With an increase in demand on deep-sea resources comes a need for appropriate and effective management of this ecosystem. The establishment of a representative network of deep-sea Marine Protected Areas offers one tool with which to address the conservation needs of the deep sea. While a number of deep-sea habitats have been identified as vulnerable to anthropogenic activities (e.g. cold-water coral reefs and sponge aggregations), poor knowledge of the distribution of these habitats hinders conservation efforts and network planning, and thus we need habitat maps. With improvements in acoustic data resolution acquired from the deep sea, and the ability to cover large areas rapidly, the use of acoustic techniques in mapping biological habitats is growing. Multibeam bathymetry and its derived terrain variables can potentially provide important information that can aid in the delineation and characterisation of biological communities. A necessary prelude to mapping is therefore the definition of biological assemblages for use as mapping units. Two megahabitat features (seamount and submarine canyons) were sampled using acoustic and ground-truthing to characterise and map the distribution of benthic assemblages. Species were identified as distinct morpho-types and catalogued, and still images quantitatively analysed. Standard multivariate community analysis was undertaken to define distinct faunal assemblage that may act as mapping units. Those clusters identified by the SIMPROF routine were taken against a set of criteria to reject/accept as robust assemblages that may be used as mapping units. Twenty two benthic assemblages or biotopes were defined from multivariate analysis of quantitative species data, 11 from the SW Approaches and 11 from Anton Dohrn Seamount, and a further one from video observations (SW Approaches). Taken against current definitions, 11 of these were considered as Vulnerable Marine Ecosystems (VME). Diversity was measured to compliment the comprehensive description of biotopes. The use of multivariate diversity indices proved better for comparing diversity of biotopes as it captures a more than one aspect of diversity of the community. Two biotopes were common to both megahabitat features, cold-water coral reef habitats, and those from Anton Dohrn Seamount were more diverse than from the SW Approaches. Modelling techniques were employed to test the relationship between biotopes and environmental and geophysical parameters, which may be used as surrogates to map VME. Generalised Additive Models of Vulnerable Marine Ecosystems revealed multibeam bathymetry and its derived parameters to be significant surrogate for mapping the distribution of some assemblages, particularly those that appear to be influenced by current regime; whilst not so well for those whose distribution is not so strongly current driven e.g. soft sediment communities. In terms of deep-sea mapping, the use of multibeam can prove a useful mapping tool if the resolution of the data is at an appropriate scale that will identify meso-scale geomorphological features, such as cliff-top mounds, that may act as proxies for occurrence of biotopes, but this relationship is still unclear. Surrogates were used to map VME across the seamount and submarine canyons, and full coverage maps were produced for all biotopes occurring on these megahabitat features.

Microphytobenthos are the dominant primary producers on estuarine mudflats playing a key role in the functioning of the ecosystem. Studies into microphytobenthic ecology have previously been limited by scale but the advent of fine scale analysis techniques (gm) as well as non-destructive sampling has enabled the system to be examined at a level not previously possible. This study examined the formation, structure and function of microphytobenthic biofilms using non-destructive (remote sensing by PAM fluorescence; fibreoptic light microprofiling) and destructive (cryo-freezing and Low temperature scanning electron microscopy) sampling. Many microphytobenthic organisms are motile and have evolved complex migratory strategies. Microphytobenthic migratory patterns are widely described but much remains to be elucidated about the controlling factors. The fluorescence parameter F015 (minimum fluorescence yield after 15 minutes dark adaptation) was used to monitor short-term changes in biomass at the sediment surface. Light, tidal state, endogeny and combinations thereof were all shown to control migration, demonstrating that predictable migratory rhythms cannot be assumed. Microscale sectioning showed that chlorophyll a was always concentrated in the top 400 gm (the photosynthetically active biomass). Clear migratory patterns were not detected using microscale sectioning therefore indicating that migration occurs over a scale < 400gm. Despite no changes in the chlorophyll a content in the surface layers, LTSEM analysis demonstrated diurnal taxonomic shifts providing circumstantial evidence that microphytobenthic cells sub-cycle at the sediment surface to optimise fitness. The light extinction co-efficient (k) of microphytobenthic biofilms significantly vaned with site, assemblage and also over time. 90% of the surface PPFD had always been attenuated by 400, and in many cases before 200. Traditional microphytobenthic primary productivity models do not account for changes in the spatial and temporal distribution of biomass or light attenuation and therefore their applicability to the real situation may be limited.

The maximum number (Nmax) of fish was recorded using baited underwater camera (BUC) techniques to study spatio-temporal changes of the fish community in localize areas. In the central North Sea (~100m depth) abundance models revealed that for both, whiting and flatfish, the Nmax was influenced by light level at the time of deployment. Nmax of hagfish was strongly related to current speed in a non-linear way with a predicted upper threshold (~11 cm.s-1) above which Nmax declined. Current speed and inter-annual variation had an important effect on haddock Nmax. Large predators that prompt avoidance mechanisms (e.g. large conger eel, marine mammals and fishing vessels) and bottom current speed >25 cm.s-1 can modify demersal fish behaviour depending on size and species and therefore have important effects on BUC-derived data. The BUC was applied for the first time to the monitoring of the Buzzard platform, a new oil and gas development in the central North Sea that host 12 demersal and benthic fish species. The benthic taxa, flatfish and hagfish, showed higher numbers closer to the platform whilst the most mobile species showed constant numbers (haddock) or highest numbers outside of the 500m of Exclusion Area (whiting). No significant changes in fish diversity were found between the areas surveyed before the platform construction. After the construction, the species richness and diversity were higher outside the 500m Exclusion Area surrounding the platform. Offshore sand banks, like oil platforms, can modify the composition of the local fish abundance. BUC and commercial trawl observations on the Jones Bank (75-150m depth, Celtic Sea) recorded 23 species, the highest richness, on top of the bank and 18 species on the slope and off-bank areas. Conger eel and Nephrops were both absent from the top of the bank site whereas haddock was only observed in the bank area.

Much of the world's oceans lie below a depth of 200 meters, but very little is known about the creatures that inhabit these deep-sea environments. The deep-sea fish family Melamphaidae (Stephanoberyciformes) is one such example of an understudied group of fishes. Samples from the MAR-ECO (www.mar-eco.no) project represent one of the largest melamphaid collections, providing an ideal opportunity to gain information on this important, but understudied, family of fishes. The key to the family presented here is the first updated, comprehensive key since those produced by Ebeling and Weed (1963) and Keene (1987). Samples from the 2004 MAR-ECO cruise and the U.S. National Museum of Natural History provided an opportunity to review two possible new species, the Scopelogadus mizolepis subspecies, and a Poromitra crassiceps species complex. Results show that Scopeloberyx americanus and Melamphaes indicoides are new species, while the two subspecies of Scopelogadus mizolepis are most likely o nly one species and the Poromitra crassiceps complex is actually several different species of Poromitra. Data collected from the MAR-ECO cruise provided an opportunity to study the distribution, reproductive characteristics and trophic ecology of the family Melamphaidae along the Mid-Atlantic Ridge (MAR). Cluster analysis showed that there are five distinct groups of melamphaid fishes along the MAR. This analysis also supported the initial observation that the melamphaid assemblage changes between the northern and southern edges of an anti-cyclonic anomaly that could be indicative of a warm-core ring. Analysis of the reproductive characteristics of the melamphaid assemblage revealed that many of the female fishes have a high gonadosomatic index (GSI) consistent with values found for other species of deep-sea fishes during their spawning seasons. / This may indicate that melamphaids use this ridge as a spawning ground. Diets of the melamphaid fishes were composed primarily of ostracods, a mphipods, copepods and euphausiids. Scopelogadus was the only genus shown to have a high percent of gelatinous prey in their digestive system, while Melamphaes had the highest concentration of chaetognaths. This work presents data on the ecology and taxonomy of the family Melamphaidae and provides a strong base for any future work on this biomass-dominant family of fishes. / by Kyle Allen Bartow. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

A variação batimétrica nos oceanos e suas mudanças ambientais associadas impõem limites à distribuição de espécies, modulando a ocorrência de indivíduos com diferentes formas, funções e histórias de vida de acordo com a profundidade, e sendo, portanto, importante para o entendimento de padrões da biodiversidade marinha. Este estudo objetiva inferir padrões de distribuição de hidroides no Oceano Atlântico e mares árticos e antárticos adjacentes a mais de 50 m de profundidade, buscando contribuir para o entendimento da diversificação e estruturação associadas à variação batimétrica que propiciaram a ocupação dos diferentes ambientes pelo grupo. Apresentamos pela primeira vez inferências das amplitudes de distribuição batimétrica das espécies, da variação de características funcionais de indivíduos e espécies com a profundidade e da distribuição da composição de espécies ao longo da profundidade e da latitude. Em conjunto, os resultados indicam que a distribuição de hidroides no Atlântico profundo está relacionada a fatores históricos e a gradientes ambientais associados às variações latitudinal e batimétrica. Os tamanhos reduzidos e a baixa fertilidade em mar profundo sugerem que a colonização e a evolução de hidroides ao longo da profundidade são principalmente influenciadas pela disponibilidade de alimento e pelas baixas densidades populacionais. Ainda, a maior proporção de espécies e indivíduos solitários em mar profundo e o maior uso de substratos não-consolidados sugerem influência da disponibilidade de substrato. A proporção de espécies capazes de liberar medusas abaixo de 50 m é geralmente menor que em águas rasas costeiras, mas a proporção aumenta com a profundidade, principalmente abaixo de 1.500 m. A liberação de medusas seria desvantajosa em um ambiente com baixas densidades populacionais, por aumentar a incerteza da fecundação dada pela dispersão de gametas, e despender mais energia para reprodução em um cenário de poucos recursos alimentares. Amplas distribuições batimétricas sugerem capacidade de dispersão vertical e alta tolerância às mudanças ambientais associadas à variação batimétrica. Os resultados indicam também que a colonização de hidroides em mar profundo ocorre em um sistema de fonte-sumidouro, no qual as populações de mar profundo seriam sustentadas por imigração de águas mais rasas. Mostramos neste estudo que hidroides são importantes habitantes do mar profundo e que o entendimento da diversidade do grupo neste ambiente se beneficiará de investigações em áreas ainda pouco amostradas, como latitudes tropicais sul e profundidades abaixo de 1.000 m / The bathymetric variation in the oceans and associated environmental changes impose limits on the distribution of species, modulating the occurrence of individuals with different forms, functions and life histories according to depth, and is therefore important for the understanding of marine biodiversity patterns. This study aims to infer patterns of hydroid distribution in the Atlantic Ocean and adjacent Arctic and Antarctic seas at more than 50 m deep, seeking to contribute to the understanding of the diversification and structuring associated with the bathymetric variation that favored the occupation of the different environments by the group. We present for the first time inferences on the bathymetric ranges of distribution of the species, on the variation of functional traits of individuals and species with depth, and on the distribution of the species composition along depth and latitude. Together, the results indicate that the distribution of hydroids in the deep Atlantic is related to historical factors and to the environmental gradients associated with latitudinal and bathymetric variations. Reduced sizes and low fertility in deep sea suggest that colonization and evolution of hydroids along depth are mainly influenced by food availability and low population densities. Also, the greater proportion of solitary species and individuals in the deep sea and the greater use of unconsolidated substrates suggest influence of substrate availability. The proportion of species capable of releasing medusae below 50 m deep is generally lower than in shallow coastal waters, but the proportion increases with depth, especially below 1,500 m. The release of medusae would be disadvantageous in an environment with low population densities, by increasing the uncertainty of fertilization given by the dispersion of gametes, and expending more energy for reproduction in a scenario of few food resources. Wide bathymetric distributions suggest vertical dispersal capacity and high tolerance to the environmental changes associated to the bathymetric variation. The results also indicate that colonization of hydroids in the deep sea occurs in a source-sink system in which deep-sea populations would be sustained by shallower water immigration. We show in this study that hydroids are important inhabitants of the deep sea and that the understanding of the diversity of the group in this environment will benefit from investigations in areas still poorly sampled, such as southern tropical latitudes and depths below 1,000 m

Understanding of the fundamental ecology of deep-sea ecosystems remains immature relative to more familiar shallow-water and terrestrial habitats, despite more than two hundred years of scientific investigation. This thesis aims to progress knowledge of deep-sea benthic ecology by the analysis of over three hundred box core samples collected from the Northwest Atlantic continental slope as part of the international NEREIDA programme. Aspects of the ecology of Peracarida (Crustacea) are studied, and this is facilitated by the coupling of a large faunal dataset with extensive environmental information. To further enhance the power of this dataset, phylogenetic and functional characteristics of assemblages are investigated. Using community phylogenetic methodology, it is demonstrated that the peracarid assemblages studied are structured more strongly by variation in environmental parameters than they are by competitive interactions. Analyses demonstrate that the intensity of bottom trawling, seafloor temperature, current speed, food availability, sediment characteristics and physical habitat heterogeneity all influence deep-sea peracarid assemblage biodiversity metrics. Further, the importance of high poriferan biomass for the promotion of peracarid assemblages of high density, biomass, richness and diversity is highlighted. Of relevance to the management of deep-sea ecosystems, the results of this thesis suggest that caution should be exercised when applying species distribution models to data-deficient environments, whilst the location of spatial closures in the NAFO Regulatory Area may not be fully optimal for the protection of all components of diverse benthic assemblages against the impacts of bottom trawling. The importance of deep-sea diversity is demonstrated by the finding of positive biodiversity – ecosystem functioning relationships. However, the form of these relationships is found to be dependent on the biodiversity and ecosystem functioning metrics employed, and a hypothesis for a generalised form of biodiversity – ecosystem functioning relationships is proposed. Finally, this thesis calls for more ambitious deep-sea ecological investigations, and it is hoped that its findings will encourage future research initiatives, helping to further illuminate this enigmatic and fascinating environment.

Biogenic “oozes” are pelagic sediments that are composed of > 30% carbonate microfossils and are estimated to cover about 50% of the ocean floor, which accounts for about 67% of calcium carbonate in oceanic surface sediments worldwide. These deposits exhibit diverse assemblages of planktonic microfossils and contribute significantly to the overall sediment supply and function of Florida’s deep-water regions. However, the composition and distribution of biogenic sediment deposits along these regions remains poorly documented. Seafloor surface sediments have been collected in situ via Johnson- Sea-Link I submersible along four of Florida’s deep-water regions during a joint research cruise between Harbor Branch Oceanographic Institute (HBOI) and Florida Atlantic University (FAU). Sedimentological analyses of the taxonomy, species diversity, and sedimentation dynamics reveal a complex interconnected development system of Florida’s deep-water habitats. Results disclose characteristic microfossil assemblages of planktonic foraminiferal ooze off the South West Florida Shelf, a foraminiferal-pteropod ooze through the Straits of Florida, and pteropod ooze deposits off Florida’s east coast. The distribution of the biogenic ooze deposits is attributed to factors such as oceanographic surface production, surface and bottom currents, off-bank transport, and deep-water sediment drifts. The application of micropaleontology, sedimentology, and oceanography facilitate in characterizing the sediment supply to Florida’s deep-water regions. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

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.

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.