Aerobic Methane Oxidation Research Articles

Bacteriohopanepolyols across the Black Sea redoxcline trace diverse bacterial metabolisms

Redox gradients in oceanic oxygen minimum zones are hotspots of diverse bacterial populations and metabolisms. Here, we test whether bacteriohopanepolyols (BHPs), a suite of membrane-regulating pentacyclic triterpenoid lipids, are suitable tracers of major bacterial metabolisms and whether their structural diversity (BHP lipidomics) allows tracing the bacterial ecology across the Black Sea chemocline. We analyzed suspended particulate matter (SPM) sampled along depth-profiles across the redox/chemocline at two sites in the eastern and western gyres and underlying core-top sediments at the western gyre site. Our results show that BHPs abundances reflect the stratification of the Black Sea and capture ecological niches across the chemocline, being highest in the lower suboxic zone and in upper to deep sulfidic waters. BHP-inferred bacterial metabolisms in the lower suboxic zone are dominated by anammox and aerobic methane oxidizers (primarily by Type I/gammaproteobacteria). Bacterial biomass production in the upper to deep sulfidic zone is mirrored by a range of BHPs that are normally associated with aerobic metabolisms, most likely explained by either survival in oxygenated micro-niches or production by anaerobic bacteria (which could possibly include sulfate reducers and nitrite-dependent methane oxidizers). Most surprisingly, this ecological niche harbors seemingly unknown anaerobic bacteria which produce abundant C-2 and C-3 methylated BHPs. Core-top sediments reflect the BHP structural diversity found in SPM, but with notable compositional differences. Most strikingly, the export dynamics seem to result in near-absence of C-2 methylated BHPs in surface sediments. Sedimentary BHP distributions therefore underestimate the importance of C-2 methylated BHPs in the water column, which has implications for the geological record.

Copper mobilisation from Cu sulphide minerals by methanobactin: Effect of pH, oxygen and natural organic matter.

Aerobic methane oxidation (MOx) depends critically on the availability of copper (Cu) as a crucial component of the metal centre of particulate methane monooxygenase, one of the main enzymes involved in MOx. Some methanotrophs have developed Cu acquisition strategies, in which they exude Cu‐binding ligands termed chalkophores under conditions of low Cu availability. A well‐characterised chalkophore is methanobactin (mb), exuded by the microaerophilic methanotroph Methylosinus trichosporium OB3b. Aerobic methanotrophs generally reside close to environmental oxic–anoxic interfaces, where the formation of Cu sulphide phases can aggravate the limitation of bioavailable Cu due to their low solubility. The reactivity of chalkophores towards such Cu sulphide mineral phases has not yet been investigated. In this study, a combination of dissolution experiments and equilibrium modelling was used to examine the dissolution and solubility of bulk and nanoparticulate Cu sulphide minerals in the presence of mb as influenced by pH, oxygen and natural organic matter. In general, we show that mb is effective at increasing the dissolved Cu concentrations in the presence of a variety of Cu sulphide phases that may potentially limit Cu bioavailability. More Cu was mobilised per mole of mb from Cu sulphide nanoparticles compared with well‐crystalline bulk covellite (CuS). In general, the efficacy of mb at mobilising Cu from Cu sulphides is pH‐dependent. At lower pH, e.g. pH 5, mb was ineffective at solubilizing Cu. The presence of mb increased dissolved Cu concentrations between pH 7 and 8.5, where the solubility of all Cu sulphides is generally low, both in the presence and absence of oxygen. These results suggest that chalkophore‐promoted Cu mobilisation from sulphide phases is an effective extracellular mechanism for increasing dissolved Cu concentrations at oxic–anoxic interfaces, particularly in the neutral to slightly alkaline pH range. This suggests that aerobic methanotrophs may be able to fulfil their Cu requirements via the exudation of mb in natural environments where the bioavailability of Cu is constrained by very stable Cu sulphide phases.

Photocatalytic Methane Conversion: Insight into the Mechanism of C(sp 3 )–H Bond Activation

Photocatalytic Methane Conversion: Insight into the Mechanism of C(sp ³ )–H Bond Activation

Rapid Field Approach to Evaluating Natural Source Zone Depletion for a Range of Light Non‐Aqueous Phase Liquid Sites

AbstractMore rapid cost‐effective approaches are required to enable field evaluation of natural source zone depletion (NSZD) at petroleum LNAPL sites. Long and costly cleanups have continued as NSZD has not become widely acceptable as a remedial option. We have developed a low cost rapid field approach (RFA) and expanded the site conceptual models (SCMs) to include NSZD. Results from two sites are presented that illustrate the benefit of the RFA in supplementing existing data and updating SCMs. At present, most NSZD guidelines follow a single generic SCM (aerobic oxidation of methane) as the primary contributor to NSZD. Aerobic oxidation of LNAPL is also possible, and can be documented by subsurface measurements of soil‐gas composition and/or heat generated from biodegradation. The RFA was developed so that sites could be easily separated into those with and without a methane plume overlying LNAPL. This distinction is important as it defines the relative rates of oxygen transport into the soil, and methane generation and release from saturated zone anaerobic biodegradation. For the RFA, evidence for direct LNAPL oxidation is absence of methane (<0.1%‐v) in the unsaturated zone above LNAPL. This measurement can be readily made in the field using existing monitoring wells. The absence of a methane plume above LNAPL would indicate that NSZD is a result of direct biodegradation of LNAPL. This alternative SCM needs to be considered and evaluated prior to implementing more costly data collection or other remediation or site management options.

Highly Selective Photocatalytic Aerobic Oxidation of Methane to Oxygenates with Water over W‐doped TiO2

Highly selective conversion of methane to oxygenates with O2 as a green oxidant remains a great challenge. It is still difficult to suppress the generation of COx (x=1, 2) as undesired by-products due to unavoidable overoxidation reaction. Hence, tungsten-doped (W-doped) TiO2 photocatalysts were designed with a tunable band structure for photocatalytic oxidation of methane to C1 oxygenates using O2 at low temperature (30 °C). The W-doping effectively modified the electronic and band structure of pristine TiO2 to enhance photocatalytic performance. Liquid oxygenates productivity could reach as high as 12.2 mmol g-1 with high selectivity of 99.4 %. Moreover, COx selectivity was effectively decreased from 21.2 % over TiO2 to 0.6 % for W-doped catalyst. Detailed characterizations further disclosed that W-doping not only enhanced light absorption, but also promoted the separation of photo-generated carriers to improve methane conversion. This work provides new insights into the design of highly efficient photocatalysts for methane oxidation.

Multiple Groups of Methanotrophic Bacteria Mediate Methane Oxidation in Anoxic Lake Sediments.

Freshwater lakes represent an important source of the potent greenhouse gas methane (CH4) to the atmosphere. Methane emissions are regulated to large parts by aerobic (MOx) and anaerobic (AOM) oxidation of methane, which are important CH4 sinks in lakes. In contrast to marine benthic environments, our knowledge about the modes of AOM and the related methanotrophic microorganisms in anoxic lake sediments is still rudimentary. Here, we demonstrate the occurrence of AOM in the anoxic sediments of Lake Sempach (Switzerland), with maximum in situ AOM rates observed within the surface sediment layers in presence of multiple groups of methanotrophic bacteria and various oxidants known to support AOM. However, substrate-amended incubations (with NO2−, NO3−, SO42−, Fe-, and Mn-oxides) revealed that none of the electron acceptors previously reported to support AOM enhanced methane turnover in Lake Sempach sediments under anoxic conditions. In contrast, the addition of oxygen to the anoxic sediments resulted in an approximately 10-fold increase in methane oxidation relative to the anoxic incubations. Phylogenetic and isotopic evidence indicate that both Type I and Type II aerobic methanotrophs were growing on methane under both oxic and anoxic conditions, although methane assimilation rates were an order of magnitude higher under oxic conditions. While the anaerobic electron acceptor responsible for AOM could not be identified, these findings expand our understanding of the metabolic versatility of canonically aerobic methanotrophs under anoxic conditions, with important implications for future investigations to identify methane oxidation processes. Bacterial AOM by facultative aerobic methane oxidizers might be of much larger environmental significance in reducing methane emissions than previously thought.

Microorganisms as bio-filters to mitigate greenhouse gas emissions from high-altitude permafrost revealed by nanopore-based metagenomics.

The distinct climatic and geographical conditions make high-altitude permafrost on the Tibetan Plateau suffer more severe degradation than polar permafrost. However, the microbial responses associated with greenhouse gas production in thawing permafrost remain obscured. Here we applied nanopore-based long-read metagenomics and high-throughput RNA-seq to explore microbial functional activities within the freeze-thaw cycle in the active layers of permafrost at the Qilian Mountain. A bioinformatic framework was established to facilitate phylogenetic and functional annotation of the unassembled nanopore metagenome. By deploying this strategy, 42% more genera could be detected and 58% more genes were annotated to nitrogen and methane cycle. With the aid of such enlarged resolution, we observed vigorous aerobic methane oxidation by Methylomonas, which could serve as a bio-filter to mitigate CH4 emissions from permafrost. Such filtering effect could be further consolidated by both on-site gas phase measurement and incubation experiment that CO2 was the major form of carbon released from permafrost. Despite the increased transcriptional activities of aceticlastic methanogenesis pathways in the thawed permafrost active layer, CH4 generated during the thawing process could be effectively consumed by the microbiome. Additionally, the nitrogen metabolism in permafrost tends to be a closed cycle and active N2O consumption by the topsoil community was detected in the near-surface gas phase. Our findings reveal that although the increased thawed state facilitated the heterotrophic nitrogen and methane metabolism, effective microbial methane oxidation in the active layer could serve as a bio-filter to relieve the overall warming potentials of greenhouse gas emitted from thawed permafrost.

Advance in Numerical Simulation Research of Marine Methane Processes

Understanding the modern marine methane processes, which can profoundly affect global climate and have far-reaching impacts on human living environments, is critical for research on the global carbon cycle. Thus, modeling of marine methane processes has attracted increasing attention due to models can accurately simulate and predict the environmental effects of methane on marine and atmospheric ecosystems. In this study, we review the applications of modeling works to marine methane processes, including methanogenesis in sediments, transport and reaction of methane in sediments and seawater, and marine methane emissions to the atmosphere. Compiled a large database of global methanogenesis rates and methane fluxes to the sulfate-methane transition zone, we estimate that the global methanogenesis budget in marine sediments is ∼0.87 Tmol yr−1 and global sedimentary dissolved inorganic carbon produced by anaerobic oxidation of methane is ∼8.9 Tmol yr−1. In addition, although anaerobic oxidation of methane in sediments and aerobic oxidation of methane in seawater act as primary filters to prevent methane leakage from sediments to the hydrosphere as well as the atmosphere, large masses of methane in extreme seafloor environments (e.g., mud volcanic eruptions and hydrate leakage) can still escape microbial oxidation and leakage to seawater or the atmosphere. There is still a lack of models that simulate methane in these extreme marine environments. Therefore, more modeling works are needed to assess the efficiency of marine ecosystems, including sediments and hydrosphere, in filtering methane in the event of large-scale methane leakage from the seafloor. This study provides an interdisciplinary view of methane processes in marine systems and helps identify future directions in the modeling of methane processes in marine system.

Phase equilibrium characteristics of natural gas hydrate formation at the deep-water environment of “Haima” cold seep

Methane seeping induced by natural gas hydrate dissociation is ubiquitous in deep-sea environment, which influences the global methane and carbon budget. Nevertheless, the phase equilibrium characteristics that control the stability of hydrate formation during the bubble ebullition process in the in-situ multi-component environment remain unclear. “Haima” cold seep is a typical active methane seeping environment associated with abundant methane hydrate, which necessitates unveiling the potential and stability of methane hydrate formation. This work investigated the hydrate phase equilibrium conditions based on the in-situ water depth with practical ion categories and concentrations for the first time. Results show that Sr2+ is an important ion that governs the thermal stability of methane hydrate. Mechanism of different ions categories (Ca2+, Mg2+, and Sr2+) effect on hydrate equilibria can be elucidated by the difference of charge and radius of the ion. Slightly difference of in-situ ion concentrations within the same salinity exerts on unobvious effect on hydrate formation. Moreover, the hydrate stability with H2S-bearing environment coupled with the anaerobic oxidation of methane in the deep-sea floor was enhanced compared to the CO2-bearing environment associated with aerobic oxidation of methane. Furthermore, thermal dynamic conditions of hydrate formation were less rigorous than that in the single methane environment. The response law of hydrate phase transition enthalpy was almost consistent with the phase equilibrium change. This work can give important fundamentals for the estimation of hydrate resources in the practical environment, and have insights for methane capture and fixation in the methane seeps.

Coupling of (methane + air)-membrane biofilms and air-membrane biofilms: Treatment of p-nitroaniline wastewater

Membrane biofilm (MBf) technology is a promising biological water treatment process that combines membrane aeration with biofilms. To expand its application in the treatment of toxic organic wastewater, methane/air gas mixture-MBfs ((CH4 + Air)-MBfs) and air-MBfs were coupled to enhance the treatment of p-nitroaniline (PNA) wastewater. Based on exploration of the membrane permeability of methane and oxygen, a hybrid MBf reactor was constructed, and the degradation characteristics of PNA and the coupling effects of (CH4 + Air)-MBfs and air-MBfs were studied. The permeation flux of methane was found to be 1.114 g/(m2 d) when using a methane/air gas mixture at an aeration pressure of 10 kPa, and this result was better than that when methane was used as the aeration gas alone. Aeration with a methane/air gas mixture provided conditions for realizing aerobic methane oxidation; the aerobic methane oxidation that occurred in the (CH4 + Air)-MBfs promoted the reduction of PNA, and the intermediates of PNA degradation were further degraded by the air-MBfs. At an influent PNA membrane area load of 1.67 g/(m2 d), the PNA removal load reached 187.30 g/(m3 d). The coupling of MBfs took advantage of different matrix-based MBfs and promoted the degradation of PNA by utilizing the synergistic effects of various functional microorganisms.

The methane-driven interaction network in terrestrial methane hotspots

BackgroundBiological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa.ResultsWe applied stable isotope probing (SIP) using 13C-CH4 coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the 13C-CH4 incubation exhibited a less connected and complex topology than the networks derived from the unlabelledC-CH4 incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity.ConclusionWe demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.

Heterogeneity of CH4-derived carbon induced by O2:CH4 mediates the bacterial community assembly processes

The mechanism by which O2:CH4 controls microbial community assembly in the process of aerobic methane oxidation coupled to denitrification (AMED) remains largely uncharacterized, which hinders the design of engineering microbiomes for the AMED. In this study, the changes in the bacterial community in fed-batch serum bottle reactors under different O2:CH4 ratios were systematically characterized. The ratios of CH4 consumption to the amount of nitrate removal in the treatment with O2:CH4 = 1.5:1, O2:CH4 = 0.5:1, and O2:CH4 = 0.25:1 were 13.1 ± 3.4, 4.7 ± 1.1, and 5.9 ± 3.0 mol-CH4 mol−1-NO3−, respectively. The α-diversity of the bacterial community increased as O2:CH4 decreased. Significantly different selection patterns were found for the high and low O2:CH4 ratios. The coherence process dominated the selection at high O2:CH4 ratios, while the diversification process played a role when O2:CH4 was low. Differences were also observed in the composition of CH4-derived carbon between treatments with O2:CH4 = 1.5:1 and O2:CH4 = 0.5:1. Compared with the treatments with O2:CH4 = 1.5:1, the concentrations of methanol, formaldehyde, acetate, and ethanol in the treatment with O2:CH4 = 0.5:1 were significantly higher, while the concentration of formate was significantly lower. The heterogeneity of CH4-derived carbon induced by O2:CH4 was likely to be responsible for the differences in the selection patterns. Our findings bridge the gaps between the observations of bacterial community perturbations and ecological community assembly theories, highlighting the potential of the bottom-up design approach to improve the nitrate removal rate of the AME-D.

Nitrogen input promotes denitrifying methanotrophs’ abundance and contribution to methane emission reduction in coastal wetland and paddy soil

Denitrifying anaerobic methane oxidation (DAMO) microorganisms, using nitrate/nitrite to oxidize methane, have been proved to be an important microbial methane sink in natural habitats. Increasing nitrogen deposit around the globe brings increased availability of substrates for these microorganisms. However, how elevated nitrogen level affects denitrifying methanotrophs has not been elucidated. In this study, sediment/soil samples from coastal wetland with continuous nitrogen input and paddy field with periodic nitrogen input were collected to investigate the influence of nitrogen input on the abundance and activity of denitrifying methanotrophs. The results indicated that nitrogen input significantly promoted DAMO microorganisms’ abundance and contribution to methane emission reduction. In the coastal wetland, the contribution rate of DAMO process to methane removal increased from 12.1% to 33.5% along with continuously elevated nitrogen level in the 3-year tracking study. In the paddy field, the DAMO process accounted for 71.9% of total methane removal when nitrogen fertilizer was applied during the growing season, exceeding the aerobic methane oxidation process. This work would help us better understand the microbial methane cycle and reduce uncertainties in the estimations of the global methane emission.

MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

Methane is a critical greenhouse gas with significant impacts on environmental and global change. However, CH4 cycling processes and coupling mechanisms with the biogeochemical cycling of carbon, nitrogen, sulfur and metals in the environment remain elusive. To fill such knowledge gaps, we constructed a manually curated methane cycling database (MCycDB) for comprehensive and accurate analysis of methane cycling microbial communities. MCycDB contains 298methane cycling gene families covering 10methane metabolism pathways with 610,208 representative sequences, and associated reference sequences from the NCBI RefSeq database with 48 phyla and 2,197genera, and five phyla and 100genera for bacteria and archaea, respectively. Also, homologous groups from public orthology databases were identified and included in MCycDB to reduce false positive assignments. We applied MCycDB to profile methane cycling gene families and associated taxonomic groups from various environments. Gene families involved in methanogenesis were abundant in hot spring sediment and less abundant in freshwater, whereas the ones involved in aerobic oxidation of methane were abundant in permafrost and peatland. This study demonstrates that MCycDB is a useful tool for studying microbially-driven methane cycling processes with high specificity, coverage and accuracy.

Analysing seasonal variations of methane oxidation processes coupled with denitrification in a stratified lake using stable isotopes and numerical modeling

Since the discovery of nitrite (n-damo) and nitrate dependent anaerobic oxidation of methane in 2006, evidence has arisen about the occurrence of this process in freshwater ecosystems. Anaerobic oxidation of methane (AOM) linked with denitrification has been proposed to be a previously overlooked sink of methane in freshwater environments. However, the occurrence and relevance of AOM coupled with denitrification in methane removal and, therefore, mitigating methane emissions in the environment is so far largely unquantified.We investigated methane oxidation processes in the water column at the seasonally stratified lake Fohnsee located in Southern Germany to determine the seasonal dynamics and to quantitatively describe the contribution of anaerobic and aerobic oxidation of methane removing CH₄ from the water column throughout nearly one year. Vertical concentration profiles and corresponding stable isotope ratios of methane (δ13C) and nitrate (δ15N and δ18O), together with dissolved oxygen concentrations were measured, and a numerical model was developed to evaluate whether anaerobic oxidation of methane coupled with denitrification is a key biogeochemical process at lake Fohnsee. Our data set together with the results of the numerical model revealed a redox zone within the water column where both denitrification and anaerobic oxidation of methane are linked, contributing to approximately 70% of methane removal between June and September. Therefore, AOM linked with denitrification represents the dominant methane sink in the water column of lake Fohnsee during summer stratification.The data patterns also showed that the anaerobic oxidation of methane zone was located near the lake bottom in May, and moved upwards following the seasonal vertical displacement of the oxycline and the availability of nitrate. This redox dynamic within the water column of lake Fohnsee had also an effect on the relevance of aerobic and anaerobic oxidation of methane removing methane from the water column during the year and the formation of a bacterial sulfate reduction zone close to the lake sediments.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Influence of methane seepage on isotopic signatures in living deep-sea benthic foraminifera, 79\xb0 N

Fossil benthic foraminifera are used to trace past methane release linked to climate change. However, it is still debated whether isotopic signatures of living foraminifera from methane-charged sediments reflect incorporation of methane-derived carbon. A deeper understanding of isotopic signatures of living benthic foraminifera from methane-rich environments will help to improve reconstructions of methane release in the past and better predict the impact of future climate warming on methane seepage. Here, we present isotopic signatures (δ13C and δ18O) of foraminiferal calcite together with biogeochemical data from Arctic seep environments from c. 1200 m water depth, Vestnesa Ridge, 79° N, Fram Strait. Lowest δ13C values were recorded in shells of Melonis barleeanus, − 5.2‰ in live specimens and − 6.5‰ in empty shells, from sediments dominated by aerobic (MOx) and anaerobic oxidation of methane (AOM), respectively. Our data indicate that foraminifera actively incorporate methane-derived carbon when living in sediments with moderate seepage activity, while in sediments with high seepage activity the poisonous sulfidic environment leads to death of the foraminifera and an overgrowth of their empty shells by methane-derived authigenic carbonates. We propose that the incorporation of methane-derived carbon in living foraminifera occurs via feeding on methanotrophic bacteria and/or incorporation of ambient dissolved inorganic carbon.

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

Lipid biomarker patterns reflect seepage activity and variable geochemical processes in sediments from the Haima cold seeps, South China Sea

The anaerobic oxidation of methane (AOM), aerobic methane oxidation and the oxidation of non-methane hydrocarbons have been demonstrated to occur in seepage ecosystems, but when they occur during seepage evolutionary is lack of constraints. Here, lipid biomarker patterns combined with total organic carbon (TOC), δ13Corg, δ13CTIC and δ18OTIC of a sediment core (~ 3 m long) from the active Haima cold seep were analyzed. The observed lipid inventories reflected the prevailing of anaerobic methane oxidizing archaea (ANME)/Desulfosarcina/Desulfococcus (DSS) and ANME-2/DSS dominated over the whole sediments. Seepage fluids originated from local gas hydrate dissociation as indicated by the pronounced δ13CTIC and δ18OTIC values, while a mixture of microbial and thermogenic methane (−65‰ to −55‰) was corroborated by back-calculation based on the predominant consortia and δ13C values of ANME-specific biomarkers. AOM occurred over the whole sediments and was strengthened between depths 40 cm and 120 cm as revealed by the extremely low δ13CTIC, δ13Corg values, and abundant lipid biomarkers of ANME such as crocetane, 2,6,10,15,19-pentamethylicosane (PMI), archaeol and sn2-OH-archaeol with strong 13C depletions (δ13C values as low as −118‰). For sediment below the depth of 120 cm, molecular fossils of aerobic methanotrophs 4α-methylcholesta-2,8(14),24-triene and C34-3β-methyl tetracyclic-ketone occurred and yielded their δ13C values of −64‰ to −61‰, indicating the prevailing of oxic condition and aerobic methane oxidation. Compared to the sediment between 40 cm and 120 cm, the abundant iso-/anteiso-C15:0 (i-/ai-C15:0) fatty acids with relatively enriched δ13C values in the bottom sediment were better explained by contribution of sulfate-reducing bacteria (SRB)-driven oxidation of non-methane hydrocarbons. The distinct biomarker patterns and the respective geochemical processes at various sediment depths revealed the microbial community succession sequence in seepage evolutionary, since the different growth rates may have led to a successive colonization of aerobic methanotrophs, SRB, and ANME in an emerging cold seep ecosystem.

Hydrocarbon seepage in the mid-Cretaceous greenhouse world: A new perspective from southern Tibet

The mid-Cretaceous greenhouse climate was induced by volcanic outgassing and the release of biogenic or thermogenic methane into the ocean-atmosphere system. During this period, major episodes of oceanic anoxic conditions enabled the large scale deposition of marine black shales rich in organic carbon, serving as a source for methane production. Studies on the anaerobic oxidation of methane, the key biogeochemical process at sites where methane is transported toward the seafloor, and its associated authigenic carbonates from mid-Cretaceous strata can contribute to elucidate such extreme climatic conditions. A total of nine layers of authigenic carbonates were recognized in the sequence of mid-Cretaceous inner shelf sedimentary rocks of the Qiangdong section, Gamba area, southern Tibet. In this study, we decipher the mode and causes of carbonate authigenesis by combining field observation, thin section petrography, mineralogy, and carbon and oxygen stable isotope geochemistry. The lowest obtained δ13Ccarb value of −30.5‰ is not low enough to exclude oil compounds as a carbon source, but since other evidence of oil seepage is lacking, methane is the most likely carbon source that was admixed to dissolved inorganic carbon to form authigenic carbonate. Typical seep carbonate phases including 13C depleted matrix micrite, clotted micrite, and banded and botryoidal cement as well as three types of authigenic pyrite comprising framboids, zoned aggregates with radial overgrowths surrounding a framboidal core, and euhedral pyrite crystals indicate the occurrence of methane seepage in the mid-Cretaceous depositional environments. In situ brecciation and subvertical tubular carbonates – the former reflecting rupture caused by local fluid overpressure and the latter interpreted as part of a plumping system – agree with widespread and vigorous seepage. Expanded shallow and deep-water anoxia in combination with low seawater sulfate concentration prior to the oceanic anoxic event 2 (OAE 2) event apparently caused an increased flux of organic matter to the methanogenic zone, stimulating methanogenesis and enabling a higher flux of methane toward the seafloor. In the water column, aerobic oxidation of methane would have enhanced oxygen depletion, thereby contributing to black shale deposition and providing a positive feedback to organic matter preservation and burial. Based on correlation with coeval authigenic carbonate deposits from the Tethyan continental margin, we conclude that organic matter accumulation and sea-level change were the main factors controlling carbonate authigenesis in the mid-Cretaceous.