Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico

At the Chapopote Knoll in the Southern Gulf of Mexico, deposits of asphalt provide the substrate for a prolific cold seep ecosystem extensively colonized by chemosynthetic communities. This study investigates microbial life and associated biological processes within the asphalts and surrounding oil-impregnated sediments by analysis of intact polar membrane lipids (IPLs), petroleum hydrocarbons and stable carbon isotopic compositions (δ¹³C) of hydrocarbon gases. Asphalt samples are lightly to heavily biodegraded suggesting that petroleum-derived hydrocarbons serve as substrates for the chemosynthetic communities. Accordingly, detection of bacterial diester and diether phospholipids in asphalt samples containing finely dispersed gas hydrate suggests the presence of hydrocarbon-degrading bacteria. Biological methanogenesis contributes a substantial fraction to the methane captured as hydrate in the shallow asphalt deposits evidenced by significant depletion in ¹³C relative to background thermogenic methane. In sediments, petroleum migrating from the subsurface stimulates both methanogenesis and methanotrophy at a sulfate-methane transition zone 6-7 m below the seafloor. In this zone, microbial IPLs are dominated by archaeal phosphohydroxyarchaeols and archaeal diglycosidic diethers and tetraethers. Bacterial IPLs dominate surface sediments that are impregnated by severely biodegraded oil. In the sulfate-reduction zone, diagnostic IPLs indicate that sulfate-reducing bacteria (SRB) play an important role in petroleum degradation. A diverse mixture of phosphohydroxyarchaeols and mixed phospho- and diglycosidic archaeal tetraethers in shallow oil-impregnated sediments point to the presence of anaerobic methane-oxidizing ANME-2 and ANME-1 archaea, respectively, or methanogens. Archaeal IPLs increase in relative abundance with increasing sediment depth and decreasing sulfate concentrations, accompanied by a shift of archaeol-based to tetraether-based archaeal IPLs. The latter shift is suggested to be indicative of a community shift from ANME-2 and/or methanogenic archaea in shallower sediments to ANME-1/methanogenic archaea and possibly benthic archaea in deeper sediments.     

Factors controlling the distribution of anaerobic methanotrophic communities in marine environments: Evidence from intact polar membrane lipids

Three distinct types of microbial consortia appear to mediate the anaerobic oxidation of methane with sulfate as electron acceptor in marine sediments and are distributed ubiquitously. These consortia consist of ANerobic MEthanotrophic (ANME) archaea of the ANME-1, ANME-2 and ANME-3 clades and their sulfate-reducing bacterial partners either of the Desulfosarcina-Desulfococcus (ANME-1/DSS and ANME-2/DSS) or Desulfobulbus spp. (ANME-3/DBB) branches. Frequently one consortium type dominates the community, but the selective factors are not well constrained. Here we analyzed patterns in the composition of intact polar lipids extracted from bacterial and archaeal communities of different marine seep environments. Further, we investigated if different environmental and geographical factors were responsible for the observed patterns, and hence could be important in the selection of seep communities. Intact polar lipids (IPLs) provide a more robust distinction of the composition of extant communities than their less polar derivatives. In ANME-1/DSS-dominated communities, glycosidic- and phospho-glyceroldialkylglyceroltetraethers were abundant, while ANME-2/DSS and ANME-3/DBB-dominated communities showed abundant archaeol-based IPLs, either with glycosidic and phospho-headgroups or only phospho-headgroups, respectively. The relative proportion of bacterial IPLs varied widely from 0% to 93% and was generally lower in samples of the ANME-1 type, suggesting lower bacterial biomasses in the respective communities. In addition to these lipid signatures, distinctive features were related to the habitat characteristics of these communities: lower amounts of phosphate-based IPLs were generally observed in communities from calcified microbial mats compared to sediments, which may reflect phosphate limitation. Based on statistical analyses of IPLs and environmental data this study constrained for the first time the occurrence of three environmental factors controlling the distribution of different ANME-associated communities in a wide range of hydrocarbon seep systems. Habitats dominated by ANME-1/DSS communities were characterized by high temperature and low oxygen content in bottom waters (or even anoxia), while ANME-2/DSS and ANME-3/DBB-dominated sediments were located in settings with lower temperatures and higher oxygen content in bottom waters. Furthermore, ANME-2/DSS communities were particularly prominent in environments in which a relatively high supply of sulfate was sustained.     

Diagnostic lipid biomarker and stable carbon isotope signatures of microbial communities mediating the anaerobic oxidation of methane with sulphate

The anaerobic oxidation of methane (AOM) with sulphate is the most important sink for methane in marine environments. This process is mediated by a consortium of methanotrophic archaea and sulphate reducing bacteria. So far, three groups of anaerobic methane oxidisers (ANME-1, -2 and -3) related to the methanogenic Methanosarcinales and Methanomicrobiales were discovered. The sulphate reducing partner of ANME-1 and -2 are two different eco-types of SRB related to the Desulfosarcina/Desulfococcus cluster (Seep-SRB1), whereas ANME-3 is associated with Desulfobulbus spp. (DBB). In this article, we reviewed literature data to assign statistically significant lipid biomarker signatures for a chemotaxonomic identification of the three known AOM communities. The lipid signatures of ANME-2/Seep-SRB1 and ANME-3/DBB are intriguingly similar, whereas ANME-1/Seep-SRB1 shows substantial differences to these AOM communities. ANME-1 can be distinguished from ANME-2 and -3 by a low ratio of the isoprenoidal dialkyl glycerol diethers sn2-hydroxyarchaeol and archaeol combined with a comparably low stable carbon isotope difference of archaeol relative to the source methane. Furthermore, only ANME-1 contains substantial amounts of isoprenoidal glycerol dialkyl glycerol tetraethers (GDGTs), however, with the probable exception of the ANME-2c sub-cluster. In contrast to the ANME-1 archaea, the tail to tail linked hydrocarbon tetramethylhexadecane (crocetane) is unique to ANME-2, whereas pentamethylicosenes (PMIs) with 4 and 5 double bonds without any higher saturated homologues were only found in ANME-3. The sulphate reducing partner of ANME-1 can be discerned from those of ANME-2 and -3 by a low ratio of the fatty acids (FAs) C_16:1ω5 relative to i-C_15:0 and, although to a lesser degree, by a high abundance of ai-C_15:0 relative to i-C_15:0. Furthermore, substantial amounts of ¹³C depleted non-isoprenoidal monoalkyl glycerol ethers (MAGEs) were only found in the sulphate reducing partners of ANME-2 and -3. A differentiation of these SRB is possible based on the characteristic presence of the FAs cy-C_17:0ω5,6 and C_17:1ω6, respectively. Generally, the data analysed here show overlaps between the different AOM communities, which highlights the need to use multiple lipid signatures for a robust identification of the dominating microbes involved.     

Archaeal lipids in Neogene dolomites (Monterey and Sisquoc Formations, California) - Planktic versus benthic archaeal sources

The distribution of archaeal lipids, including archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs), in dolomite concretions and surrounding sediment from the Monterey Formation (Miocene) and the Sisquoc Formation (Miocene-Pliocene) were examined to distinguish planktic from benthic contributions. For this purpose, dolomites with positive δ¹³C values (+7‰ to +13‰) were chosen; such highly positive values point to pronounced methanogenesis of benthic archaea in the sedimentary column. At first glance, distributions and relative abundances of GDGTs in both dolomites and background sediment were similar, resembling patterns of marine planktic crenarchaea. A contribution of benthic euryarchaea to the GDGT pool became evident only from variations in the δ¹³C values of different biphytanes obtained after ether cleavage of GDGTs. Whereas bi- and tricyclic biphytanes had an isotopic signal typical of planktic archaea (δ¹³C −23.6‰ to −20.5‰ and −23.4‰ to −21.2‰, respectively) for both dolomite and background sediment, acyclic and monocyclic biphytanes showed lower values for dolomite samples (−25.1‰ to −22.6‰ and −27.6‰ to −24.7‰, respectively), indicating a contribution of lipids from benthic archaea. The isoprenoid diether archaeol (δ¹³C −23.9‰ to −22.9‰), assigned to euryarchaea, was only detected in dolomite samples, also reflecting additional input from sedimentary archaea, probably autotrophic methanogens. The occurrence of lipids derived from methanogenic archaea agrees with the strong ¹³C-enrichment of dolomites and with mineral formation taking place in the zone of archaeal methanogenesis. This implies that the lipid biomarker inventory of sedimentary strata needs to be interpreted carefully, as it is often not straightforward to discriminate between input from the water column and sedimentary microbial activity.     

Intact Polar and Core Tetraether Lipids in Sediments from the Haiyang 4 Cold-seep of the Northern South China Sea and their Implications

A number of cold seeps have been discovered in the northern South China Sea (SCS) including the Haiyang 4 cold-seep area where Core 973-5 was collected. Intact polar lipids (IPLs) and core lipids (CLs) were analyzed separately in sediments from Core 973-5. The most abundant lipid biomarkers were isoprenoidal GDGTs (isoGDGTs), with Crenarchaeol and GDGT-0 predominating. IPL-isoGDGTs and CL-isoGDGTs were mainly derived from Thaumarchaeota. IPL-isoGDGTs were mainly produced and retained in situ thus containing most of the in situ microbiological information. Branched GDGTs were predominantly derived from generated in marine production, and mixed with some terrestrial inputs. All IPLs groups presented a high value in the sulfate-methane transition zone (SMTZ). Furthermore, IPL and CL-MI, IPL-R0/4 showed the highest values within the SMTZ, while IPL and CL-R4/i had the lowest values at the SMTZ, suggesting that the contribution of Methanophila and methanogenic to GDGTs increased, while the contribution of ammonia-oxidizing Archaea to GDGTs decreased at the SMTZ.     

Comparison of extraction and work up techniques for analysis of core and intact polar tetraether lipids from sedimentary environments

Glycerol dibiphytanyl glycerol tetraether-based intact polar lipids (IPL GDGTs) are used as biomarkers for living Archaea and are analyzed utilizing a variety of extraction and quantification techniques. Most IPL GDGT studies have used a modified Bligh–Dyer extraction method, but it has been suggested that Soxhlet extraction may be more efficient for environmental samples and biomass. We investigated the impact of three different extractions (Soxhlet, Bligh–Dyer and accelerated solvent extraction, ASE), two IPL quantification methods and two work up techniques (Na₂SO₄ and SiO₂ column) on the amount and distribution of CL (core lipid)- and IPL-derived GDGTs and crenarchaeol-based IPLs in marine sediments from the Arabian Sea and Icelandic shelf, as well as a microbial mat from a Dutch beach. The different extraction procedures gave a similar yield of CL- and IPL-derived GDGTs. Direct analysis of crenarchaeol IPLs showed, however, that, while GDGTs with a monohexose head group were not affected by the extraction method, there was a large effect on IPL GDGTs containing dihexose or hexose, phosphohexose head groups. Quantification of IPL-derived GDGTs by way of either separation over a silica column or by subtraction of CL GDGTs in the total lipid extract before and after hydrolysis gave similar results, but the ‘subtraction-method’ had a relatively large quantification error. However, the silica column, as well as drying over a Na₂SO₄ column, resulted in a loss of the hexose, phosphohexose IPLs by up to 80%. Based on the results, a modified Bligh–Dyer extraction with as little further treatment as possible is recommended to allow measurement of the full range of IPL GDGTs in sediments.     

Extraordinary C enrichment of diether lipids at the Lost City Hydrothermal Field indicates a carbon-limited ecosystem

Active and inactive carbonate chimneys from the Lost City Hydrothermal Field contain up to 0.6% organic carbon with diverse lipid assemblages. The δ¹³C values of total organic carbon range from −21.5‰ vs. VPDB at an extinct carbonate chimney to −2.8‰ at a 70 °C, actively venting carbonate chimney. Samples collected at locations with total organic carbon with δ¹³C > −15‰ also contained high abundances of isoprenoidal and nonisoprenoidal diether lipids. Samples with TOC more depleted in ¹³C lacked or contained lower amounts of these diethers.Isoprenoidal diethers, including sn-2 hydroxyarchaeol, sn-3 hydroxyarchaeol, and putative dihydroxyarchaeol, are likely to derive from methanogenic archaea. These compounds have δ¹³C values ranging from −2.9 to +6.7‰ vs. VPDB. Nonisoprenoidal diethers and monoethers are presumably derived from bacteria, and have structures similar to those produced by sulfate-reducing bacteria in culture and at cold seeps. In samples that also contained abundant hydroxyarchaeols, these diethers have δ¹³C values between −11.8 and +3.6‰. In samples without abundant hydroxyarchaeols, the nonisoprenoidal diethers were typically more depleted in ¹³C, with δ¹³C as low as −28.7‰ in chimneys and −45‰ in fissures.The diethers at Lost City are probably derived from hydrogen-consuming methanogens and bacteria. High hydrogen concentrations favor methanogenesis over methanotrophy and allow the concurrent growth of methanogens and sulfate-reducing bacteria. The unusual enrichment of ¹³C in lipids can be attributed to nearly complete consumption of bioavailable carbon in vent fluids. Under carbon-limited conditions, the isotope effects that usually lead to ¹³C-depletion in organic material cannot be expressed. Consequently, metabolic products such as lipids and methane have δ¹³C values typical of abiotic carbon.     

Differential degradation of intact polar and core glycerol dialkyl glycerol tetraether lipids upon post-depositional oxidation

Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids (GDGTs) are used in various proxies, such as TEX₈₆ and the BIT index. In living organism, they contain polar head groups (intact polar lipids – IPLs). IPL GDGTs have also been detected in ancient marine sediments and it is unclear whether or not they are fossil entities or are part of living cells. In order to determine the extent of degradation of IPL GDGTs over geological timescales, we analyzed turbidite deposits, which had been partly reoxidized for several kyr after deposition on the Madeira Abyssal Plain. Analysis of core lipid (CL) and IPL-derived GDGTs showed a reduction in concentration by two orders of magnitude upon post-depositional oxidation, while IPL GDGTs with a mono- or dihexose head group decreased by 2–3 orders of magnitude. The BIT index for CL- and IPL-derived GDGTs increased substantially upon oxidation from 0.1 to up to 0.5. Together with changing MBT/CBT values, this indicates preferential preservation of soil-derived branched GDGTs over marine isoprenoid GDGTs, combined with in situ production of branched GDGTs in the sediment. The TEX₈₆ value for IPL-derived GDGTs decreased by 0.07 upon oxidation, while that of CL GDGTs showed no significant change. Isolation of IPLs revealed that the TEX₈₆ value for monohexose GDGTs was 0.55, while the that for dihexose GDGTs was substantially higher, 0.70. Thus, the decrease in TEX₈₆ for IPL-derived GDGTs was in agreement with the dominance of monohexose GDGTs in the oxidized turbidite, probably caused by a combination of in situ production as well as selective preservation of terrestrial isoprenoid GDGTs. Due to the low amount of IPL GDGTs vs. CL GDGTs, the impact of IPL degradation on CL-based TEX₈₆ paleotemperature estimates was negligible.     

Carbon and hydrogen isotope ratio characterization of methane dynamics for Fluxnet Peatland Ecosystems

Methane concentration [CH₄] and stable isotope ratio values (δ¹³C) characterize methanogenic and methanotrophic processes within two contrasting peatland ecosystems of the Fluxnet Canada Research Network: (i) a western Canada peatland fen in northern Alberta (Fen) and (ii) an eastern Canada peatland bog in southeastern Ontario (Bog). We use carbon isotope ratio discrimination of produced methane (δ¹³C_CH4) from the precursor carbon compounds (δ¹³C_preC) to estimate the relative proportions of archaebacterial acetoclastic methanogenesis (AM) and hydrogenotrophic carbonate reduction methanogenesis (HM) in these terrestrial ecosystems. The [CH₄] and δ¹³C_CH4 signatures describe contrasts in the methanogenic and methanotrophic processes between the Fen and the Bog. The differences are substantiated by stable hydrogen isotope ratio (δD) separation between the dissolved δD_CH4 and co-existing δD_H2O. Methanogenesis at the Fen is dominated by AM, in contrast to the Bog, which is essentially HM. We suggest that this is potentially a result of differences in type/quality of organic substrates. The trajectory of ¹³C enrichment in δ¹³C_CH4 values with depth at the Bog reflects a closed system, substrate depletion effect. Our Rayleigh distillation model estimates 58-76% depletion in the source dissolved inorganic carbon (DIC).     

Advection and diffusion determine vertical distribution of microbial communities in intertidal sediments as revealed by combined biogeochemical and molecular biological analysis

Porewater advection stimulates nutrient exchange and microbial activity in shallow marine sediments, whereas element cycling in deeper diffusion-dominated sediments is comparatively slow due to limited nutrient supply. We studied the vertical distribution of microbial communities and organic matter (OM) cycling in these contrasting porewater regimes down to 5 m depth at an intertidal flat of the southern North Sea. Archaea, Bacteria and Eukarya were targeted, combining intact polar lipid (IPL) analysis with qualitative and quantitative molecular biological techniques. The largely sandy section 1 of the core (<75 cm) is characterized by rapid burial of fresh marine OM and intense porewater advection. This supply fuels heterotrophic microbes, as evident from the ¹³C isotopic composition of total organic carbon and IPL derivatives. Major sources of OM are algae and cyanobacteria, as suggested by the elevated amount of eukaryotic 18S rRNA gene copies and phosphate-free IPLs. The relative abundance of most phospholipids remained largely constant over the entire core, except for diphosphatidylglycerol, which represented about half of total IPL abundance in the lower part of section 1 (>50 cm) and the diffusion-dominated section 2 (75–490 cm). This suggests bacteria adapting their membranes in response to increasing physicochemical stress and starvation in the nutrient limited, fine grained sediments of section 2 with less bioavailable, predominantly terrestrial, OM. Relative amounts of bacterial acyl ether and diether phospholipids increased in this lower section and were assigned to sulfate reducers and yet uncultured myxobacteria. Archaea were an order of magnitude less abundant than Bacteria, and were affiliated mainly with Methanosarcinales and Methanomicrobiales. Accordingly, the archaeal IPL composition was typical for a methanogenic community. IPLs not exclusively derived from in situ microbial production emphasize that these biomarkers have to be interpreted with caution in sediments with complex hydrogeology. Our results demonstrate that contrasting subsurface flow regimes significantly impact on the vertical zonation of biogeochemical properties and microorganisms in marine sediments.     

Identification and distribution of intact polar branched tetraether lipids in peat and soil

Branched glycerol dialkyl glycerol tetraether lipids (GDGTs) are membrane lipids of soil bacteria that occur ubiquitously in soil, but their occurrence as intact polar lipids (IPLs) has not been well studied. Here, we report the identification and distribution of IPL-branched GDGTs throughout a depth profile of a Swedish peat bog. In addition to two reported glycosidic IPL branched GDGTs, we identified IPL branched GDGTs with a hexose-glycuronic acid, phospho-hexose, or hexose-phosphoglycerol head group, based on mass spectrometry. A selected reaction monitoring (SRM) assay was developed to monitor changes in head group distribution with depth. The abundance of the IPL branched GDGTs increased below the water table, suggesting that they were primarily produced in this part of the peat. This was supported by the concentrations of core lipid and IPL-derived branched GDGTs, which also substantially increased below the water table. However, individual IPL trends differed, which may be due to changes in the microbial community composition with depth or to different degradation rates for the different IPL branched GDGTs. The SRM method was also applied to two different soil types, which showed that similar IPL branched GDGTs as those in peat were present, albeit with different distributions.     

The stable carbon isotope biogeochemistry of acetate and other dissolved carbon species in deep subseafloor sediments at the northern Cascadia Margin

Ocean drilling has revealed the existence of vast microbial populations in the deep subseafloor, but to date little is known about their metabolic activities. To better understand the biogeochemical processes in the deep biosphere, we investigate the stable carbon isotope chemistry of acetate and other carbon-bearing metabolites in sediment pore-waters. Acetate is a key metabolite in the cycling of carbon in anoxic sediments. Its stable carbon isotopic composition provides information on the metabolic processes dominating acetate turnover in situ. This study reports our findings for a methane-rich site at the northern Cascadia Margin (NE Pacific) where Expedition 311 of the Integrated Ocean Drilling Program (IODP) sampled the upper 190 m of sediment. At Site U1329, δ¹³C values of acetate span a wide range from −46.0‰ to −11.0‰ vs. VPDB and change systematically with sediment depth. In contrast, δ¹³C values of both the bulk dissolved organic carbon (DOC) (−21.6 ± 1.3‰ vs. VPDB) and the low-molecular-weight compound lactate (−20.9 ± 1.8‰ vs. VPDB) show little variability. These species are interpreted to represent the carbon isotopic composition of fermentation products. Relative to DOC, acetate is up to 23.1‰ depleted and up to 9.1‰ enriched in ¹³C. Broadly, ¹³C-depletions of acetate relative to DOC indicate flux of carbon from acetogenesis into the acetate pool while ¹³C-enrichments of pore-water acetate relative to DOC suggest consumption of acetate by acetoclastic methanogenesis. Isotopic relationships between acetate and lactate or DOC provide new information on the carbon flow and the presence and activity of specific functional microbial communities in distinct biogeochemical horizons of the sediment. In particular, they suggest that acetogenic CO₂-reduction can coexist with methanogenic CO₂-reduction, a notion contrary to the hypothesis that hydrogen levels are controlled by the thermodynamically most favorable electron-accepting process. Further, the isotopic relationship suggests a relative increase in acetate flow to acetoclastic methanogenesis with depth although its contribution to total methanogenesis is probably small. Our study demonstrates how the stable carbon isotope biogeochemistry of acetate can be used to identify pathways of microbial carbon turnover in subsurface environments. Our observations also raise new questions regarding the factors controlling acetate turnover in marine sediments.     

A comprehensive approach to the study of methane-seep deposits from the Lincoln Creek Formation, western Washington State, USA

ABSTRACT A comprehensive approach using palaeontology, petrography, stable isotope geochemistry and biomarker analyses was applied to the study of seven small methane‐seep carbonate deposits. These deposits are in the Oligocene part of the Lincoln Creek Formation, exposed along the Canyon and Satsop Rivers in western Washington. Each deposit preserves invertebrate fossils, many representing typical seep biota. Authigenic carbonates with δ¹³C values as low as ?51‰ PDB reveal that the carbon is predominately methane derived. Carbonates contain the irregular isoprenoid hydrocarbons 2,6,11,15‐tetramethylhexadecane (crocetane) and 2,6,10,15,19‐pentamethylicosane (PMI), lipid biomarkers diagnostic for archaea. These lipids are strongly depleted in ¹³C (δ¹³C values as low as ?120‰ PDB), indicating that archaea were involved in the anaerobic oxidation of methane. Small filaments preserved in the carbonate may represent methanotrophic archaea. Archaeal methanogenesis induced the formation of a late diagenetic phase, brownish calcite, consisting of dumbbell‐shaped crystal aggregates that exhibit δ¹³C values as high as +7‰ PDB. Clotted microfabrics of primary origin point to microbial mediation of carbonate precipitation. Downward‐directed carbonate aggregation in the seeps produced inverted stromatactoid cavities. Large filaments, interpreted as green algae based on their size, shape, arrangement and biomarkers, imply that deposition occurred, in places, in water no deeper than 210 m.     

Polar and neutral isopranyl glycerol ether lipids as biomarkers of archaea in near-surface sediments from the Nankai Trough

The molecular and carbon isotopic compositions of polar isopranyl glycerol ether lipids, which are direct indicators of viable archaea, and neutral isopranyl glycerol ether lipids, which are derived from polar lipids via hydrolysis, in near-surface sediments from a methane seep in the Nankai Trough (off central Japan) were investigated. Procedures for extracting, separating and derivatizing polar and neutral ether lipids for detection using gas chromatography were first examined with one sediment sample and a cultivated methanogen. For all sediment samples, archaeol and hydroxyarchaeol were detected in both the polar and neutral ether lipid fractions. Acyclic and cyclic biphytanes were also detected in both types of lipid fractions after treatment with HI/LiAlH₄ for ether cleavage and alkylation. The δ¹³C values of archaeol, sn-2-hydroxyarchaeol, and sn-3-hydroxyarchaeol in the sample from 0.82 m below the seafloor were lower than −100‰ relative to PDB, indicating that diverse living methanotrophic archaea are present in the seep sediments. Biphytanes released from polar ether lipids in the same sample were less depleted in δ¹³C (−71‰ to −36‰). The wide range of δ¹³C values suggests that the biphytanes were derived not only from methanotrophic but also from non-methanotrophic archaea, and that the relative contributions of the methanotrophic and non-methanotrophic archaea differed, depending on the biphytane compound. The vertical profiles and δ¹³C values of the neutral ether lipids were similar to those of the intact polar ether lipids, suggesting that neutral ether lipids derived from fossil archaea in the samples had mainly been lost by the time of sampling.     

Comparison of fluid geochemistry and microbiology of multiple organic-rich reservoirs in the Illinois Basin, USA: Evidence for controls on methanogenesis and microbial transport

Microbial methane in sedimentary basins comprises approximately 20% of global natural gas resources, yet little is known about the environmental requirements and metabolic rates of these subsurface microbial communities. The Illinois Basin, located in the midcontinent of the United States, is an ideal location to investigate hydrogeochemical factors controlling methanogenesis as microbial methane accumulations occur: (1) in three organic-rich reservoirs of different geologic ages and organic matter types - Upper Devonian New Albany Shale (up to 900 m depth), Pennsylvanian coals (up to 600 m depth), and Quaternary glacial sediments (shallow aquifers); (2) across steep salinity gradients; and (3) with variable concentrations of . For all three organic-rich reservoirs aqueous geochemical conditions are favorable for microbial methanogenesis, with near neutral pH, concentrations <2 mM, and Cl⁻ concentrations <3 M. Also, carbon isotopic fractionation of CH₄, CO₂, and DIC is consistent with microbial methanogenesis, and increased carbon isotopic fractionation with average reservoir depth corresponds to a decrease of groundwater flushing rates with average depth of reservoir. Plots of stable isotopes of water and Cl⁻ show mixing between a brine endmember and freshwater, suggesting that meteoric groundwater recharge has affected all microbial methanogenic systems. Additionally, similar methanogenic communities are present in all three reservoirs with comparable cell counts (8.69E3-2.58E6 cells/mL). TRFLP results show low numbers of archaea species with only two dominant groups of base pairs in coals, shale, and limestone aquifers. These results compare favorably with other methanogen-containing deep subsurface environments. Individual hydrogeochemical parameters that have a Spearman correlation coefficient greater than 0.3 to variations in methanogenic species include stable isotopes of water (δ¹⁸O and δD), type of substrate (i.e. coals versus shale), pH, and Cl⁻ concentration. The matching of variations between methanogenic TRFLP data and conservative tracers suggests that deep circulation of meteoric waters influenced archaeal communities in the Illinois Basin. In addition, coalification and burial estimates suggest that in the study area, coals and shale reservoirs were previously sterilized (>80 °C in nutrient poor environments), necessitating the re-introduction of microbes into the subsurface via groundwater transport.     

Quantifying seasonal precipitation using high-resolution carbon isotope analyses in evergreen wood

High-resolution natural abundance stable carbon isotope analyses across annual growth rings in evergreen trees reveal a cyclic increase and decrease in the measured carbon isotopic composition (δ¹³C), but the causes of this pattern are poorly understood. We compiled new and published high-resolution δ¹³C data from across annual growth rings of 33 modern evergreen trees from 10 genera and 15 globally distributed sites to quantify the parameters that affect the observed δ¹³C pattern. Across a broad range of latitude, temperature, and precipitation regimes, we found that the average, measured seasonal change in δ¹³C (Δδ¹³C_meas, ‰) within tree rings of evergreen species reflects changes in the carbon isotopic composition of atmospheric carbon dioxide (Δδ¹³C_CO2) and changes in seasonal precipitation (ΔP) according to the following equation: Δδ¹³C_meas = Δδ¹³C_CO2 - 0.82(ΔP) + 0.73; R² = 0.96. Seasonal changes in temperature, pCO₂, and light levels were not found to significantly affect Δδ¹³C_meas. We propose that this relationship can be used to quantify seasonal patterns in paleoprecipitation from intra-ring profiles of δ¹³C measured from non-permineralized, fossil wood.     

Different types of methane monooxygenases produce similar carbon and hydrogen isotope fractionation patterns during methane oxidation

We determined the stable carbon and hydrogen isotope fractionation factors for methane oxidation under oxic conditions using strains with known degradation pathways. The aerobic oxidation of methane can be initiated by two different forms of enzymes known as methane monooxygenases (MMO). The expression of these enzymes is type-specific and dependent upon the adjusted copper concentration in the medium (or environment). In this study, the expression of either the soluble MMO or the particulate MMO was supported by adjusting the copper concentrations in the growth medium. Taxonomically different aerobic methanotrophic strains, mainly belonging to the alpha- and gamma- classes of Proteobacteria, produced methane isotope enrichment factors (ε_bulk) ranging from −14.8 to −27.9‰ for carbon, and from −110.0 to −231.5‰ for hydrogen. The ratio of hydrogen versus carbon discrimination (Λ = (α_H⁻¹ − 1)/(α_C⁻¹ − 1) ≈ Δ(δ²H)/Δ(δ¹³C)) were similar for all tested cultures, and are also identical to values calculated from previously published enrichment factors for aerobic and anaerobic methane degradation. In contrast, Λ-values for the abiotic oxidation of methane with OH radicals (this process is considered as the main removal process for methane from the atmosphere) were significantly higher than the values derived from biotic oxidation. Due to the low variability of microbial methane isotope fractionation patterns, we propose that combined carbon and hydrogen isotope fractionation analyses can be used to monitor and assess the occurrence of microbial methane oxidation in marine or terrestrial environments. However, it is not possible to distinguish distinct aerobic or anaerobic methane-oxidation pathways by this approach.     

Fossilization and degradation of intact polar lipids in deep subsurface sediments: A theoretical approach

Intact polar membrane lipids (IPLs) are frequently used as markers for living microbial cells in sedimentary environments. The assumption with these studies is that IPLs are rapidly degraded upon cell lysis and therefore IPLs present in sediments are derived from in situ microbial production. We used a theoretical approach to assess whether IPLs in surface sediments can potentially represent fossilized IPLs derived from the upper part of the water column and whether IPLs can be preserved during sediment burial. Previous studies which examined the degradation kinetics of IPLs show that phospholipids, i.e. ester-linked lipids with a phosphor-containing head group, degrade more rapidly than glycosidic ether lipids, i.e. ether-linked lipids with a glycosidically bound sugar moiety. Based on these studies, we calculate that only a minor fraction of phospholipids but a major fraction of glycosidic ether lipids biosynthesized in the upper part of the water column can potentially reach deep-sea surface sediments. Using a simple model and power law kinetic degradation parameters reported in the literature, we also evaluated the degradation of IPLs during sediment burial. Our model predicts a log-log relationship between IPL concentrations and depth, consistent with what has been observed in studies of IPLs in subsurface sediments. Although our results do not exclude production of IPLs in subsurface sediment, they do suggest that IPLs present in the deep biosphere may contain a substantial fossil component potentially masking in situ IPL production.     

Compound-specific carbon isotope study on the hydrocarbon biomarkers in lacustrine source rocks from Songliao Basin

Stable carbon isotopic composition of organic matter (δ¹³C_org) and compound-specific δ¹³C values of biomarkers from 15 lacustrine source rocks were analyzed to identify the original paleoenvironment and source organisms. The δ¹³C values of hopanes (δ¹³C_hop) ranged from −68.7‰ to −32‰ and exhibit strongly ¹³C-depleted values in the lower part of Member 1 of the Nenjiang Formation (K₂n¹, up to −68.7‰), suggesting an origin from predominantly methanotrophic bacteria. ¹³C-enriched δ¹³C_Ga values and significantly ¹³C-depleted δ¹³C_hop in K₂n¹, which coincide with water stratification and an intermittent anoxic photic zone, represents a shallow chemocline. The presence of an intermittent anoxic photic zone, which means that the anoxia expanded into the euphotic zone, is beneficial for OM preservation and results in high values of TOC and HI in this section. However, the absence of gammacerane and ¹³C-enrichment of δ¹³C_hop in Member 2 of Nenjiang Formation (K₂n²) reflect a deeper chemocline, corresponding to relatively oxidizing conditions and low values of TOC and HI. Moreover, the negative correlation of TOC vs δ¹³C_org and HI vs δ¹³C_org reflects the control of OM formation by sedimentary environments rather than productivity in the water column. Thus, the depth of the chemocline not only controls the abundance of OM but also affects the development of the microbial community, such as chemoautotrophic bacteria in the deep chemocline and chemoautotrophic and methanotrophic bacteria in the shallow chemocline. Moreover, δ¹³C_Ga and δ¹³C values for 4-methyl steranes are related to water salinity, with a higher salinity accompanied by ¹³C-enrichment in gammacerane and 4-methyl steranes.     

海洋沉积物中现存微生物化学标志物完整极性膜脂研究进展

完整极性膜脂作为活的微生物细胞的化学标志物,能够反映海洋沉积物中现存微生物群落结构和生物量等信息.与生物学方法相比,完整极性膜脂分析技术具有无需培养、快速和普适性等特点.综述了海洋沉积物中细菌和古菌的细胞膜完整极性膜脂的组成特点及其在生物地球化学和微生物生态学等研究中的应用,重点评述了在生物地球化学循环中有特殊作用的微生物,如厌氧氨氧化细菌、甲烷氧化古菌、氨氧化古菌、具有四醚膜脂结构的海洋泉古菌等,或者是一些特殊生态系统,如冷泉、海底深部生物圈等研究中完整极性膜脂应用的进展.还简要介绍了完整极性膜脂的分析方法,并对其应用前景进行了展望.