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Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.

Past changes in the input/output, and internal cycling, of bioavailable nitrogen (N) in marine and lacustrine environments can be reconstructed by analyzing the N isotopic composition (δ15N) of organic matter in the sedimentary record. To verify, and eliminate, potential biases of bulk sedimentary δ15N (δ15Nbulk) signatures by diagenetic alteration and external N inputs, we applied, for the first time, the diatom‐bound N isotope (δ15Ndb) paleo‐proxy to lake sediments. By comparing δ15Nbulk and δ15Ndb in a sedimentary record from eutrophic Lake Lugano (Switzerland), we demonstrate that changing redox conditions influence the degree of N‐isotopic alteration of the bulk sediment, emphasizing the need for caution when interpreting δ15Nbulk in paleolimnological studies. Furthermore, in combining δ15Ndb measurements with X‐ray fluorescence scanning and state‐of‐the‐art molecular biomarker analyses, we reconstruct nutrient cycling and paleoenvironmental conditions in the lake over the past ~ 125 yr. Coeval with the period of severe eutrophication in Lake Lugano in the 1960s, our proxy data indicate that export production, δ15Ndb, and the concentration of heterocyst glycolipids (a biomarker for N2‐fixing cyanobacteria) increased simultaneously. Together, these data suggest that the rise in δ15Ndb is likely the result of enhanced water‐column denitrification in response to increased phytoplankton productivity. We hypothesize that greater export production during eutrophication led to anoxic conditions in the hypolimnion as a result of enhanced organic matter remineralization, raising water‐column denitrification. Enhanced N loss and remobilization of phosphorous (P) from the sediments under anoxic conditions lowered the N : P ratio in the lake, fostering cyanobacterial N2 fixation in surface waters. [ABSTRACT FROM AUTHOR]

Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R(2) = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell(-1)·d(-1) increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86 Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature.

The Coal Oil Point seep field located offshore Santa Barbara, CA, consists of dozens of named seeps, including a peripheral ∼200 m2 area known as Brian Seep, located in 10 m water depth. A single comprehensive survey of gas flux at Brian Seep yielded a methane release rate of ∼450 moles of CH4 per day, originating from 68 persistent gas vents and 23 intermittent vents, with gas flux among persistent vents displaying a log normal frequency distribution. A subsequent series of 33 repeat surveys conducted over a period of 6 months tracked eight persistent vents, and revealed substantial temporal variability in gas venting, with flux from each individual vent varying by more than a factor of 4. During wintertime surveys sediment was largely absent from the site, and carbonate concretions were exposed at the seafloor. The presence of the carbonates was unexpected, as the thermogenic seep gas contains 6.7% CO2, which should act to dissolve carbonates. The average δ13C of the carbonates was −29.2 ± 2.8‰ VPDB, compared to a range of −1.0 to +7.8‰ for CO2 in the seep gas, indicating that CO2 from the seep gas is quantitatively not as important as 13C-depleted bicarbonate derived from methane oxidation. Methane, with a δ13C of approximately −43‰, is oxidized and the resulting inorganic carbon precipitates as high-magnesium calcite and other carbonate minerals. This finding is supported by 13C-depleted biomarkers typically associated with anaerobic methanotrophic archaea and their bacterial syntrophic partners in the carbonates (lipid biomarker δ13C ranged from −84 to −25‰). The inconsistency in δ13C between the carbonates and the seeping CO2 was resolved by discovering pockets of gas trapped near the base of the sediment column with δ13C-CO2 values ranging from −26.9 to −11.6‰. A mechanism of carbonate formation is proposed in which carbonates form near the sediment–bedrock interface during times of sufficient sediment coverage, in which anaerobic oxidation of methane is favored. Precipitation occurs at a sufficient distance from active venting for the molecular and isotopic composition of seep gas to be masked by the generation of carbonate alkalinity from anaerobic methane oxidation. Figure Processes modulating carbonate formation at Brian Seep (California) during times of high and low sediment burden

Detailed knowledge of the extent of post-genetic modifications affecting shallow submarine hydrocarbons fueled from the deep subsurface is fundamental for evaluating source and reservoir properties. We investigated gases from a submarine high-flux seepage site in the anoxic Eastern Black Sea in order to elucidate molecular and isotopic alterations of low-molecular-weight hydrocarbons (LMWHC) associated with upward migration through the sediment and precipitation of shallow gas hydrates. For this, near-surface sediment pressure cores and free gas venting from the seafloor were collected using autoclave technology at the Batumi seep area at 845 m water depth within the gas hydrate stability zone. Vent gas, gas from pressure core degassing, and from hydrate dissociation were strongly dominated by methane (> 99.85 mol.% of ∑[C1-C4, CO2]). Molecular ratios of LMWHC (C1/[C2 + C3] > 1000) and stable isotopic compositions of methane (δ13C = - 53.5‰ V-PDB; D/H around - 175‰ SMOW) indicated predominant microbial methane formation. C1/C2+ ratios and stable isotopic compositions of LMWHC distinguished three gas types prevailing in the seepage area. Vent gas discharged into bottom waters was depleted in methane by > 0.03 mol.% (∑[C1-C4, CO2]) relative to the other gas types and the virtual lack of 14C-CH4 indicated a negligible input of methane from degradation of fresh organic matter. Of all gas types analyzed, vent gas was least affected by molecular fractionation, thus, its origin from the deep subsurface rather than from decomposing hydrates in near-surface sediments is likely. As a result of the anaerobic oxidation of methane, LMWHC in pressure cores in top sediments included smaller methane fractions [0.03 mol.% ∑(C1-C4, CO2)] than gas released from pressure cores of more deeply buried sediments, where the fraction of methane was maximal due to its preferential incorporation in hydrate lattices. No indications for stable carbon isotopic fractionations of methane during hydrate crystallization from vent gas were found. Enrichments of 14C-CH4 (1.4 pMC) in short cores relative to lower abundances (max. 0.6 pMC) in gas from long cores and gas hydrates substantiates recent methanogenesis utilizing modern organic matter deposited in top sediments of this high-flux hydrocarbon seep area. © 2009 Elsevier B.V. All rights reserved.