Microbial Anaerobic Oxidation Research Articles

Nitrite-driven anaerobic ethane oxidation

Ethane, the second most abundant gaseous hydrocarbon in vast anoxic environments, is an overlooked greenhouse gas. Microbial anaerobic oxidation of ethane can be driven by available electron acceptors such as sulfate and nitrate. However, despite nitrite being a more thermodynamically feasible electron acceptor than sulfate or nitrate, little is known about nitrite-driven anaerobic ethane oxidation. In this study, a microbial culture capable of nitrite-driven anaerobic ethane oxidation was enriched through the long-term operation of a nitrite-and-ethane-fed bioreactor. During continuous operation, the nitrite removal rate and the theoretical ethane oxidation rate remained stable at approximately 25.0 mg NO2–N L−1 d−1 and 11.48 mg C2H6 L−1 d−1, respectively. Batch tests demonstrated that ethane is essential for nitrite removal in this microbial culture. Metabolic function analysis revealed that a species affiliated with a novel genus within the family Rhodocyclaceae, designated as 'Candidatus Alkanivoras nitrosoreducens', may perform the nitrite-driven anaerobic ethane oxidation. In the proposed metabolic model, despite the absence of known genes for ethane conversion to ethyl-succinate and succinate-CoA ligase, 'Ca. A. nitrosoreducens' encodes a prospective fumarate addition pathway for anaerobic ethane oxidation and a complete denitrification pathway for nitrite reduction to nitrogen. These findings advance our understanding of nitrite-driven anaerobic ethane oxidation, highlighting the previously overlooked impact of anaerobic ethane oxidation in natural ecosystems.

Methane diffusion affects characteristics of benthic communities in and around microbial mat-covered sediments in the northeastern Japan sea

We investigated relationships between features of benthic macrofaunal communities and geochemical parameters in and around microbial mat-covered sediments associated with a methane seepage on Sakata Knoll in the eastern Japan Sea. A depression on top of the knoll corresponds to a gas-hydrate-bearing area with seepage of methane-rich fluid, and microbial mats cover the seafloor sediments. Sediment cores were collected at three sites for this study: one within a microbial mat, a second a few meters outside of the microbial mat, and a third from a reference site outside the gas-hydrate-bearing areas. Morphological analysis showed that the site inside the microbial mat had higher macrofaunal density and biomass compared with the other sites. 18S rRNA gene analysis showed that annelids were dominant in the surface sediment inside the microbial mat with the possible occurrence of microbial anaerobic oxidation of methane (AOM), whereas in the surface sediments outside the microbial mat and at the reference site the predominant species belonged to phylum Cercozoa. Morphological analysis also showed that the surface sediment inside the microbial mat noticeably favored annelids, with dorvilleid Ophryotrocha sp. and ampharetid Neosabellides sp. identified as major constituents. Statistical analysis showed that sulfidic sediment conditions with concentrations of H2S up to 121 μM resulting from AOM likely resulted in the predominance of annelids with tolerance to sulfide. Both the 18S rRNA genes and macrofaunal characteristics showed that benthic biodiversity among the three sites was greatest outside the microbial mat. The site outside the microbial mat may represent geochemical transition conditions, including a lower rate of upward methane gas-flow compared with the site inside the microbial mat. The high biodiversity there might result from the presence of species specifically suited to the transition zone as well as species also found in photosynthesis-based communities of the background environment.

Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation.

Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM-often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)-are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al., Sci. Rep. 4, 1-9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al., Appl. Environ. Microbiol. 88, e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al., Geology 48, 862-866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.

The microbial oxidation of pharmaceuticals in an anaerobic aqueous environment: Effect of dissolved organic matter fractions from different sources

Previous studies have demonstrated the importance of dissolved organic matter (DOM) on the biodegradation of trace organic contaminants occurred in the hyporheic zone. However, the role of diverse DOM fractions with distinct physicochemical properties on the biodegradation of pharmaceuticals under reducing conditions is scarcely known. To address this knowledge gap, DOMs derived from road-deposited sediment, soil, and active sludge (namely allochthonous DOM) and algae (namely autochthonous DOM) were collected and isolated into different fractions. Thereafter, the effect of DOM fractions on the anaerobic microbial oxidation of two typical pharmaceuticals, i.e., ritonavir (RTV) and tetracycline (TC) was explored by using simulated anaerobic microcosms. Mechanistic insights into how DOM fractions from different sources influence pharmaceutical biodegradation processes were provided by optical and electrochemical analyses. Results showed that humic acid and fulvic acid fractions from allochthonous DOM could enhance the biodegradation of TC (12.2 % per mgC/L) and RTV (14.5 % per mgC/L), while no significant impact was observed for that of hydrophilic fractions. However, autochthonous DOM promoted the biodegradation of TC (4.17 % per mgC/L) and inhibited that of RTV. Mechanistic analysis showed that the higher of humification and aromatization level of DOM components, the stronger their promotive effect on the biodegradation of TC and RTV. Further, the promotive mechanism could be attributed to the response of quinone moieties in DOM as extracellular electron acceptors that yields more energy to support microbial metabolism. These results provide a more comprehensive understanding of diverse DOM fractions mediating microbial anaerobic oxidation of trace organic pollutants, and extend our insights into contamination control and remediation technologies.

Thermochemical oxidation of methane by manganese oxides in hydrothermal sediments

Microbial anaerobic oxidation of methane coupled to the reduction of Mn(IV)-oxides, typically MnO2, derived from continental weathering and riverine transport has been proposed as a globally important sink of methane. However, the potential role of hydrothermal Mn(IV) oxide-rich sediments as a methane sink, and the mechanisms of underpinning methane oxidation at high-temperature hydrothermal fields remain poorly understood. Here, we report the occurrence of almost pure rhodochrosite with extremely negative δ13CPDB values (as low as –76.4‰) in direct association with hausmannite formed through hydrothermal activity in the Late Triassic Heqing Mn deposit in Southern China. Based on detailed petrography and geochemistry, this rhodochrosite is interpreted as the result of the thermochemical oxidation of methane by hausmannite during early diagenesis. Given high hydrothermal Mn2+ and CH4 release coupled to low sulfate concentration observed in the Archean oceans, we propose that hydrothermal Mn(IV) oxides may have been effective methane sinks in Earth’s ancient oceans.

Reversibility controls on extreme methane clumped isotope signatures from anaerobic oxidation of methane

Microbial anaerobic oxidation of methane (AOM) substantially mitigates atmospheric methane emissions on Earth and is a process to consider for astrobiological targets where methane has been detected. The measurement of doubly substituted, or “clumped”, methane isotopes has proven useful in tracing processes of methane formation and oxidation. Both near-equilibrium and extreme disequilibrium methane clumped isotope signatures can be attributed to AOM, but, to date, understanding the mechanistic and environmental controls on those signatures has been lacking. We report measurements of methane clumped isotope compositions of residual methane in AOM-active microbial incubations using sediment slurries from Svalbard and Santa Barbara Channel methane seeps. Incubation experiments of Svalbard sediment slurries resulted in residual methane with very high Δ13CH3D and Δ12CH2D2 values up to 19.5‰ and 65.1‰, respectively. We found similarly high Δ13CH3D and Δ12CH2D2 values in fluid samples from the Chamorro Seamount, a serpentinite mud volcano in the Mariana forearc, suggesting that minimal reversibility of AOM intracellular reactions leads to kinetic fractionation of clumped isotopologues. When conditions were consistent with a low thermodynamic drive for AOM, however, methane isotopologues approached intra-species quasi-equilibrium. This was clearly observed in isotope exchange experiments with methyl-coenzyme M reductase (Mcr) and in microbial incubations of the Santa Barbara Channel sediment slurries. Using an isotopologue fractionation model, we highlight the critical role of reversibility in controlling the trajectory of gases in Δ13CH3D vs. Δ12CH2D2 space during AOM. The near-equilibrium methane isotopologue signatures are generalized as a result of the Mcr-catalyzed intracellular isotope exchange operating under near-threshold free energy conditions, as shown in the deep-biosphere incubations. Our results show that the reversibility of the Mcr-catalyzed reaction is central to understanding the meaning of methane isotopologue ratios affected by microbial production and oxidation.

Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture.

Anaerobic microbial manganese oxidation (AMMO) has been considered an ancient biological metabolism for Mn element cycling on Archaean Earth before the presence of oxygen. A light-dependent AMMO was recently observed under strictly anoxic conditions, providing a new proxy for the interpretation of the evolution of oxygenic photosynthesis. However, the feasibility of biotic Mn(II) oxidation in dark geological habitats that must have been abundant remains unknown. Therefore, we discovered that it would be possible to achieve AMMO in a light-independent electrosyntrophic coculture between Rhodopseudomonas palustris and Geobacter metallireducens. Transmission electron microscopy analysis revealed insoluble particle formation in the coculture with Mn(II) addition. X-ray diffraction and X-ray photoelectron spectroscopy analysis verified that these particles were a mixture of MnO2 and Mn3O4. The absence of Mn oxides in either of the monocultures indicated that the Mn(II)-oxidizing activity was induced via electrosyntrophic interactions. Radical quenching and isotopic experiments demonstrated that hydroxyl radicals (•OH) produced from H2O dissociation by R. palustris in the coculture contributed to Mn(II) oxidation. All these findings suggest a new, symbiosis-dependent and light-independent AMMO route, with potential importance to the evolution of oxygenic photosynthesis and the biogeochemical cycling of manganese on Archaean and modern Earth.

Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia

Anaerobic microorganisms are thought to play a critical role in regulating the flux of short-chain gaseous alkanes (SCGAs; including ethane, propane and butane) from terrestrial and aquatic ecosystems to the atmosphere. Sulfate has been confirmed to act as electron acceptor supporting microbial anaerobic oxidation of SCGAs, yet several other energetically more favourable acceptors co-exist with these gases in anaerobic environments. Here, we show that a bioreactor seeded with biomass from a wastewater treatment facility can perform anaerobic propane oxidation coupled to nitrate reduction to dinitrogen gas and ammonium. The bioreactor was operated for more than 1000 days, and we used 13C- and 15N-labelling experiments, metagenomic, metatranscriptomic, metaproteomic and metabolite analyses to characterize the microbial community and the metabolic processes. The data collectively suggest that a species representing a novel order within the bacterial class Symbiobacteriia is responsible for the observed nitrate-dependent propane oxidation. The closed genome of this organism, which we designate as ‘Candidatus Alkanivorans nitratireducens’, encodes pathways for oxidation of propane to CO2 via fumarate addition, and for nitrate reduction, with all the key genes expressed during nitrate-dependent propane oxidation. Our results suggest that nitrate is a relevant electron sink for SCGA oxidation in anaerobic environments, constituting a new microbially-mediated link between the carbon and nitrogen cycles.

Anaerobic oxidation of methane and trace-element geochemistry in microbial mat-covered sediments related to methane seepage, northeastern Japan Sea

We evaluated the spatial variability of geochemical features, including trace-element cycles, associated with methane seepage in a knoll off Sakata (called Sakata Knoll) in the eastern Japan Sea. Seafloor observations from a remotely operated vehicle and environmental visualization around Sakata Knoll by an optical mapping device revealed large patches of white and gray microbial mats covering sediment in the depression on the top of the knoll. Push core samples were collected inside and a few meters outside microbial mats, and outside the gas hydrate-bearing areas. For these cores, the interstitial sulfate ion (SO42−) concentrations, sedimentary total organic carbon, total sulfur (TS), and trace-element contents, and bulk carbonate minerals δ13C were analyzed. In the entire core samples below the microbial mats and in sediments below 10 cm depth outside microbial mats, TS contents were substantially higher than those at the reference site, and bulk carbonate minerals δ13C was strongly negative (−20‰ to −40‰). These results imply that the formations of sulfide minerals and authigenic carbonates occur in the anoxic sediments via microbial anaerobic oxidation of methane (AOM) coupled with sulfate reduction. Although a rapid and linear decrease of interstitial water SO42− concentration in the sediments collected inside microbial mats supports the occurrence of AOM, there is no fall in SO42− concentration outside microbial mats, which may be explained by the higher upward flow of methane gas inside than outside the mats. The AOM-impacted sediments at Sakata Knoll were characterized by enrichments in Mo and As that were well correlated with TS contents and the authigenic iron fraction, and by strong enrichment of authigenic Mo relative to U, indicated by higher Mo/U ratios than those of seawater. These observations suggest that Mo and As are effectively transferred from the water column to AOM-impacted sulfidic sediments at Sakata Knoll via precipitation of particulate iron–manganese oxyhydroxides in the water column that have adsorbed Mo and As.

A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.

Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.

Long-term effects of four environment-related iron minerals on microbial anaerobic oxidation of methane in paddy soil: A previously overlooked role of widespread goethite

Due to a suitable ecological environment, the iron-dependent anaerobic oxidation of methane (Fe-AOM) occurs in paddy soil, reducing methane emissions to the atmosphere. Paddy soil contains a variety of iron minerals whose effects on Fe-AOM remain unclear. Here, paddy soil in the ferruginous zone was collected, and four environment-related iron minerals (ferrihydrite, goethite, hematite, and magnetite) were used as electron acceptors to cultivate Fe-AOM for 380 days. The Fe-AOM activity and microbial community structure were monitored using isotope activity assays and molecular biological methods, including quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. The inoculum Fe-AOM rate was the highest with ferrihydrite, followed by goethite, hematite, and magnetite. However, it was ranked in the order goethite > ferrihydrite > hematite > magnetite after long-term cultivation. The specific activity of goethite-dependent AOM increased 14.2 times (from 0.9 ± 0.2 to 12.9 ± 0.4 nmol d−1 g−1 dry soil) during the 380 days, while that of ferrihydrite increased by only 1.2 times (from 7.9 ± 2.4 to 9.1 ± 0.3 nmol d−1 g−1 dry soil). The microbial community changed significantly after the emendation of ferrihydrite or goethite, while the other two did not. This implies that ferrihydrite and goethite had a significant impact on microbial processes, including Fe-AOM. Notably, although ferrihydrite promoted Fe-AOM, its reduction product of Fe(II) greatly stimulated methanogenesis and increased methane emission, whereas goethite was able to reduce methane emissions and did not stimulate methanogenesis. Thus, these findings indicate that goethite-dependent AOM occurs in paddy soils and, although previously overlooked, is a crucial sink of the global methane cycle.

Carbon and hydrogen isotope fractionation during aerobic oxidation of short-chain alkanes in experimental incubations of vent fluids

Aerobic oxidation of short-chain alkanes was observed in gas samples from the Lutao intertidal hydrothermal vents in Taiwan, during storage at 20 °C for up to 29 months without adding bacterial strains and replenishing substrates. The carbon isotope fractionation factors (εC) of methane (C1), ethane (C2), and propane (C3), were calculated using the Rayleigh fractionation equation to be −37.1 ± 7.5‰, −14.8 ± 4.8‰, and −4.7 ± 5.2‰, respectively. The hydrogen isotope fractionation factor (εH) of methane was determined to be −281 ± 187‰. DNA sequencing of the 16S rRNA gene in the vent fluids suggests that aerobic oxidation is dominated by methanotrophs of the genera Methylomicrobium and Methylophaga, which use the ribulose monophosphate pathway (RuMP). The degrees of isotope fractionation (εC and εH values) herein are larger than previously reported values, possibly due to the limited O2 supply and low abundance of aerobic methane-oxidizing bacteria in the experiments. Since the fractionation factor of methane is higher than those of ethane and propane, the aerobic oxidation of thermogenic or microbial alkanes could produce a carbon isotope reversal, which is frequently noted as a trait of abiotic hydrocarbons. This work demonstrates that in addition to anaerobic microbial oxidation, aerobic oxidation with a low cell density can also produce significant isotope fractionation of alkanes in geological closed/semi-closed environments and open flow reaction systems that are characterized by moderate temperatures and a limited supply of substrates and O2; these environments include cold seeps, mud volcanoes, and low-temperature hydrothermal plumes/aquifers/reservoirs.

Roles and opportunities for microbial anaerobic oxidation of methane in natural and engineered systems

Anaerobic oxidation of methane (AOM) is a crucial bioprocess in global methane mitigation. Adoption of AOM in an engineered system provides an opportunity for the development of methane-based biotechnologies.

Nitrite Accumulation Is Required for Microbial Anaerobic Iron Oxidation, but Not for Arsenite Oxidation, in Two Heterotrophic Denitrifiers.

Phylogenetically diverse species of bacteria can mediate anaerobic oxidation of ferrous iron [Fe(II)] and/or arsenite [As(III)] coupled to nitrate reduction, impacting the biogeochemical cycles of Fe and As. However, the mechanisms for nitrate-dependent anaerobic oxidation of Fe(II) and As(III) remain unclear. In this study, we isolated two bacterial strains from arsenic-contaminated paddy soils, Ensifer sp. ST2 and Paracoccus sp. QY30. Both strains were capable of anaerobic As(III) oxidation, but only QY30 could oxidize Fe(II) under nitrate-reducing conditions. Both strains contain the As(III) oxidase gene aioA, whose expression was induced greatly by As(III) exposure. Both strains contain the whole suite of genes for complete denitrification, but the nitrite reductase gene nirK was not expressed in QY30 and nitrite accumulated under nitrate-reducing conditions. When the functional nirK gene was knocked out in strain ST2, its nitrite reduction ability was completely abolished and nitrite accumulated in the medium. Moreover, the ST2ΔnirK mutant gained the ability to oxidize Fe(II). When nirK gene from ST2 was introduced to QY30, the recombinant strain QY30::nirK gained the ability to reduce nitrite but lost the ability to oxidize Fe(II). These genetic manipulations did not affect the ability of both strains to oxidize As(III). Our results indicate that nitrite accumulation is required for anaerobic oxidation of Fe(II) but not for As(III) oxidation in these strains. The results suggest that anaerobic Fe(II) oxidation in the two bacterial strains is primarily driven by abiotic reaction of Fe(II) with nitrite, while reduction of nitrate to nitrite is sufficient for redox coupling with anaerobic As(III) oxidation catalyzed by Aio. Deletion of nirK gene in denitrifiers can enhance anaerobic Fe(II) oxidation.

Biogeochemical Consequences of Nonvertical Methane Transport in Sediment Offshore Northwestern Svalbard

AbstractA site at the gas hydrate stability limit was investigated offshore northwestern Svalbard to study methane transport in sediment. The site was characterized by chemosynthetic communities (sulfur bacteria mats, tubeworms) and gas venting. Sediments were sampled with in situ porewater collectors and by gravity coring followed by analyses of porewater constituents, sediment and carbonate geochemistry, and microbial activity, taxonomy, and lipid biomarkers. Sulfide and alkalinity concentrations showed concentration maxima in near‐surface sediments at the bacterial mat and deeper maxima at the gas vent site. Sediments at the periphery of the chemosynthetic field were characterized by two sulfate‐methane transition zones (SMTZs) at ~204 and 45 cm depth, where activity maxima of microbial anaerobic oxidation of methane (AOM) with sulfate were found. Amplicon sequencing and lipid biomarker indicate that AOM at the SMTZs was mediated by ANME‐1 archaea. A 1D numerical transport reaction model suggests that the deeper SMTZ‐1 formed on centennial scale by vertical advection of methane, while the shallower SMTZ‐2 could only be reproduced by nonvertical methane injections starting on decadal scale. Model results were supported by age distribution of authigenic carbonates, showing youngest carbonates within SMTZ‐2. We propose that nonvertical methane injection was induced by increasing blockage of vertical transport or formation of sediment fractures. Our study further suggests that the methanotrophic response to the nonvertical methane injection was commensurate with new methane supply. This finding provides new information about for the response time and efficiency of the benthic methane filter in environments with fluctuating methane transport.

Fluid transport and reaction processes within a serpentinite mud volcano: South Chamorro Seamount

Natural fluids with a pH (25 °C) up to 12.3 were collected from a sub-seafloor borehole observatory (Ocean Drilling Program (ODP) Hole 1200C) on South Chamorro Seamount, a serpentinite mud volcano in the Mariana forearc. We used systematic differences in the chemical compositions of pore waters from drilling operations during ODP Leg 195 and borehole fluids collected subsequently from Hole 1200C to define two endmember solutions, one of which was a sulfate-rich fluid with a methane concentration of 50 mM that ascends from the subduction channel and the other was a low-sulfate fluid. The sequence of sample collection and fluid compositions constrain subsurface hydrologic conditions. Deep-sourced, sulfate- and methane-rich, sterile fluids from the subduction channel can reach the seafloor unchanged within the central conduit, whereas other fluid pathways likely intersect the pelagic sediment that underlies the serpentinite mud volcano, providing potentially suitable conditions and inoculum for microbial anaerobic oxidation of methane (AOM). These AOM-affected, low-sulfate fluids also make it to the seafloor where they discharge. The source of the sulfate- and methane-rich fluid in the subduction channel is attributed to abiotic methane production fueled by hydrogen production from serpentinization and carbonate dissolution. This methane production includes a mechanism to raise the pH above values from serpentinization alone. Results from South Chamorro Seamount represent an end member along a transect defined by the distance from the trench. Results from this site are applied to other serpentinite mud volcanoes along this transect to speculate on likely chemical conditions within shallower and cooler portions of the subduction channel.

Evaluating radioisotope‐based approaches to measure anaerobic methane oxidation rates in lacustrine sediments

AbstractThe microbial anaerobic oxidation of methane (AOM) is the dominant sink for methane in anoxic sediments. AOM rate measurements are essential for assessing the efficacy of the benthic methane filter to mitigate the evasion of this potent greenhouse gas to the atmosphere. Incubation techniques with trace amounts of radiolabeled substrate (typically 14CH4) represent the most sensitive approach for methane oxidation rate measurements. Yet, radiotracer application can be performed in different ways, rendering the comparability of AOM rate measurements in field and laboratory investigations problematic. We compared four different 14CH4‐based short‐term incubation approaches to quantify methane turnover rates in lake sediments. Three of the applied methods yielded similar and reliable downcore rate profiles. They provided clear evidence for AOM with maximum rates of 15 nmol cm−3 d−1 at ~ 17 cm sediment depth. Using the short‐term slurry incubation (SL) method, however, we were unable to detect the AOM activity maximum that we observed with the other approaches. We hypothesize that changes in the microbial structure and disruption of physical interactions due to mixing of sediments negatively affected the activity of AOM communities and longer incubation times are necessary to enhance the sensitivity of this approach. Minor variabilities in rate measurement that we found in the non‐SL incubations may be related to small‐scale sediment heterogeneity, differential partial methane loss during sample handling, and/or an uneven application of the radiotracer. Whole‐core incubations interfere the least with the in situ conditions, but the ultimate choice of the AOM rate measurement method will depend on the individual sampling requirements.

Intramolecular isotopic evidence for bacterial oxidation of propane in subsurface natural gas reservoirs

Microbial anaerobic oxidation of hydrocarbons is a key process potentially involved in a myriad of geological and biochemical environments yet has remained notoriously difficult to identify and quantify in natural environments. We performed position-specific carbon isotope analysis of propane from cracking and incubation experiments. Anaerobic bacterial oxidation of propane leads to a pronounced and previously unidentified 13C enrichment in the central position of propane, which contrasts with the isotope signature associated with the thermogenic process. This distinctive signature allows the detection and quantification of anaerobic oxidation of hydrocarbons in diverse natural gas reservoirs and suggests that this process may be more widespread than previously thought. Position-specific isotope analysis can elucidate the fate of natural gas hydrocarbons and provide insight into a major but previously cryptic process controlling the biogeochemical cycling of globally significant greenhouse gases.

Carbonate formation in salt dome cap rocks by microbial anaerobic oxidation of methane

Major hydrocarbon accumulations occur in traps associated with salt domes. Whereas some of these hydrocarbons remain to be extracted for economic use, significant amounts have degraded in the subsurface, yielding mineral precipitates as byproducts. Salt domes of the Gulf of Mexico Basin typically exhibit extensive deposits of carbonate that form as cap rock atop salt structures. Despite previous efforts to model cap rock formation, the details of subsurface reactions (including the role of microorganisms) remain largely unknown. Here we show that cap rock mineral precipitation occurred via closed-system sulfate reduction, as indicated by new sulfur isotope data. 13C-depleted carbonate carbon isotope compositions and low clumped isotope-derived carbonate formation temperatures indicate that microbial, sulfate-dependent, anaerobic oxidation of methane (AOM) contributed to carbonate formation. These findings suggest that AOM serves as an unrecognized methane sink that reduces methane emissions in salt dome settings perhaps associated with an extensive, deep subsurface biosphere.

Methane biotransformation in the ocean and its effects on climate change: A review

Methane is a potent greenhouse gas. Continental margins contain large reservoirs of methane as solid gas hydrate and the dissolved and gaseous forms of methane. Submarine methane seeps along the global continental margins, including the coastal seas, have been estimated to contribute 0.01 to 0.05 Gt of carbon to the atmosphere annually, accounting for between 1% and 5% of the global methane emissions to the atmosphere. Much of this methane is exhausted via microbial anaerobic methane oxidation. Methane biotransformation in the ocean has effects on global climate change. This review mainly introduces the mechanisms of methanogenesis and methane oxidation and describes new findings that will provide information that will improve the understanding of the balance in terms of the generation, migration and consumption of methane in marine environments. Moreover, this review provides new insights into methane biogeochemical cycles and the effects of marine methane budgets on global climate.