The anomuran sub-family Lithodinae comprises a great diversity of morphological and ecological forms, whose global radiation has not been specifically addressed since the modern syntheses of plate tectonics, oceanography, species theory and cladistic systematics. The focus of this thesis was to investigate the origin and radiations of the deep-sea Lithodinae as a case study for interchanges between deep and shallow oceans in mobile benthic fauna. Molecular sequences were obtained from six genes (for 47 species belonging to 10 genera of Lithodidae) and different aspects of morphology were examined in order to identify nested monophyletic groups based on shared, derived characteristics. The hypothesis that lineage-specific temperature tolerances influence the distribution of deep- and shallow-water groups was tested by examining habitat alongside phylogeny. Lithodid ancestors are likely to have had a north Pacific, shallow-water distribution and planktotrophic larvae. Some shallow-water populations of Lithodidae are tied to locations north of 30°N because of the restricted thermal tolerance of pelagic larval stages; however, life-history changes allowed the subfamily Lithodinae to expand through the global deep sea, where they are now living at the frontier of their lower temperature threshold in the Southern Ocean. Phylogenies indicate the importance of large-scale dispersals within deep-sea groups, linked to the cold deep-water currents that connect the major oceans. The subfamily Lithodinae includes examples of at least two genera in which diverse morphologies have arisen within the deep ocean in the absence of discernable barriers to gene flow. Adult migration and larval dispersal partially explain the widespread occurrence of the Lithodidae, but this does not indicate that lithodids roam the ocean depths unconstrained by physical or chemical conditions. Climate change throughout the Cenozoic has substantially altered the marine environment and shaped the distribution and radiation of the extant Lithodidae. In the forthcoming years, measurable changes in ocean temperature, ocean currents and benthic habitat will affect the distribution of the lithodids and the communities they live in, as they have in the past.

Marine phytoplankton are central to biogeochemical cycling within the ocean, driving enzyme catalysed redox reactions using a set of evolutionary conserved metabolic proteins. Data are presented from four cruises in the North Atlantic in both the sub-tropics (D326, winter 2008 and FeAST, summer 2008) and the high latitudes (D350, spring 2010 and D354, summer 2010). Optimisation of quantitative immunoblotting enabled detection of target photosynthetic proteins and resulted in a method which provided extraction efficiencies averaging 71% 12% and good reproducibility. Quantification of target proteins within natural marine communities, are combined with photophysiological measurements and biochemical data, to determine protein distribution patterns and suggest potential acclimation patterns in response to environmental forcing. Quantification of photosystem II (PSII) and Rubisco, was achieved from phytoplankton communities in the sub-tropical North Atlantic, in both surface waters and from the deep-chlorophyll maximum (DCM). Increased PSII abundance, relative to total protein, observed in samples from the DCM suggest that phytoplankton within the sub-tropical North Atlantic, photoacclimate to lower irradiance by increasing the abundance of PSII reaction centres. Data collected from the high latitude North Atlantic (HLNA) during spring and summer 2010 suggest that, during summer, primary productivity in the Irminger Basin was limited by iron (Fe) availability while co-limitation by Fe and nitrate was constraining phytoplankton growth in the Iceland Basin. The most significant inter-season difference in protein abundance was a decrease in Rubisco in summer. This decline was potentially attributed to a decrease in nitrate availability between spring and summer. Low PSII:Chl a ratios, coupled with depressed photosynthetic efficiency (Fv/Fm), were observed in the Irminger basin during summer, potentially as a result of larger antenna sizes and/or excess uncoupled Chl-binding proteins, in response to Fe limitation. Nutrient addition incubation experiments in the HLNA, during summer 2010, further supported the in situ data. In particular, the molecular level response of these communities to Fe addition was characterised by a marked increase in PSII:Chl a. Overall this thesis has enabled absolute quantification of key photosynthetic proteins from natural communities in the North Atlantic and has addressed potential environmental drivers for changes in protein abundance. Future quantification of key photosynthetic proteins, in natural communities, will provide applications in primary productivity estimates.

Despite its extreme environmental conditions, the deep sea harbours a unique and species-rich fauna of mostly unknown age and phylogeny. Pennatulids (Anthozoa: Octocorallia) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied, in spite of their abundance and ecological importance in softbottom communities. Phylogenetic analysis of a combination of partial ND2 and msh1 sequences produced well-supported phylogenetic relationships for representative deepsea (and shallow-water) pennatulids at familial, generic and specific taxonomic levels. Generally, molecular data were congruent with current classification and previous phylogenetic reconstructions of the O. Pennatulacea based on morphology. Discrepancies were evident concerning the finer details for some families and genera: this can be attributable to the high frequency of homoplasy in pennatulids where reversals in evolution have led to taxa that possess apomorphic character states that are analogous with plesiomorphic traits. Genetic analysis gave strong support that highly-derived taxa occur in both shallow and deep water and that many may have differentiated and dispersed from the deep sea to the shallows. The Renillidae, which is considered one of the most primitive shallow-water families, evolved recently from deep-water ancestors. Conversely, the bathyal Anthoptilidae was the most primitive of families, and although more evidence is required, pennatulids as a group may have originated in deep water. The systematics of the exclusively deep-sea genus Umbellula, which contains fortytwo species, remains unclear despite the repeated attempts of revision. Incorporating new morphological and distributional data from the examination of recently collected material, together with type specimens, genetic analysis, and a critical study of the literature, fifteen Umbellula species are here considered valid, including three new to science. Eight species lack sclerites in the autozooids, U. magniflora, U. encrinus, U. antarctica, U. carpenteri and Umbellula sp.1 n. sp. (quadrangular axes), and U. huxleyi and U. pellucida (round axes); and seven possess autozooid sclerites, U. thomsoni and U. hemigymna (quadrangular axes), and U. monocephalus, U. aciculifera, U. durissima, Umbellula sp.2 n. sp. and Umbellula sp.3 n. sp. (round axes). Biogeographic data and genetic evidence supported the hypothesis that species of Umbellula differentiated in the Indo-Pacific. Many radiated southwards to the Antarctic and later north into the Atlantic, E Pacific, Indian and Arctic oceans, occupying bathyal and abyssal depths. Other, older species that evolved via a separate evolutionary pathway, may have originated in the Indo-Pacific, and dispersed to the Subantarctic (U. sp.2 n. sp.) or Indian and Atlantic oceans (U. monocephalus). Further, morphological examination of Umbellula showed it adapted to the oligotrophic conditions of the deep sea by reducing the number but increasing the size of the autozooids, and in doing so, enlarged the food-catchment area; abyssal species have done so even more extremely.

This thesis presents one of the most comprehensive studies on submarine canyons yet. It integrates data on the geology, geochemistry, sedimentology and oceanography of the Nazaré, Setúbal and Cascais canyons, west Iberian margin, in order to constrain the processes and controls of past and present sedimentation in this area. The results indicate that, during the glacial stages, turbidity currents are the dominant process of sediment transport, erosion and deposition in these canyons. Turbidity currents are mostly in the form of small-volume, high-frequency events that are generated by fluvial and hydrodynamic processes, and the flows remain mainly within the upper canyon. A smaller proportion of turbidity currents are large-volume, low-frequency, seismictriggered events that flush through the entire canyons. Catastrophic mass wasting is most prominent in Setúbal Canyon due to its closer proximity to the region’s active fault zone along the southern Iberian margin. During the Holocene, sedimentary activity in Setúbal and Cascais canyons continued in the form of frequent, canyon-flushing turbidity currents that ceased abruptly ca 6.4 ka. This interval corresponds to both a regional aridification event that affected the Mediterranean and northern African regions, and to a decline in rising sea level. A combination of the two events is interpreted as being the direct cause of the cessation in sedimentary activity on the continental margin. In Nazaré Canyon, sedimentary activity during the last ~1000 years has been dominated by a mid-canyon resuspension depocentre that is controlled by small-volume, low-energy, hydrodynamic-generated turbidity currents. This depocentre provides a unique high-resolution record of recent sedimentation in a deep-sea setting, preserving a potential forest fire debris signal that is linked to a change in climate during the Little Ice Age. The conclusions from this work are that sedimentation in the west Iberian canyons is controlled by the complex interplay between several variables, the most important ones being the source and supply of sediment, the hydrodynamic conditions on the shelf and slope, and the canyon morphology. The sedimentary activity in the river-fed Setúbal and Cascais canyons is found to be affected more by regional climatic changes than by eustatic sea-level changes, and in Nazaré Canyon by the supply of sediment along the shelf.

The formation of new ocean lithosphere at mid-ocean ridges is a fundamental component of the plate tectonic cycle, and through hydrothermal interactions with seawater is a major control on the composition of the oceans, ocean crust, and upper mantle. Two complementary approaches are used to investigate the thermal implications of endmember theoretical models that describe the accretion of the lower oceanic crust at fast spreading rates. The first approach uses the record of hydrothermal alteration of the ocean crust, including Sr and O-isotopes, to investigate and quantify the role of hydrothermal circulation during the accretion of the ocean crust. The second method uses diffusion based geospeedometry techniques to determine cooling rates in the ocean crust. Samples from two locations of ocean crust formed at fast spreading rates at the East Pacific Rise are used in these investigations, ODP Hole 1256D and Hess Deep. Hole 1256D provides the first intact sampling of a complete section of upper oceanic crust formed at a fast spreading rate and recovered the first in situ sampling of the dike/-gabbro boundary. Hess Deep is a tectonic window where the westward propagation of the Cocos-Naza Ridge has rifted ocean crust formed at the EPR and exposed the lower ocean crust at the seafloor. The whole rock profile for Hole 1256D reveals Sr isotopes in the volcanic sequence to be only slightly shifted from primary MORB values (0.70284-0.703814 compared to 1256 MORB of 0.70283). In contrast, Sr isotopes in the sheeted dike complex (0.70294-0.70536) are strongly elevated towards hydrothermal fluid compositions (0.70505-0.70525). Rocks of the plutonic complex are characterised by elevated Sr ratios along igneous contacts (up to 0.70524) but only limited increases in Sr isotopes relative to MORB in the centres of the gabbro bodies (0.70290-0.70396). The complementary oxygen isotope profile records the downwards transition from low temperature to high temperature hydrothermal alteration but contains small scale variation associated with changes in secondary mineral abundances and local fluid/rock ratios. Both the detailed Sr and O isotope profiles document the importance of dike margins and other igneous contacts as focussed pathways for fluid flow through the crust. The time-integrated fluid flux required to cause the observed Sr isotope profile through the sheeted dike complex is 2.0 - 2.6 x 106 kg/m2 and is consistent with fluid fluxes calculated for other crustal locations (e.g, Hole 504B, Pito Deep, Hess Deep). The heat flux required to sustain this fluid flux is equivalent to half of the latent heat released during the crystallisation of the lower ocean crust. At Hole 1256D the removal of heat by hydrothermal fluids was effcient and demonstrates that the fluid flux in the sheeted dikes must have removed some portion of the heat flux out of the lower ocean crust. In order to remove all of the latent heat of crystallisation from the lower crust, there must be significant hydrothermal circulation in the lower ocean crust.

No description available.

Naturally occurring sedimentation is an important habitat-structuring factor. Increased sedimentation through anthropogenic actions can result in adverse effects to organisms and communities. With industrial activities moving further offshore, new habitats and organisms are affected. Particular in the North-East Atlantic, anthropogenic activities including oil and gas exploration and trawling have been recognised as major hazards to organisms that are sensitive to sedimentation. Sessile filter-feeders, such as sponges, provide vital functions to benthic habitats in many ecosystems and are believed to be adversely affected by turbid waters and settling particles. This project aimed to investigate the effects of sedimentation events from natural and anthropogenic sources on three different sponge species from contrasting habitats, Suberites ficus (shallow water, high sedimentation rates), Sycon ciliatum (shallow water, low sedimentation rates) and Phakellia ventilabrum (deep water, low sedimentation rates). The responses of the three species to increased concentrations of sediment were assessed on a physiological and a transcriptional level. Exposure to drill cuttings from oil exploration was investigated in Sycon ciliatum and Phakellia ventilabrum. It was shown that contrary to the expectations, respiration rates of all investigated sponges were not affected by sedimentation. However, on a molecular level the genes of the stress protein heat shock protein (hsp70) and the enzyme nitric oxide synthase (nos) were significantly regulated during exposure to sediment. Surprisingly, the expression pattern of hsp70 and nos was not consistent between the sponge species. Hsp70 transcription did not change in Suberites ficus, it was down-regulated in Sycon ciliatum and up-regulated in Phakellia ventilabrum. The expression of nos was down-regulated in Suberites ficus and up-regulated in Sycon ciliatum and Phakellia ventilabrum. Stress reaction seemed to be specific to each sponge species and might be dependent on the exposure to sedimentation that naturally occurs in their habitat.

No description available.

When active venting has ceased, reduced minerals in hydrothermal mounds and sediments continue to provide an inorganic energy source for chemolithotrophic microbes. This research focuses on the nature of microbially-mediated metal transformations in hydrothermal sediments during sulphide alteration and their impact on the ultimate fate of hydrothermal sulphides on the seafloor. The core studied is more seawater altered than other cores studied at TAG and provides an insight into the bacterial and archaeal communities as well as the geochemical processes taking place in highly altered metalliferous sediments. This study combines geochemical approaches with microbiological and organic biomarker measurements within the suboxic transition zone of sulphidic sediments to characterise the reactions and microbial communities present. This integrated approach demonstrates that (a) there is biogeochemical zonation within the sediment sequence with distinct microbial communities present at the sulphide-oxic seawater transition, (b) the microbes identified are associated with Fe and S redox cycling, (c) Marinobacter sp. are dominant at the sulphide interface. There is a significant shift in the microbiological community across the redox transition zone in these sulphidic sediments. The microbial assemblage of the suboxic transition zone is dominated by Bacillus sp. which are microaerophilic whereas the sulphide layer assemblage is dominated by Marinobacter sp. which are Fe oxidisers. Based on biomarker assemblages and genetic analyses, archaeal (and to a certain degree bacterial) communities are comparable to other hydrothermal settings despite the low biomass present. Processes inferred to be important in this sediment include the S, Fe and N cycle, all potentially coupled to the release and uptake of a range of transition metals. Significant recycling of redox active species occurs in the suboxic transition zones present in the sediment core. Uranium concentrations are low compared with other less altered sulphidic hydrothermal sediments, and U is associated with the upper regions of the suboxic transition zone and is associated with enrichment of a suite of other transition metals (e.g. Cu, Mo, As and V). Massive electrodes were constructed from CuFeS2 (from Ireland and TAG) and FeS2 (from TAG) and studied in oxygenated artificial seawater under circumneutral conditions using electrochemical methods. The results can be explained by existing hypotheses about pyrite and chalcopyrite oxidation and their oxidation products. The oxidation status of Cu in covellite could be identified as Cu+1. Impurities found (as expected because natural samples were used) have no effect on the electrochemical behaviour of the electrodes. The impact of Marinobacter sp. on sulphide alteration was studied in detail using an electrochemical approach. The results demonstrate that Marinobacter aquaeolei enhances the rates of oxidation. Marinobacter species seem to be of special importance for weathering reactions on the seafloor and in hydrothermal settings like the TAG area.

Gromiids are large amoeboid protozoans with an organic test and filose pseudopodia, which protrude through a shell aperture that is surrounded by an oral capsule. The first shallow-water gromiid, Gromia oviformis, was described by Dujardin in 1835 and is found worldwide. It was only in 1994, however, that gromiids were found for the first time at bathyal depths in a nonfjord setting, when the first deep-sea gromiid, G. sphaerica, was recovered from below the oxygen minimum zone on the continental slope off Oman in the Arabian Sea. The present study is based on the largest sample set of undescribed deep-sea gromiids thus far. The core of this thesis is the description of twelve new morphospecies from bathyal and abyssal depths (1180 m – 4800 m) in the Weddell Sea, Antarctica, using a combination of morphological and molecular criteria. All species possess a distinct oral capsule and a layer of “honeycomb membranes”, which form the inner part of the organic test wall. Both these features are characteristic of gromiids. Their identification as gromiids is confirmed by analyses of partial small subunit ribosomal DNA (SSU rDNA) gene sequences for three of the twelve new species: Gromia marmorea sp. nov., Gromia melinus sp. nov., and Gromia winnetoui sp. nov. Phylogenetic analysis using the maximum likelihood method revealed that G. marmorea and G. melinus form two distinct clades reflecting the morphological differences amongst the Weddell Sea species, and between deep-water Southern Ocean Gromia and previously described shallow-water gromiid G. oviformis, as well as gromiids from the deep Arabian Sea. Gromia winnetoui forms a third clade which branches with one of the Arabian Sea species. Both these species are morphologically very distinct and therefore the molecular results are inconsistent with the morphological characteristics. Based solely on morphological criteria, another sixteen morphospecies from the Northeast Atlantic are described, including specimens from the Northwest African margin (1320 m), the Porcupine Seabight and the Rockall Trough (1028- 3000 m), the Skagerrak (664 m), and the fjords of Møre along the western coast of Norway (65- 667 m). Most deep-sea gromiids appear to range in size between 0.1 and 4.0 mm, except for morphospecies B2 from the Skagerrak as well as most of the Arabian Sea species, which display a wider size range. The different morphospecies exhibit a variety of shapes, including spherical, droplet, conical, grape, elongate oval, sausage, bowling pin, vermiform, and irregular. The results of this thesis support the hypothesis that gromiids occur at depths >200 m in all major oceans. They are predominantly found along continental margins between 1000 and 3000 m. This thesis presents the only two records of Gromia (G. melinus and Species 154) from depths >4000 m in the Weddell Sea. It is hypothesized that further sampling will increase the number of species and novel morphotypes. Gromiids appear to be found in highest abundances in areas with elevated fluxes of organic matter. They are likely to play an important role in carbon and nitrogen cycling, as well as increasing local biodiversity.