The deep-sea is a vast and relatively sparsely characterized domain. As little as 0.01% of deep-sea benthic habitats have been characterized in detail. Characterizing the distribution of organisms and environmental components of the deep-sea is pivotal to the creation and implementation of successful resource management. Benthic habitat maps are a good method to inventory and characterize deep-sea habitats. Recent advances in technology, such as multibeam sonar and remotely operated vehicles (ROVs), have allowed for greater understanding of these ecosystems. As it is difficult and expensive to collect data deep-sea benthic community composition, environmental surrogates of biological data would be economically beneficial. Ideally, a surrogate is an easily-measured abiotic indicator that greatly influences benthic community composition. The quality of a surrogate can be extrapolated to represent the quality of benthic habitat. The Miami Terrace is a deep-sea ecosystem that has begun to be explored and characterized. Previous studies noted that community compositions vary with broad-scale geomorphology on the Miami Terrace. This study addresses a swath of data collected from the Miami Terrace to determine if geomorphology in high resolution bathymetry could serve as a viable surrogate to biological data for the initial characterization of benthic habitats on the Miami Terrace. Data from cable impact assessment surveys for the South Florida Ocean Measurement Facility (SFOMF) and the Department of Energy were utilized in this study. Images from these surveys were analyzed to generate and detail twelve transects across a section of the Miami Terrace. This cross section of the terrace had previously been sectioned into distinct geomorphologic zones (Messing et al., 2012). The geomorphologic zones assessed in this study were High Slope Inner Terrace (HSIT), Low Slope Inner Terrace (LSIT), High Slope Outer Terrace Platform (HSOTP), Low Slope Outer Terrace Platform (LSOTP), High Slope Outer Terrace Ridge (HSOTR), and Low Slope Outer Terrace Ridge (LSOTR). Images from these transects were analyzed to generate percent cover and community data. This data includes overall organism density, species richness, and an inventory of all organisms greater than 4 cm identified to the lowest taxonomic level possible. This data was taken in concert with previously collected environmental data (e.g. depth, slope, and geomorphology) and subjected to multivariate statistical analysis. Patterns in organism density across the transects align with the progression of the transects by slope and geomorphologic region. Depth was seen to increase from Inner Terrace to Outer Terrace Platform. The Outer Terrace Ridge exhibited an increase in the percent cover of hardbottom habitat; which is preferential for many organisms. This corresponded to a shift in the organism density of multiple Cnidarians and Poriferans. In particular, the density of stylasterids and several sponges increased towards the Outer Terrace Ridge. One High Slope Inner Terrace transect juts into the Outer Terrace Platform, and it was more similar to Outer Terrace Platform transects than those of the Inner Terrace. This suggests that area of Inner Terrace jutting into the Outer Terrace Platform may need to be reassigned as Outer Terrace Platform. Analysis of variance by region and slope yielded that the density of multiple species varies with geomorphology across the study area, and high slope areas had significantly higher species richness than areas of low slope. These results support that geomorphology could serve as a surrogate for the Miami Terrace; however, it is likely a combination of geomorphology and another environmental factor (e.g., percent cover substrate or depth) would better serve to predict distribution of species on the Miami Terrace. The results of this study support that geomorphologic region, slope, depth, and percent cover of substrate can be used to determine different deep-sea habitats on the Miami Terrace. The influence of geomorphology on organism densities was varied, and thus its predictive capacity and efficacy as a surrogate remains limited. Nevertheless, the necessity for ecological baselines to guide management decisions is greater than the uncertainty associated with the use of geomorphology as a surrogate on the Miami Terrace.

This thesis presents: 1) the first statistically rigorous support for the longstanding hypothesis that state of satiation modifies diel vertical migration patterns of deep-sea micronektonic crustaceans and fishes; and, 2) the first assessment of microplastic ingestion by deep-pelagic micronekton in the Gulf of Mexico and Straits of Florida. Deep-sea pelagic crustaceans and fishes significantly contribute to abundance and biomass of pelagic ecosystems, are frequently consumed by commercially valuable fishery species, and serve to transport both nutrients and pollutants between shallow and deep waters. The results presented herein will be valuable for assessing risk associated with potential biomagnification of plastic through consumption or indirect consumption of deep-sea biota. Moreover, these data demonstrate that the extent of feeding at depth by non-migratory taxa as well as non-migrating individuals of migratory taxa is substantial. Feeding at depth is usually excluded from biogeochemical models, and these data demonstrate that this is an important factor that must be included to obtain more precise estimates of active nutrient flux by micronekton.

Thesis. 1975. M.S.--Massachusetts Institute of Technology. Dept. of Meteorology. / Bibliography: leaves 70-72. / M.S.

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.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20442号 / 農博第2227号 / 新制||農||1050(附属図書館) / 学位論文||H29||N5063(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 澤山 茂樹, 教授 左子 芳彦, 准教授 中川 聡 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

The distribution of biodiversity on the planet faces dramatic spatial reorganization from climate change. This is especially true in the marine realm, where species often live near their physiological limits. Thus, effective conservation agendas for marine biodiversity must be predicated upon robust multi-scenario projections of climate-driven changes in oceanographic conditions. However, much of the theory and empirical work on distributional changes in marine biodiversity comes from shallow-water ecosystems. The deep seafloor (> 200 m) has received comparably little attention despite mounting evidence of the accrual of climatic changes within this largest habitable area of the planet. Here, I present a number of case studies predicting the effects of climate change on the distributions of cold-water coral (CWC) reef habitats and their associated fauna, using both modelling approaches and empirical data collected on multiple oceanographic cruises to the CWC reefs of the southeast USA (SEUS) in 2018-2019. These reefs are persistent features of continental margins (~200 – 4000 m ) around the globe, important biodiversity and biogeochemical cycling hotspots, and sentinels of marine climate change. In Chapter 2, I fit global habitat suitability models (HSMs) using publicly available oceanographic and biogeographic products to predict the occurrence of reef-forming CWC species and the reef habitat they form, testing for taxonomic and regional differences in their ecological niches. I then use an ensemble of global climate model outputs as inputs for ensemble HSMs projecting the distributions of these same taxa to 2100 in a range of climate scenarios, and test for differences in distribution changes across species and bioregions. In Chapter 3, I use higher-resolution regional and global climate products and data from multiple oceanographic cruises to the SEUS to build HSMs for this region; this data collation revealed the largest known, essentially continuous CWC reef province on the planet. The models located pivotal climate refugia primarily at deeper (> 600 m) eastward reef sites – notably including those outside of areas designated to protect coral from bottom-contact fisheries – that may remain suitable to 2100 while shallower sites are projected to experience catastrophic declines. In Chapters 4 and 5 I present community ecological work based from research expeditions to CWC reefs of the SEUS described in Chapter 2. In Chapter 4, I use video imagery and in situ collections of intact seafloor communities to test how the abundance, taxonomic and functional diversity, and community structure of invertebrate communities in hard-substratum ecosystems along the SEUS margin, including CWC reefs and submarine canyons change along biocomplexity (e.g. the percentage of live coral cover), bathymetric, and oceanographic gradients. In Chapter 5, I synthesize invertebrate and fish data from SEUS CWC reefs to fit Bayesian community-level joint HSMs predicting the occurrence and abundance of these faunas as functions of their ecological traits. These models reveal strong distinctions fish and invertebrates in their climate and habitat preferences at CWC reefs, suggesting opposing responses to climate change. Overall, Chapters 3-5 expand upon baseline descriptions of reef habitats and coral-associated fauna in the SEUS, testing for mechanisms driving observed ecological patterns across large environmental gradients. Together, this volume improves our understanding of the ecological drivers of vulnerable marine ecosystem occurrence and biodiversity, augmenting conservation efforts for these critical components of the global ocean. / Biology

As the largest and most poorly environment on Earth, the deep-sea is facing global threats from climate change and anthropogenic disturbance further compounded by the lack of critical baseline data on seafloor species composition and community structure. Many data-deficient regions include those in geographically-isolated offshore environments, like low-latitude seamounts, where sampling and surveys have been limited, resulting in critical knowledge gaps that do not allow for effective conservation measures to be realized. This work seeks to characterize the coral fauna of tropical seamount environments greater than 150 m depth and understand the environmental controls on species distribution and community assembly for long-lived, ecologically-important species, primarily from the Octocorallia, Antipatharia, Stylasteridae, and Scleractinia. Methodologies for accomplishing this research have included analysis of remotely operated vehicle (ROV) video surveys and identification of collected voucher specimens to understand biogeographic patterns within coral communities on seamounts and other rugged seafloor features in 3 different regions: the tropical western Atlantic (Anegada Passage), the equatorial central Pacific (Phoenix Islands), and the tropical eastern Pacific (Costa Rica). These regions represent vastly different oceanographic regimes in terms of biological productivity and water column structure resulting in differential effects on deep-sea coral communities. Evidence from these three regions has shown significant effects of the role that oceanic water masses have on structuring deep-water coral biodiversity and suggests that these features, along with other abiotic environmental variables, are important indicators for understanding species distribution patterns, community structure, and global biogeographic patterns. More broadly, the results of this work have demonstrated the capabilities of exploratory ROV surveys, across multiple platforms, to add practical knowledge to coral species inventories and identify bathyal biogeographic patterns in remote regions of the deep sea. The results of this work, serving as baseline coral biodiversity surveys for each area, are also germane to evaluating the effects of human-mediated disturbance and global climate change in the deep ocean. These disturbances also include ocean acidification, ocean deoxygenation, deep-sea mining, and bottom-contact fishing, all of which have been identified as threats to the seamount benthos. / Biology

Human population growth and global industrial development are driving potentially irreversible anthropogenic impacts on the natural world, including altering global climate and ocean conditions and exposing oceanic environments to a wide range of pollutants. While there are numerous studies highlighting the variable effects of climate change and pollution on marine organisms independently, there are very few studies focusing on the potential interactive effects of these stressors. The deep-sea is under increasing threat from these anthropogenic stressors, especially cold-water coral (CWC) communities which contribute to nutrient and carbon cycling, as well as providing biogenic habitats, feeding grounds, and nurseries for many fishes and invertebrates. The primary goals of this dissertation are to assess the vulnerability of CWCs to independent and interacting anthropogenic stressors in their environment; including natural hydrocarbon seepage, hydrocarbon and dispersant concentrations released during an accidental oil spill (i.e. Deepwater Horizon), and the interacting effects of climate change-related factors and hydrocarbon/dispersant exposure. To address these goals, multiple stressor experiments were implemented to assess the effects of current and future conditions [(a) temp: 8C and pH: 7.9; (b) temp: 8C and pH: 7.6; (c) temp: 12C and pH: 7.9; (d) temp: 12C and pH: 7.6] and oil spill exposure (oil, dispersant, oil + dispersant combined) on coral health using the CWC Lophelia pertusa. Phenotypic response was assessed through observations of diagnostic characteristics that were combined into an average health rating at four points during exposure and recovery. Regardless of environmental condition, average health significantly declined during 24-hour exposure to dispersant alone and increased temperature resulted in a delay in recovery (72 hours) from dispersant exposure. The overall gene expression patterns varied by coral colony, but the dispersant exposure elicited the strongest response. Gene ontology (GO) enrichment analysis revealed that L. pertusa likely experienced varying stages of the cellular stress response (CSR) during exposure to oil, dispersant, and a decrease in pH. The most severe responses were associated with the dispersant exposure including GO terms related to apoptosis, the immune system, wound healing, and stress-related responses. However, the oil exposure induced an upregulation of metabolic pathways and energy transfer but a downregulation of cell growth and development, indicating that the coral nubbins could have been reallocating resources and reducing growth to maintain cellular homeostasis. The decrease in seawater pH elicited a similar response to oil through the enrichment of terms associated with a reduction in the cell cycle and development. Interestingly, the increase in temperature did not elicit a CSR that was detectable in the gene expression data. To further investigate the influence of hydrocarbon exposure on CWCs, comparisons of gene expression profiles were conducted using Callogorgia delta colonies that live in close proximity to active hydrocarbon seepage (“seep”) areas with no current active seepage (“non-seep”) at two different sites in the Gulf of Mexico. There were fewer differentially expressed genes in the “seep” versus “non-seep” comparison (n=21) than the site comparison (n=118) but both analyses revealed GO terms indicating slight alterations in natural biological housekeeping processes, as opposed to a CSR. Our results indicate that distinct stages of the CSR are induced depending on the intensity of stress. This bolsters the idea that there is a stress response shared by all corals in response to a variety of stressors. These data provide evidence that CWCs can be more negatively impacted, both on the phenotypic and molecular levels, by exposure to chemical dispersants than to hydrocarbons alone. Gaining an understanding of how these communities respond, not only to independent stressors, but the combination of these stressors, provides vital information about how CWC communities will fair in current and future conditions. / Biology

The Coastal and Marine Ecological Classification Standard (CMECS) provides a comprehensive framework of common terminology for organizing physical, chemical, biological, and geological information about marine ecosystems. Federally endorsed as a dynamic content standard, all federally funded data must be compliant by 2018; however, applying CMECS to deep sea datasets and underwater video have not been extensively examined. The presented research demonstrates the extent to which CMECS can be applied to deep sea benthic habitats, assesses the feasibility of applying CMECS to remotely operated vehicle (ROV) video data in near-real-time, and establishes best practices for mapping environmental aspects and observed deep sea habitats as viewed by the ROV’s forwardacing camera. All data were collected during 2014 in the Northern Gulf of Mexico by the National Oceanic and Atmospheric Administration’s (NOAA) ROV Deep Discoverer and ship Okeanos Explorer.

The chemical diversity of the phylum Porifera have provided marine natural products (MNPs) such as alkaloids, terpenoids and peptides with ranging biological activity. Every two days a novel compound deriving from sponges are discovered. The aim of this report is to explore the metabolic diversity of deep-sea sponges collected from five different geographical locations. The metabolome of the deep-sea sponges was studied with tandem mass spectrometry (UPLC- MS/MS) and screened for peptides and other major compounds. The aim also includes the selection, isolation and characterisation of a compound obtained from the metabolic profiling of the sponges. The metabolic profiles of 25 sponges were screened. The specimens analysed in this report displayed great metabolic diversity and peptides, halogenated compounds as well as presumable alkaloids were found. The spectra of some specimens displayed low sensitivity which required optimisation such as increase of volume injection. Nevertheless, the report offers novel discoveries for sponges that have never previously been examined. The brominated compound derived from the sponge Desmacella annexa was analysed using large-scale extraction and different analytical techniques such as preparative-HPLC, Q-Tof-MS and NMR. However, the isolation of the target compound was unsuccessful due to co-extractant compounds and insufficient amount of the compound to perform further purification.  Nevertheless, the discoveries made from the metabolic profiles of the sponges may be of assistance when selecting potential bioactive compounds for further studies. Furthermore, bioassays may be performed in the future on the extracts obtained from the sponge Desmacella annexa.