Papers by Shane S O'Reilly
The microbial contribution to soil organic matter has been shown to be much larger than previousl... more The microbial contribution to soil organic matter has been shown to be much larger than previously thought and thus it plays a major role in carbon cycling. Among soil microorganisms, chemoautotrophs can fix CO 2 without sunlight and can glean energy through the oxidation of reduced elements such as sulfur. Here we show that the addition of sulfur to soil results in an initial surge in production of CO 2 through microbial respiration, followed by an order of magnitude increase in the capture of carbon from the atmosphere as elemental sulfur is oxidised to sulfate. Thiobacillus spp., take advantage of specific conditions to become the dominant chemoautotrophic group that consumes CO 2. We discern the direct incorporation of atmospheric carbon into soil carbohydrate, protein and aliphatic compounds and differentiate these from existing biomass. These results suggest that chemoautotrophs can play a large role in carbon cycling and that this carbon is heavily influenced by land management practises. Traditionally, humic substances were thought of as the main repository of organic carbon in agricultural soils. However, studies show that most soil biomass is actually present as bacterial and fungal cellular material 1, 2. This is a critical observation: microbial biomass, unlike humic materials, can potentially play a direct role in global carbon cycles, actively releasing or trapping greenhouse gases, such as CO 2 and CH 4 , under specific conditions. As one third of greenhouse gas emissions are associated with agriculture and soil accounts for more than half of this carbon 3 there is a need to understand the influence of agriculture on carbon fluxes modulated by soil microbes 4. The contribution of photoautotrophic microorganisms to CO 2 uptake, is well known 5 and there is now a reali-sation that they play a significant role in the sequestration of soil carbon 6. However, the contribution of chemoau-totrophic microorganisms, through chemosynthesis or " dark carbon fixation " (DCF) has been generally neglected as a pathway to carbon assimilation 7. Despite this, recent studies show that DCF is a quantitatively important CO 2 uptake mechanism 8–11. Chemoautotrophy describes metabolic processes that are used to convert CO 2 into organic materials (bio-mass) by microbes, using energy obtained from the oxidation of reduced organic or inorganic molecules. Unlike photoautotrophs, energy from light is therefore not needed for CO 2 fixation. Chemoautotrophs can be further subdivided into two groups: 1) The chemolithotrophs, that use inorganic electron donors (e.g. NH 4 + , NO 2− , Fe 2+ and S 2 O 3 2−) to provide energy while fixing CO 2 ; 2) The mixotrophs – a group of organisms that are facultative chemoautotrophs, i.e. assimilating CO 2 but also using heterotrophic carbon metabolism when the right environmental circumstances apply. Previously, we showed that the addition of thiosulfate to soils resulted in an order of magnitude increase in the uptake of CO 2 by chemoautotrophs 12, 13. Thiosulfate acts as an electron donor and provides the energy for a large increase in CO 2 uptake. The uptake events occurred over the space of 48 hours in conditions conducive to chemoautotrophic growth.
The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities
Marine Pollution Bulletin, 2016
The source, concentration, and potential impact of sewage discharge and incomplete organic matter... more The source, concentration, and potential impact of sewage discharge and incomplete organic matter (OM) combustion on sedimentary microbial populations were assessed in Dublin Bay, Ireland. Polycyclic aromatic hydrocarbons (PAHs) and faecal steroids were investigated in 30 surface sediment stations in the bay. Phospholipid fatty acid (PLFA) content at each station was used to identify and quantify the broad microbial groups present and the impact of particle size, total organic carbon (%TOC), total hydrogen (%H) and total nitrogen (%N) was also considered. Faecal sterols were found to be highest in areas with historical point sources of sewage discharge. PAH distribution was more strongly associated with areas of deposition containing high %silt and %clay content, suggesting that PAHs are from diffuse sources such as rainwater run-off and atmospheric deposition. The PAHs ranged from 12 to 3072ng/g, with 10 stations exceeding the suggested effect range low (ERL) for PAHs in marine sediments. PAH isomer pair ratios and sterol ratios were used to determine the source and extent of pollution. PLFAs were not impacted by sediment type or water depth but were strongly correlated to, and influenced by PAH and sewage levels. Certain biomarkers such as 10Me16:0, i17:0 and a17:0 were closely associated with PAH polluted sediments, while 16:1Ω9, 16:1Ω7c, Cy17:0, 18:1Ω6, i16:0 and 15:0 all have strong positive correlations with faecal sterols. Overall, the results show that sedimentary microbial communities are impacted by anthropogenic pollution.
Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation ... more Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation is still actively debated, which limits our understanding of the significance and meaning of these grains in Earth's history. Central questions include the role played by microbes in the formation of ooids and the sources of ubiquitous organic matter within ooid cortices. To address these issues, we investigated the microbial community composition and associated lipids in modern oolitic sands at Pigeon Cay on Cat Island, The Bahamas. Surface samples were taken along a transect from the shallow, turbulent surf zone to calmer, deeper water. Grains transitioned from shiny and abraded ooids in the surf zone, to biofilm-coated ooids at about 3 m water depth. Further offshore, grapestones (cemented aggregates of ooids) dominated. Benthic diatoms and Proteobacteria dominated biofilms. Taxa that may promote carbonate precipitation were abundant, particularly those associated with sulfur cycling. Compared to the lipids associated with surface biofilms, relict lipids bound within carbonate exhibited remarkably similar profiles in all grain types. The enhanced abundance of methyl-branched fatty acids and β-hydroxy fatty acids, 1-O-monoalkyl glycerol ethers and hopanoids bound within ooid and grapestone carbonate confirms a clear association of benthic sedimentary bacteria with these grains. Lipids bound within ooid cortices also contain molecular indicators of microbial heterotrophic degradation of organic matter, possibly in locally reducing conditions. These included the loss of labile unsaturated fatty acids, enhanced long-chain fatty acids/short-chain fatty acids, enriched stable carbon isotopes ratios of fatty acids, and very high stanol/stenol ratios. To what extent some of these molecular signals are derived from later heterotrophic endolithic activity remains to be fully resolved. We speculate that some ooid carbonate forms in microbial biofilms and that early diagenetic degradation of biofilms may also play a role in early stage carbonate precipitation around ooids.
Phospholipid ester-linked fatty acids 16S rRNA gene barcoded pyrosequencing Shelf sediment Irish ... more Phospholipid ester-linked fatty acids 16S rRNA gene barcoded pyrosequencing Shelf sediment Irish Sea a b s t r a c t The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12–111 m), organic carbon content (0.09–1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal poly-unsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclo-propyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavo-bacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.
Marine Geology 357, 139-150, Aug 23, 2014
Methane-derived authigenic carbonate (MDAC) mound features at the Codling Fault Zone (CFZ), locat... more Methane-derived authigenic carbonate (MDAC) mound features at the Codling Fault Zone (CFZ), located in shallow waters (50–120 m) of the western Irish Sea were investigated and provide a comparison to deep sea MDAC settings. Carbonates consisted of aragonite as the major mineral phase, with δ13C depletion to −50‰ and δ18O enrichment to ~ 2‰. These isotope signatures, together with the co-precipitation of framboidal pyrite confirm that anaerobic oxidation of methane (AOM) is an important process mediating methane release to thewater column
and the atmosphere in this region. 18O-enrichment could be a result of MDAC precipitation with seawater in colder than present day conditions, or precipitation with 18O-enriched water transported from deep petroleum sources. The 13C depletion of bulk carbonate and sampled gas (−70‰) suggests a biogenic source, but significant
mixing of thermogenic gas and depletion of the original isotope signature cannot be ruled out. Active seepage was recorded from one mound and together with extensive areas of reduced sediment, confirms that seepage is ongoing. The mounds appear to be composed of stacked pavements that are largely covered by sand and extensively
eroded. The CFZ mounds are colonized by abundant Sabellaria polychaetes and possible Nemertesia hydroids, which benefit indirectly from available hard substrate. In contrast to deep sea MDAC settings where seep-related macrofauna are commonly reported, seep-specialist fauna appear to be lacking at the CFZ. In addition,
unlike MDAC in deep waters where organic carbon input from photosynthesis is limited, lipid biomarkers and isotope signatures related to marine planktonic production (e.g. sterols, alkanols) were most abundant. Evidence for microbes involved in AOM was limited from samples taken; possibly due to this dilution effect from
organic matter derived from the photic zone, and will require further investigation.
Estuarine, Coastal and Shelf Science 136, 157-171, Nov 13, 2013
A suite of lipid biomarkers were investigated from surface sediments and particulate matter acros... more A suite of lipid biomarkers were investigated from surface sediments and particulate matter 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.
Organic carbon cycling in marine sediments and seabed seepage features in Irish waters
PhD Thesis, Nov 8, 2013
Cycling of organic carbon in marine sediments is of fundamental importance for marine ecosystem f... more 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).
Reassessment of the Microbial Role in Mn-Fe Nodule Genesis in Andean Paleosols
The presence of Mn-Fe nodules in the epipedons (surface horizons) of paleosols of presumed Upper ... more The presence of Mn-Fe nodules in the epipedons (surface horizons) of paleosols of presumed Upper Neogene age in the northwestern Venezuelan Andes have been interpreted as products of inorganic oxidation and reduction processes operating over the full range of glacial and interglacial cycles that affected paleosol morphogenesis. New microscopic/chemical data from combined SEM-EDS-FIB analyses of representative Mn-Fe nodules indicate microbes play an important role in Mn/Fe precipitation leading to their genesis in alpine Mollisols (Argiustolls). While the prevailing new data is based mainly on fossil forms of filamentous bacteria and fungi and other biogenic pseudomorphs that may represent the former resident bacteria, the presence of extant microbes must await field experiments/collection, followed by a molecular microbiology approach to determine the biological drivers of metal precipitation. As in other terrestrial niche environments, microbes are seen here to play a role, perhaps a key one, in the morphogenesis of paleosols of importance in upper Neogene paleoenvironmental reconstruction.
Open Journal of Marine Science 3, 175-181
A marine sediment core obtained from a methane seepage site off the northern coast of Ireland was... more A marine sediment core obtained from a methane seepage site off the northern coast of Ireland was analysed, at 3 depths, for catabolic genes associated with the aerobic and anaerobic degradation of aromatic compounds. Catabolic gene copy numbers varied through the core peaking at 2.1 meters below sediment surface (mbsf)-just above the sulphate boundary. Beyond the sulphate boundary gene copy numbers fell considerably, suggesting the boundary may be a critical factor in the degradation of aromatic compounds within marine sediments. At the 2.1 mbsf depth our data also suggest that known benzoyl CoA reductase utilizing bacteria are readily detectable.
Aquatic Biology 15, 215-224, Jun 6, 2012
Living (LM) and non-living maerl (NLM) rhodoliths of the species Lithothamnion corallioides (Crou... more Living (LM) and non-living maerl (NLM) rhodoliths of the species Lithothamnion corallioides (Crouan & Crouan, 1867) from Kingstown Bay, Galway, were sampled and compared in relation to their physical structure and lipid and low molecular weight carbohydrate (LMWC) composition. Saturated (SATFA) and polyunsaturated fatty acids (PUFA) were dominant, in particular 16:0, 20:4n-6 and 20:5n-3, but a diverse range of fatty acids were identified. The abundance of n-alkanals was high, and sterol composition was simple, with cholesterol accounting for over 90% of the total sterols. Mono-, di-, and trisaccharides, with galactose units being dominant, and floridoside were present in high abundance. Notably, the fatty acid and LMWC profiles varied little between NLM and LM. The relatively high abundance of PUFA and floridoside, in particular, suggests that NLM may have further potential for research and commercial purposes in a variety of food, biomedical and industrial applications. Previously reported unidentified ‘globular inclusions’ were more abundant in NLM and exhibited a crystalline morphology. Together with the bacterial fatty acid composition of LM and NLM, the results indicate that these structures are not bacterial in nature.
Geochemistry, Geophysics and Geosystems 13, 1-18, Jan 1, 2012
[1] Marine pockmarks are a specific type of seabed geological setting resembling craters or pits ... more [1] Marine pockmarks are a specific type of seabed geological setting resembling craters or pits and are considered seabed surface expressions of fluid flow in the subsurface. A large composite pockmark on the Malin Shelf, off the northern coast of Ireland was surveyed and ground truthed to assess its activity and investigate fluid related processes in the subsurface. Geophysical (including acoustic and electromagnetic) data confirmed the subsurface presence of signatures typical of fluids within the sediment. Shallow seismic profiling revealed a large shallow gas pocket and typical gas related indicators such as acoustic blanking and enhanced reflectors present underneath and around the large pockmark. Sulphate profiles indicate that gas from the shallow reservoir has been migrating upwards, at least recently. However, there are no chimney structures observed in the sub-bottom data and the migration pathways are not apparent. Electromagnetic data show slightly elevated electrical conductivity on the edges of the pockmarks and a drop below regional levels within the confines of the pockmark, suggesting changes in physical properties of the sediment. Nuclear Magnetic Resonance (NMR) experiments were employed to characterize the organic component of sediments from selected depths. Very strong microbial signatures were evident in all NMR spectra but microbes outside the pockmark appear to be much more active than inside. These observations coincide with spikes in conductivity and the lateral gas bearing body suggesting that there is an increase in microbial activity and biomass when gas is present.
Planetary and Space Science 60, 386-398, Jan 1, 2012
Bulk paleosol samples collected from a Middle to Early Miocene moraine in the New Mountain area o... more Bulk paleosol samples collected from a Middle to Early Miocene moraine in the New Mountain area of the Dry Valleys, Antarctica, yielded Coleoptera exoskeletons and occasional endoskeletons showing considerable diagenetic effects along with several species of bacteria, all lodged in a dry-frozen but salt-rich horizon at shallow depth to the land surface. The till is at the older end of a chronologic sequence of glacial deposits, thought to have been deposited before the transition from wet-based to cold-based ice (∼15 Ma), and hence, entirely weathered in contact with the subaerial atmosphere. It is possible, though not absolutely verifiable, that the skeletons date from this early stage of emplacement having undergone modifications whenever light snowmelt occurred or salt concentrations lowered the freezing temperature to maintain water as liquid. Correlation of the Coleoptera species with cultured bacteria in the sample and the likelihood of co-habitation with Beauveria bassiani found in two adjacent, although younger paleosols, leads to new questions about the antiquity of the Coleoptera and the source of N and glucose from chitinase derived from the insects. The skeletons in the 831 section may date close to the oldest preserved chitin (Oligocene) yet found on Earth. While harsh Martian conditions make it seemingly intolerable for complex, multicellular organisms such as insects to exist in the near-surface and subaerially, life within similar cold, dry paleosol microenvironments (Cryosols) of Antarctica point to life potential for the Red Planet, especially when considering the relatively diverse microbe (bacteria and fungi) population.
Sedimentary Geology 237, 84-94, May 15, 2011
Pyrophosphate-extractable Al has been used to establish the presence of organically-complexed com... more Pyrophosphate-extractable Al has been used to establish the presence of organically-complexed compounds in middle latitude and tropical soils and paleosols on Earth. As proxy data used to establish the presence of organic molecules and trace movement within profiles, it has proved an accurate indicator of downward translocation in Spodosols (podzols). Antarctic paleosols, dating from Middle to Early Miocene age (15–20 Ma), are mineralic weathering profiles lacking A and B horizons. These profiles exhibit pavement/Cox/Cz/Cu horizons, largely with sandy silt textures, little clay, and exceedingly low concentrations of organic matter. Recent chemical investigations of 33 soil samples from the New Mountain and Aztec Mountain areas near the Inland Ice, adjacent to the Taylor Glacier, show that pyrophosphate-extractable Al concentrations vary in phase with organic carbon as determined by loss-on-ignition. While Al-extract concentrations in selected samples are low (< 0.15%), increasing values above nil approximately correlate positively with increases in bacterial populations of several common phylum, the extreme high numbers with more advanced biota including fossil Coleoptera. Available data suggest Alp extracts may target samples which may have undergone minor chelation, and which over long periods of time might have a cumulative weathering effect resulting in the accumulation of small concentrations of organic matter.
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Papers by Shane S O'Reilly
and the atmosphere in this region. 18O-enrichment could be a result of MDAC precipitation with seawater in colder than present day conditions, or precipitation with 18O-enriched water transported from deep petroleum sources. The 13C depletion of bulk carbonate and sampled gas (−70‰) suggests a biogenic source, but significant
mixing of thermogenic gas and depletion of the original isotope signature cannot be ruled out. Active seepage was recorded from one mound and together with extensive areas of reduced sediment, confirms that seepage is ongoing. The mounds appear to be composed of stacked pavements that are largely covered by sand and extensively
eroded. The CFZ mounds are colonized by abundant Sabellaria polychaetes and possible Nemertesia hydroids, which benefit indirectly from available hard substrate. In contrast to deep sea MDAC settings where seep-related macrofauna are commonly reported, seep-specialist fauna appear to be lacking at the CFZ. In addition,
unlike MDAC in deep waters where organic carbon input from photosynthesis is limited, lipid biomarkers and isotope signatures related to marine planktonic production (e.g. sterols, alkanols) were most abundant. Evidence for microbes involved in AOM was limited from samples taken; possibly due to this dilution effect from
organic matter derived from the photic zone, and will require further investigation.
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).