Sedimentos de mar profundo são ambientes estáveis e homogêneos, apesar disso, eles apresentam uma grande variedade de habitats disponíveis, possibilitando uma alta diversidade microbiana. A distribuição espacial dos micro-organismos é influenciada por fatores locais e regionais. Os fatores locais são associados à estrutura do ambiente e os fatores regionais, a limitação na dispersão dos micro-organismos que compõem as comunidades e eventos históricos que eventualmente podem modificar o ambiente. Eventos como a liberação de hidrocarbonetos das camadas mais profundas do sedimento para superfície podem alterar os padrões de distribuição espacial das comunidades microbianas, devido o aumento na disponibilidade de carbono e consequentemente selecionando as espécies capazes de degradá-los. Esses eventos são denominados de exsudações de asfalto e foram encontradas na região de estudo. Considerando a falta de conhecimento e a importância dos micro-organismos em sedimentos de mar profundo do oceano Atlântico Sul, o objetivo desse estudo foi compreender os padrões de diversidade microbiana nessas regiões e também investigar como o óleo proveniente da exsudação de asfalto influência as comunidades de micro-organismos no seu entorno. Esse estudo foi realizado na região do Platô de São Paulo que foi dividido em duas regiões, norte e sul. A diversidade microbiana foi estudada em 14 amostras de sedimento de mar profundo, nove amostras na região norte e cinco na sul. A exsudação de asfalto foi encontrada na região norte, influenciando diretamente três das nove amostras. As comunidades foram estudadas através dos métodos de eletroforese em gel de gradiente desnaturante (DGGE), PCR quantitativa (qPCR) e sequenciamento de última geração (Ion Torrent). A distribuição espacial das comunidades foi analisada em diferentes escalas espaciais: verticalmente, variando com a profundidade do sedimento (≤ 4 cm), localmente, em cada uma das regiões amostradas (1-34 Km) e regionalmente, comparando as regiões norte e sul (> 250 Km). O perfil da comunidade obtido com a técnica de DGGE mostrou que as comunidades microbianas foram menos similares entre as regiões e apresentaram relação com a distância geográfica para arqueia e bactéria. Os valores de similaridade foi maior localmente do que regionalmente. A similaridade obtida nas camadas de profundidade analisadas foi alta e não houve relação com a distância geográfica. O número de células entre as camadas de profundidades foi diferente, com tendência de diminuição com o aumento da profundidade. As classes bacterianas mais abundantes foram Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). A composição das comunidades influenciadas pela exsudação de asfalto não teve relação com a presença do óleo ou com as camadas de profundidade. A distância geográfica e a exsudação de asfalto foram importantes fatores para determinação da distribuição geográfica das comunidades microbianas em sedimento marinhos profundos do Platô de São Paulo. Apesar da ausência de relação entre o óleo proveniente da exsudação de asfalto e a composição das comunidades, a alta abundância de Alphaproteobacteria e a importância da distância dentro da região norte são indicativos do aumento da heterogeneidade causado pela exsudação de asfalto. Mais estudos procurando compreender a composição geoquímica dos sedimentos e do óleo são necessários para explicar como esses fatores influenciam a estruturação das comunidades microbianas estudadas. / Deep-sea sediments are stable and homogeneous environments, however, they have a high variety of available habitats, allowing a high microbial diversity to occur. Microbial spatial distribution is determined by local and regional factors. Local factors are associated to environment structure and regional factors, to microbial dispersal limitation and historical events that may cause environmental changes. Historical events such as hydrocarbon emanation from sub-seafloor to seafloor may change the patterns of microbial spatial distribution, due to an increase of carbon, thus, selecting species capable to degrade them. These events are denominated as asphalt seep and they were found on the studied region. Considering the lack of knowledge and the importance of microorganisms on deep-sea sediments from South Atlantic ocean, this study aims to understand the patterns of microbial spatial distribution and how the oil from asphalt seep influence the microbial communities. This study was realized in São Paulo Plateau region. The plateau was divided in two regions, north and south. Microbial diversity was studied from 14 deep-sea sediment samples, nine samples from north region and five from south region. The asphalt seep was found in north region from São Paulo Plateau, directly affecting three of the nine samples. The communities were studied through denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR) and next generation sequencing (Ion Torrent). The spatial distribution of the communities was analyzed at different spatial scales: sediment depth (≤ 4 cm), local (1-34 Km) and regional (> 250 Km). Microbial communities were less similar between regions and showing relation with geographic distance to achaea and bacteria. Similarity values within regions were higher then between them, but the geographic distance was also important to both domains, despite samples being closer. Similarity values between sediment depths were high and have no relation with geographic distance. The cell number between sediment depths was different, with tendency to decrease with depth increase. The most abundant classes were Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). The communities composition influenced by asphalt seep have no relation with oil presence and sediment depths. Geographic distance and asphalt seep were important factors to determine the spatial distribution of microbial communities in deep-sea sediments from São Paulo Plateau. Despite the absence of relation between oil from asphalt seep and communities composition, the high abundance of Alphaproteobacteria and the importance of distance within north region are indicative of heterogeneity increase caused by asphalt seep. More studies aiming to understand the geochemical composition from sediments and oil are necessary to explain how these factors influence the communities structure.

Parcelas orgânicas de macroalgas, madeira e carcaças de baleia criam importantes oasis de enriquecimento orgânico no assoalho marinho de regiões profundas, mas a estrutura e sucessão ecológica da macrofauna sedimentar ao redor destes ambientes ainda é pouco conhecida. Parcelas de macroalgas e madeira foram artificialmente implantadas próximas a uma carcaça de baleia de 30-ton hà uma profundidade de 1670 m na Bacia de Santa Cruz, Pacífico NE. Ao redor de cada ilha orgânica, foram estudados os padrões espaciais e temporais de enriquecimento sedimentar orgânico e a estrutura e sucessão temporal da macrofauna em escalas temporais que variam de 0.25 à 7 anos. Ainda, o nível de sobreposição entre espécies colonizadoras das parcelas orgânicas e na baleia, foram comparados com comunidades de exudações frias (uma localizada na bacia de São Clemente, Pacífico NE) e fontes hidrotermais. Em geral, a abundância da macrofauna sedimentar foi altamente elevada em períodos de intenso enriquecimento orgânico, com decréscimo da diversidade da macrofauna num raio de 0.5 metros das parcelas. Nas parcelas de macroalgas e madeira, espécies oportunistas e tolerantes à sulfetos atingiram altas densidades após o pico de enriquecimento orgânico sedimentar (0.25 e 1.8 anos, respectivamente), enquanto que ao redor da carcaça de baleia, a macrofauna foi também dominada por organismos quimiossintéticos com associações simbióticas bacterianas, e ainda espécies oportunistas que se alimentavam do abundante carpete bacteriano sobre a superfície sedimentar. Os sedimentos ao redor das parcelas de macroalgas e madeira sustentam baixas taxas de degradação microbiana e sulfeto intersticial, recrutando assim um limitado número de organismos quimioautotróficos e consequentemente com baixa sobreposição de espécies com outros ambientes redutores. Na carcaça de baleia, os sedimentos sustentam intensa degradação microbiana e altos níveis de sulfeto, mas diferenças marcantes nas biogeoquímica e nas cadeias tróficas presentes nestas carcaças resultam em baixa sobreposição de espécies com a fauna de exsudações frias e fontes hidrotermais. Conclui-se que sedimentos enriquecidos organicamente ao redor de macroalgas, madeiras e carcaças de baleia criam importantes hábitats para a persistência e evolução de espécies dependentes de condições sedimentares redutoras, e assim estas ilhas devem contribuir para a diversidade regional e global dos ecossistemas de mar profundo. / Sunken parcels of macroalgae, wood and whale carcasses provide important oases of organic enrichment at the deep-sea floor, but sediment community structure and succession around these habitat islands are poorly evaluated. We experimentally implanted parcels of kelp and wood falls nearby a 30-ton deep-sea whale-fall at 1670 m in the Santa Cruz Basin (SCr; NE Pacific). At each organic island, we aimed to evaluate patterns of organic enrichment and spatial and temporal patterns of macrofaunal community structure and succession over time scales of 0.25 to 7y. Additionally, species overlap between kelp-, wood- and whale-falls with nearby cold-seep communities were investigated. In general, the abundance of infaunal macrobenthos was highly elevated at periods of intense organic enrichment at all organic falls, with decreased macrofaunal diversity and evenness within 0.5 meters of the falls. At kelp and wood falls opportunistic species and sulfide tolerant microbial grazers (dorvilleid polychaetes) abounded after the peak of sedimentary enrichment (0.25y and 1.8y, respectively), while the whale-fall macrofauna was highly abundant from 4.5 to 6.8 y, and was dominated by enrichment opportunist, chemoautotrophic-symbiont-hosting and heterotrophic species grazing sulfur-oxidizing bacterial mats. Sediments around kelp and wood parcels provided lowintensity reducing conditions, which sustain a limited chemoautotrophically-based fauna, with low levels of species overlap among other chemosynthetic habitats in the deep NE Pacific. Whale-fall sediments harbor many species and trophic types not present in background sediments, but there were low levels of species overlap between the whalefall, cold seeps and hydrothermal vents, explained by differences in biogeochemistry and food webs among these habitats. We conclude that organically enriched sediments around kelp, wood and whale-falls may provide important habitat islands for the persistence and evolution of species dependent on organic- and sulfide-rich conditions at the deep-sea floor and contribute to regional and global diversity in deep-sea ecosystems.

Crude oil causes both lethal and sublethal effects on marine organisms, but the impact upon sensory function remains unexplored. Elasmobranchs rely upon the effective functioning of their sensory systems for use in feeding, mating, and predator avoidance. The objective of this study was to test the effect of crude oil upon the olfactory and electroreceptive sensitivity of the Atlantic stingray, Dasyatis sabina. The magnitudes of the electro-olfactogram (EOG) responses were significantly depressed by 26% (Glutamic Acid) to 157% (Cysteine) for all amino acids when stingrays were exposed to crude oil. The shapes of the EOG responses when exposed to oil were also significantly different, exhibiting a more protracted response compared to un-exposed stingrays. Oil exposed stingrays exhibited a significant decrease in orientation distance to prey-simulating electric fields. This study is the first to quantify the effects of crude oil on olfactory and electrosensory sensitivity of marine predators. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

Notre connaissance de la diversité virale associée aux microorganismes procaryotiques issus des sources hydrothermales océaniques profondes demeure encore limitée. Peu d’études se sont intéressées à l’abondance virale ou à l’impact des virus sur la mortalité microbienne au sein de ces écosystèmes. Le nombre de virus caractérisés, issus de ces environnements, reste faible. Deux virus, PAV1 et TPV1, associés à des archées hyperthermophiles anaérobies appartenant à l’ordre des Thermococcales ont été décrits dans notre laboratoire. Afin de poursuivre nos recherches sur la diversité virale infectant les microorganismes hydrothermaux marins, l’ordre bactérien des Thermotogales a été ciblé. Cet ordre est composé de bactéries chimioorganotrophes anaérobies pour la plupart hyper/thermophiles. Elles partagent la même niche écologique que les Thermococcales et sont métaboliquement proches. De nombreux transferts latéraux de gènes ont, par ailleurs, contribué à l’histoire évolutive des Thermotogales, subodorant l’implication potentielle de virus. La présence de séquences CRISPR a également été rapportée au sein de plusieurs génomes de Thermotogales, suggérant que les Thermotogales sont ou ont certainement déjà été exposées à des infections virales. Pour autant, à ce jour, les seuls éléments génétiques mobiles à avoir réellement été décrits chez les Thermotogales sont 3 miniplasmides et aucun virus. Une cinquantaine de souches de Thermotogales provenant majoritairement de la collection de notre laboratoire (Souchothèque de Bretagne et Collection Ifremer) a été passée au crible quant à la présence d’éventuels bactériovirus associés. A l’issue de ce criblage, des éléments à ADN extra-chromosomiques, incluant 2 plasmides et 7 bactériovirus (du type Siphoviridae) ont été découverts au sein de souches appartenant aux genres Thermosipho et Marnitoga. Des analyses préliminaires ont été réalisées sur ces différents éléments et l’un des nouveaux systèmes hôte/virus a été caractérisé en détail. MPV1 (Marinitoga piezophila virus 1) est un siphovirus-like tempéré isolé d’une bactérie piezophile, il constitue le premier bactériovirus associé à l’ordre des Thermotogales. La souche hôte est piezophile mais aisément cultivable à pression atmosphérique au terme de plusieurs repiquages. Si l’essentiel des analyses a été mené à pression atmosphérique, la production virale s’est avérée tout à fait effective à pression hydrostatique. Nous avons réalisé les analyses de la séquence complète du génome MPV1 (43,7 kb, extrait des capsides virales purifiées) et sa comparaison avec le provirus présent au sein du génome séquencé de Marinitoga piezophila KA3. Les analyses de ce génome viral ont suggéré une proximité évolutive de MPV1 avec les bactériovirus de Firmicutes. Nous avons également mis en évidence que le bactériovirus partage son hôte avec un élément génétique extra chromosomique circulaire de 13,3 kb (pMP1). Ce « ménage à 3 » est surprenant dans le sens où l’élément de 13,3 kb, contenant 13 ORF de fonctions majoritairement inconnues, utilise les capsides virales afin de se propager. Ceci pourrait, ainsi, illustrer un nouvel exemple de piratage moléculaire. / Our knowledge of the viral diversity associated to procaryotic microorganisms inhabiting the deep sea hydrothermal vents is still limited. Only few studies have focused on viral abundance and impact on microbial mortality within these ecosystems. A limited number of viruses from these environments were isolated and characterized. Two viruses, PAV1 and TPV1, associated to hyperthermophilic anaerobic Archaea, Thermococcales order, have ever been described in our laboratory. The topic of this phD thesis was to extend our investigation to other deep sea vent microorganisms in order to deepen our knowledge on the marine hydrothermal virosphere. We decided to focus more precisely on the bacterial order of Thermotogales. This order is composed of anaerobic chemoorganotrophic bacteria that are, for almost, hyper/thermophilic. They share the same ecological niche as the Thermococcales and are metabolically close. Numerous lateral gene transfers have contributed to the evolutionary history of the Thermotogales, implying the potential involvement of viruses. The presence of CRISPRs has also been reported in many genomes, suggesting that Thermotogales certainly are or have been exposed to viral infections. However, up till now, only 3 miniplasmids have been described within Thermotogales and no viruses. Fifty strains of Thermotogales, mostly from the LM2E culture collection (Ifremer and “UBOCC”), were screened for the presence of potential bacteriovirus. Extrachromosomal DNA elements, including 2 plasmids and 7 bacterioviruses (siphovirus-like), were discovered amongst strains belonging to both Thermosipho and Marinitoga genera. Preliminary studies were performed on these elements and one of the new virus-host systems was characterized in details. MPV1 (Marinitoga piezophila virus 1) is a temperate siphovirus-like isolated from a piezophilic bacterium, it is the first bacteriovirus associated to the Thermotogales order. This host strain is piezophilic but easily cultivable at atmospheric pressure after several subcultures. Whether most experiments were performed at atmospheric pressure, the viral production appeared to be effective at hydrostatic pressure. We reported the analyses of the complete sequence of the MPV1 genome (43.7 kb, extracted from purified virions) and its comparison to the provirus present in the sequenced genome of Marinitoga piezophila KA3. Analyses of the viral genome suggested a close evolutionary relationship of MPV1 to Firmicutes bacterioviruses .We also reported that this bacteriovirus shares its host with a circular extrachromosomal genetic element of 13.3 kb (pMP1). This ‘ménage à trois’ is surprising in the sense where the 13.3kb element, that contains 13 ORFs of mostly unknown function, uses the viral capsid to propagate. Therefore, it would likely correspond to a new example of molecular piracy.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. / by Santiago Herrera Monroy. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 145-161). / Chemoautotrophic ecosystems at deep-sea hydrothermal vents were discovered in 1977, but not until 1995 were free-living autotrophic Epsilonproteobacteria identified as important microbial community members. Because the deep-sea is food-starved, the autotrophic metabolism of hydrothermal vent Epsilonproteobacteria may be very important for deep-sea consumers. However, quantifying their metabolic activities in situ has remained difficult, and biochemical mechanisms underlying their autotrophic physiology are poorly described. To gain insight into environmental processes, an approach was developed for incubations of microbes at in situ pressure and temperature (25 MPa, 24°C) with various combinations of electron donors/acceptors (H₂ , O₂ and NO₃- and ¹³HCO₃-) as a tracer to track carbon fixation. During short (18-24 h) incubations of low-temperature vent fluids from Crab Spa (9°N East Pacific Rise), the concentration of electron donors/acceptors and cell numbers were monitored to quantify microbial processes. Measured rates were generally higher than previous studies, and the stoichiometry of microbially-catalyzed redox reactions revealed new insights into sulfur and nitrogen cycling. Single-cell, taxonomically-resolved tracer incorporation showed Epsilonproteobacteria dominated carbon fixation, and their growth efficiency was calculated based on electron acceptor consumption. Using these data, in situ primary productivity, microbial standing stock, and average biomass residence time of the deep-sea vent subseafloor biosphere were estimated. Finally, the population structures of the most abundant genera Sulfurimonas and Thioreductor were shown to be strongly influenced by pO₂ and temperature respectively, providing a mechanism for niche differentiation in situ. To gain insights into the core biochemical reactions underlying autotrophy in Epsilonprotebacteria, a theoretical metabolic model of Sulfurimonas denitrificans was developed. Validated iteratively by comparing in silico yields with data from chemostat experiments, the model generated hypotheses explaining critical, yet so far unresolved reactions supporting chemoautotrophy in Epsilonproteo bacteria. For example, it provides insight into how energy is conserved during sulfur oxidation coupled to denitrification, how reverse electron transport produces ferredoxin for carbon fixation, and why aerobic growth yields are only slightly higher compared to denitrification. As a whole, this thesis provides important contributions towards understanding core mechanisms of chemoautrophy, as well as the in situ productivity, physiology and ecology of autotrophic Epsilonproteobacteria. / by Jesse Christopher McNichol. / Ph. D.

This thesis aims to characterize the annelid diversity of whale bones implanted in the SW Atlantic at two different depths (1500 and 3300 m) and its relation with other whale falls and chemosynthetic environments. The first chapter presents a general introduction with a brief review on whale-fall composition and its importance to the deep-sea ecosystem. Chapter 1 also exhibits the distribution of annelid families showing that assemblages are probably under the control of oceanographic processes, such as water masses characteristics and direction of flow. The diversity of the most important whale fall specialist, Osedax, is explored in chapter 2. The distribution of Osedax species on the studied depths reinforces the importance of oceanographic processes for community structure. In this chapter we also compare Atlantic and Pacific populations of Osedax frankpressi. Interestingly, the family Capitellidae was the most abundant annelid in whale bones and, for this reason, the diversity of Capitella is evaluated in chapter 3, the only capitellid genus found in whale falls. The phylogenetic relationships of shallow-water and deep-sea Capitella are present in chapter 3, providing insights for the invasion and diversification of this genus in the deep-sea environment. In Chapter 4, the diversity and phylogeny of Sirsoe and Vrijenhoekia is investigated. The phylogenic analysis of both genera indicates the inclusion of Vrijenhoekia inside Sirsoe. Ten new Sirsoe species were found, some of them cryptic and some shared between Atlantic and Pacific whale falls. Only one new species was previously found in vents. Finally, chapter 5 highlights the contribution of this thesis to the knowledge of whale fall diversity, suggesting important issues for future studies. / Esta tese tem como objetivo caracterizar a diversidade de anelídeos de ossos de baleia implantados no Atlântico Sudoeste em duas profundidades diferentes (1500 e 3300 m), e a relação com outras carcaças de baleia e ambientes quimiossintetizantes. O primeiro capítulo apresenta uma introdução geral com uma breve revisão sobre a composição da fauna e sua importância ecológica para o ecossistema de mar profundo. O capítulo 1 também mostra a distribuição das famílias de anelídeos evidenciando que as assembleias provavelmente estão sob influência dos processos oceanográficos, tais como as características das massas d\'águas e seu fluxo direcional. A diversidade do especialista de carcaça, Osedax, é abordado no capítulo 2. A distribuição das espécies de Osedax nas profundidades estudadas reforçam a importância dos processos oceanográficos na estrutura da comunidade. Neste capítulo nós também comparamos as populações do Atlântico e do Pacífico de Osedax frankpressi. Surpreendentemente, a família Capitellidae foi o anelídeo mais abundante nos ossos de baleia, e por esta razão, a diversidade de Capitella, o único gênero de capitelídeo encontrado nas carcaças, é avaliada no capítulo 3. As relações filogenéticas entre Capitella de águas rasas e de mar profundo são apresentadas no capítulo 3, gerando percepções sobre a invasão e diversificação do gênero no mar profundo. No capítulo 4, a diversidade e filogenia de Sirsoe e Vrijenhoekia são investigadas, evidenciando a inclusão de Vrijenhoekia dentro de Sirsoe. Dez novas espécies de Sirsoe foram descritas, algumas delas crípticas e outras compartilhadas entre as carcaças de baleia do Atlântico e do Pacífico. Apenas uma espécie nova foi previamente registrada em fontes hidrotermais. Por último, o capítulo 5 ressalta a contribuição desta tese para o conhecimento da diversidade de carcaças de baleia, sugerindo questões importantes para futuros estudos.

Sedimentos de mar profundo são ambientes estáveis e homogêneos, apesar disso, eles apresentam uma grande variedade de habitats disponíveis, possibilitando uma alta diversidade microbiana. A distribuição espacial dos micro-organismos é influenciada por fatores locais e regionais. Os fatores locais são associados à estrutura do ambiente e os fatores regionais, a limitação na dispersão dos micro-organismos que compõem as comunidades e eventos históricos que eventualmente podem modificar o ambiente. Eventos como a liberação de hidrocarbonetos das camadas mais profundas do sedimento para superfície podem alterar os padrões de distribuição espacial das comunidades microbianas, devido o aumento na disponibilidade de carbono e consequentemente selecionando as espécies capazes de degradá-los. Esses eventos são denominados de exsudações de asfalto e foram encontradas na região de estudo. Considerando a falta de conhecimento e a importância dos micro-organismos em sedimentos de mar profundo do oceano Atlântico Sul, o objetivo desse estudo foi compreender os padrões de diversidade microbiana nessas regiões e também investigar como o óleo proveniente da exsudação de asfalto influência as comunidades de micro-organismos no seu entorno. Esse estudo foi realizado na região do Platô de São Paulo que foi dividido em duas regiões, norte e sul. A diversidade microbiana foi estudada em 14 amostras de sedimento de mar profundo, nove amostras na região norte e cinco na sul. A exsudação de asfalto foi encontrada na região norte, influenciando diretamente três das nove amostras. As comunidades foram estudadas através dos métodos de eletroforese em gel de gradiente desnaturante (DGGE), PCR quantitativa (qPCR) e sequenciamento de última geração (Ion Torrent). A distribuição espacial das comunidades foi analisada em diferentes escalas espaciais: verticalmente, variando com a profundidade do sedimento (≤ 4 cm), localmente, em cada uma das regiões amostradas (1-34 Km) e regionalmente, comparando as regiões norte e sul (> 250 Km). O perfil da comunidade obtido com a técnica de DGGE mostrou que as comunidades microbianas foram menos similares entre as regiões e apresentaram relação com a distância geográfica para arqueia e bactéria. Os valores de similaridade foi maior localmente do que regionalmente. A similaridade obtida nas camadas de profundidade analisadas foi alta e não houve relação com a distância geográfica. O número de células entre as camadas de profundidades foi diferente, com tendência de diminuição com o aumento da profundidade. As classes bacterianas mais abundantes foram Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). A composição das comunidades influenciadas pela exsudação de asfalto não teve relação com a presença do óleo ou com as camadas de profundidade. A distância geográfica e a exsudação de asfalto foram importantes fatores para determinação da distribuição geográfica das comunidades microbianas em sedimento marinhos profundos do Platô de São Paulo. Apesar da ausência de relação entre o óleo proveniente da exsudação de asfalto e a composição das comunidades, a alta abundância de Alphaproteobacteria e a importância da distância dentro da região norte são indicativos do aumento da heterogeneidade causado pela exsudação de asfalto. Mais estudos procurando compreender a composição geoquímica dos sedimentos e do óleo são necessários para explicar como esses fatores influenciam a estruturação das comunidades microbianas estudadas. / Deep-sea sediments are stable and homogeneous environments, however, they have a high variety of available habitats, allowing a high microbial diversity to occur. Microbial spatial distribution is determined by local and regional factors. Local factors are associated to environment structure and regional factors, to microbial dispersal limitation and historical events that may cause environmental changes. Historical events such as hydrocarbon emanation from sub-seafloor to seafloor may change the patterns of microbial spatial distribution, due to an increase of carbon, thus, selecting species capable to degrade them. These events are denominated as asphalt seep and they were found on the studied region. Considering the lack of knowledge and the importance of microorganisms on deep-sea sediments from South Atlantic ocean, this study aims to understand the patterns of microbial spatial distribution and how the oil from asphalt seep influence the microbial communities. This study was realized in São Paulo Plateau region. The plateau was divided in two regions, north and south. Microbial diversity was studied from 14 deep-sea sediment samples, nine samples from north region and five from south region. The asphalt seep was found in north region from São Paulo Plateau, directly affecting three of the nine samples. The communities were studied through denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR) and next generation sequencing (Ion Torrent). The spatial distribution of the communities was analyzed at different spatial scales: sediment depth (≤ 4 cm), local (1-34 Km) and regional (> 250 Km). Microbial communities were less similar between regions and showing relation with geographic distance to achaea and bacteria. Similarity values within regions were higher then between them, but the geographic distance was also important to both domains, despite samples being closer. Similarity values between sediment depths were high and have no relation with geographic distance. The cell number between sediment depths was different, with tendency to decrease with depth increase. The most abundant classes were Alphaproteobacteria (30%), Acidimicrobiia (18%), Gammaproteobacteria (16%), Deltaproteobacteria e Gemmatimonadetes (3%). The communities composition influenced by asphalt seep have no relation with oil presence and sediment depths. Geographic distance and asphalt seep were important factors to determine the spatial distribution of microbial communities in deep-sea sediments from São Paulo Plateau. Despite the absence of relation between oil from asphalt seep and communities composition, the high abundance of Alphaproteobacteria and the importance of distance within north region are indicative of heterogeneity increase caused by asphalt seep. More studies aiming to understand the geochemical composition from sediments and oil are necessary to explain how these factors influence the communities structure.

Parcelas orgânicas de macroalgas, madeira e carcaças de baleia criam importantes oasis de enriquecimento orgânico no assoalho marinho de regiões profundas, mas a estrutura e sucessão ecológica da macrofauna sedimentar ao redor destes ambientes ainda é pouco conhecida. Parcelas de macroalgas e madeira foram artificialmente implantadas próximas a uma carcaça de baleia de 30-ton hà uma profundidade de 1670 m na Bacia de Santa Cruz, Pacífico NE. Ao redor de cada ilha orgânica, foram estudados os padrões espaciais e temporais de enriquecimento sedimentar orgânico e a estrutura e sucessão temporal da macrofauna em escalas temporais que variam de 0.25 à 7 anos. Ainda, o nível de sobreposição entre espécies colonizadoras das parcelas orgânicas e na baleia, foram comparados com comunidades de exudações frias (uma localizada na bacia de São Clemente, Pacífico NE) e fontes hidrotermais. Em geral, a abundância da macrofauna sedimentar foi altamente elevada em períodos de intenso enriquecimento orgânico, com decréscimo da diversidade da macrofauna num raio de 0.5 metros das parcelas. Nas parcelas de macroalgas e madeira, espécies oportunistas e tolerantes à sulfetos atingiram altas densidades após o pico de enriquecimento orgânico sedimentar (0.25 e 1.8 anos, respectivamente), enquanto que ao redor da carcaça de baleia, a macrofauna foi também dominada por organismos quimiossintéticos com associações simbióticas bacterianas, e ainda espécies oportunistas que se alimentavam do abundante carpete bacteriano sobre a superfície sedimentar. Os sedimentos ao redor das parcelas de macroalgas e madeira sustentam baixas taxas de degradação microbiana e sulfeto intersticial, recrutando assim um limitado número de organismos quimioautotróficos e consequentemente com baixa sobreposição de espécies com outros ambientes redutores. Na carcaça de baleia, os sedimentos sustentam intensa degradação microbiana e altos níveis de sulfeto, mas diferenças marcantes nas biogeoquímica e nas cadeias tróficas presentes nestas carcaças resultam em baixa sobreposição de espécies com a fauna de exsudações frias e fontes hidrotermais. Conclui-se que sedimentos enriquecidos organicamente ao redor de macroalgas, madeiras e carcaças de baleia criam importantes hábitats para a persistência e evolução de espécies dependentes de condições sedimentares redutoras, e assim estas ilhas devem contribuir para a diversidade regional e global dos ecossistemas de mar profundo. / Sunken parcels of macroalgae, wood and whale carcasses provide important oases of organic enrichment at the deep-sea floor, but sediment community structure and succession around these habitat islands are poorly evaluated. We experimentally implanted parcels of kelp and wood falls nearby a 30-ton deep-sea whale-fall at 1670 m in the Santa Cruz Basin (SCr; NE Pacific). At each organic island, we aimed to evaluate patterns of organic enrichment and spatial and temporal patterns of macrofaunal community structure and succession over time scales of 0.25 to 7y. Additionally, species overlap between kelp-, wood- and whale-falls with nearby cold-seep communities were investigated. In general, the abundance of infaunal macrobenthos was highly elevated at periods of intense organic enrichment at all organic falls, with decreased macrofaunal diversity and evenness within 0.5 meters of the falls. At kelp and wood falls opportunistic species and sulfide tolerant microbial grazers (dorvilleid polychaetes) abounded after the peak of sedimentary enrichment (0.25y and 1.8y, respectively), while the whale-fall macrofauna was highly abundant from 4.5 to 6.8 y, and was dominated by enrichment opportunist, chemoautotrophic-symbiont-hosting and heterotrophic species grazing sulfur-oxidizing bacterial mats. Sediments around kelp and wood parcels provided lowintensity reducing conditions, which sustain a limited chemoautotrophically-based fauna, with low levels of species overlap among other chemosynthetic habitats in the deep NE Pacific. Whale-fall sediments harbor many species and trophic types not present in background sediments, but there were low levels of species overlap between the whalefall, cold seeps and hydrothermal vents, explained by differences in biogeochemistry and food webs among these habitats. We conclude that organically enriched sediments around kelp, wood and whale-falls may provide important habitat islands for the persistence and evolution of species dependent on organic- and sulfide-rich conditions at the deep-sea floor and contribute to regional and global diversity in deep-sea ecosystems.

The deep ocean (> 200-m depth) covers more than 65 percent of earth's surface and is known as the largest active carbon sink of the planet. Photosynthesis fixes inorganic carbon into organic rich-compounds to fuel the biological production in the upper ocean. A small portion of the photosynthetic carbon eventually sinks to the seafloor to support diverse deep-sea life. In this dissertation, the phytoplankton production and export flux of particulate organic carbon (POC) to the seafloor were linked to standing stocks and compositional changes of the deep-sea soft bottom assemblages. The pattern and processes of energy transfer from the surface ocean to the deep sea was examined by modeling the global benthic bacteria, meiofauna, macrofauna, and megafauna biomass from remotely sensed ocean color images and the seafloor relief. The analysis was then scaled down to the macrofauna of the Gulf of Mexico (GoM) to examine the global pattern on regional oceanic features with contrasting productivity regimes. These results suggested a universal decline of benthic standing stocks down the continental margins that is caused by an exponential decrease of export POC flux with depth. A revisit of historical epibenthic invertebrate sampling in the North Atlantic showed that both individual species and multi-species assemblages occurred in narrow depth bands that hugged the topography from the upper continental slope out to the Hatteras Abyssal Plain. The continuum compositional change suggested that the continuous decline of benthic food supply with depth was the potential driving force for the pattern of bathymetric faunal zonation. A broad, systematic survey across multiple depth transects in the northern GoM suggested that macrofauna zonation is not only taking place across isobaths, but also form the northeast to the northwest GoM due to a horizontal productivity gradient created by the nutrient-laden Mississippi River. Analyses of long-term demersal fish data from 1964 to 2002 in the northern GoM showed no evidence of large-scale faunal change across different sampling times. Base on the pooled data, a shift in rate of fish species replacement may be caused by complex biological interactions or changes in environmental heterogeneity along depth or productivity gradients.