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The deep sea is a dynamic environment over various spatio-temporal scales. But, the characteristics of deep-sea natural variations and underlying processes remain poorly understood, which prevents contextualising any anthropogenic impact on this environment. Long-term observations, from which inter-annual variations can be detected, as well as detailed broad-scale spatial observations, are scarce in the deep sea. In this thesis, I examined changes in both spatial (~ 0.1-10s km scale) and temporal (inter-annual scale) domains in abyssal benthic fauna at two abyssal stations in the North East Pacific (Station M, 1991 to 2011) and in the North East Atlantic (Porcupine Abyssal Plain, PAP, 1991 to 2012) using Polychaeta as study organisms. Four main results were found. 1) At intermediate scales (0.1 to 10s km), the macrofauna and polychaete family composition were related to the sediment grain size distribution (Chapter 2). Differences in sediment grain size distribution between and among abyssal hills created habitat heterogeneity. Differences in near-bed current flows, and thus in particle size and food settling conditions, may be the primary factors influencing the sediment particle size distribution and macrofauna. Overall polychaetes and macrofauna may be more spatially variable than previously thought in abyssal areas when considering that abyssal hills might be one of the most common topographic features on Earth. 2) At inter-annual scale, polychaete families and functional groups varied in density, diversity and community structure at Sta. M and PAP (chapter 3). Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Differences may be related to the quantity and quality of the particulate organic carbon reaching the seafloor. Overall, changes in the dominance of functional groups imply changes in abyssal ecosystem functioning. 3) At inter-annual scale, the dynamics of polychaete abundances and body sizes suggested that migration/enhanced survivorship and recruitment events occurred (chapter 4). The densities and median body sizes of the five density-dominant species at Sta. M were analysed over time to help elucidate population dynamics as population parameters such as reproduction or growth rate could not be directly measured. The results indicated that the density dynamics of Paradoneis cf. lyra may have be related to enhanced survivorship or immigration of adult individuals, while the density dynamics of Cossura cf. rostrata may have be linked to individuals shifting between growth and reproduction. 4) At inter-annual scale, Sta. M polychaete changes were detected in standing stocks, rank distributions, species and functional group composition (chapter 5). Although a change in sampling location occurred after 2005, preventing ascribing the assemblage change unequivocally to particular environmental drivers, analyses prior to 2005 showed that the polychaete assemblage composition dynamics were primary driven by food supply variation. Overall, energetic zero-sum dynamics were not clearly observed at polychaete assemblage level, but were evident in the greater macrofauna community that includes the polychaetes. Polychaete displayed stability in body size structure in space and time, following the predictions of the metabolic theory of ecology. In conclusion, this work highlighted that abyssal polychaete communities can change over spatial scales of tens of square kilometres and time scales of months or more; this work found a large but as yet underappreciated variability.

It has long been recognised that some oceanic regions have persistently low chlorophyll levels, even though inorganic nutrients are plentiful. Studies have shown that these high-nutrient, low-chlorophyll (HNLC) areas are depleted in iron, which is an essential micronutrient for phytoplankton growth. In HNLC regions biological production can be enhanced with artificial mesoscale iron fertilisation. However, the ability of artificially induced phytoplankton blooms to efficiently sequester carbon to mesopelagic depths is still an open question. SubAntarctic islands in the HNLC Southern Ocean are a natural source of iron and thus fuel the annual phytoplankton blooms observed in their proximity. One such bloom, tied to the Crozet Islands (52ºE, 46ºS), provided the opportunity to examine particulate organic carbon (POC) export during the austral summer of 2004/5. This work was imbedded into the multi-disciplinary CROZEX project thus providing a rich context for data interpretation. Based on satellite imagery, a high chlorophyll region (max = 4 µg l-1) north and downstream of the Crozet Islands was distinguished from a low chlorophyll region (typically 0.3 µg l-1) south and upstream of the islands. POC export estimates, obtained with the naturally occurring particle reactive radionuclide tracer, 234Th, were initially D15 mmol C m-2 d-1 in the high chlorophyll region, compared with D5 mmol C m-2 d-1 in the low chlorophyll region. After a moderately small increase in chlorophyll in the south (max = 0.7 µg l-1) the spatial variability in POC export was lost, resulting in equally high levels of POC export (ca. 20 mmol C m-2 d-1) throughout the study area. After comparing the daily rates of POC export with temporally integrated new production calculated from nitrate budgets, a different spatial pattern emerged. New production (NP) presented consistently higher values in the north, when compared to the south. Two hypotheses were formulated to explain this, 1) dissolved organic matter (DOM) and suspended particulate organic matter (sPOM) produced from NP was stored in the mixed layer with this effect relatively greater in the north, 2) the export event in the north was longer resulting in greater seasonal POC export. Investigation of the DOM pool revealed that DOM accounted for 46±7% of NP and was consistent across the whole study area. In contrast, sPOM accumulated at differential rates of 18±7% in the north and 0±7% in the south. This suggested that differential storage of sPOM was responsible for the lack of a latitudinal gradient in POC export after the relatively small increase in chlorophyll in the south. After investigating the second hypothesis, the daily rates of POC export were scaled to seasonal integrals using a silicon budget, which allowed the formulation of a seasonal carbon budget. This revealed that over the timescale of the study the magnitude of NP and POC export were not the same with this difference greatest within the northern high chlorophyll region. This was the result of relatively greater storage of sPOM in the north and had the effect of reducing the amount of easily exportable POC to mesopelagic depths. Thus both hypotheses contributed to better understanding carbon export in the Crozet region.

Submarine canyons are considered potential hotspots of biodiversity and abundance, which makes them an important focus for scientific investigation and for policy-makers who seek to manage their resources. This study investigates the structure and dynamics of megafaunal communities in relation to inherent environmental parameters within submarine canyons; understanding the distribution and resilience of hotspot ecosystems is important in creating ecologically-sustainable resource-management plans. Data were collected from Nazaré, Setúbal, Lisbon and Cascais Canyons (Portuguese margin) and a channel and adjacent slope on the Pakistan margin, using passively-towed camera platforms and a remotely operated vehicle. Photographic data were analysed from a range of canyon habitats; abundance and distribution of megafauna were recorded and diversity indices calculated. Environmental variables were used to interpret patterns of species distribution, abundance and diversity. Community analyses were used to assess changes in community structure within and among canyons, and the adjacent slope. Portuguese margin: The canyons were ranked in order of decreasing activity: Nazaré, Lisbon, Setúbal and Cascais Canyons. Expected species richness conformed to Connell’s intermediate disturbance hypothesis, reflecting the activity of the canyons. Megabenthic abundance did not exceed that reported in studies of nearby slope communities, suggesting that the canyons are not hotspots of megabenthic abundance. Suspension-feeders dominated all canyons though were most abundant in Nazaré Canyon, which was linked to observed higher activity. All canyons showed a higher proportion of suspension-feeders than are reported in studies from nearby slope environments. There was high variability in habitat type within and between the canyons, which was reflected in the megabenthic assemblages. Pakistan margin: Observations of turbidity and current velocity indicated that the Pakistan margin channel is relatively inactive. Megafaunal abundance was significantly lower, and diversity higher, within the channel than on the adjacent slope. Suspension-feeders dominated all sites, though were significantly more numerous on the slope. The sites were located below the base of the OMZ core, and communities displayed OMZ edge-effects with a peak in abundance at ~ 1000 m WD, high dominance and a high rate of species turnover. Community analysis suggested that the communities were more heavily influenced by the proximity to the OMZ than by the channel, which indicated that either the influence of the OMZ masks any potential channel-induced patterns, or that the channel is too small to influence megafaunal communities.

Echinoderms are keystone organisms that have representatives in virtually every marine ecosystem. They possess a number of features that makes them an excellent model system, namely 1) their susceptibility to changes in the chemistry of seawater and temperature 2) their ossified skeletons are major contributors to many carbonate formations 3) their variety of life history strategies that enable successful reproduction (e.g. asexual reproduction, fission, cloning and regeneration). In most parts of the ocean, CO2 and temperature co-vary, making it difficult to extrapolate isolated effects of any one variable to natural scenarios. Laboratory and field work was conducted to assess the physiological and biogeochemical response of sea urchin Psammechinus miliaris larvae to changes in water carbonate chemistry. This study used two approaches: 1) the incubation of the larvae with naturally CO2-enriched deep-seawater, and 2) the study of the effect of ocean acidification and ocean warming. It is reported that there was no effect of in situ naturally high CO2 seawater, or laboratory induced CO2 concentrations, on larval physiology or morphology. However, elevated CO2 was found to cause a decrease in fertilization and calcification. An increase in temperature appeared to counteract significantly the negative effect that high CO2 has on fertilization and biocalcification. Therefore, it is argued that the developmental stages of sea urchins may adapt to predicted ocean acidification and increasing temperature scenarios, which is advantageous to maintaining stability and survival of populations under environmental selection pressure. Furthermore, the regeneration capability of the Pacific seastar larvae Pisaster ochraceus and Orthasterias koehleri was investigated. The successful complete re-growth of the larvae can be considered a specific developmental strategy that facilitates the species’ survival. This research suggests that echinoderm larvae are resilient to conditions in a changing ocean, due to their high acclimation capabilities and to their reproduction life history strategies. In this context, echinoderms may be considered an evolutionary success.

There is no longer any part of the ocean that is inaccessible, however, spanning 361 million km2 across the earth's surface and, with approximately 50% of its volume at a depth greater than 2000 m, it is the very sheer size and complex nature of the deep ocean, that means it still remains one of the least understood environments on earth. Deep-sea hydrothermal vents are insular and ephemeral sea oor habitats that host locally abundant populations of vent endemic taxa, supported by in situ primary production through chemolithoautotrophy. Since the initial discovery along the Galapagos rift in 1977, global vent communities have been shown to exhibit significant variation in the taxonomic composition of their assemblages and, as a result, a number of biogeographic provinces have been proposed. In 2009, the ChEsSO consortium (Chemosynthetic Ecosystem Science in the Southern Ocean) initiated a three-cruise program for the discovery and exploration of chemosynthetic environments south of the Polar front. One of the major findings was the discovery of the E2 and E9 vent fields on the East Scotia Ridge (ESR), revealing faunal assemblages distinct from those of other vent biogeographic provinces. Using precision high-definition ROV videography to create broad-extent mosaic images, this thesis examines the spatial dynamics and ecological processes that govern the zonation of the faunal assemblages associated with the Antarctic vent environment. Analysis of faunal microdistribution reveals a consistent pattern of zonation with increasing distance from vent fluid exits, which can be attributed to ecological processes such as nutritional mode and reproductive development. In addition, by examining the variation in microdistribution on chimneys with differing levels of activity, suggests a possible successional sequence for vent fauna in this new biogeographic province. Finally, with over three years of visual observations, this study reveals constancy in the broad taxonomic composition of assemblages, and stability in the spatial distribution in reproductive development of dominant motile vent fauna (Kiwa n. sp.) on an intermediate-spreading ridge, which challenges the widespread perception and understanding of deep-sea vent environments.

This thesis presents an investigation into the reproductive processes of a collapsing population of the European flat oyster Ostrea edulis in the Solent, UK. Oyster populations are in decline worldwide. Their ecological and economic importance requires research to address the many uncertainties still existing regarding their reproduction and recruitment, in order to manage or restore populations successfully. The Solent oyster population supported a productive local fishery from 1972 to about 2006, when catch rates started to decline sharply until the fishery became economically unviable in 2011. Recurrent recruitment failures suggested that the collapse might have been caused by a disturbance of the reproductive processes. This study set out to determine if the reproductive processes were indeed inhibited, and if so, at which life history stage. Population fitness was good and gave no reason to assume that the oysters were incapable of successful reproduction due to poor condition. Histological and visual examination of the reproductive status of 362 animals revealed a significant skew towards male phase oysters (chisquare, P 0.001), while gametogenesis as such was normal in each gender. Fecundity was similar to literature values. No relationship was found between the recruitment failures or the sex ratio shift and prevalence of bonamiosis, as only two animals of the 25 examined with a PCR assay were infected. Ostrea edulis larvae were found in the plankton with a peak of 9 larvae 100 l-1 in August 2010. Larval abundance was within the range of previous records for the Solent from 1984-87. Development of Ostrea edulis larvae cultured in the laboratory was found to be normal. No apparent adverse effects of exposure to air with an increased pCO2 of 1500 atm were found either, leading to hope that the long term viability of the species will not be jeopardized by ocean acidification. No spat settlement was observed in this study. Predation pressure from Ocenebra erinacea was found to be low, and hopefully would not jeopardize restoration attempts. Overall this study showed that while there is a lack of females in the Solent oyster population, the reproductive processes as such function well enough to enable regeneration and maintenance of the population. This study demonstrated the importance of investigating the reproductive processes of a population before planning its regeneration, but it also showed that the basic factors of habitat destruction and unsustainable �shing pressure must not be overlooked.

To achieve long-term planning and whole-ecosystem management of the oceans requires data on the extent of human impacts and the wider availability of data on human activities. This study, which aimed to provide the first detailed assessment of the extent of human activities in the deep North East Atlantic, OSPAR Maritime Area, revealed that during 2005 bottom-trawl fisheries affected an area of seafloor at least one order of magnitude greater than all the other the activities in the study combined. It was also found that identifying data sources, access to data and data quality presented significant barriers to implementing whole-ecosystem management and governance in the North East Atlantic. Additional work, in the North West Atlantic, to investigate the availability of data on human activities and to identify examples of best practice, revealed similar problems to those encountered in the North East Atlantic. Legal and policy frameworks and reporting requirements for human activities in the North East Atlantic were reviewed and recommendations made. This study identified access to fisheries’ vessel-monitoring data (VMS) and data quality as particular problems. Currently the location of bottom-trawling can only be identified by analysis of these data. This information is vital for ecosystem management. Current European Commission legislation, regarding access to environmental data and more specifically fisheries data, were discussed and the responses to applications made to European Member States for VMS data were analyzed. The results revealed a variety of interpretations of the Regulation. While the ecosystem approach is incorporated into many conventions and agreements, its implementation is not straightforward. For whole-ecosystem governance and management of the oceans, it is necessary to move beyond the traditional sector-based, piecemeal approaches. To do so requires significant improvements in availability and management of human-activities data and a shift in thinking towards a more integrated approach.

For well over a century a great deal of effort has been expended into investigation of how polychaetes capture their food but there has been a relative lack of attention paid to the processing of ingested material in the various forms and functioning of the anterior gut in errant polychaetes. The principal focus of this study was the examination of the functional anatomy of the anterior digestive tracts from three families of polychaetes; the Arenicolidae; sedentary detritivores, the Nereidae; errant omnivores and the Nephtyidae; errant carnivores. Comparisons were made with the already well-studied gut anatomy and particularly the pharyngeal anatomy of Arenicola marina, so as to establish a baseline for the other families of polychaetes. Particular attention was focused on the method of pharyngeal stabilisation in relation to food capture and processing. It is universally accepted that ‘coelomic pressure’ has been the primary factor in the eversion of the pharynx and proboscis in polychaete worms. This study challenges this hypothesis. This was done with the use of micro-dissection in anaesthetised polychaetes, electro-stimulation, modern light microscopy methods and novel application of micro-computed x-ray tomography. Investigations using scanning electron microscopy with freeze dried and freeze fractured specimens have revealed a very unusual interlacing muscle fibre pattern, in the Nephtys pharynx. This suggests that specialised pharyngeal muscles, and particularly a newly named muscle, the ventral coelomic muscle (VCM), in Nephtys, may be a primary mover of proboscis eversion rather than as a consequence of an increase in coelomic pressure. To date, only one other study has recognised this muscle, describing it as a ‘ventral retensor’ that possibly aided in the retraction of the extruded pharynx. The VCM has its origin in the ventral pharynx; it is connected to the anterior intestine, and inserted into the ventral body wall from segment 40-45. This, at least, suggests a stabilising muscle for the pharynx and proximal intestine. The present study’s observations suggest that this muscle is in fact a major player in a primarily muscular driving force for proboscis extrusion. These findings strongly suggest that coelomic pressure increases, associated with proboscis extrusion, are secondary factors in proboscis extrusion in the Nephtyidae. In the Nereidae, it would appear, that the combined action of the powerful longitudinal and circular muscles, together with the firm integrity of the outer body wall, are important players in the muscular extrusion of the pharynx and jaws. Associated increases in coelomic pressure are possibly a secondary effect and linked more with burrowing and body movement and hydrostatic support. In errant polychaetes with relatively short straight guts the anterior sections of the gut should be expected to play an important role in food processing, especially as examination of the intestines of many species, especially Nephtyidae, have revealed many of them to be empty.

Little is known about the fauna that inhabits non-chemosynthetic environments associated with mid-ocean ridges. This thesis investigates a ridge and fracture zone system to assess its influence as a barrier to faunal dispersal, and as a unique bathyal habitat. It also describes the ecology of megabenthic communities inhabiting a ridge. Sites were chosen on the Mid-Atlantic Ridge in the vicinity of the Charlie-Gibbs Fracture Zone, at a target depth of 2,500 m. Four superstations were chosen north and south of the Fracture Zone, on either side of the ridge. Different productivity levels and hydrographic features were characteristic for the northern and southern sites. In order to characterise the benthic megafauna 50 ha were trawled and 32,000 m2 of seafloor were sampled with HD video footage, targeting both flat and 10 ◦ sloped habitats. Holothurians were the most abundant megafauna. In order to assess their evolutionary relationship 43 holothurian specimens were genetically studied by modelling five of their genes (16S, 18S, 28S, COI, H3) in a phylogenetic analysis. All four sites exhibited noticeably different faunal characteristics. The biomass was highest at the SE, and lowest at the NW site. Body sizes differed between sites for most taxa, that were sufficient in numbers to be compared between sites, most likely as a result of different adaptations to food supply. Differences in species richness were observed between the sampling methods, with the highest richness at the SE site in trawl samples, and highest at the NW and SW sites in the video survey. Species densities were highest at the northern sites with both methods. Differences in diversity were also observed, with trawl samples providing a higher taxonomic resolution than the video survey and showing highest diversity at the SE site and lowest at the NE site. Community composition was significantly different between sites. Variations in the composition of megabenthic assemblages were observed between flat and 10 ◦ sloped habitats, although the effect of slope appears to be site dependent. The genetic analyses revealed a close relationship between individuals from different families. The extent to which the Ridge acts as a faunal barrier was unclear as the southern sites lacked an obvious difference in community composition. Faunal differences to the north and south of the Fracture Zone, however, suggest that this feature is a barrier to dispersal. The contrasting megafaunal assemblages of the sites probably reflect a combination of environmental drivers including sediment type, phytodetrital quality, hydrography, and habitat complexity.