod shrimp are consumed by a variety of organisms occupying higher trophic levels. One of the most abundant and diverse groups of decapods is the Family Oplophoridae. Their roles in pelagic food webs in the Gulf of Mexico (GOM) and other deep-sea ecosystems makes them ideal candidates for study; however, only a limited amount of research has been conducted on their distribution and reproductive biology. In the northeastern GOM, all previous studies have been conducted at Standard Station in the eastern Gulf (27°N, 86°W) (Hopkins and Lancraft, 1984; Hopkins et al., 1989; Hopkins and Gartner, 1992; Hopkins et al., 1994). The current study is unique because 1) it provides data from regions of the Gulf where oplophorids have never been studied, 2) allows for comparisons of distributions and abundances of oplophorid species in both the mesopelagic and bathypelagic zones by using a continuous data set, and 3) compares assemblages from two distinct bathymetric environments in the northeastern GOM: continental slope (200-1000 m bottom depth) and offshore (>1000 m). As the study site also encompasses the region most strongly impacted by the Deepwater Horizon oil spill, these data represent the first quantification of any component of the decapod crustacean assemblage in this location after the oil spill, and will be used for comparison with data obtained during future DEEPEND Consortium (Deep Pelagic Nekton Dynamics of the Gulf of Mexico) cruises to monitor changes, or lack thereof, in the assemblage after exposure to Deepwater Horizon oil and dispersants in the water column.

Cold-water corals, similar to tropical corals, contain a diverse and complex microbial landscape. Comprised of vital microscopic organisms (i.e. bacteria, viruses, archaea), the coral microbiome is a driving factor in the proliferation and survival of the coral host. Bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and a new genus. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the host genus was the primary driver of bacterial composition. The new coral genus, dominated by Alteromonadales and Pirellulales, had much higher species richness and a distinct bacterial community compared to Anthothela samples. Anthothela species had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Core bacterial diversity present across 90% of the Anthothela samples revealed genus-level conservation. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and Spirochaeta; the functional abilities of which contribute to a nearly complete nitrogen cycle. Dominant bacterial members of the new coral genus also had functional capabilities in nitrogen cycling. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Temperature microstructure observations obtained in Howe Sound are presented and related to their oceanographic context, In some instances, two free-falling probes have been launched simultaneously with separations of 10 to 20 m at the surface in an attempt to look at the lateral extent of temperature microstructure features. Patches of temperature gradient variance were found where the gradient presented peak values of both signs at smaller scales. These patches were usually observed by one probe only and seem to extend laterally over less than 20 m. In other instances the peak gradient values took mostly the same sign within a given patch. Such patches were usually detected by both probes, indicating that their horizontal extent is significantly larger than 20 m. These types of temperature microstructure are also discussed in terms of mechanisms that could provide an explanation for their existence. In Howe Sound's Inner Basin, the Deep Water occasionally receives large influxes of water from the Strait of Georgia. Otherwise, it stays essentially trapped behind a 75 m deep sill and becomes more homogeneous with time. A model is presented which relates the rate at which temperature becomes homogeneous to temperature gradient variance and the molecular coefficient of heat diffusion. Other parts of the water column are discussed in terms of the Osborn-Cox (1972) model of vertical heat transport. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Unknown

Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-06-29T17:44:44Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) 2011-Dissertação-VeronicaOliveira.pdf: 1667348 bytes, checksum: 414658d0814de55828e22ff1ca12623b (MD5) / Made available in DSpace on 2017-06-29T17:44:44Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) 2011-Dissertação-VeronicaOliveira.pdf: 1667348 bytes, checksum: 414658d0814de55828e22ff1ca12623b (MD5) Previous issue date: 2011-02-18 / Esse estudo representa a primeira avaliação da meiofauna em cânions submarinos no Atlântico Sul e, em especial, na Bacia de Campos. A meiofauna dos cânions Almirante Câmara e Grussaí e, em transectos adjacentes, foi analisada em quatro isóbatas (400m, 700m, 1.000m e 1.300m), em duas campanhas (maio/2008 e fevereiro/2009), considerando três estratos sedimentares (0-2cm, 2-5cm e 5-10cm). Para testar a significância da densidade e da riqueza da meiofauna, utilizou-se uma análise de variância fatorial com um “desenho amostral balanceado”, considerando como fatores: áreas, campanhas, isóbatas e estratos. A composição taxonômica da meiofauna, registrada nos cânions e em suas áreas adjacentes, foi semelhante à outros estudos realizados em áreas de mar profundo, sendo composta por 23 táxons, com Nematoda sendo o mais freqüente e abundante. As densidades da meiofauna nos sedimentos dos cânions e nas áreas adjacentes na Bacia de Campos foram altas, sendo aquelas encontradas dentro dos cânions mais elevadas do que nos seus transectos adjacentes correspondentes. As densidades foram, significativamente, maiores no estrato sedimentar superior em relação aos demais, em ambas as campanhas. No presente estudo observou-se que a abundância da meiofauna e a riqueza de grupos não apresentaram variações significativas em função do aumento da profundidade.O teste de correlação não indicou a presença de umarelação entre o carbono orgânico total e a riqueza/abundância da meiofauna. / This study represents the first meiofauna evaluation in submarine canyons from South Atlantic, with emphasis in Campos Basin. The meiofauna from Almirante Câmara and Grussaí canyons and adjacent transects were analyzed in 4 different isobaths (400m, 700m, 1000m and 1300m) during two campaigns (May/2008 and February/2009). Meiofauna core was divided in 0-2cm, 2-5cm and 5-10cm. A balanced four-way analysis of variance was applied in order to evaluate the difference in density and richness; for this analysis area, campaign, isobaths and layers were used as factors. Meiofauna composition from canyons and their adjacent areas were similar to other studies in deep-sea areas being composed of 23 taxa. Nematoda was the most frequent and abundant taxon. Meiofauna density from canyons and adjacent areas was high, but the density from canyons was higher than in their adjacent area in both sampling campaigns. The densities were significantly higher in the upper sedimentary strata in relation to others, in both campaigns. In this study we observed that the abundance and richness of meiofauna groups showed no significant variations as a function of increasing depth. There was no correlation between total organic carbon and meiofauna richness/abundance.

L'exploration de la diversité des êtres vivants dans les profondeurs marines est une histoire récente. C'est seulement à partir du XIXe siècle, sur un terrain vierge de toute connaissance, aussi bien géologique que biologique, que les scientifiques y révèlent progressivement la présence d'organismes, le plus souvent à l'occasion d'expédition à but économique. Par exemple, la pose de câbles télégraphiques a permis de découvrir fortuitement des organismes inattendus, ce qui a initié l'intérêt des naturalistes pour les grands fonds. Aujourd'hui, la connaissance de la diversité du vivant dans les profondeurs reste partielle. Les biologistes y font souvent face à la nouveauté et à l'imprévu, ce qui suscite un régime original de production des connaissances scientifiques reposant sur la description, elle-même fondée sur des hypothèses rarement explicitées, mal fondées sur un état de connaissance incomplet. D'autre part, ce sont souvent des intérêts économiques (tournés vers l'exploitation minière ou halieutique) qui orientent les explorations de la diversité des grands fonds vers certaines zones. Le présent travail doctoral développe une approche à la fois scientifique, historique et épistémologique liée des explorations marines et des données de biodiversité des profondeurs qui en résultent. Il s'agit de caractériser la transformation des représentations scientifiques du vivant et de sa diversité dans les profondeurs et d'identifier les facteurs et les éventuels biais méthodologiques qui déterminent l'acquisition et la structure de ces connaissances. Ce travail s'appuie sur un vaste corpus de documents rattachés au programme de campagnes océanographiques, initié en 1976 et mené conjointement par le MNHN (Muséum National d'Histoire Naturelle) et l'IRD (Institut de Recherche pour le Développement), appelé « Tropical Deep-Sea Benthos » (TDSB), anciennement « MUSORSTOM ». Ce programme informel d'exploration naturaliste cible depuis quarante ans la zone aphotique intertropicale principalement dans l'Indo-Ouest Pacifique. Une grande partie du travail a consisté en la structuration et la mise à disposition des données et des connaissances acquises pendant ce programme dans les bases de données du MNHN. Il a notamment permis de construire et d'alimenter la base de données des expéditions du MNHN (expeditions.mnhn.fr) dont le but est de fournir non seulement un référentiel géographique auquel les autres bases de données du MNHN peuvent se référer, mais aussi de documenter les métadonnées associées aux expéditions (rôle et spécialité des scientifiques participant aux campagnes, comptes-rendus de mission, photographies des spécimens et des récoltes). Parallèlement, un référentiel bibliographique a été conçu, qui permet de relier des publications aux différentes campagnes. Cette structuration des données au sens large permet de formuler des hypothèses sur la façon dont se construisent les représentations de la biodiversité et les explications qui s'y rapportent. L'analyse de ce corpus de publications a été menée en deux temps. Un premier moment descriptif a permis de dégager des tendances historiques et géographiques ainsi que des hypothèses sur les facteurs qui structurent le jeu de données obtenu. Une seconde approche a visé à étayer ces hypothèses en analysant finement le contenu des publications. Une grande partie de ces publications étant des travaux de taxonomie descriptive, cette analyse met en avant des constantes et des évolutions dans les pratiques de ce champ disciplinaire. En plus de l'analyse des documents associés au programme, un travail de contextualisation mené à partir de quinze entretiens de chercheurs permet de situer le programme TDSB dans l'histoire plus générale de l'exploration des grands fonds. / Exploring the diversity of living being in the deep sea is a recent story. It is only from the nineteenth century, on a virgin land of all knowledge, both geological and biological, that scientists gradually reveal the presence of organisms, usually on the occasion of expedition for economic purposes. For example, the laying of telegraphic cables has unexpectedly discovered organisms, which has initiated the interest of naturalists for the deep sea fauna. Today, the knowledge of the diversity of life in the depths remains partial. Biologists often face the novelty and the unexpected, which gives rise to an original regime for the production of scientific knowledge based on the description, which itself is based on hypotheses that are rarely explained and that are based on a state of incomplete knowledge. On the other hand, it is often economic interests (turned towards mining or fishing) that guide explorations of the diversity of the deep sea towards certain zones. The present doctoral work develops a scientific, historical and epistemological approach of the marine explorations and of the knowledge on biodiversity produces by this program. It is a question of characterizing the transformation of the scientific representations of the fauna and its diversity in the depths and of identifying the factors and the possible methodological biases which determine the acquisition and the structure of this knowledge. This work is based on a large corpus of documents related to the oceanographic cruises program, initiated in 1976 and conducted jointly by the MNHN (National Museum of Natural History) and the IRD (Research Institute for Development), called " Tropical Deep-Sea Benthos "(TDSB), formerly" MUSORSTOM ". This informal program of naturalist exploration has for forty years been targeting the intertropical zone, mainly in the Indo-West Pacific. Much of the work involved structuring and making available the data and knowledge gained during this program in the MNHN databases. In particular, it has helped to develop and complete the MNHN expedition database (expeditions.mnhn.fr), which aims to provide not only a geographical repository to which the other MNHN databases can refer, but also to document the metadata associated with the expeditions (role and specialty of the scientists participating in the cruises, mission reports, photographs of the specimens and substrate). At the same time, a bibliographic repository has been designed that links publications to different campaigns. This structuring of data in a broad sense makes it possible to formulate hypotheses on the way in which the representations of biodiversity and the explanations related to it are constructed. The analysis of this corpus of publications was conducted in two steps. A first descriptive approach made it possible to identify historical and geographical trends as well as hypotheses on the factors that structure the dataset obtained. A second approach aimed to support these hypotheses by finely analyzing the content of publications. Since most of these publications refer to a descriptive taxonomy field, this analysis highlights constants and evolutions in the practices of this disciplinary field. In addition to the analysis of the documents associated with the program, a contextualization work carried out from fifteen interviews of researchers makes it possible to situate the TDSB program in the more general history of deep-sea exploration.

Deep-sea corals have long been regarded as cold-water coral; however a reevaluation of their habitat limitations has been suggested after the discovery of deep-sea coral in the Red Sea where temperatures exceed 20˚C. To gain further insight into the biology of deep-sea corals at these temperatures, the work in this PhD employed a holotranscriptomic approach, looking at coral animal host and bacterial symbiont gene expression in Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus sp. sampled from the deep Red Sea. Bacterial community composition was analyzed via amplicon-based 16S surveys and cultured bacterial strains were subjected to bioprospecting in order to gauge the pharmaceutical potential of coralassociated microbes. Coral host transcriptome data suggest that coral can employ mitochondrial hypometabolism, anaerobic glycolysis, and surface cilia to enhance mass transport rates to manage the low oxygen and highly oligotrophic Red Sea waters. In the microbial community associated with these corals, ribokinases and retron-type reverse transcriptases are abundantly expressed. In its first application to deep-sea coral associated microbial communities, 16S-based next-generation sequencing found that a single operational taxonomic unit can comprise the majority of sequence reads and that a large number of low abundance populations are present, which cannot be visualized with first generation sequencing. Bioactivity testing of selected bacterial isolates was surveyed over 100 cytological parameters with high content screening, covering several major organelles and key proteins involved in a variety of signaling cascades. Some of these cytological profiles were similar to those of several reference pharmacologically active compounds, which suggest that the bacteria isolates produce compounds with similar mechanisms of action as the reference compounds. The sum of this work offers several mechanisms by which Red Sea deep-sea corals cope with environmental conditions in which no other deep-sea corals have yet to be reported. These deep-sea coral are associated with rich microbial communities, which produce molecules that induce bioactivity. The aggregate of this work provides direction for future research of Red Sea deep-sea coral and highlights the potential pharmacological benefit of conserving these species and their unique ecosystem.