A deep-sea time-lapse camera and several temperature probes were deployed on the Gulf of Mexico continental shelf at a biological community associated with a gas hydrate outcropping to study topographic and hydrologic changes over time. The deployment site, Bush Hill (GC 185), is located at 27°47.5' N and 91°15.0' W at depths of ~540m. The digital camera recorded one still image every six hours for three months in 2001, every two hours for the month of June 2002 and every six hours for the month of July 2002. Temperature probes were in place at the site for the entire experimental period. The data recovered provide a record of processes that occur at gas hydrate mounds. Biological activity was documented by identifying the fauna observed in the time-lapse record and recording the number of individuals and species in each image. 1,381 individual organisms representing 16 species were observed. Sediment resuspension and redistribution were regular occurrences during the deployment periods. By digitally analyzing the luminosity of the water column above the mound and plotting the results over time, the turbidity at the site was quantified. A significant diurnal pattern can be seen in both luminosity and temperature records, indicating a possible tidal or inertial component to deep-sea currents in this area. Contrary to expectations, there was no major change in shape or size of the gas hydrate outcrop at this site on the time frame of this study. This indicates that this particular mound was more stable than suggested by laboratory studies and prior in situ observations. The stable topography of the gas hydrate mound combined with high bacterial activity and sediment turnover appears to focus benthic predatory activity in the mound area. The frequency and recurrence of sediment resuspension indicates that short-term change in the depth and distribution of surface sediments is a feature of the benthos at the site. Because the sediment interface is a critical environment for hydrocarbon oxidation and chemosynthesis, short-term variability and heterogeneity may be important characteristics of these settings.

Density, species diversity, species richness, and evenness of bivalve mollusks were measured in the deep (0.2km to 3.7km) northern Gulf of Mexico to describe the community structure of benthic bivalve mollusks. Density decreased gradually from shallow continental slope depths, with remarkably high values in the Mississippi canyon, to the deepest sites. Diversity of bivalve mollusks increased from shallow continental slope depths, with low values in the Mississippi canyon, to a maximum at intermediate depths (1-2km), followed by a decrease down to the deepest locations (3.7km). Nine distinct groups were formed on the basis of the similarity in species composition. The pattern varied more abruptly on the slope compared to the deeper depths, possibly due to steeper gradients in physical variables. ANOVA indicated that the density of bivalve mollusks was not significantly different at different depths, was not significantly different on different transects, was not significantly different between basin and non-basin, but was significantly different in canyon and non-canyon locations. Similar distinctions were observed in diversity, except that basins were lower than non-basins. The patterns observed reflect the intense elevated input of terrigenous sediments accompanied by high surface-water plankton production from the Mississippi River to the north central gulf.

No description available.

Graduation date: 1997

Thesis (Ph. D.)--Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 1989. / Includes bibliographical references.

Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2009. / Includes bibliographical references.

Thesis (Ph.D.)--Aberdeen University, 2008. / "Oceanlab" Includes bibliographical references.

The discovery of deep-sea chemosynthesis-based ecosystems including hydrothermal vents and cold seeps has greatly expanded our view of life on Earth. Nevertheless, for many benthic organisms in these ecosystems, little is known about where they come from, how scattered populations are connected by larval dispersal, and how they adapt to the local environments. Mussels of Bathymodiolus platifrons (Bivalvia: Mytilidae) are one of the dominant and foundation species in deep-sea chemosynthesis-based ecosystems. They are known to have a wide geographic distribution, and are also one of the few deep-sea species capable of living in both hydrothermal vents [in Okinawa Trough (OT)] and methane seeps [in the South China Sea (SCS) and Sagami Bay (SB)]. Previous population genetics studies of B. platifrons mostly relied on one to several genes, which suffered from the lack of sensitivity required to resolve their fine-scale genetic structure, and were unable to reveal their adaptation to the local environments. With the repaid development of molecular techniques, it is now possible to address their demographic mechanisms and local adaptation from a genome-wide perspective. Therefore, in the first part of my thesis, I aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for B. platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) approach, assess the potential use of SNPs in detecting fine-scale population genetic structure and signatures of diversifying selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781 720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified from 28 B. platifrons individuals collected from a methane seep in the SCS and a hydrothermal vent in the middle OT (M-OT), with nine outlier SNPs showed significant evidence of diversifying selection. The small FST value (0.0126) estimated based on the neutral SNPs indicated high genetic connectivity between the two populations. However, the permutation test detected significant differences (P < 0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the neutral or outlier SNPs also showed that the two populations were genetically differentiated. This initial study successfully demonstrated the applicability of combining genome sequencing and 2b-RAD in population genomics studies of B. platifrons. Besides, using the survey genome of B. platifrons as a reference, a total of 10 199, 6429, and 3811 single nucleotide variants (SNVs) were detected from three bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides, and Idas sp. These results highlighted the potential of cross-species and cross-genus applications of the B. platifrons genome for SNV/SNP identification among different bathymodioline lineages, which can be further used in various evolutionary and genetic studies. To have a deeper understanding of how individuals of B. platifrons are connected among and adapt to their habitats, in the second part of my thesis, I used both mitochondrial genes and genome-wide SNPs to conduct a more comprehensive population genetics/genomics study of B. platifrons. Three mitochondrial genes (i.e. atp6, cox1, and nad4) and 6398 SNPs generated by 2b-RAD were obtained from 110 B. platifrons individuals from six representative locations along their known distribution range in the Northwestern Pacific. The small FST values based on both types of genetic markers all revealed high genetic connectivity of B. platifrons, which may have been driven by the strong ocean currents (i.e. Kuroshio Current, North Pacific Intermediate Water). However, when using SNP datasets rather than mitochondrial genes, individuals in the SCS were identified as a distinct genetic group, indicating the Luzon Strait may serve as a dispersal barrier that limits their larval exchange between the SCS and the open area in the Northwestern Pacific. Moreover, a genetic subdivision of B. platifrons in the southern OT (S-OT) from those in M-OT and SB was observed when using 125 outlier SNPs for data analyses. The outlier-associated proteins were found to be involved in various biological processes, such as DNA and protein metabolism, transcription and translation, and response to stimulus, indicating local adaptation of B. platifrons even they are confronted with extensive gene flow in the OT-SB region. Furthermore, by using SNP datasets, populations in S-OT were revealed to be the source of gene flow to those in the SCS, M-OT, and SB. Overall, these results offered novel perspectives on the potential forces that may have led to the genetic differentiation and local adaptation of B. platifrons, which can serve as an example for other deep-sea species with high dispersal potential, and contribute to the designation of marine protected areas and conservation of deep-sea chemosynthesis-based ecosystems. Molluscan shell formation is one of the most common and abundant biomineralization processes in metazoans. Although composed of less than 5 wt% of the molluscan shells, shell matrix proteins (SMPs) are known to play multiple key roles during shell formation, such as providing a gel-like micro-environment to favour mineral precipitation, promoting crystal nucleation, as well as guiding and inhibiting crystal growth. To date, all studies on SMPs have focused on molluscs in terrestrial and shallow-water ecosystems with no reports for those living in the deep ocean. Herein, the third part of my thesis was to study the shell proteomes of B. platifrons and its shallow-water relative Modiolus philippinarum with the aim to bridge such knowledge gaps in biomineralization studies. A total of 94 and 55 SMPs were identified from the shell matrices of B. platifrons and M. philippinarum, respectively, with 31 SMPs shared between two species. These SMPs can be assigned into six broad categories, comprising calcium binding, polysaccharide interaction, enzyme, extracellular matrix-related proteins, immunity-related proteins, and those with uncharacterized functions. Many of them, such as tyrosinases, carbonic anhydrases, collagens, chitin-related proteins, peroxidases, as well as proteinase and proteinase inhibitor domain-containing proteins, have been widely found in molluscan shell matrices and other metazoan calcified tissues (e.g. exoskeletons of corals, tubes of tubeworms), whereas some others, such as cystatins, were found for the first time in molluscan shell matrices, and ferric-chelate reductase-like proteins and heme-binding proteins were to be detected for the first time in metazoan calcified tissues. This is the first report of the shell proteome of deep-sea molluscs, which will support various follow-up studies to better understand the functions of these SMPs, especially in relation to environmental adaptation. Overall, my population genetics/genomics studies have improved our understanding of the population dynamics, genetic connectivity, fine-scale genetic structure, and local adaptation of B. platifrons in the Northwestern Pacific, and my proteomics study has shed light on the biomineralization processes of molluscs in the deep ocean.

Organismos de mar profundo encontram limitações na disponibilidade de alimentos e exploram enriquecimentos orgânicos esporádicos que chegam ao assoalho oceânico. O objetivo deste trabalho foi descrever a diversidade das comunidades bacterianas associadas a parcelas sintéticas e orgânicas (vértebras de baleia e blocos de madeira) no Espírito Santo, Rio de Janeiro e São Paulo a 3.300 m de profundidade, avaliando a influência dos substratos e da localização geográfica sobre essas comunidades. Foi realizada a extração de DNA e amplificação do gene RNAr 16S para sequenciamento por Illumina Miseq e análises estatísticas pelo Qiime. Os Gêneros dominantes nos substratos sintéticos, madeira e vértebras foram Psychroserpens (Flavobacteriia), Phaeobacter, (Alphaproteobacteria), Desulfobacter, (Deltaproteobacteria), respectivamente. Com base nos resultados obtidos, afirma-se que o tipo de substrato teve maior influência do que a localização geográfica sobre a estrutura das comunidades bacterianas. / Deep sea organisms found limitations in the availability of food and exploit sporadic organic enrichments that reach the ocean floor. The aim of this study was to describe the diversity of bacterial communities associated with synthetic and organic substrate (whale bone and wood blocks) in Espírito Santo, Rio de Janeiro and Sao Paulo to 3,300 m deep, assessing the influence of substrates and location geographical about these communities. 16S rRNA sequencing was performed by Illumina Miseq and statistical analysis by Qiime. The dominant genera in synthetic substrates, wood and vertebrae were Psychroserpens (Flavobacteriia), Phaeobacter (Alphaproteobacteria) and Desulfobacter, (Deltaproteobacteria), respectively. Based on these results, it is stated that the substrate type had greater influence than geographic location on the structure of bacterial communities.

abstract: This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities in the deep-sea water of the Pacific Ocean. Both RT-PCR and qRT-PCR approaches were employed to detect expression of the genes involved in photosynthesis of photoautotrophic organisms. Positive results were obtained and further proved the functional activity of these detected photosynthetic microbes in the deep-sea. Metagenomic and metatranscriptomic data was obtained, integrated, and analyzed from deep-sea microbial communities, including both prokaryotes and eukaryotes, from four different deep-sea sites ranging from the mesopelagic to the pelagic ocean. The RNA/DNA ratio was employed as an index to show the strength of metabolic activity of deep-sea microbes. These taxonomic and functional analyses of deep-sea microbial communities revealed a `defensive' life style of microbial communities living in the deep-sea water. Pseudoalteromonas sp.WG07 was subjected to transcriptomic analysis by application of RNA-Seq technology through the transcriptomic annotation using the genomes of closely related surface-water strain Pseudoalteromonas haloplanktis TAC125 and sediment strain Pseudoalteromonas sp. SM9913. The transcriptome survey and related functional analysis of WG07 revealed unique features different from TAC125 and SM9913 and provided clues as to how it adapted to its environmental niche. Also, a comparative transcriptomic analysis of WG07 revealed transcriptome changes between its exponential and stationary growing phases. / Dissertation/Thesis / Ph.D. Civil and Environmental Engineering 2013