Emerging topics in marine methane biogeochemistry

Distribution and sea-to-air fluxes of nitrous oxide and methane from a seasonally hypoxic coastal zone in the southeastern Arabian Sea

The seasonal variability, pathways, and sea-to-air fluxes of nitrous oxide (N2O) and methane (CH4) in the coastal environment, where coastal upwelling and mudbanks co-exist are presented based on the monthly time-series measurements from November 2021 to December 2022. Upwelling-driven hypoxic water's shoreward propagation and persistence were the major factors controlling the N2O concentrations, while the freshwater influx and sedimentary fluxes modulate CH4 concentrations. The N2O concentrations were high during the southwest monsoon (up to 35 nM; 19 ± 8 nM)), followed by spring inter-monsoon (up to 19 nM; 10 ± 5 nM), and lowest during the northeast monsoon (up to 13 nM; 8 ± 2 nM), whereas the CH4 levels were high during the spring inter-monsoon (8.4 to 65 nM), followed by southwest monsoon (6.8 to 53.1 nM) and relatively lower concentrations during the northeast monsoon (3.3 to 32.6 nM). The positive correlations of excess N2O with Apparent Oxygen Utilisation (AOU) and the sum of nitrate and nitrite (NOx) indicate that nitrification is the primary source of N2O in the mudbank regime. The negative correlation of CH4 concentrations with salinity indicates considerable input of CH4 through freshwater influx. CH4 exhibited a highly significant positive correlation with Chlorophyll-a throughout the study period. Furthermore, it displayed a statistically significant positive correlation with phosphate (PO43-) during the northeast monsoon while a strong negative correlation with PO43- during the spring inter-monsoon, pointing towards the role of aerobic CH4 production pathways in the mudbank regime. N2O and CH4 exhibited a contrasting seasonal pattern of sea-to-air fluxes, characterised by the highest N2O fluxes during the southwest monsoon (hypoxia) (13 ± 10 μM m-2 d-1), followed by spring inter-monsoon (12 ± 16 μM m-2 d-1), and the lowest during the northeast monsoon (0.6 ± 3 μM m-2 d-1). Conversely, the highest sea-to-air fluxes of CH4 were noticed during the spring inter-monsoon (74 ± 56 μM m-2 d-1), followed by the southwest monsoon (45 ± 35 μM m-2 d-1), and the lowest values during the northeast monsoon (19 ± 16 μM m-2d-1). Long-term time-series measurements will be invaluable in understanding the longer-term impacts of climate-driven variability on marine biogeochemical cycles in dynamic nearshore systems.

Cold seep formation from salt diapir-controlled deep biosphere oases

Deep sea cold seeps are sites where hydrogen sulfide, methane, and other hydrocarbon-rich fluids vent from the ocean floor. They are an important component of Earth's carbon cycle in which subsurface hydrocarbons form the energy source for highly diverse benthic micro- and macro-fauna in what is otherwise vast and spartan sea scape. Passive continental margin cold seeps are typically attributed to the migration of hydrocarbons generated from deeply buried source rocks. Many of these seeps occur over salt tectonic provinces, where the movement of salt generates complex fault systems that can enable fluid migration or create seals and traps associated with reservoir formation. The elevated advective heat transport of the salt also produces a chimney effect directly over these structures. Here, we provide geophysical and geochemical evidence that the salt chimney effect in conjunction with diapiric faulting drives a subsurface groundwater circulation system that brings dissolved inorganic carbon, nutrient-rich deep basinal fluids, and potentially overlying seawater onto the crests of deeply buried salt diapirs. The mobilized fluids fuel methanogenic archaea locally enhancing the deep biosphere. The resulting elevated biogenic methane production, alongside the upward heat-driven fluid transport, represents a previously unrecognized mechanism of cold seep formation and regulation.

The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea

The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.

Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis

Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2 as an electron donor to reduce CO2 to CH4, but in the absence of H2 many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for the reduction of coenzyme F420 or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is unknown. Using Methanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420 at similar rates. F420 reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1 mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in the loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth, and the metal content of the proteins suggested that isoforms are dependent on either molybdenum or tungsten for activity. These data suggest that both isoforms of Fdh are functionally redundant, but their activities in vivo may be limited by gene regulation or metal availability under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.

Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13C/12C and D/H) and multiply substituted (13CH3D and 12CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.

Earthquake-enhanced dissolved carbon cycles in ultra-deep ocean sediments

Hadal trenches are unique geological and ecological systems located along subduction zones. Earthquake-triggered turbidites act as efficient transport pathways of organic carbon (OC), yet remineralization and transformation of OC in these systems are not comprehensively understood. Here we measure concentrations and stable- and radiocarbon isotope signatures of dissolved organic and inorganic carbon (DOC, DIC) in the subsurface sediment interstitial water along the Japan Trench axis collected during the IODP Expedition 386. We find accumulation and aging of DOC and DIC in the subsurface sediments, which we interpret as enhanced production of labile dissolved carbon owing to earthquake-triggered turbidites, which supports intensive microbial methanogenesis in the trench sediments. The residual dissolved carbon accumulates in deep subsurface sediments and may continue to fuel the deep biosphere. Tectonic events can therefore enhance carbon accumulation and stimulate carbon transformation in plate convergent trench systems, which may accelerate carbon export into the subduction zones.

Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments

The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH₄) seepage. However, the role of prokaryotes in influencing this CH₄ release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2-0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H₂/CO₂ or acetate. Also, CH₄ production occurred in 50% of methylated substrate slurries and only methylotrophic CH₄ production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. "Aminicenantes." Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles.

The ProkaBioDen database, a global database of benthic prokaryotic biomasses and densities in the marine realm

Benthic prokaryotes include Bacteria and Archaea and dominate densities of marine benthos. They play major roles in element cycles and heterotrophic, chemoautotrophic, and phototrophic carbon production. To understand how anthropogenic disturbances and climate change might affect these processes, better estimates of prokaryotic biomasses and densities are required. Hence, I developed the ProkaBioDen database, the largest open-access database of benthic prokaryotic biomasses and densities in marine surface sediments. In total, the database comprises 1,089 georeferenced benthic prokaryotic biomass and 1,875 density records extracted from 85 and 112 studies, respectively. I identified all references applying the procedures for systematic reviews and meta analyses and report prokaryotic biomasses as g C cm⁻³ sediment, g C g⁻¹ sediment, and g C m⁻². Density records are presented as cell cm⁻³ sediment, cell g⁻¹ sediment/ sulfide/ vent precipitate, and cell m⁻². This database should serve as reference to close sampling gaps in the future.

Measurement(s)	prokaryotic benthic biomass • prokaryotic benthic density
Technology Type(s)	PLFA • microscopy • ATP
Sample Characteristic - Organism	unclassified Bacteria
Sample Characteristic - Environment	marine sediment • deep marine sediment • shallow marine sediment
Sample Characteristic - Location	Pacific Ocean • Atlantic Ocean • Indian Ocean • Southern Ocean • Arctic Ocean

A GC-SSIM-CRDS system: Coupling a gas chromatograph with a Cavity Ring-Down Spectrometer for onboard Twofold analysis of molecular and isotopic compositions of natural gases during ocean-going research expeditions

Carbon dioxide (CO₂) and methane (CH₄) are two climate-sensitive components of gases migrating within sediments and emitted into the water column on continental margins. They are involved in several key biogeochemical processes entering into the global carbon cycle. In order to perform onboard measurements of both the molecular and stable carbon isotope ratios (δ¹³C) of CH₄ and CO₂ of natural gases during oceanic cruises, we have developed a novel approach coupling gas chromatography (GC) with cavity ring-down spectroscopy (CRDS). The coupled devices are connected to a small sample isotope module (SSIM) to form a system called GC-SSIM-CRDS. Small volumes of natural gas samples (<1 mL) are injected into the GC using a headspace autosampler or a gas-tight syringe to separate the chemical components using a Shincarbon ST packed column and for molecular quantification by thermal conductivity detection (TCD). Subsequently, CO₂ from the sample is trapped in a 7 mL loop at 32 °C before being transferred to the CRDS analyzer for sequential determination of the stable carbon isotope ratios of CH₄ and CO₂ in 24 min. The loop is an open column (without stationary phase). This approach does not require the use of adsorbents or cooling for the trapping step. Optimization of the separation step prior to analysis was focused on the influence of two key separation factors 1) the flow of the carrier gas and 2) the temperature of the oven. Our analytical system and the measurement protocol were validated on samples collected from gas seeps in the Sea of Marmara (Turkey). Our results show that the GC-SSIM-CRDS system provides a reliable determination of the molecular identification of CH₄ and CO₂ in complex natural gases, followed by the stable carbon isotope ratios of methane and carbon dioxide.

Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker

Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.

Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay

Seabed hydrocarbon seeps present natural laboratories for investigating responses of marine ecosystems to petroleum input. A hydrocarbon seep near Scott Inlet, Baffin Bay, was visited for in situ observations and sampling in the summer of 2018. Video evidence of an active hydrocarbon seep was confirmed by methane and hydrocarbon analysis of the overlying water column, which is 260 m at this site. Elevated methane concentrations in bottom water above and down current from the seep decreased to background seawater levels in the mid-water column >150 m above the seafloor. Seafloor microbial mats morphologically resembling sulfide-oxidizing bacteria surrounded areas of bubble ebullition. Calcareous tube worms, brittle stars, shrimp, sponges, sea stars, sea anemones, sea urchins, small fish and soft corals were observed near the seep, with soft corals showing evidence for hydrocarbon incorporation. Sediment microbial communities included putative methane-oxidizing Methyloprofundus, sulfate-reducing Desulfobulbaceae and sulfide-oxidizing Sulfurovum. A metabolic gene diagnostic for aerobic methanotrophs (pmoA) was detected in the sediment and bottom water above the seep epicentre and up to 5 km away. Both 16S rRNA gene and pmoA amplicon sequencing revealed that pelagic microbial communities oriented along the geologic basement rise associated with methane seepage (running SW to NE) differed from communities in off-axis water up to 5 km away. Relative abundances of aerobic methanotrophs and putative hydrocarbon-degrading bacteria were elevated in the bottom water down current from the seep. Detection of bacterial clades typically associated with hydrocarbon and methane oxidation highlights the importance of Arctic marine microbial communities in mitigating hydrocarbon emissions from natural geologic sources.

Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps

Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.

Bubble-mediated transport of benthic microorganisms into the water column: Identification of methanotrophs and implication of seepage intensity on transport efficiency

Benthic microorganisms transported into the water column potentially influence biogeochemical cycles and the pelagic food web structure. In the present study six gas-releasing vent sites in the Coal Oil Point seep field (California) were investigated, and the dislocation of microorganisms from the sediment into the water column via gas bubbles released from the seabed was documented. It was found that the methanotrophs transport efficiency was dependent on the volumetric gas flow, with the highest transport rate of 22.7 × 10³ cells mL_gas⁻¹ at a volumetric gas flow of 0.07 mL_gas s⁻¹, and the lowest rate of 0.2 × 10³ cells mL_gas⁻¹ at a gas flow of 2.2 mL_gas s⁻¹. A simple budget approach showed that this bubble-mediated transport has the potential to maintain a relevant part of the water-column methanotrophs in the seep field. The bubble-mediated link between the benthic and pelagic environment was further supported by genetic analyses, indicating a transportation of methanotrophs of the family Methylomonaceae and oil degrading bacteria of the genus Cycloclasticus from the sediment into the water column. These findings demonstrate that the bubble-mediated transport of microorganisms influences the pelagic microbial abundance and community composition at gas-releasing seep sites.

Physiological limits to life in anoxic subseafloor sediment

In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?' from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life-death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life.

Ocean Dumping of Containerized DDT Waste Was a Sloppy Process

Industrial-scale dumping of organic waste to the deep ocean was once common practice, leaving a legacy of chemical pollution for which a paucity of information exists. Using a nested approach with autonomous and remotely operated underwater vehicles, a dumpsite offshore California was surveyed and sampled. Discarded waste containers littered the site and structured the suboxic benthic environment. Dichlorodiphenyltrichloroethane (DDT) was reportedly dumped in the area, and sediment analysis revealed substantial variability in concentrations of p, p-DDT and its analogs, with a peak concentration of 257 μg g^-1, ∼40 times greater than the highest level of surface sediment contamination at the nearby DDT Superfund site. The occurrence of a conspicuous hydrocarbon mixture suggests that multiple petroleum distillates, potentially used in DDT manufacture, contributed to the waste stream. Application of a two end-member mixing model with DDTs and polychlorinated biphenyls enabled source differentiation between shelf discharge versus containerized waste. Ocean dumping was found to be the major source of DDT to more than 3000 km² of the region's deep seafloor. These results reveal that ocean dumping of containerized DDT waste was inherently sloppy, with the contents readily breaching containment and leading to regional scale contamination of the deep benthos.

Manifestation, Drivers, and Emergence of Open Ocean Deoxygenation

Oxygen loss in the ocean, termed deoxygenation, is a major consequence of climate change and is exacerbated by other aspects of global change. An average global loss of 2% or more has been recorded in the open ocean over the past 50-100 years, but with greater oxygen declines in intermediate waters (100-600 m) of the North Pacific, the East Pacific, tropical waters, and the Southern Ocean. Although ocean warming contributions to oxygen declines through a reduction in oxygen solubility and stratification effects on ventilation are reasonably well understood, it has been a major challenge to identify drivers and modifying factors that explain different regional patterns, especially in the tropical oceans. Changes in respiration, circulation (including upwelling), nutrient inputs, and possibly methane release contribute to oxygen loss, often indirectly through stimulation of biological production and biological consumption. Microbes mediate many feedbacks in oxygen minimum zones that can either exacerbate or ameliorate deoxygenation via interacting nitrogen, sulfur, and carbon cycles. The paleo-record reflects drivers of and feedbacks to deoxygenation that have played out through the Phanerozoic on centennial, millennial, and hundred-million-year timescales. Natural oxygen variability has made it difficult to detect the emergence of a climate-forced signal of oxygen loss, but new modeling efforts now project emergence to occur in many areas in 15-25 years. Continued global deoxygenation is projected for the next 100 or more years under most emissions scenarios, but with regional heterogeneity. Notably, even small changes in oxygenation can have significant biological effects. New efforts to systematically observe oxygen changes throughout the open ocean are needed to help address gaps in understanding of ocean deoxygenation patterns and drivers.

Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments

Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ¹³C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ¹³C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.

Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.

Methanotroph-derived bacteriohopanepolyol signatures as a function of temperature related growth, survival, cell death and preservation in the geological record

Interpretation of bacteriohopanepolyol (BHP) biomarkers tracing microbiological processes in modern and ancient sediments relies on understanding environmental controls of production and preservation. BHPs from methanotrophs (35-aminoBHPs) were studied in methane-amended aerobic river-sediment incubations at different temperatures. It was found that: (i) With increasing temperature (4°C-40°C) a 10-fold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; (ii) A further increase in temperature (50°C) saw selection for the thermophile Methylocaldum and mixtures of aminopentol and C-3 methylated aminopentol, again, with no increase in aminotriol and aminotetrol. (iii) At 30°C, more aminopentol and an aminopentol isomer and unsaturated aminopentol were produced after methanotroph growth and the onset of substrate starvation/oxygen depletion. (iv) At 50°C, aminopentol and C-3 methylated aminopentol, only accumulated during growth but were clearly resistant to remineralization despite cell death. These results have profound implications for the interpretation of aminoBHP distributions and abundances in modern and past environments. For instance, a temperature regulation of aminopentol production but not aminotetrol or aminotriol is consistent with and, corroborative of, observed aminopentol sensitivity to climate warming recorded in a stratigraphic sequence deposited during the Paleocene-Eocene thermal maximum (PETM).

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark

Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.

Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone

Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (<15 m) water column profiles revealed a 300 m thick layer of elevated methane (20-105 nM) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water. Further incubations characterised a methanogenic potential in the presence of both porewater sulphate and nitrate of up to 88 nmol g-1day-1 in the sediment surface layer. In these methane-producing sediments, the majority (85%) of methyl coenzyme M reductase alpha subunit (mcrA) gene sequences clustered with Methanosarcinaceae (⩾96% similarity to Methanococcoides sp.), a family capable of performing non-competitive methanogenesis. Incubations with 13C-CH4 showed potential for both aerobic and anaerobic methane oxidation in the waters within and above the OMZ. Both aerobic and anaerobic methane oxidation is corroborated by the presence of particulate methane monooxygenase (pmoA) gene sequences, related to type I methanotrophs and the lineage of Candidatus Methylomirabilis oxyfera, known to perform nitrite-dependent anaerobic methane oxidation (N-DAMO), respectively.

False Negatives for Remote Life Detection on Ocean-Bearing Planets: Lessons from the Early Earth

Ocean-atmosphere chemistry on Earth has undergone dramatic evolutionary changes throughout its long history, with potentially significant ramifications for the emergence and long-term stability of atmospheric biosignatures. Though a great deal of work has centered on refining our understanding of false positives for remote life detection, much less attention has been paid to the possibility of false negatives, that is, cryptic biospheres that are widespread and active on a planet's surface but are ultimately undetectable or difficult to detect in the composition of a planet's atmosphere. Here, we summarize recent developments from geochemical proxy records and Earth system models that provide insight into the long-term evolution of the most readily detectable potential biosignature gases on Earth-oxygen (O2), ozone (O3), and methane (CH4). We suggest that the canonical O2-CH4 disequilibrium biosignature would perhaps have been challenging to detect remotely during Earth's ∼4.5-billion-year history and that in general atmospheric O2/O3 levels have been a poor proxy for the presence of Earth's biosphere for all but the last ∼500 million years. We further suggest that detecting atmospheric CH4 would have been problematic for most of the last ∼2.5 billion years of Earth's history. More broadly, we stress that internal oceanic recycling of biosignature gases will often render surface biospheres on ocean-bearing silicate worlds cryptic, with the implication that the planets most conducive to the development and maintenance of a pervasive biosphere will often be challenging to characterize via conventional atmospheric biosignatures. Key Words: Biosignatures-Oxygen-Methane-Ozone-Exoplanets-Planetary habitability. Astrobiology 17, 287-297.

A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity

River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.

A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments

Methane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major-capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Pequeñovirus.

Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria

The oxygenated surface waters of the world's oceans are supersaturated with methane relative to the atmosphere, a phenomenon termed the 'marine methane paradox'. The production of methylphosphonic acid (MPn) by marine archaea related to Nitrosopumilus maritimus and subsequent decomposition of MPn by phosphate-starved bacterioplankton may partially explain the excess methane in surface waters. Here we show that Pelagibacterales sp. strain HTCC7211, an isolate of the SAR11 clade of marine α-proteobacteria, produces methane from MPn, stoichiometric to phosphorus consumption, when starved for phosphate. Gene transcripts encoding phosphonate transport and hydrolysis proteins are upregulated under phosphate limitation, suggesting a genetic basis for the methanogenic phenotype. Strain HTCC7211 can also use 2-aminoethylphosphonate and assorted phosphate esters for phosphorus nutrition. Despite strain-specific differences in phosphorus utilization, these findings identify Pelagibacterales bacteria as a source of biogenic methane and further implicate phosphate starvation of chemoheterotrophic bacteria in the long-observed methane supersaturation in oxygenated waters.

Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin

The phylum Chloroflexi is one of the most frequently detected phyla in the subseafloor of the Pacific Ocean margins. Dehalogenating Chloroflexi (Dehalococcoidetes) was originally discovered as the key microorganisms mediating reductive dehalogenation via their key enzymes reductive dehalogenases (Rdh) as sole mode of energy conservation in terrestrial environments. The frequent detection of Dehalococcoidetes-related 16S rRNA and rdh genes in the marine subsurface implies a role for dissimilatory dehalorespiration in this environment; however, the two genes have never been linked to each other. To provide fundamental insights into the metabolism, genomic population structure and evolution of marine subsurface Dehalococcoidetes sp., we analyzed a non-contaminated deep-sea sediment core sample from the Peruvian Margin Ocean Drilling Program (ODP) site 1230, collected 7.3 m below the seafloor by a single cell genomic approach. We present for the first time single cell genomic data on three deep-sea Chloroflexi (Dsc) single cells from a marine subsurface environment. Two of the single cells were considered to be part of a local Dehalococcoidetes population and assembled together into a 1.38-Mb genome, which appears to be at least 85% complete. Despite a high degree of sequence-level similarity between the shared proteins in the Dsc and terrestrial Dehalococcoidetes, no evidence for catabolic reductive dehalogenation was found in Dsc. The genome content is however consistent with a strictly anaerobic organotrophic or lithotrophic lifestyle.

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO2 or oxidation of organics completely to CO2. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.

Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C₂), propane (C₃), and butane (C₄) in anoxic sediments in contrast to methane (C₁). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV, Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C₁–C₄ alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C₁–C₄ alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75°C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C₁–C₄ alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C₂–C₄ alkanes. Maximum C₁–C₄ alkane oxidation rates occurred at 55°C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C₃ was oxidized at the highest rate over time, then C₄, C₂, and C₁, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C₂–C₄alkanes with AOM for available oxidants and the influence on the fate of C₁ derived from these hydrothermal systems.

Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and decoupling from sulfate reduction

The anaerobic oxidation of methane (AOM) is a globally significant sink that regulates methane flux from sediments into the oceans and atmosphere. Here we examine mesophilic to thermophilic AOM in hydrothermal sediments recovered from the Middle Valley vent field, on the Juan de Fuca Ridge. Using continuous-flow sediment bioreactors and batch incubations, we characterized (i) the degree to which AOM contributes to net dissolved inorganic carbon flux, (ii) AOM and sulfate reduction (SR) rates as a function of temperature and (iii) the distribution and density of known anaerobic methanotrophs (ANMEs). In sediment bioreactors, inorganic carbon stable isotope mass balances results indicated that AOM accounted for between 16% and 86% of the inorganic carbon produced, underscoring the role of AOM in governing inorganic carbon flux from these sediments. At 90°C, AOM occurred in the absence of SR, demonstrating a striking decoupling of AOM from SR. An abundance of Fe(III)-bearing minerals resembling mixed valent Fe oxides, such as green rust, suggests the potential for a coupling of AOM to Fe(III) reduction in these metalliferous sediments. While SR bacteria were only observed in cooler temperature sediments, ANMEs allied to ANME-1 ribotypes, including a putative ANME-1c group, were found across all temperature regimes and represented a substantial proportion of the archaeal community. In concert, these results extend and reshape our understanding of the nature of high temperature methane biogeochemistry, providing insight into the physiology and ecology of thermophilic anaerobic methanotrophy and suggesting that AOM may play a central role in regulating biological dissolved inorganic carbon fluxes to the deep ocean from the organic-poor, metalliferous sediments of the global mid-ocean ridge hydrothermal vent system.

Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production

Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group.

The effect of nitrogen enrichment on c(1)-cycling microorganisms and methane flux in salt marsh sediments

Methane (CH₄) flux from ecosystems is driven by C₁-cycling microorganisms – the methanogens and the methylotrophs. Little is understood about what regulates these communities, complicating predictions about how global change drivers such as nitrogen enrichment will affect methane cycling. Using a nitrogen addition gradient experiment in three Southern California salt marshes, we show that sediment CH₄ flux increased linearly with increasing nitrogen addition (1.23 μg CH₄ m⁻² day⁻¹ for each g N m⁻² year⁻¹ applied) after 7 months of fertilization. To test the reason behind this increased CH₄ flux, we conducted a microcosm experiment altering both nitrogen and carbon availability under aerobic and anaerobic conditions. Methanogenesis appeared to be both nitrogen and carbon (acetate) limited. N and C each increased methanogenesis by 18%, and together by 44%. In contrast, methanotrophy was stimulated by carbon (methane) addition (830%), but was unchanged by nitrogen addition. Sequence analysis of the sediment methylotroph community with the methanol dehydrogenase gene (mxaF) revealed three distinct clades that fall outside of known lineages. However, in agreement with the microcosm results, methylotroph abundance (assayed by qPCR) and composition (assayed by terminal restriction fragment length polymorphism analysis) did not vary across the experimental nitrogen gradient in the field. Together, these results suggest that nitrogen enrichment to salt marsh sediments increases methane flux by stimulating the methanogen community.

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

BACKGROUND

Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation.

RESULTS

Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade.

CONCLUSIONS

Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences. The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions.