Description: Butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs) are membrane lipids, recently discovered in sedimentary environments and in the methanogenic archaeon Methanomassiliicoccus luminyensis. They possess an unusual structure, which challenges fundamental assumptions in lipid biochemistry. Indeed, they bear a butanetriol or a pentanetriol backbone instead of a glycerol at one end of their core structure. In this study, we unambiguously located the additional methyl group of the BDGT compound on the C3 carbon of the lipid backbone via high-field nuclear magnetic resonance (NMR) experiments. We further systematically explored the abundance, distribution and isotopic composition of BDGTs and PDGTs as both intact polar and core lipid forms in marine sediments collected in contrasting environments of the Mediterranean Sea and Black Sea. High proportions of intact polar BDGTs and PDGTs in the deeper methane-laden sedimentary layers and relatively C-13-depleted BDGTs, especially in the Rhone Delta and in the Black Sea, are in agreement with a probable methanogenic source for these lipids. However, contributions from heterotrophic Archaea to BDGTs (and PDGTs) cannot be excluded, particularly in the eastern Mediterranean Sea, and contrasting BDGT and PDGT headgroup distribution patterns were observed between the different sites studied. This points to additional, non-methanogenic, archaeal sources for these lipids.

Description: The occurrence of microbially induced smectite-to-illite (S-I) reaction has challenged both the notions of solely inorganic chemical control for this reaction and the conventional concept of a semiquantitative illite geothermometer for the reconstruction of the thermal and tectonic histories of sedimentary basins. Here, we present evidence for a naturally occurring microbially induced S-I transition, via biotic reduction of phyllosilicate structural Fe(III), in mudstones buried at the Nankai Trough, offshore Japan (International Ocean Discovery Program Site C0023). Biotic S-I reaction is a consequence of a bacterial survival and growth strategy at diagenetic temperatures up to 80 °C within the Nankai Trough mudstones. These results have considerable implications for petroleum exploration, modification of fault behavior, and the understanding of microbial communities in the deep biosphere.

Description: Highlights: • Constraining sources of core and intact archaeal lipids with stable C isotopic ratios. • No evidence for sedimentary sources of IPL crenarchaeol. • Evidence of sedimentary production of IPL caldarchaeol and BDGT-0. • Higher organic matter content promotes higher activity of sedimentary archaea. • Archaeol is a sensitive indicator of sedimentary archaea. Archaea occupy an important niche in the global carbon cycle and their lipids are widely used as indicators of environmental conditions in both paleoenvironmental and modern biogeochemical studies. The principal sources of archaeal lipids in marine sediments are benthic archaea, fossil remnants of planktonic archaea, and allochthonous sources such as soils. However, the relative contributions of these sources to the sedimentary lipid pool have not been comprehensively constrained, complicating a mechanistic understanding of archaeal lipid proxies. In order to provide insights into the relative contributions of these sources and identify signals derived from sedimentary activity, we performed a systematic survey of stable carbon isotopic compositions (delta C-13) of both core and intact archaeal lipids via analyses of their phytanyl (Phy) and biphytanyl (BP) moieties in diverse marine sediments. The sample set consisted of 44 sediment horizons from the Mediterranean and adjacent basins and represented diverse sources of organic matter and depositional conditions. Complementary geochemical data enabled the comparison of lipid distributions and carbon isotopic signatures with prevailing redox conditions. The delta C-13 of tricyclic BP (BPcren) from the core and intact forms of crenarchaeol ranged from -19.1 to -28.6% and -18.1 to -27.4%, respectively. delta C-13 values of core and intact BPcren did not differ, suggesting that intact crenarchaeol is either a fossil relic from planktonic archaea or a product of lipid recycling by benthic archaea, as opposed to being synthesized de novo by sedimentary archaea. delta C-13 values of BP0 derived from core and intact forms of glycerol and butanetriol dibiphytanyl glycerol tetraethers (GDGTs and BGDTs, respectively), but predominantly from caldarchaeol (GDGT-0), ranged from -19.4 to -32.0% and -20.9 to -37.0%, respectively. In contrast to BPcren, intact-lipid derived BP0 was often C-13-depleted relative to its core counterpart, consistent with in situ production by sedimentary archaea. This relative depletion was most pronounced in sulfate reduction zones, likely due to heterotrophic activity. Core and intact archaeol exhibited the largest ranges in delta C-13 values, from -21.6 to -42.1% and -22.7 to -58.9%, respectively. This strong C-13-depletion relative to both total organic carbon and dissolved inorganic carbon is consistent with mixtures of functional sources of sedimentary chemolithoautotrophic, methanotrophic, methanogenic and heterotrophic archaea. Based on the substantial C-13-depletion of BPcren and BP0 in samples in the vicinity of the Rhone River delta relative to a distal marine reference site, we infer that the terrestrial soil contribution of archaeal lipids to these sediments is as high as 43%. Hence, terrestrial input of archaeal lipids, including their intact forms, can be substantial and suggests caution when using existing molecular proxies aimed at constraining riverine input. In summary, our comparative isotopic analysis of sedimentary core versus intact archaeal lipids improves the apportionment of their diverse sources and confidence in distinguishing in situ lipid production by sedimentary archaea.

Description: An understanding of how the coupled cycles of carbon, iron and sulfur in sediments respond to environmental change throughout Earth history requires the reconstruction of biogeochemical processes over a range of spatial and temporal scales. In this study, sediment cores from the southwestern Black Sea were analyzed to gain insight into past changes in biogeochemical processes with particular focus on the cycling of dissolved organic carbon (DOC). The sediment consists of Late Pleistocene deposits of iron oxide-rich and organic-poor lacustrine sediments, a Holocene sapropel layer deposited after the inflow of saline Mediterranean seawater about 9300 yr BP, and overlying recent marine sediments. The porewaters displayed high concentrations of DOC, acetate, dissolved iron and an extended depth interval over which sulfate and methane were both present. The historical fluctuations of the fluxes of carbon, sulfur and iron species at the seafloor that led to these present-day geochemical profiles, and which cannot be easily interpreted from the measured data alone, were hindcasted with a reaction-transport model. The model suggests that the inflow of Mediterranean seawater impacted the rain rate and reactivity of organic matter reaching the sediments, which shifted the sedimentary redox regimes throughout the Holocene that now are reflected on different lithology units. Organic matter in the sapropel layer is apparently the main source of modern-day accumulations of DOC and acetate, both of which probably sustained subsurface microbial activity throughout the post-glacial period. The ratio between DOC and dissolved inorganic carbon (DIC) flux to the bottom water decreased from ∼40% before the inflow of Mediterranean water to ∼2% at the present day. We suggest that the coexistence of methanogenesis and sulfate reduction was associated with sulfate-reducing bacteria and methanogens sharing common substrates of acetate and lactate and utilizing non-competitive substrates such as methylated compounds in the sapropel layer and in the bottom of modern marine deposits. Intense sulfur and iron cycling mainly took place in the organic-poor freshwater deposits, today characterized by high concentrations of dissolved iron and methane. In contrast to previous studies in similar environments, anaerobic oxidation of methane coupled to the reduction of ferric iron was negligible. The results have broad implications for coastal environments that are currently experiencing deoxygenation and seawater intrusion and also for understanding the role of DOC in the sedimentary carbon cycle.

Description: The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (delta 13C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative delta 13C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable delta 13C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86, CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.

Description: Low-molecular-weight (LMW) alcohols are produced during the microbial degradation of organic matter from precursors such as lignin, pectin, and carbohydrates. The biogeochemical behavior of these alcohols in marine sediment is poorly constrained but potentially central to carbon cycling. Little is known about LMW alcohols in sediment pore waters because of their low concentrations and high water miscibility, both of which pose substantial analytical challenges. In this study, three alternative methods were adapted for the analysis of trace amounts of methanol and ethanol in small volumes of saline pore waters: direct aqueous injection (DAI), solid-phase microextraction (SPME), and purge and trap (P&T) in combination with gas chromatography (GC) coupled to either a flame ionization detector (FID) or a mass spectrometer (MS). Key modifications included the desalination of samples prior to DAI, the use of a threaded midget bubbler to purge small-volume samples under heated conditions and the addition of salt during P&T. All three methods were validated for LMW alcohol analysis, and the lowest detection limit (60 nM and 40 nM for methanol and ethanol, respectively) was achieved with the P&T technique. With these methods, ambient concentrations of volatile alcohols were determined for the first time in marine sediment pore waters of the Black Sea and the Gulf of Mexico. A strong correlation between the two compounds was observed and tentatively interpreted as being controlled by similar sources and sinks at the examined stations.

Description: Methylated amines and sulfides are ubiquitous organic nitrogen and sulfur compounds in the marine environment and could serve as important energy substrates to methanogens inhabiting anoxic sediments. However, their abundance and isotopic values remain largely unconstrained in marine sediments. In this study, we investigated the distribution of trimethylamine (TMA), dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) in Aarhus Bay, Denmark and provided the first report for their stable carbon isotopic composition. Simultaneous measurement of those two compounds in small volumes of pore waters and sediments was accomplished with gas chromatography in combination with either a purge and trap system for quantification or a headspace method for carbon isotopic analysis. TMA in the solid phase (exchangeable pool, 0.3-6.6 µmol/kg wet sediment; base-extractable pool, 2-18 µmol/kg) was much more abundant than the dissolved pool (〈 20 nM), indicating strong adsorption of TMA to sediments. Likewise, total base-hydrolyzable DMS(P)t (including DMS and base-released DMS from DMSP) in sediment was at least three orders of magnitude higher (11-65 µmol/kg) than the dissolved pool of DMS(P)d in the pore water (including DMS and dissolved DMSP; 1-12 nM). TMA and DMS(P) contents in the solid phase peaked in the surface sediment, consistent with their phytodetrital origin. TMA was more 13C-depleted than DMS(P) (TMA: -36.4 per mil to -39.2 per mil; DMS: -18.6 per mil to -23.4 per mil), presumably due to different biological or biosynthetic origins of the respective methyl groups. Both compounds showed a downcore decrease in their solid-phase concentration, a feature that was attributed to microbial degradation, but progressive enrichment in 13C (up to 4 per mil) with depth was observed only for DMS(P). The considerable pool size of TMA and DMS(P) outlined in this study and geochemical evidence of their degradability suggested these two compounds could be potentially important substrates for methane production in sulfate-reducing environments.