Description: Hydrocarbon seeps are ubiquitous at gas-prone Cenozoic deltas such as the Nile Deep Sea Fan (NDSF2) where seepage into the bottom water has been observed at several mud volcanoes (MVs3) including North Alex MV (NAMV4). Here we investigated the sources of hydrocarbon gases and sedimentary organic matter together with biomarkers of microbial activity at four locations of NAMV to constrain how venting at the seafloor relates to the generation of hydrocarbon gases in deeper sediments. At the centre, high upward flux of hot (70 °C) hydrocarbon-rich fluids is indicated by an absence of biomarkers of Anaerobic Oxidation of Methane (AOM) and nearly constant methane (CH4) concentration depth-profile. The presence of lipids of incompatible thermal maturities points to mixing between early-mature petroleum and immature organic matter, indicating that shallow mud has been mobilized by the influx of deep-sourced hydrocarbon-rich fluids. Methane is enriched in the heavier isotopes, with values of δ13C∼−46.6‰VPDB and δD ∼−228‰VSMOW, and is associated with high amounts of heavier homologues (C2+) suggesting a co-genetic origin with the petroleum. On the contrary at the periphery, a lower but sustained CH4 flux is indicated by deeper sulphate–methane transition zones and the presence of 13C-depleted biomarkers of AOM, consistent with predominantly immature organic matter. Values of δ13C-CH4∼−60‰VPDB and decreased concentrations of 13C-enriched C2+ are typical of mixed microbial CH4 and biodegraded thermogenic gas from Plio-Pleistocene reservoirs of the region. The maturity of gas condensate migrated from pre-Miocene sources into Miocene reservoirs of the Western NDSF is higher than that of the gas vented at the centre of NAMV, supporting the hypothesis that it is rather released from the degradation of oil in Neogene reservoirs. Combined with the finding of hot pore water and petroleum at the centre, our results suggest that clay mineral dehydration of Neogene sediments, which takes place posterior to reservoir filling, may contribute to intense gas generation at high sedimentation rate deltas.

Description: Anaerobic oxidation of methane (AOM) was shown to reduce methane emissions by over 50% in freshwater systems, its main natural contributor to the atmosphere. In these environments iron oxides can become main agents for AOM, but the underlying mechanism for this process has remained enigmatic. By conducting anoxic slurry incubations with lake sediments amended with 13C-labeled methane and naturally abundant iron oxides the process was evidenced by significant 13C-enrichment of the dissolved inorganic carbon pool and most pronounced when poorly reactive iron minerals such as magnetite and hematite were applied. Methane incorporation into biomass was apparent by strong uptake of 13C into fatty acids indicative of methanotrophic bacteria, associated with increasing copy numbers of the functional methane monooxygenase pmoA gene. Archaea were not directly involved in full methane oxidation, but their crucial participation, likely being mediators in electron transfer, was indicated by specific inhibition of their activity that fully stopped iron-coupled AOM. By contrast, inhibition of sulfur cycling increased 13C-methane turnover, pointing to sulfur species involvement in a competing process. Our findings suggest that the mechanism of iron-coupled AOM is accomplished by a complex microbe-mineral reaction network, being likely representative of many similar but hidden interactions sustaining life under highly reducing low energy conditions.

Description: Hydrocarbon seeps are ubiquitous at gas-prone Cenozoic deltas such as the Nile Deep Sea Fan (NDSF2) where seepage into the bottom water has been observed at several mud volcanoes (MVs3) including North Alex MV (NAMV4). Here we investigated the sources of hydrocarbon gases and sedimentary organic matter together with biomarkers of microbial activity at four locations of NAMV to constrain how venting at the seafloor relates to the generation of hydrocarbon gases in deeper sediments. At the centre, high upward flux of hot (70 °C) hydrocarbon-rich fluids is indicated by an absence of biomarkers of Anaerobic Oxidation of Methane (AOM) and nearly constant methane (CH4) concentration depth-profile. The presence of lipids of incompatible thermal maturities points to mixing between early-mature petroleum and immature organic matter, indicating that shallow mud has been mobilized by the influx of deep-sourced hydrocarbon-rich fluids. Methane is enriched in the heavier isotopes, with values of δ13C∼−46.6‰VPDB and δD ∼−228‰VSMOW, and is associated with high amounts of heavier homologues (C2+) suggesting a co-genetic origin with the petroleum. On the contrary at the periphery, a lower but sustained CH4 flux is indicated by deeper sulphate–methane transition zones and the presence of 13C-depleted biomarkers of AOM, consistent with predominantly immature organic matter. Values of δ13C-CH4∼−60‰VPDB and decreased concentrations of 13C-enriched C2+ are typical of mixed microbial CH4 and biodegraded thermogenic gas from Plio-Pleistocene reservoirs of the region. The maturity of gas condensate migrated from pre-Miocene sources into Miocene reservoirs of the Western NDSF is higher than that of the gas vented at the centre of NAMV, supporting the hypothesis that it is rather released from the degradation of oil in Neogene reservoirs. Combined with the finding of hot pore water and petroleum at the centre, our results suggest that clay mineral dehydration of Neogene sediments, which takes place posterior to reservoir filling, may contribute to intense gas generation at high sedimentation rate deltas. Highlights ► Extensive seepage of biodegraded gas at the periphery of North Alex mud volcano. ► At the centre seepage of deeper-sourced hot water, oil and thermogenic gas. ► At the centre, degradation of reservoired-oil to gas is most likely. ► Multivariate statistics on biomarkers show oil degradation at the centre and AOM at the periphery. ► Shallow gas production is enhanced by hot water influx from actively dewatering clays.

Description: Cold seeps in the Aleutian deep-sea trench support prolific benthic communities and generate carbonate precipitates which are dependent on carbon dioxide delivered from anaerobic methane oxidation. This process is active in the anaerobic sediments at the sulfate reduction-methane production boundary and is probably performed by archaea working in syntrophic co-operation with sulfate-reducing bacteria. Diagnostic lipid biomarkers of archaeal origin include irregular isoprenoids such as 2,6,11,15-tetramethylhexadecane (crocetane) and 2,6,10,15,19-pentamethylicosane (PMI) as well as the glycerol ether lipid archaeol (2,3-di-O-phytanyl-sn-glycerol). These biomarkers are prominent lipid constituents in the anaerobic sediments as well as in the carbonate precipitates. Carbon isotopic compositions of the biomarkers are strongly depleted in 13C with values of δ13C as low as −130.3‰ PDB. The process of anaerobic methane oxidation is also reflected in the carbon isotope composition of organic matter with δ13C-values of −39.2 and −41.8‰ and of the carbonate precipitates with values of −45.4 and −48.7‰. This suggests that methane-oxidizing archaea have accumulated within the microbial community, which is active at the cold seep sites. The dominance of crocetane in sediments at one station indicates that, probably due to decreased methane venting, archaea might no longer be growing, whereas high amounts of crocetenes found at other more active stations may indicate recent fluid venting and active archaea. Comparison with other biomarker studies suggests that various archaeal assemblages might be involved in the anaerobic consumption of methane. The assemblages are apparently dependent on specific conditions found at each cold seep environment. Selective conditions probably include water depth, temperature, degree of anoxia, and supply of free methane.

Description: Saanich Inlet has been a highly productive fjord since the last glaciation. During ODP Leg 169S, nearly 70 m of Holocene sediments were recovered from Hole 1034 at the center of the inlet. The younger sediments are laminated, anaerobic, and rich in organic material (1–2.5 wt.% Corg), whereas the older sediments below 70 mbsf are non-laminated, aerobic, with glacio-marine characteristics and have a significantly lower organic matter content. This difference is also reflected in the changes of interstitial fluids, and in biomarker compositions and their carbon isotope signals. The bacterially-derived hopanoid 17α(H),21β(H)-hop-22(29)-ene (diploptene) occurs in Saanich Inlet sediments throughout the Holocene but is not present in Pleistocene glacio-marine sediments. Its concentration increases after ∼6000 years BP up to present time to about 70 μg/g Corg, whereas terrigenous biomarkers such as the n-alkane C31 are low throughout the Holocene (〈51 μg/g Corg) and even slightly decrease to 36 μg/g Corg at the most recent time. The increasing concentrations of diploptene in sediments younger than ∼6000 years BP separate a recent period of higher primary productivity, stronger anoxic bottom waters, and higher bacterial activity from an older period with lesser activity, heretofore undifferentiated. Carbon isotopic compositions of diploptene in the Holocene are between −31.5 and −39.6‰ PDB after ∼6000 years BP. These differences in the carbon isotopic record of diploptene probably reflect changes in microbial community structure of bacteria living at the oxic–anoxic interface of the overlying water column. The heavier isotope values are consistent with the activity of nitrifying bacteria and the lighter isotope values with that of aerobic methanotrophic bacteria. Therefore, intermediate δ13C values probably represent mixtures between the populations. In contrast, carbon isotopic compositions of n-C31 are roughly constant at −31.4±1.1‰ PDB throughout the Holocene, indicating a uniform input from cuticular waxes of higher plants. Prior to ∼6000 years BP, diploptene enriched in 13C of up to −26.3‰ PDB is indicative of cyanobacteria living in the photic zone and suggests a period of lower primary productivity, more oxygenated bottom waters, and hence lower bacterial activity during the earliest Holocene.

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: Dissolved organic matter (DOM) in marine sediment pore waters derives largely from decomposition of particulate organic matter and its composition is influenced by various biogeochemical and oceanographic processes in yet undetermined ways. Here, we determine the molecular inventory of pore water DOM in marine sediments of contrasting depositional regimes with ultrahigh-resolution mass spectrometry and complementary bulk chemical analyses in order to elucidate the factors that shape DOM composition. Our sample sets from the Mediterranean, Marmara and Black Seas covered different sediment depths, ages and a range of marine environments with different (i) organic matter sources, (ii) balances of organic matter production and preservation, and (iii) geochemical conditions in sediment and water column including anoxic, sulfidic and hypersaline conditions. Pore water DOM had a higher molecular formula richness than overlying water with up to 11,295 vs. 2114 different molecular formulas in the mass range of 299–600 Da and covered a broader range of element ratios (H/C = 0.35–2.19, O/C = 0.03–1.19 vs. H/C = 0.56–2.13, O/C = 0.15–1.14). Formula richness was independent of concentrations of DOC and TOC. Near-surface pore water DOM was more similar to water column DOM than to deep pore water DOM from the same core with respect to formula richness and the molecular composition, suggesting exchange at the sediment–water interface. The DOM composition in the deeper sediments was controlled by organic matter source, selective decomposition of specific DOM fractions and early diagenetic molecule transformations. Compounds in pelagic sediment pore waters were predominantly highly unsaturated and N-bearing formulas, whereas oxygen-rich CHO-formulas and aromatic compounds were more abundant in pore water DOM from terrigenous sediments. The increase of S-bearing molecular formulas in the water column and pore waters of the Black Sea and the Mediterranean Discovery Basin was consistent with elevated HS- concentrations reflecting the incorporation of sulfur into biomolecules during early diagenesis. Sulfurization resulted in an increased average molecular mass of DOM and higher formula richness (up to 5899 formulas per sample). In sediments from the methanogenic zone in the Black Sea, the DOM pool was distinctly more reduced than overlying sediments from the sulfate-reducing zone. Bottom and pore water DOM from the Discovery Basin contained the highest abundances of aliphatic compounds in the entire dataset; a large fraction of abundant N-bearing formulas possibly represented peptide and nucleotide formulas suggesting preservation of these molecules in the life inhibiting environment of the Discovery Basin. Our unique data set provides the basis for a comprehensive understanding of the molecular signatures in pore water DOM and the turnover of sedimentary organic matter in marine sediments.

Description: Colonization of newly ice-free areas by marine benthic organisms intensifies burial of macroalgae detritus in Potter Cove coastal surface sediments (Western Antarctic Peninsula). Thus, fresh and labile macroalgal detritus serves as primary organic matter (OM) source for microbial degradation. Here, we investigated the effects on post-depositional microbial iron reduction in Potter Cove using sediment incubations amended with pulverized macroalgal detritus as OM source, acetate as primary product of OM degradation and lepidocrocite as reactive iron oxide to mimic in situ conditions. Humic substances analogue anthraquinone-2,6-disulfonic acid (AQDS) was also added to some treatments to simulate potential for electron shuttling. Microbial iron reduction was promoted by macroalgae and further enhanced by up to 30-folds with AQDS. Notably, while acetate amendment alone did not stimulate iron reduction, adding macroalgae alone did. Acetate, formate, lactate, butyrate and propionate were detected as fermentation products from macroalgae degradation. By combining 16S rRNA gene sequencing and RNA stable isotope probing, we reconstructed the potential microbial food chain from macroalgae degraders to iron reducers. Psychromonas, Marinifilum, Moritella, and Colwellia were detected as potential fermenters of macroalgae and fermentation products such as lactate. Members of class deltaproteobacteria including Sva1033, Desulfuromonas, and Desulfuromusa together with Arcobacter (former phylum Epsilonbacteraeota, now Campylobacterota) acted as dissimilatory iron reducers. Our findings demonstrate that increasing burial of macroalgal detritus in an Antarctic fjord affected by glacier retreat intensifies early diagenetic processes such as iron reduction. Under scenarios of global warming, the active microbial populations identified above will expand their environmental function, facilitate OM remineralisation, and contribute to an increased release of iron and CO2 from sediments. Such indirect consequences of glacial retreat are often overlooked but might, on a regional scale, be relevant for the assessment of future nutrient and carbon fluxes.