Molecular composition in surface and subsurface sediments of the Helgoland mud area, North Sea

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30-530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments.

Organic matter composition and sulfate reduction intensity in Oman Margin sediments

Petrographical and geochemical studies of Neogene marine sediments from the Oman Sea (Leg 117, Sites 720, 724, 726 and 730), show a close relationship between the nature and amount of the organic matter, and the degree of degradation of organic matter by sulfate reduction, i.e. pyritization. Petrographically, three major pyritization types were observed: (1) Finely dispersed pyrite framboids in sediments from Oman Margin and Indus Fan, enriched in autochthonous marine organic matter. (2) Infilling of pores by massive pyrite crystals in Oman Margin sediments with a low TOC and a high microfossil content. (3) Pyrite mineralization of lignaceous fragments in organic-depleted sediments from the Indus Fan leading to more massive pyrite. Geochemically, we can define a sulfate reduction index (SRI) as the percentage of initial organic carbon versus that of residual organic carbon. Finely laminated Pliocene-Pleistocene sediments from the Oman Margin exclusively contain organic matter deriving from organic phytoplankton, for which the quantity (TOC) positively correlates with the geochemical quality (Hydrogen Index). We think that the occurrence of this residual organic matter is linked mainly to a high primary paleo-productivity. The intensity of sulfate reduction is constant for sediments with TOC up to 2% and becomes more important when organic input decreases. This degradation process can destroy up to 50% of the initial organic matter, but is not sufficient to explain some of the encountered very low TOC values. It can be seen that sharp increases of certain plankton species (with mineral skeletons) are responsible for a pronounced degradation of organic matter, due to increased sulfate reduction. In that case, the organic matter may be strongly degraded (high SRI), although deposited in an oxygen-depleted environment. Conversely, Miocene-Pliocene sediments contain an autochthonous organic matter that is typical of both low productivity and oxic processes; their very low sulfate reduction index indicates that very little metabolizable organic matter was initially present.

Organic carbon and humic substances contents, carbon isotope composition and peroxidase activity in sediments from DSDP Sites 15-147 and 75-532

Sediment samples from the Cariaco Trench (DSDP Leg 15) and the Walvis Ridge (DSDP Leg 75) ranging in age from Holocene to Upper Miocene (approximately 8 million years BP) and in depth from 5 to 258 m were extracted with basic sodium pyrophosphate and the extract analyzed for enzymic activity. Since no dehydrogenase, alkaline phosphatase or esterase activity was found, it is estimated from these data that the maximum bacterial population does not exceed 1000 cells per gram dry sediment. Peroxidase activity was, however, found in most samples: this showed marked dependence on the humic substance concentration (expressed as percent of the organic carbon content) and increased with depth at a rate of 33 units per meter. To explain this observation, we favor an hypothesis based on the presence of active humic-enzyme association. The humic substances absorb and stabilize peroxidase which is liberated throughout the sediment column by lysis of cells. The association of the enzyme with the humic substances protects it from biodegradation and denaturation. This hypothesis agrees with laboratory experiments which show the enhanced stability of humic-enzyme complexes towards degradation by biological, chemical and thermal effects.

(Table 2) Composition of the deapest pore fluids from ODP Holes 168-1030B and 168-1031A

On the eastern flank of the Juan de Fuca Ridge, reaction between upwelling basement fluid and sediment alters hydrothermal fluxes of Ca, SiO2(aq), SO4, PO4, NH4, and alkalinity. We used the Global Implicit Multicomponent Reactive Transport (GIMRT) code to model the processes occurring in the sediment column (diagenesis, sediment burial, fluid advection, and multicomponent diffusion) and to estimate net seafloor fluxes of solutes. Within the sediment section, the reactions controlling the concentrations of the solutes listed above are organic matter degradation via SO4 reduction, dissolution of amorphous silica, reductive dissolution of amorphous Fe(III)-(hydr)oxide, and precipitation of calcite, carbonate fluorapatite, and amorphous Fe(II)-sulfide. Rates of specific discharge estimated from pore-water Mg profiles are 2 to 3 mm/yr. At this site the basement hydrothermal system is a source of NH4, SiO2(aq), and Ca, and a sink of SO4, PO4, and alkalinity. Reaction within the sediment column increases the hydrothermal sources of NH4 and SiO2(aq), increases the hydrothermal sinks of SO4 and PO4, and decreases the hydrothermal source of Ca. Reaction within the sediment column has a spatially variable effect on the hydrothermal flux of alkalinity. Because the model we used was capable of simulating the observed pore-water chemistry by using mechanistic descriptions of the biogeochemical processes occurring in the sediment column, it could be used to examine the physical controls on hydrothermal fluxes of solutes in this setting. Two series of simulations in which we varied fluid flow rate (1 to 100 mm/yr) and sediment thickness (10 to 100 m) predict that given the reactions modeled in this study, the sediment section will contribute most significantly to fluxes of SO4 and NH4 at slow flow rates and intermediate sediment thickness and to fluxes of SiO2(aq) at slow flow rates and large sediment thickness. Reaction within the sediment section could approximately double the hydrothermal sink of PO4 over a range of flow rates and sediment thickness, and could slightly decrease (by

Sediment and pore water C and N composition of ODP Holes 201-1227A and 201-1230A

This study addresses the problem of diagenetic fractionation of d15N in sedimentary organic matter by constructing isotopic mass balances for the sedimentary nitrogen and pore water ammonium at two Ocean Drilling Program (ODP) sites, 1227 and 1230. At Site 1230, ammonium production flux integrated through the sedimentary column indicates that >60% of organic matter is lost to decomposition. The d15N of pore water ammonium is <0.7 per mil different from that of the sedimentary organic matter, which implies that very little isotopic fractionation is associated with degradation of organic matter at this site. The constant d15N of the solid-phase sedimentary nitrogen through the whole profile supports this conclusion. Atomic C/N ratios (9-12) indicate that organic matter at this site is primarily of marine origin. At Site 1227, the sedimentary organic matter appears to be a mixture of terrestrial and marine components. Ammonium is ~4 heavier than the organic matter. The observed isotopic enrichment of pore water ammonium relative to the sedimentary nitrogen might indicate either the preferential decomposition of isotopically heavier marine fraction of the organic matter, or possibly, a nonsteady-state condition of the ammonium concentration and d15N profiles. Interpretation of the results at Site 1227 is further complicated by the contribution of ammonium with d15N of ~4 per mil that is diffusing upward from Miocene brines.

Mass spectrometric and capillary electrophoretic investigation of the enzymatic degradation of heparin-like glycosaminoglycans

Difficulties in determining composition and sequence of glycosaminoglycans, such as those related to heparin, have limited the investigation of these biologically important molecules. Here, we report methodology, based on matrix-assisted laser desorption ionization MS and capillary electrophoresis, to follow the time course of the enzymatic degradation of heparin-like glycosaminoglycans through the intermediate stages to the end products. MS allows the determination of the molecular weights of the sulfated carbohydrate intermediates and their approximate relative abundances at different time points of the experiment. Capillary electrophoresis subsequently is used to follow more accurately the abundance of the components and also to measure sulfated disaccharides for which MS is not well applicable. For those substrates that produce identical or isomeric intermediates, the reducing end of the carbohydrate chain was converted to the semicarbazone. This conversion increases the molecular weight of all products retaining the reducing terminus by the “mass tag” (in this case 56 Da) and thus distinguishes them from other products. A few picomoles of heparin-derived, sulfated hexa- to decasaccharides of known structure were subjected to heparinase I digestion and analyzed. The results indicate that the enzyme acts primarily exolytically and in a processive mode. The methodology described should be equally useful for other enzymes, including those modified by site-directed mutagenesis, and may lead to the development of an approach to the sequencing of complex glycosaminoglycans.

Potential Shifts in Canadian High Arctic Sedimentary Organic Matter Composition With Permafrost Active Layer Detachments

Increased temperature and precipitation in Arctic regions have led to deeper thawing and structural instability in permafrost soil. The resulting localized disturbances, referred to as active layer detachments (ALDs), may transport organic matter (OM) to more biogeochemically active zones. To examine this further, solid state cross polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS NMR) and biomarker analysis were used to evaluate potential shifts in riverine sediment OM composition due to nearby ALDs within the Cape Bounty Arctic Watershed Observatory, Nunavut, Canada. In sedimentary OM near ALDs, NMR analysis revealed signals indicative of unaltered plant-derived material, likely derived from permafrost. Long chain acyclic aliphatic lipids, steroids, cutin, suberin and lignin occurred in the sediments, consistent with a dominance of plant-derived compounds, some of which may have originated from permafrost-derived OM released by ALDs. OM degradation proxies for sediments near ALDs revealed less alteration in acyclic aliphatic lipids, while constituents such as steroids, cutin, suberin and lignin were found at a relatively advanced stage of degradation. Phospholipid fatty acid analysis indicated that microbial activity was higher near ALDs than downstream but microbial substrate limitation was prevalent within disturbed regions. Our study suggests that, as these systems recover from disturbance, ALDs likely provide permafrost-derived OM to sedimentary environments. This source of OM, which is enriched in labile OM, may alter biogeochemical patterns and enhance microbial respiration within these ecosystems.

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

Radiocarbon ages, dose rates, water isotopic composition and hydrochemistry of samples from Komakuk Beach and Herschel Island

Terrestrial permafrost archives along the Yukon Coastal Plain (northwest Canada) have recorded landscape development and environmental change since the Late Wisconsinan at the interface of unglaciated Beringia (i.e. Komakuk Beach) and the northwestern limit of the Laurentide Ice Sheet (i.e. Herschel Island). The objective of this paper is to compare the late glacial and Holocene landscape development on both sides of the former ice margin based on permafrost sequences and ground ice. Analyses at these sites involved a multi-proxy approach including: sedimentology, cryostratigraphy, palaeoecology of ostracods, stable water isotopes in ground ice, hydrochemistry, and AMS radiocarbon and infrared stimulated luminescence (IRSL) dating. AMS and IRSL age determinations yielded full glacial ages at Komakuk Beach that is the northeastern limit of ice-free Beringia. Herschel Island to the east marks the Late Wisconsinan limit of the northwest Laurentide Ice Sheet and is composed of ice-thrust sediments containing plant detritus as young as 16.2 cal ka BP that might provide a maximum age on ice arrival. Late Wisconsinan ice wedges with sediment-rich fillings on Herschel Island are depleted in heavy oxygen isotopes (mean d18O of -29.1 per mil); this, together with low d-excess values, indicates colder-than-modern winter temperatures and probably reduced snow depths. Grain-size distribution and fossil ostracod assemblages indicate that deglaciation of the Herschel Island ice-thrust moraine was accompanied by alluvial, proluvial, and eolian sedimentation on the adjacent unglaciated Yukon Coastal Plain until ~11 cal ka BP during a period of low glacio-eustatic sea level. The late glacial-Holocene transition was marked by higher-than-modern summer temperatures leading to permafrost degradation that began no later than 11.2 cal ka BP and caused a regional thaw unconformity. Cryostructures and ice wedges were truncated while organic matter was incorporated and soluble ions were leached in the thaw zone. Thermokarst activity led to the formation of ice-wedge casts and deposition of thermokarst lake sediments. These were subsequently covered by rapidly accumulating peat during the early Holocene Thermal Maximum. A rising permafrost table, reduced peat accumulation, and extensive ice-wedge growth resulted from climate cooling starting in the middle Holocene until the late 20th century. The reconstruction of palaeolandscape dynamics on the Yukon Coastal Plain and the eastern Beringian edge contributes to unraveling the linkages between ice sheet, ocean, and permafrost that have existed since the Late Wisconsinan.

Organic and inorganic geochemistry and archaeal community composition of hypersaline sediments from Orca Basin, RV Atlantis Expedition AT18-02

Among the most extreme habitats on Earth, dark, deep, anoxic brines host unique microbial ecosystems that remain largely unexplored. As the terminal step of anaerobic degradation of organic matter, methanogenesis is a potentially significant but poorly constrained process in deep-sea hypersaline environments. We combined biogeochemical and phylogenetic analyses as well as incubation experiments to unravel the origin of methane in hypersaline sediments of Orca Basin in the northern Gulf of Mexico. Substantial concentrations of methane (up to 3.4 mM) coexisted with high concentrations of sulfate (16-43 mM) in two sediment cores retrieved from the northern and southern parts of Orca Basin. The strong depletion of 13C in methane (-77 to -89 per mill) pointed towards a biological source. While low concentrations of competitive substrates limited the significance of hydrogenotrophic and acetoclastic methanogenesis, the presence of non-competitive methylated substrates (methanol, trimethylamine, dimethyl sulfide, dimethylsulfoniopropionate) supported the potential for methane generation through methylotrophic methanogenesis. Thermodynamic calculations demonstrated that hydrogenotrophic and acetoclastic methanogenesis were unlikely to occur under in situ conditions, while methylotrophic methanogenesis from a variety of substrates was highly favorable. Likewise, carbon isotope relationships between methylated substrates and methane supported methylotrophic methanogenesis as the major source of methane. Stable isotope tracer and radiotracer experiments with 13C bicarbonate, acetate and methanol as well as 14C-labeled methylamine indicated that methylotrophic methanogenesis was the predominant methanogenic pathway. Based on 16S rRNA gene sequences, halophilic methylotrophic methanogens related to the genus Methanohalophilus dominated the benthic archaeal community in the northern basin but also occurred in the southern basin. High abundances of methanogen lipid biomarkers such as intact polar and polyunsaturated hydroxyarchaeols were detected in sediments from the northern basin, with lower abundances in the southern basin. Strong 13C-depletion of saturated and monounsaturated hydroxyarchaeol were consistent with methylotrophic methanogenesis as the major methanogenic pathway. Collectively, the availability of methylated substrates, thermodynamic calculations, experimentally determined methanogenic activity as well as lipid and gene biomarkers strongly suggested methylotrophic methanogenesis as predominant pathway of methane formation in the presence of sulfate in Orca Basin sediments.