Organic carbon cycling in marine sediments and seabed seepage features in Irish waters

Cycling of organic carbon in marine sediments is of fundamental importance for marine ecosystem function, for marine and atmospheric chemistry, for the petroleum and natural gas industry, and for paleoclimatic and paleoenvironmental studies. While most of this carbon is derived from marine and terrestrial sources, significant improvements in mapping and remote investigation have revealed that seabed fluid flow, principally in the form of thermogenic or microbial methane, is also of fundamental importance. In this thesis, the cycling of organic carbon at a number of sites in Irish waters was conducted, with a focus on recently mapped seabed seepage features. A spatial study of the distribution of lipid biomarkers in surface sediments and water column plankton in the western Irish Sea revealed zonation in diatom, zooplankton and dinoflagellate biomass and detrital input in line with hydrographic zonation and seasonal primary production (Chapter 2). Active gas seepage was recorded from carbonate mounds at the Codling Fault Zone, western Irish Sea as well as extensive eroded nodules, largely covered hard ground pavements, patches of anoxic seabed and extensive fossil tube worms and colonising hydroids. Analysis of retrieved samples has confirmed that these hard grounds are methane-derived authogenic carbonates and that anaerobic oxidation of methane is likely a significant process at this site (Chapter 3). The microbial diversity at a large composite but apparently dormant pockmark in the Malin Sea, NW Ireland was found to be dominated by non-seepage associated microbes and suggests a shift in population structure over a pockmarks lifetime. Bacterial species diversity was low and dominated by Psychrobacter and Sulfitobacter genera, although downcore microdiversity is apparent and could indicate niche specialisation with depth (Chapter 4). A shallow pockmark field in Dunmanus Bay was found to coincide with regions of acoustic gas signatures in the upper 3 m of seabed. This has been confirmed to be gas, which most likely accumulated below fine-grained impermeable muddy sediment. Numerous lines of evidence suggest that gaseous products, including methane, are produced in situ rather than transported from the subsurface, suggesting that the role of microbial activity in pockmark formation in this setting could be underestimated(Chapter 5)

CV10_28 Irish Sea cruise report

Cruise CV10_28 mobilized and demobilized from Howth, Co. Dublin, on the 2nd and 7th June 2010 respectively, and totalled over 112 operational hours. The objectives of this cruise were primarily to investigate and sample previously identified methane-related seepage structures in the Irish Designated Seabed Zone (IDSZ) of the Irish Sea, to carry out sampling grids of Dublin Bay and of the region of the IDSZ from Dublin Bay to Dundalk Bay for multidisciplinary geochemical and microbiological studies, and also to sample the water column for dissolved organic matter studies. A total of 113 sampling stations were successfully sampled: 46 grabs; 55 boxcores (0.25m2); 5 gravity cores (1m); and 7 vibrocores (3m). Gas-related seepage features successfully investigated were methane-derived authigenic carbonates (MDAC) in the Codling Fault Zone (CFZ), the Lambay Deep mud diapir, and also a shallow pockmark in the northen mudbelt region. Four videolines with over six hours of video footage were acquired in the MDAC target sites. Video footage and image stills of clusters of MDAC slabs, nodules and outcroppings, as well as indications enhanced anaerobic oxidation of methane (AOM) were successfully obtained. These features were subsequently successfully ground-truthed, sampled and preliminary geochemical analysis was carried out, thereby proving MDAC mounds in the CFZ are distinct features caused by active sub-surface seepage of methane. The Lambay Deep mud diapir was investigated by videoline deployment, whereby no distinct differences in seabed structure or biodiversity were observed. Fine sandy muds with relatively high macrofaunal biodiversity characterized seabed both inside and outside of Lambay Deep. The feature and surrounding seabed was ground-truthed by vibrocore and boxcore, and results supported the videoline findings. Sub-surface sediment (0-3m) was characterized by homogenous well-sorted fine sandy mud, with low infauna and shell presence, and little or no evidence of sub-surface anoxia. The mudbelt pockmark was investigated by videoline deployment and also subsequently ground-truthed by gravity core and boxcore. Videoline and sampling evidence suggests that the pockmark and reference samples from the surrounding seabed is uniform, and characterized by very fine mud with little sub-surface zonation. Previous sub-bottom profiling of the feature suggests no evidence of gas seepage or accumulations in the vicinity of the pockmark. The weather and sampling conditions were overall favourable throughout the cruise but the lack of dynamic positioning aboard the Celtic Voyager and also the restriction on the vibrocore to slack water and day-time use resulted in some sampling limitations and incomplete secondary objectives. Overall CV10_28 achieved the vast majority of its objectives, and a comprehensive foundation for numerous studies and peer-reviewed publications has been established

Hydrographic controls on marine organic matter fate and microbial diversity in the western Irish Sea

Cycling of organic matter (OM) is the key biological process in the marine environment and knowledge of the sources and the reactivity of OM, in addition to factors controlling its distribution in estuarine, coastal and shelf sediments are of key importance for understanding global biogeochemical cycles. With recent advances in cultivation-independent molecular approaches to microbial ecology, the key role of prokaryotes in global biogeochemical cycling in marine ecosystems has been emphasised. However, spatial studies combining the distribution and fate of OM with microbial community abundance and diversity remain rare. Here, a combined spatial lipid biomarker and 16S rRNA tagged pyrosequencing study was conducted in surface sediments and particulate matter across hydrographically distinct zones associated with the seasonal western Irish Sea gyre. The aim was to assess the spatial variation of, and factors controlling, marine organic cycling and sedimentary microbial communities across these distinct zones. The distribution of phospholipid fatty acids, source-specific sterols, wax esters and C25 highly branched isoprenoids indicate that diatoms, dinoflagellates and green algae were the major contributors of marine organic matter, while the distribution of cholesterol, wax esters and C20 and C22 polyunsaturated fatty acids have highlighted the importance of copepod grazing for mineralizing organic matter in the water column5. This marine OM production and mineralisation was greatest in well-mixed waters compared to offshore stratified waters. Lipid analysis and 16S rRNA PCR-DGGE profiling also suggests that sedimentary bacterial abundance increases while community diversity decreases in offshore stratified waters. The major bacterial classes are the Deltaproteobacteria, Clostridia, Flavobacteriia, Gammaproteobactera and Bacteroiidia. At the family/genus level most groups appear to be associated with organoheterotrophic processing of sedimentary OM, ranging from degradation of complex organic matter (e.g. Tepidibacter sp.) to sulfur-dependent utilisation of simple organic molecules (e.g. Desulfobulbaceae and Desulfuromonadaceae)

Ireland’s unseen majority – microbial diversity of the seabed

Despite their size, prokaryote (bacteria and archaea) biomass is estimated to represent between 15 and 30% of total living biomass1,2. Prokaryotes play major roles in marine ecosystems and in global biogeochemical cycling3,4. Molecular phylogenetic approaches have revolutionised microbiology and have revealed that the complexity of microbial life is orders of magnitude greater than previous estimates based on cultivation-based approaches5. This highlights how little we currently know about the microbial world and the clear potential of this vast untapped resource for human application. Here we present the first in-depth analysis of microbial community diversity and composition in the Irish Sea. The western Irish Sea is characterised by distinct hydrographic conditions, resulting in summer stratified offshore deeper waters and settling of fine mud, while well-mixed waters and coarser sediment type dominate in the south and coastal regions. We wished to assess whether these factors play a role in prokaryote abundance and diversity

Taphonomy of Biosignatures in Microbial Mats on Little Ambergris Cay, Turks and Caicos Islands

Microbial mats are taxonomically and metabolically diverse microbial ecosystems, with a characteristic layering that reflects vertical gradients in light and oxygen availability. Silicified microbial mats in Proterozoic carbonate successions are generally interpreted in terms of the surficial, mat building community. However, information about biodiversity in the once-surface-layer can be lost through decay as the mats accrete. To better understand how information about surface microbial communities is impacted by processes of decay within the mat, we studied microbial mats from Little Ambergris Cay, Turks and Caicos Islands. We used molecular techniques, microscopy and geochemistry to investigate microbial mat taphonomy – how processes of degradation affect biological signatures in sedimentary rocks, including fossils, molecular fossils and isotopic records. The top < 1 cm of these mats host cyanobacteria-rich communities overlying and admixed with diverse bacterial and eukaryotic taxa. Lower layers contain abundant, often empty, sheaths of large filamentous cyanobacteria, preserving their record as key mat-builders. Morphological remains and free lipid biomarkers of several bacterial groups, as well as diatoms, arthropods, and other eukaryotes also persist in lower mat layers, although at lower abundances than in surface layers. Carbon isotope signatures of organic matter were consistent with the majority of the biomass being sourced from CO2-limited cyanobacteria. Porewater sulfide sulfur isotope values were lower than seawater sulfate sulfur isotope values by ∼45–50‰, consistent with microbial sulfate reduction under sulfate-replete conditions. Our findings provide insight into how processes of degradation and decay bias biosignatures in the geological record of microbial mats, especially mats that formed widely during the Proterozoic (2,500–541 million years ago) Eon. Cyanobacteria were the key mat-builders, their robust and cohesive fabric retained at depth. Additionally, eukaryotic remains and eukaryotic biosignatures were preserved at depth, which suggests that microbial mats are not inherently biased against eukaryote preservation, either today or in the past

Biomarkers reveal the effects of hydrography on the sources and fate of marine and terrestrial organic matter in the western Irish Sea

A suite of lipid biomarkers were investigated from surface sediments and particulatematter across hydrographically distinct zones associated with the western Irish Sea gyre and the seasonal bloom. The aim was to assess the variation of organic matter (OM) composition, production, distribution and fate associated with coastal and southern mixed regions and also the summer stratified region. Based on the distribution of a suite of diagnostic biomarkers, including phospholipid fatty acids, source-specific sterols, wax esters and C25 highly branched isoprenoids, diatoms, dinoflagellates and green algae were identified as major contributors of marine organic matter (MOM) in this setting. The distribution of cholesterol, wax esters and C20 and C22 polyunsaturated fatty acids indicate that copepod grazing represents an important process for mineralising this primary production. Net tow data from 2010 revealed much greater phytoplankton and zooplankton biomass in well-mixed waters compared to stratified waters. This appears to be largely reflected in MOM input to surface sediments. Terrestrial organic matter (TOM), derived from higher plants, was identified as a major source of OM regionally, but was concentrated in proximity to major riverine input at the Boyne Estuary and Dundalk Bay. Near-bottom residual circulation and the seasonal gyre also likely play a role in the fate of TOM in the western Irish Sea

Active Ooid Growth Driven By Sediment Transport in a High-Energy Shoal, Little Ambergris Cay, Turks and Caicos Islands

Ooids are a common component of carbonate successions of all ages and present significant potential as paleoenvironmental proxies, if the mechanisms that control their formation and growth can be understood quantitatively. There are a number of hypotheses about the controls on ooid growth, each offering different ideas on where and how ooids accrete and what role, if any, sediment transport and abrasion might play. These hypotheses have not been well tested in the field, largely due to the inherent challenges of tracking individual grains over long timescales. This study presents a detailed field test of ooid-growth hypotheses on Little Ambergris Cay in the Turks and Caicos Islands, British Overseas Territories. This field site is characterized by westward net sediment transport from waves driven by persistent easterly trade winds. This configuration makes it possible to track changes in ooid properties along their transport path as a proxy for changes in time. Ooid size, shape, and radiocarbon age were compared along this path to determine in which environments ooids are growing or abrading. Ooid surface textures, petrographic fabrics, stable-isotope compositions (δ^(13)C, δ^(18)O, and δ^(34)S), lipid geochemistry, and genetic data were compared to characterize mechanisms of precipitation and degradation and to determine the relative contributions of abiotic (e.g., abiotic precipitation, physical abrasion) and biologically influenced processes (e.g., biologically mediated precipitation, fabric destruction through microbial microboring and micritization) to grain size and character. A convergence of evidence shows that active ooid growth occurs along the transport path in a high-energy shoal environment characterized by frequent suspended-load transport: median ooid size increases by more than 100 μm and bulk radiocarbon ages decrease by 360 yr westward along the ∼ 20 km length of the shoal crest. Lipid and 16S rRNA data highlight a spatial disconnect between the environments with the most extensive biofilm colonization and environments with active ooid growth. Stable-isotope compositions are indistinguishable among samples, and are consistent with abiotic precipitation of aragonite from seawater. Westward increases in ooid sphericity and the abundance of well-polished ooids illustrate that ooids experience subequal amounts of growth and abrasion—in favor of net growth—as they are transported along the shoal crest. Overall, these results demonstrate that, in the Ambergris system, the mechanism of ooid growth is dominantly abiotic and the loci of ooid growth is determined by both carbonate saturation and sediment transport mode. Microbes play a largely destructive, rather than constructive, role in ooid size and fabric

epiCaPture: a urine DNA methylation test for early detection of aggressive prostate cancer

Purpose Liquid biopsies that noninvasively detect molecular correlates of aggressive prostate cancer (PCa) could be used to triage patients, reducing the burdens of unnecessary invasive prostate biopsy and enabling early detection of high-risk disease. DNA hypermethylation is among the earliest and most frequent aberrations in PCa. We investigated the accuracy of a six-gene DNA methylation panel (Epigenetic Cancer of the Prostate Test in Urine [epiCaPture]) at detecting PCa, high-grade (Gleason score greater than or equal to 8) and high-risk (D'Amico and Cancer of the Prostate Risk Assessment] PCa from urine. Patients and Methods Prognostic utility of epiCaPture genes was first validated in two independent prostate tissue cohorts. epiCaPture was assessed in a multicenter prospective study of 463 men undergoing prostate biopsy. epiCaPture was performed by quantitative methylation-specific polymerase chain reaction in DNA isolated from prebiopsy urine sediments and evaluated by receiver operating characteristic and decision curves (clinical benefit). The epiCaPture score was developed and validated on a two thirds training set to one third test set. Results Higher methylation of epiCaPture genes was significantly associated with increasing aggressiveness in PCa tissues. In urine, area under the receiver operating characteristic curve was 0.64, 0.86, and 0.83 for detecting PCa, high-grade PCa, and highrisk PCa, respectively. Decision curves revealed a net benefit across relevant threshold probabilities. Independent analysis of two epiCaPture genes in the same clinical cohort provided analytical validation. Parallel epiCaPture analysis in urine and matched biopsy cores showed added value of a liquid biopsy. Conclusion epiCaPture is a urine DNA methylation test for high-risk PCa. Its tumor specificity out-performs that of prostate-specific antigen (greater than 3 ng/mL). Used as an adjunct to prostate-specific antigen, epiCaPture could aid patient stratification to determine need for biopsy

Active Ooid Growth Driven By Sediment Transport in a High-Energy Shoal, Little Ambergris Cay, Turks and Caicos Islands

Ooids are a common component of carbonate successions of all ages and present significant potential as paleoenvironmental proxies, if the mechanisms that control their formation and growth can be understood quantitatively. There are a number of hypotheses about the controls on ooid growth, each offering different ideas on where and how ooids accrete and what role, if any, sediment transport and abrasion might play. These hypotheses have not been well tested in the field, largely due to the inherent challenges of tracking individual grains over long timescales. This study presents a detailed field test of ooid-growth hypotheses on Little Ambergris Cay in the Turks and Caicos Islands, British Overseas Territories. This field site is characterized by westward net sediment transport from waves driven by persistent easterly trade winds. This configuration makes it possible to track changes in ooid properties along their transport path as a proxy for changes in time. Ooid size, shape, and radiocarbon age were compared along this path to determine in which environments ooids are growing or abrading. Ooid surface textures, petrographic fabrics, stable-isotope compositions (δ^(13)C, δ^(18)O, and δ^(34)S), lipid geochemistry, and genetic data were compared to characterize mechanisms of precipitation and degradation and to determine the relative contributions of abiotic (e.g., abiotic precipitation, physical abrasion) and biologically influenced processes (e.g., biologically mediated precipitation, fabric destruction through microbial microboring and micritization) to grain size and character. A convergence of evidence shows that active ooid growth occurs along the transport path in a high-energy shoal environment characterized by frequent suspended-load transport: median ooid size increases by more than 100 μm and bulk radiocarbon ages decrease by 360 yr westward along the ∼ 20 km length of the shoal crest. Lipid and 16S rRNA data highlight a spatial disconnect between the environments with the most extensive biofilm colonization and environments with active ooid growth. Stable-isotope compositions are indistinguishable among samples, and are consistent with abiotic precipitation of aragonite from seawater. Westward increases in ooid sphericity and the abundance of well-polished ooids illustrate that ooids experience subequal amounts of growth and abrasion—in favor of net growth—as they are transported along the shoal crest. Overall, these results demonstrate that, in the Ambergris system, the mechanism of ooid growth is dominantly abiotic and the loci of ooid growth is determined by both carbonate saturation and sediment transport mode. Microbes play a largely destructive, rather than constructive, role in ooid size and fabric