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

A wealth of empirical and theoretical studies has investigated the consequences of biodiversity loss on ecosystem properties. Whilst the importance of biodiversity in mediating ecosystem properties has been established, the magnitude and direction of effects vary between studies and are dependent on the biotic and abiotic conditions of the experimental system. Consequently there are still significant gaps in our understanding of how species loss may affect ecosystem properties, what the underlying mechanisms are, and how the effects of species loss are modified by environmental context.

Previous pulse-chase experiments have revealed a wide diversity of benthic response patterns to organic matter (OM) input depending on environmental setting, benthic community structure and experimental conditions i.e. quantity and quality of the added OM.  However, the mechanisms and interaction of environmental and biological factors that produce an observed response pattern are poorly understood. The present thesis set out to improve our current understanding on the set of parameters that determine benthic response patterns.  The core of this study was based on two pulse-chase experiments in two bathyal settings: the Faroe-Shetland Channel (FSC) and the SW Cretan slope in the E. Mediterranean (E. Med).  The sub-zero temperatures in the FSC enabled the observation of the benthic response in “slow-motion” and showed that the response is not static but instead might go through various “phases”.  In the warm E. Med, C processing rates were considerably lower compared to previous measurements in adjacent regions.  The discrepancy was attributed to the particularly refractory sedimentary OM at the sampling station with apparent consequences for the physiological state of the bacterial community.  Both experiments showed that bacterial metabolism and its regulation is a key factor determining the reaction of the benthic community to OM inputs.  This thesis provided further understanding on the short-term fate of organic C in deep-sea sediments but also raised certain issues that could be addressed in future studies.

Thesis (Ph. D.)--Rutgers University, 2007. / "Graduate Program in Microbiology and Molecular Genetics." Includes bibliographical references (p. 102-114).

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / The mechanisms of faunal dispersal across ocean basins are key unknowns toward understanding of the modern biogeography and biodiversity of deep-sea fauna. Seamounts are considered to play a defining role in faunal evolution, acting as regional centers of speciation, "stepping-stones" for dispersal, and/or refugia for deep-sea populations. The overarching goal of this dissertation was to examine the role of seamounts in structuring marine biodiversity and biogeography. This study focused on North Atlantic seamounts, specifically the New England seamount chain, the Corner Rise seamounts, and Muir seamount, areas damaged and threatened by deep-sea fisheries and currently a focus of conservation efforts. Videographic analyses of biological community structure revealed distinct faunal assemblages, dominated by the Porifera, Cnidaria, and Echinodermata and structured by geographic region, depth regions (with apparent taxonomic breaks at 1300 m, 2300 m, and 2600 m), and substrate type (including natural/anthropogenic and abiotic substrates and biotic substrates). Amongst these assemblages, seven highly specific coral host- invertebrate associate relationships were identified. To investigate whether or not these broad community patterns were discernible at a genetic level, the 16S mtDNA gene was utilized as a genetic "barcode" within the Class Ophiuroidea, through which 22 putative species were identified, including four target species (Asteroschema clavigera, Ophiocreas oedipus, Ophioplinthaca abyssalis, and Ophioplinthaca chelys) for subsequent population genetic studies. Analyses of mitochondrial 16S and COI gene sequences revealed evidence for recent population expansion and estimates of recent high gene flow across all four species throughout the North Atlantic seamount region. / (cont.) However, genetic differentiation within populations of A. clavigera and 0. chelys within seamount regions was significant, suggesting that historical diversification has been mediated by a long-distance dispersal mechanism that homogenizes this genetic signal on a regional scale. In addition, comparisons of all ophiuroid populations revealed no congruent pattern of historical migration amongst seamounts, which may also be attributed to the varying levels of host specificity and reproductive strategy of each ophiuroid species. These results will guide future studies and conservation efforts to protect seamount communities vulnerable to deep-sea fishery activities. / by Walter W. Cho. / 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), 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.

There are a large number of research vessels and fishing vessels equipped with echosounders plying the world ocean, making continual observations of the ocean interior. Developing data collation programmes (e.g. Integrated Marine Observing System) and automated, repeatable analyses techniques enable the upper c. 1,200 meters of the world ocean to be sampled routinely, and for their characteristic deep scattering layers (DSLs) to be compared. Deep scattering layers are comprised of zooplankton (e.g. euphausiids) and fish, particularly myctophids or lantern fish, and comprise the majority of sub-surface biomass. Here we present, by the analysis of a global acoustic dataset, a mesopelagic biogeography of the sea. This was accomplished by (i) the collation and processing of a global active acoustic dataset, (ii) the development of a standardised and automated method of sound scattering layer (SSL) extraction and description, (iii) the derivation of the environmental drivers of DSL depth and biomass, (iv) the definition of a mesopelagic biogeography based on the drivers of DSL metrics and (v) the prediction, using output from the NEMO-MEDUSA-2.0 coupled model, of how the metrics and biogeography may change by 2100. Key findings include, the development of the Sound Scattering Layer Extraction Method (SSLEM) the inference that primary production, water temperature and wind stress are key drivers in DSL depth and biomass and that mesopelagic fish biomass may increase by 2100. Such an increase is a result of increased trophic efficiency from the shallowing of DSLs and rising water temperatures, suggesting, that as the climate warms the ocean is becoming more efficient. The biophysical relationships and biogeography derived here, serve to improve our understanding of mesopelagic mid-trophic level dynamics in open-ocean ecosystems. This will aid both fisheries and conservation management, which now adopt more holistic approaches when monitoring and evaluating ecosystem health and stability.

No description available.