Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction

Recent findings in methanotrophs: genetics, molecular ecology, and biopotential

The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.

Anaerobic oxidation of methane driven by different electron acceptors: A review

Methane, the most significant reduced form of carbon on Earth, acts as a crucial fuel and greenhouse gas. Globally, microbial methane sinks encompass both aerobic oxidation of methane (AeOM), conducted by oxygen-utilizing methanotrophs, and anaerobic oxidation of methane (AOM), performed by anaerobic methanotrophs employing various alternative electron acceptors. These electron acceptors involved in AOM include sulfate, nitrate/nitrite, humic substances, and diverse metal oxides. The known anaerobic methanotrophic pathways comprise the internal aerobic oxidation pathway found in NC10 bacteria and the reverse methanogenesis pathway utilized by anaerobic methanotrophic archaea (ANME). Diverse anaerobic methanotrophs can perform AOM independently or in cooperation with symbiotic partners through several extracellular electron transfer (EET) pathways. AOM has been documented in various environments, including seafloor methane seepages, coastal wetlands, freshwater lakes, soils, and even extreme environments like hydrothermal vents. The environmental activities of AOM processes, driven by different electron acceptors, primarily depend on the energy yields, availability of electron acceptors, and environmental adaptability of methanotrophs. It has been suggested that different electron acceptors driving AOM may occur across a wider range of habitats than previously recognized. Additionally, it is proposed that methanotrophs have evolved flexible metabolic strategies to adapt to complex environmental conditions. This review primarily focuses on AOM, driven by different electron acceptors, discussing the associated reaction mechanisms and the habitats where these processes are active. Furthermore, it emphasizes the pivotal role of AOM in mitigating methane emissions.

Reveling the micromolecular biological mechanism of acetate, thiosulfate and Fe0 in ecological floating beds for treating low C/N wastewater: Insight into nitrogen removals and greenhouse gases reductions

Selecting an appropriate electron donor to enhance nitrogen removal for treating low C/N wastewater in ecological floating beds (EFBs) is controversy. In this study, a systematic and comprehensive evaluation of sodium acetate (EFB-C), sodium thiosulfate (EFB-S) and iron scraps (EFB-Fe) was performed in a 2-year experiment on long-term viability including nitrogen removal and greenhouse gas emissions associated with key molecular biological mechanisms. The results showed that EFB-C (43-85 %) and EFB-S (40-88 %) exhibited superior total nitrogen (TN) removal. Temperature and hydraulic retention time (HRT) have significant impacts on TN removal of EFB-Fe, however, it could reach 86 % under high temperature (30-35 °C) and a long HRT (3 days), and it has lowest N2O (0-6.2 mg m-2 d-1) and CH4 (0-5.3 mg m-2 d-1) fluxes. Microbial network analysis revealed that the microbes changed from competing to cooperating after adding electron donors. A higher abundance of anammox genera was enriched in EFB-Fe. The Mantel's test and structural equation model provided proof of the differences, which showed that acetate and thiosulfate were similar, whereas Fe0 was different in the nitrogen removal mechanism. Molecular biology analyses further verified that heterotrophic, autotrophic, and mixotrophic coupled with anammox were the main TN removal pathways for EFB-C, EFB-S, and EFB-Fe, respectively. These findings provide a better understanding of the biological mechanisms for selecting appropriate electron donors for treating low C/N wastewater.

Characterization of the redox-active extracellular polymeric substances in an anaerobic methanotrophic consortium

Anaerobic oxidation of methane (AOM) is a microbial process of importance in the global carbon cycle. AOM is predominantly mediated by anaerobic methanotrophic archaea (ANME), the physiology of which is still poorly understood. Here we present a new addition to the current physiological understanding of ANME by examining, for the first time, the biochemical and redox-active properties of the extracellular polymeric substances (EPS) of an ANME enrichment culture. Using a 'Candidatus Methanoperedens nitroreducens'-dominated methanotrophic consortium as the representative, we found it can produce an EPS matrix featuring a high protein-to-polysaccharide ratio of ∼8. Characterization of EPS using FTIR revealed the dominance of protein-associated amide I and amide II bands in the EPS. XPS characterization revealed the functional group of C-(O/N) from proteins accounted for 63.7% of total carbon. Heme-reactive staining and spectroscopic characterization confirmed the distribution of c-type cytochromes in this protein-dominated EPS, which potentially enabled its electroactive characteristic. Redox-active c-type cytochromes in EPS mediated the EET of 'Ca. M. nitroreducens' for the reduction of Ag+ to metallic Ag, which was confirmed by both ex-situ experiments with extracted soluble EPS and in-situ experiments with pristine EPS matrix surrounding cells. The formation of nanoparticles in the EPS matrix during in-situ extracellular Ag + reduction resulted in a relatively lower intracellular Ag distribution fraction, beneficial for alleviating the Ag toxicity to cells. The results of this study provide the first biochemical information on EPS of anaerobic methanotrophic consortia and a new insight into its physiological role in AOM process.

Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications

Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F430, a nickel-containing tetrahydrocorphin. Several modified versions of F430 have been discovered, including the 172-methylthio-F430 (mtF430) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F430 compared to 172-thioether coenzyme F430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 172 methylthio modification in ANME-1 MCR. Modifications at the 172 position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH3-S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme's organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.

Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. KEY POINTS: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes.

Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments

Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.

Diversity, Methane Oxidation Activity, and Metabolic Potential of Microbial Communities in Terrestrial Mud Volcanos of the Taman Peninsula

Microbial communities of terrestrial mud volcanoes are involved in aerobic and anaerobic methane oxidation, but the biological mechanisms of these processes are still understudied. We have investigated the taxonomic composition, rates of methane oxidation, and metabolic potential of microbial communities in five mud volcanoes of the Taman Peninsula, Russia. Methane oxidation rates measured by the radiotracer technique varied from 2.0 to 460 nmol CH4 cm-3 day-1 in different mud samples. This is the first measurement of high activity of microbial methane oxidation in terrestrial mud volcanos. 16S rRNA gene amplicon sequencing has shown that Bacteria accounted for 65-99% of prokaryotic diversity in all samples. The most abundant phyla were Pseudomonadota, Desulfobacterota, and Halobacterota. A total of 32 prokaryotic genera, which include methanotrophs, sulfur or iron reducers, and facultative anaerobes with broad metabolic capabilities, were detected in relative abundance >5%. The most highly represented genus of aerobic methanotrophs was Methyloprofundus reaching 36%. The most numerous group of anaerobic methanotrophs was ANME-2a-b (Ca. Methanocomedenaceae), identified in 60% of the samples and attaining relative abundance of 54%. The analysis of the metagenome-assembled genomes of a community with high methane oxidation rate indicates the importance of CO2 fixation, Fe(III) and nitrate reduction, and sulfide oxidation. This study expands current knowledge on the occurrence, distribution, and activity of microorganisms associated with methane cycle in terrestrial mud volcanoes.

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent

Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.

Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications

Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.

Electron Transfer in the Biogeochemical Sulfur Cycle

Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.

Effects of methane emissions on multiple myeloma-related mortality rates: A World Health Organization perspective

In this research, it was aimed to evaluate effects of methane emissions on multiple myeloma related mortality rates. Two countries in Europe (Germany and Netherlands) and 1 country for each region (Turkey, USA, Brazil, Egypt, and Australia) were selected within The World Health Organization Database. Multiple myeloma mortality rates of countries between 2009 and 2019 were used as dependent variable of the research. Methane emission level and agriculture methane levels of countries were used as independent variables from The World Bank Database. Current health expenditure and healthy life expectancy were used as controlling variables. Multiple myeloma-related mortality rate was the highest in the USA, followed by Germany, Brazil, Turkey, Australia, Netherlands, and Egypt. Difference analysis results were significant (P < .05). Methane and agriculture methane emissions were the highest in the USA. Multiple myeloma mortality was positively correlated with methane emissions (R = 0.504; P < .01), agricultural methane emissions (R = 0.705; P < .01), and current health expenditure (R = 0.528; P < .01). According to year and country controlled correlation analysis results, multiple myeloma mortality (MMM) was positively correlated with methane emissions (R = 0.889; P < .01), agricultural methane emissions (R = 0.495; P < .01), and current health expenditure (R = 0.704; P < .01). Methane emission (B = 0.01; P < .05), Germany (B = 9010.81; P < .01), the USA (B = 26516.77; P < .01), and Brazil (B = 4886.14; P < .01) had significant effect on MMM. Nonagricultural methane production has an increasing effect on MMM. Therefore, by looking at the differences between agricultural methane emissions and general methane emissions, studies can be conducted that allow for more effective global comparisons.

Humic substances as electron acceptor for anaerobic oxidation of methane (AOM) and electron shuttle in Mn (IV)-dependent AOM

Anaerobic methanotrophic archaea (ANME) belonging to the family Methanoperedenaceae are crucial for the global carbon cycle and different biogeochemical processes, owing to their metabolic versatility to couple anaerobic oxidation of methane (AOM) with different electron acceptors. A universal feature of Methanoperedenaceae is the abundant genes encoded in their genomes associated with extracellular electron transfer (EET) pathways. Candidatus. 'Methanoperedens manganicus', an archaeon belonging to the family Methanoperedenaceae, was recently enriched in a bioreactor performing AOM coupled with Mn (IV) reduction. Using this EET-capable ANME, we tested the hypothesis in this study that ANME can catalyse the humic-dependent AOM for growth. A two-year incubation showed that AOM activity can be sustained by Ca. 'M. manganicus' consortium in a bioreactor fed only with humic acids and methane. An isotopic mass balance batch test confirmed that the observed AOM was coupled to the reduction of humic acids. The increase of relative abundance of Ca. 'M. manganicus', and the total archaea population in the microbial community suggested that Ca. 'M. manganicus' can grow on methane and humic acids. The observation of humic-dependent AOM led to a subsequent hypothesis that humic acids could be used as the electron shuttle to mediate the EET in dissimilatory Mn (IV) reduction by Ca. 'M. manganicus'. We tested this hypothesis by adding humic acids to a Ca. 'M. manganicus' dominated-culture, which showed that the AOM rate was doubled by the addition of humic acids. X-ray photoelectron spectroscopy (XPS) showed that quinone moieties were consumed when humic acids worked as electron acceptors while remaining stable when functioning as a shuttle for electron transfer. The results of our study suggest that humic acids may serve as electron shuttles to allow ANME to access more electron acceptors through long-range EET.

Assessing the effect of sulfate on the anaerobic oxidation of methane coupled with Cr(VI) bioreduction by sludge characteristic and metagenomics analysis

Methane-driven hexavalent chromium (Cr(VI)) reduction in a microbial fuel cell (MFC) has attracted much attention. However, whether the presence of sulfate (SO42-) affects the reduction of Cr(VI) is still lacking in systematic studies. This study involved constructing a MFC-granular sludge (MFC-GS) coupling system with dissolved methane (CH4) was used as the electron donor to investigate the effect of SO42- on Cr(VI) bioreduction, sludge characteristic, and functional metabolic mechanisms. When the SO42- concentration was 10 mg/L, the average removal rate of Cr(VI) in the anaerobic stage decreased to the lowest value (22.25 ± 2.06%). Adding 10 mg/L SO42- obviously inhibited the electrochemical performance of the system. Increasing SO42- concentration weakened the fluorescence peaks of tryptophan and aromatic proteins in the extracellular polymeric substance of sludge. Under the influence of SO42-, Methanothrix_soehngenii decreased from 14.44% to 5.89%. The relative abundance of methane metabolic was down-regulated from 1.47% to 0.98%, while the sulfur metabolic was up-regulated from 0.09% to 0.21% when SO42- was added. These findings provided some reference for the treatment of wastewater containing Cr(VI) and SO42- complex pollutants in the MFC-GS coupling system.

Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization

Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.

Challenges and Approaches of Culturing the Unculturable Archaea

Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.

Conventional Fossil Fuel Extraction, Associated Biogeochemical Processes, and Topography Influence Methane Groundwater Concentrations in Appalachia

The production of fossil fuels, including oil, gas, and coal, retains a dominant share in US energy production and serves as a major anthropogenic source of methane, a greenhouse gas with a high warming potential. In addition to directly emitting methane into the air, fossil fuel production can release methane into groundwater, and that methane may eventually reach the atmosphere. In this study, we collected 311 water samples from an unconventional oil and gas (UOG) production region in Pennsylvania and an oil and gas (O&G) and coal production region across Ohio and West Virginia. Methane concentration was negatively correlated to distance to the nearest O&G well in the second region, but such a correlation was shown to be driven by topography as a confounding variable. Furthermore, sulfate concentration was negatively correlated with methane concentration and with distance to coal mining in the second region, and these correlations were robust even when considering topography. We hypothesized that coal mining enriched sulfate in groundwater, which in turn inhibited methanogenesis and enhanced microbial methane oxidation. Thus, this study highlights the complex interplay of multiple factors in shaping groundwater methane concentrations, including biogeochemical conversion, topography, and conventional fossil extraction.

Biosensing systems for the detection and quantification of methane gas

Climate change due to the continuous increase in the release of green-house gasses associated with anthropogenic activity has made a significant impact on the sustainability of life on our planet. Methane (CH4) is a green-house gas whose concentrations in the atmosphere are on the rise. CH4 measurement is important for both the environment and the safety at the industrial and household level. Methanotrophs are distinguished for their unique characteristic of using CH4 as the sole source of carbon and energy, due to the presence of the methane monooxygenases that oxidize CH4 under ambient temperature conditions. This has attracted interest in the use of methanotrophs in biotechnological applications as well as in the development of biosensing systems for CH4 quantification and monitoring. Biosensing systems using methanotrophs rely on the use of whole microbial cells that oxidize CH4 in presence of O2, so that the CH4 concentration is determined in an indirect manner by measuring the decrease of O2 level in the system. Although several biological properties of methanotrophic microorganisms still need to be characterized, different studies have demonstrated the feasibility of the use of methanotrophs in CH4 measurement. This review summarizes the contributions in methane biosensing systems and presents a prospective of the valid use of methanotrophs in this field. KEY POINTS: • Methanotroph environmental relevance in methane oxidation • Methanotroph biotechnological application in the field of biosensing • Methane monooxygenase as a feasible biorecognition element in biosensors.

Salinity effect on an anaerobic methane- and ammonium-oxidising consortium: Shifts in activity, morphology, osmoregulation and syntrophic relationship

Nitrate-dependent anaerobic methane oxidation (AOM) is a microbial process of both ecological significance for global methane mitigation and application potential for wastewater treatment. It is mediated by organisms belonging to the archaeal family 'Candidatus Methanoperedenaceae', which have so far mainly been found in freshwater environments. Their potential distribution in saline environments and their physiological responses to salinity variation were still poorly understood. In this study, the responses of the freshwater 'Candidatus Methanoperedens nitroreducens'-dominated consortium to different salinities were investigated using short- and long-term setups. Short-term exposure to salt stress significantly affected nitrate reduction and methane oxidation activities over the tested concentration range of 15-200‰ NaCl, and 'Ca. M. nitroreducens' showed the higher tolerance to high salinity stress than its partner of anammox bacteria. At high salinity concentration, near marine conditions of 37‰, the target organism 'Ca. M. nitroreducens' showed stabilized nitrate reduction activity of 208.5 µmol day-1 gCDW-1 in long-term bioreactors over 300 days, in comparison to 362.9 and 334.3 µmol day-1 gCDW-1 under low-salinity conditions (1.7‰ NaCl) and control conditions (∼15‰ NaCl). Different partners of 'Ca.  M. nitroreducens' evolved in the consortia with three different salinity conditions, suggesting the different syntrophic mechanisms shaped by changes in salinity. A new syntrophic relationship between 'Ca. M. nitroreducens' and Fimicutes and/or Chloroflexi denitrifying populations was identified under the marine salinity condition. Metaproteomic analysis shows that the salinity changes lead to higher expression of response regulators and selective ion (Na+/H+) channeling proteins that can regulate the osmotic pressure between the cell and its environment. The reverse methanogenesis pathway was, however, not impacted. The finding of this study has important implications for the ecological distribution of the nitrate-dependent AOM process in marine environments and the potential of this biotechnological process for the treatment of high-salinity industrial wastewater.

Variation in epibiotic bacteria on two squat lobster species of Munidopsidae

The relationships between epibiotic bacteria on deep-sea hosts and host lifestyle factors are of particular interest in the field of deep-sea chemoautotrophic environmental adaptations. The squat lobsters Shinkaia crosnieri and Munidopsis verrilli are both dominant species in cold-seep ecosystems, and they have different distributions and feeding behaviors. These species may have evolved to have distinct epibiotic microbiota. Here, we compared the epibiotic bacterial communities on the M. verrilli carapace (MV_carapace), S. crosnieri carapace (SC_carapace), and S. crosnieri ventral plumose setae (SC_setae). The epibiotic bacteria on SC_setae were dense and diverse and had a multi-layer configuration, while those on MV_carapace and SC_carapace were sparse and had a monolayer configuration. Chemoautotrophic bacteria had the highest relative abundance in all epibiotic bacterial communities. The relative abundance of amplicon sequence variant 3 (ASV3; unknown species in order Thiotrichales), which is associated with sulfide oxidation, was significantly higher in SC_setae than MV_carapace and SC_carapace. Thiotrichales species seemed to be specifically enriched on SC_setae, potentially due to the synthetic substrate supply, adhesion preference, and host behaviors. We hypothesize that the S. crosnieri episymbionts use chemical fluxes near cold seeps more efficiently, thereby supporting the host's nutrient strategies, resulting in a different distribution of the two species of squat lobster.

Microbial communities and their roles in the Cenozoic sulfurous oil reservoirs in the Southwestern Qaidam Basin, Western China

The latest discovery of sulfurous natural gas marked a breakthrough in the Cenozoic natural gas exploration in the southwestern margin of Qaidam Basin. The 16S rRNA analyses were performed on the crude oil samples from H₂S-rich reservoirs in the Yuejin, Shizigou and Huatugou profiles, to understand the sulfurous gas origin, which was also integrated with carbon and hydrogen isotopes of alkane and sulfur isotopes of H₂S collected from the Yingxiongling Area. Results show that the microorganisms in samples can survive in the hypersaline reservoirs, and can be classified into multiple phyla, including Proteobacteria, Planctomycetes, Firmicutes, Bacteroidetes, and Haloanaerobiaeota. Methanogens are abundant in all of the three profiles, while sulfate-reducing bacteria are abundant in Yuejin and Huatugou profiles, contributing to the methane and H₂S components in the natural gas. The carbon, hydrogen and sulfur isotopes of sulfurous natural gas in the Yingxiongling Area show that the natural gas is a mixture of coal-type gas and oil-type gas, which was primarily derived from thermal degradation, and natural gas from the Yuejin and Huatugou profiles also originated from biodegradation. The isotopic analysis agrees well with the 16S rRNA results, i.e., H₂S-rich natural gas from the Cenozoic reservoirs in the southwest margin of the Qaidam Basin was primarily of thermal genesis, with microbial genesis of secondary importance.

Fe(III) enhances Cr(VI) bioreduction in a MFC-granular sludge coupling system: Experimental evidence and metagenomics analysis

The influence of Fe(III) on the bioreduction efficiency of Cr(VI) in a microbial fuel cell (MFC)-granular sludge coupling system using dissolved methane as an electron donor and carbon source was explored, and the mechanism of Fe(III) mediating enhancement in the bioreduction process of Cr(VI) in the coupling system was also investigated. Results showed that the presence of Fe(III) enhanced the ability of the coupling system to reduce Cr(VI). The average removal efficiencies of Cr(VI) in the anaerobic zone in response to 0, 5, and 20 mg/L of Fe(III) were 16.53±2.12%, 24.17±2.10%, and 46.33±4.41%, respectively. Fe(III) improved the reducing ability and output power of the system. In addition, Fe(III) enhanced the electron transport systems activity of the sludge, the polysaccharide and protein content in the anaerobic sludge. Meanwhile, X-ray photoelectron spectrometer (XPS) spectra demonstrated that Cr(VI) was reduced to Cr(III), while Fe2p participated in reducing Cr(VI) in the form of Fe(III) and Fe(II). Proteobacteria, Chloroflexi, and Bacteroidetes were the dominant phylum in the Fe(III)-enhanced MFC-granular sludge coupling system, accounting for 49.7%-81.83% of the microbial community. The relative abundance of Syntrophobacter and Geobacter increased after adding Fe(III), indicating that Fe(III) contributed to the microbial mediated anaerobic oxidation of methane (AOM) and bioreduction of Cr(VI). The genes mcr, hdr, and mtr were highly expressed in the coupling system after the Fe(III) concentration increased. Meanwhile, the relative abundances of coo and aacs genes were up-regulated by 0.014% and 0.075%, respectively. Overall, these findings deepen understanding of the mechanism of the Cr(VI) bioreduction in the MFC-granular sludge coupling system driven by methane under the influence of Fe(III).

Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps

Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.

Microbial survival mechanisms within serpentinizing Mariana forearc sediments

Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.5 and depleted nutrients. The International Ocean Discovery Program Expedition 366 to the Mariana Convergent Margin sampled three serpentinizing seamounts located along the Mariana forearc chain with elevated concentrations of methane, hydrogen, and sulfide. Across all three seamount summits, the most abundant transcripts were for cellular maintenance such as cell wall and membrane repair, and the most abundant metabolic pathways were the Entner-Doudoroff pathway and tricarboxylic acid cycle. At flank samples, sulfur cycling involving taurine assimilation dominated the metatranscriptomes. The in situ activity of these pathways was supported by the detection of their metabolic intermediates. All samples had transcripts from all three domains of Bacteria, Archaea, and Eukarya, dominated by Burkholderiales, Deinococcales, and Pseudomonales, as well as the fungal group Opisthokonta. All samples contained transcripts for aerobic methane oxidation (pmoABC) and denitrification (nirKS). The Mariana forearc microbial communities show activity not only consistent with basic survival mechanisms, but also coupled metabolic reactions.

Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH₄ dm^-3. Methane carbon isotopic composition (δ¹³C-CH₄) varied from -98.9 to -77.6‱, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4-5.0 nmol dm^-3 day^-1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm^-3 day^-1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a-2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

Microbial one‑carbon and nitrogen metabolisms are beneficial to the reservoir recovery after cyanobacterial bloom

Cyanobacterial blooms have profound effects on the structure and function of plankton communities in inland waters, but few studies have focused on the effects of microbial-based processes in one‑carbon and nitrogen cycling on water quality improvement following the bloom. Here, we compared the structure and function of the bacterial community, focusing on microbial one‑carbon and nitrogen metabolisms during and after a cyanobacterial Microcystis bloom in a deep subtropical reservoir. Our data showed that microbial one‑carbon and nitrogen cycles were closely related to different periods of the bloom, and the changes of functional genes in microbial carbon and nitrogen cycling showed the same consistent trend as that of Methylomonas sp. With the receding of the bloom, the abundance of Methylomonas as well as the functional genes of microbial one‑carbon and nitrogen cycling reached the peak and then recovered. Our results indicate that microbial one‑carbon and nitrogen metabolisms were beneficial to the recovery of water quality from the cyanobacterial bloom. This study lays a foundation for a deep understanding of the cyanobacterial decomposition mediated by microbes in one‑carbon and nitrogen cycles in inland freshwaters.

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.

Characterization of archaeal and bacterial communities thriving in methane-seeping on-land mud volcanoes, Niigata, Japan

Submarine mud volcanoes (MVs) have attracted significant interest in the scientific community for obtaining clues on the subsurface biosphere. On-land MVs, which are much less focused in this context, are equally important, and they may even provide insights also for astrobiology of extraterrestrial mud volcanism. Hereby, we characterized microbial communities of two active methane-seeping on-land MVs, Murono and Kamou, in central Japan. 16S rRNA gene profiling of those sites recovered the dominant archaeal sequences affiliated with methanogens. Anaerobic methanotrophs (ANME), with the subgroups ANME-1b and ANME-3, were recovered only from the Murono site albeit a greatly reduced relative abundance in the community compared to those of typical submarine MVs. The bacterial sequences affiliated to Caldatribacteriota JS1 were recovered from both sites; on the other hand, sulfate-reducing bacteria (SRB) of Desulfobulbaceae was recovered only from the Murono site. The major difference of on-land MVs from submarine MVs is that the high concentrations of sulfate are not always introduced to the subsurface from above. In addition, the XRD analysis of Murono shows the absence of sulfate-, sulfur-related mineral. Therefore, we hypothesize one scenario of ANME-1b and ANME-3 thriving at the depth of the Murono site independently from SRB, which is similar to the situations reported in some other methane-seeping sites with a sulfate-depleted condition. We note that previous investigations speculate that the erupted materials from Murono and Kamou originate from the Miocene marine strata. The fact that SRB (Desulfobulbaceae) capable of associating with ANME-3 was recovered from the Murono site presents an alternative scenario: the old sea-related juvenile water somehow worked as the source of additional sulfur-related components for the SRB-ANME syntrophic consortium forming at a deeper zone of the site. However, the reason for the differences between Murono and Kamou is still unknown, and this requires further investigation.

Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea

Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.

Polyhydroxyalkanoate-driven current generation via acetate by an anaerobic methanotrophic consortium

Anaerobic oxidation of methane (AOM) is an important microbial process mitigating methane (CH₄) emission from natural sediments. Anaerobic methanotrophic archaea (ANME) have been shown to mediate AOM coupled to the reduction of several compounds, either directly (i.e. nitrate, metal oxides) or in consortia with syntrophic bacterial partners (i.e. sulfate). However, the mechanisms underlying extracellular electron transfer (EET) between ANME and their bacterial partners or external electron acceptors are poorly understood. In this study, we investigated electron and carbon flow for an anaerobic methanotrophic consortium dominated by 'Candidatus Methanoperedens nitroreducens' in a CH₄-fed microbial electrolysis cell (MEC). Acetate was identified as a likely intermediate for the methanotrophic consortium, which stimulated the growth of the known electroactive genus Geobacter. Electrochemical characterization, stoichiometric calculations of the system, along with stable isotope-based assays, revealed that acetate was not produced from CH₄ directly. In the absence of CH₄, current was still generated and the microbial community remained largely unchanged. A substantial portion of the generated current in the absence of CH₄ was linked to the oxidation of the intracellular polyhydroxybutyrate (PHB) and the breakdown of extracellular polymeric substances (EPSs). The ability of 'Ca. M. nitroreducens' to use stored PHB as a carbon and energy source, and its ability to donate acetate as a diffusible electron carrier expands the known metabolic diversity of this lineage that likely underpins its success in natural systems.

Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring

Lost Hammer Spring, located in the High Arctic of Nunavut, Canada, is one of the coldest and saltiest terrestrial springs discovered to date. It perennially discharges anoxic (<1 ppm dissolved oxygen), sub-zero (~-5 °C), and hypersaline (~24% salinity) brines from the subsurface through up to 600 m of permafrost. The sediment is sulfate-rich (1 M) and continually emits gases composed primarily of methane (~50%), making Lost Hammer the coldest known terrestrial methane seep and an analog to extraterrestrial habits on Mars, Europa, and Enceladus. A multi-omics approach utilizing metagenome, metatranscriptome, and single-amplified genome sequencing revealed a rare surface terrestrial habitat supporting a predominantly lithoautotrophic active microbial community driven in part by sulfide-oxidizing Gammaproteobacteria scavenging trace oxygen. Genomes from active anaerobic methane-oxidizing archaea (ANME-1) showed evidence of putative metabolic flexibility and hypersaline and cold adaptations. Evidence of anaerobic heterotrophic and fermentative lifestyles were found in candidate phyla DPANN archaea and CG03 bacteria genomes. Our results demonstrate Mars-relevant metabolisms including sulfide oxidation, sulfate reduction, anaerobic oxidation of methane, and oxidation of trace gases (H₂, CO₂) detected under anoxic, hypersaline, and sub-zero ambient conditions, providing evidence that similar extant microbial life could potentially survive in similar habitats on Mars.

Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression

Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F₄₃₀. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.

Response of the Anaerobic Methanotrophic Archaeon Candidatus "Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment

Anaerobic methanotrophic (ANME) archaea can drive anaerobic oxidation of methane (AOM) using solid iron or manganese oxides as the electron acceptors, hypothetically via direct extracellular electron transfer (EET). This study investigated the response of Candidatus "Methanoperedens nitroreducens TS" (type strain), an ANME archaeon previously characterized to perform nitrate-dependent AOM, to an Fe(III)-amended condition over a prolonged period. Simultaneous consumption of methane and production of dissolved Fe(II) were observed for more than 500 days in the presence of Ca. "M. nitroreducens TS," indicating that this archaeon can carry out Fe(III)-dependent AOM for a long period. Ca. "M. nitroreducens TS" possesses multiple multiheme c-type cytochromes (MHCs), suggesting that it may have the capability to reduce Fe(III) via EET. Intriguingly, most of these MHCs are orthologous to those identified in Candidatus "Methanoperedens ferrireducens," an Fe(III)-reducing ANME archaeon. In contrast, the population of Ca. "M. nitroreducens TS" declined and was eventually replaced by Ca. "M. ferrireducens," implying niche differentiation between these two ANME archaea in the environment.

Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption

Cold seeps are a major methane source in marine systems, and microbe-mediated anaerobic oxidation of methane (AOM) serves as an effective barrier for preventing methane emissions from sediment to water. However, how the periodic eruption of cold seeps drives the microbial community shift and further affects carbon cycling has been largely neglected, mainly due to the technical challenge of analyzing the in situ communities undergoing such geological events. Using a continuously running high-pressure bioreactor to simulate these events, we found that under the condition of simulated eruptions, the abundance of AOM-related species decreased, and some methane was oxidized to methyl compounds to feed heterotrophs. The methanogenic archaeon Methanolobus replaced ANME-2a as the dominant archaeal group; moreover, the levels of methylotrophic bacteria, such as Pseudomonas, Halomonas, and Methylobacter, quickly increased, while those of sulfate-reducing bacteria decreased. According to the genomic analysis, Methylobacter played an important role in incomplete methane oxidation during eruptions; this process was catalyzed by the genes pmoABC under anaerobic conditions when the methane pressure was high, possibly generating organic carbon. Additionally, the findings showed that methyl compounds can also be released to the environment during methanogenesis and AOM under eruption conditions when the methane pressure is high.

Progress and Challenges in Studying the Ecophysiology of Archaea

It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.

Temperature sensitivity of anaerobic methane oxidation versus methanogenesis in paddy soil: Implications for the CH4 balance under global warming

The global methane (CH₄ ) budget is based on a sensitive balance between methanogenesis and CH₄ oxidation (aerobic and anaerobic). The response of these processes to climate warming, however, is not quantified. This largely reflects our lack of knowledge about the temperature sensitivity (Q₁₀ ) of the anaerobic oxidation of CH₄ (AOM)-a ubiquitous process in soils. Based on a ¹³ CH₄ labeling experiment, we determined the rate, Q₁₀ and activation energy of AOM and of methanogenesis in a paddy soil at three temperatures (5, 20, 35°C). The rates of AOM and of methanogenesis increased exponentially with temperature, whereby the AOM rate was significantly lower than methanogenesis. Both the activation energy and Q₁₀ of AOM dropped significantly from 5-20 to 20-35°C, indicating that AOM is a highly temperature-dependent microbial process. Nonetheless, the Q₁₀ of AOM and of methanogenesis were similar at 5-35°C, implying a comparable temperature dependence of AOM and methanogenesis in paddy soil. The continuous increase of AOM Q₁₀ over the 28-day experiment reflects the successive utilization of electron acceptors according to their thermodynamic efficiency. The basic constant for Q₁₀ of AOM was calculated to be 0.1 units for each 3.2 kJ mol^-1 increase of activation energy. We estimate the AOM in paddy soils to consume 2.2~5.5 Tg CH₄ per year on a global scale. Considering these results in conjunction with literature data, the terrestrial AOM in total consumes ~30% of overall CH₄ production. Our data corroborate a similar Q₁₀ of AOM and methanogenesis. As the rate of AOM in paddy soils is lower than methanogenesis, however, it will not fully compensate for an increased methane production under climate warming.

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation

Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.

Anaerobic oxidation of methane mediated by microbial extracellular respiration

Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET-mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET-mediated AOM is discussed with both methane-oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET-mediated AOM, raising open research questions for future research.

Biologically-oriented mud volcano database: muddy_db

Mud volcanoes (MVs) are naturally occurring hydrocarbon hotbeds with continuous methane discharge, contributing to global warming. They host microbial communities adapted to hydrocarbon oxidation. Given their research value, MVs still represent a niche topic in microbiology and are neglected by hydrocarbon-oriented research. All the data regarding MVs is sporadic and decentralized. To mitigate this problem, we built a custom Natural Language Processing pipeline (muddy_mine), and collected all the available MV data from open-access articles. Based on this data, we built the muddy_db database. The muddy_db represents the first biologically oriented database rendered as a user-friendly web app. This database includes all the relevant MV data, ranging from microbial taxonomy to hydrocarbon occurrence and geology. The muddy_mine and muddy_db tools are licensed under the GPLv3. muddy_db R Shiny web app: https://muddy-db.shinyapps.io/muddy_db/ muddy_db R package: https://github.com/TracyRage/muddy_db muddy_mine Conda package: https://github.com/TracyRage/muddy_mine.

Influence of nitrate supplementation on in-vitro methane emission, milk production, ruminal fermentation, and microbial methanotrophs in dairy cows fed at two forage levels

Modifying the chemical composition of a diet can be a good strategy for reducing methane emission in the rumen. However, this strategy can have adverse effects on the ruminal microbial flora. The aim of our study was to reduce methane without disturbing ruminal function by stimulating the growth and propagation of methanotrophs. In this study, we randomly divided twenty multiparous Holstein dairy cows into 4 groups in a 2×2 factorial design with two forage levels (40% and 60%) and two nitrate supplementation levels (3.5% and zero). We examined the effect of experimental diets on cow performance, ruminal fermentation, blood metabolites and changes of ruminal microbial flora throughout the experimental period (45-day). Additionally, in vitro methane emission was evaluated. Animals fed diet with 60% forage had greater dry matter intake (DMI) and milk fat content, but lower lactose and milk urea content compared with those fed 40% forage diet. Moreover, nitrate supplementation had no significant effect on DMI and milk yield. Furthermore, the interactions showed that nitrate reduces DMI and milk fat independently of forage levels. Our findings showed that nitrate can increase ammonia concentration, pH, nitrite, and acetate while reducing the total volatile fatty acids concentration, propionate, and butyrate in the rumen. With increasing nitrate, methane emission was considerably decreased possibly due to the stimulated growth of Fibrobacteria, Proteobacteria, type II Methanotrophs, and Methanoperedense nitroreducens, especially with high forage level. Overall, nitrate supplementation could potentially increase methane oxidizing microorganisms without adversely affecting cattle performance.

Biogenic formation of amorphous carbon by anaerobic methanotrophs and select methanogens

Elemental carbon exists in different structural forms including graphite, diamond, fullerenes, and amorphous carbon. In nature, these materials are produced through abiotic chemical processes under high temperature and pressure but are considered generally inaccessible to biochemical synthesis or breakdown. Here, we identified and characterized elemental carbon isolated from consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), which together carry out the anaerobic oxidation of methane (AOM). Two different AOM consortia, ANME-1a/HotSeep-1 and ANME-2a/c/Seep-SRB, produce a black material with similar characteristics to disordered graphite and amorphous carbon. Stable isotope probing studies revealed that the carbon is microbially generated during AOM. In addition, we found that select methanogens also produce amorphous carbon with similar characteristics to the carbon from AOM consortia. Biogenic amorphous carbon may serve as a conductive element to facilitate electron transfer, or redox active functional groups associated with the carbon could act as electron donors and acceptors.

Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea

Cold seeps are globally widespread seafloor ecosystems that feature abundant methane production and flourishing chemotrophic benthic communities. Chemical evidence indicates that cold seep methane is largely biogenic; however, the primary methane-producing organisms and associated pathways involved in methanogenesis remain elusive. This work detected methane production when glycine betaine (GBT) or trimethylamine (TMA) was added to the sediment microcosms of the Formosa cold seep, South China Sea. The methane production was suppressed by antibiotic inhibition of bacteria, while GBT was accumulated. This suggests that the widely used osmoprotectant GBT could be converted to cold seep biogenic methane via the synergistic activity of bacteria and methanogenic archaea because archaea are not sensitive to antibiotics and no bacteria are known to produce ample methane (mM). 16S rRNA gene diversity analyses revealed that the predominant bacterial and archaeal genera in the GBT-amended methanogenic microcosms included Oceanirhabdus and Methanococcoides. Moreover, metagenomic analyses detected the presence of grdH and mtgB genes that are involved in GBT reduction and demethylation, respectively. Two novel species were obtained, including bacterium Oceanirhabdus seepicola, which reduces GBT to TMA, and a methanogenic archaeon, Methanococcoides seepicolus, which produces methane from TMA and GBT. The two strains reconstituted coculture efficiently converted GBT to methane at 18°C; however, at 4°C addition of dimethylglycine (DMG), the GBT demethylation product, was necessary. Therefore, this work demonstrated that GBT is the precursor not only of the biogenic methane but also of the cryoprotectant DMG to the microorganisms at the Formosa cold seep.

IMPORTANCE Numerous cold seeps have been found in global continental margins where methane is enriched in pore waters that are forced upward from sediments. Therefore, high concerns have been focused on the methane-producing organisms and the metabolic pathways in these environments because methane is a potent greenhouse gas. In this study, GBT was identified as the main precursor for methane in the Formosa cold seep of the South China Sea. Further, synergism of bacteria and methanogenic archaea was identified in GBT conversion to methane via the GBT reduction pathway, while methanogen-mediated GBT demethylation to methane was also observed. In addition, GBT-demethylated product dimethyl glycine acted as a cryoprotectant that promoted the cold seep microorganisms at cold temperatures. GBT is an osmoprotectant that is widely used by marine organisms, and therefore, the GBT-derived methanogenic pathway reported here could be widely distributed among global cold seep environments.

Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane

Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.

Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea

Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.

Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies

Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NO_x consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.

Simultaneous nitrate and sulfate dependent anaerobic oxidation of methane linking carbon, nitrogen and sulfur cycles

ANaerobic MEthanotrophic (ANME) archaea are critical microorganisms mitigating methane emission from anoxic zones. In previous studies, sulfate-dependent anaerobic oxidation of methane (AOM) and nitrate-dependent AOM, performed by different clades of ANME archaea, were detected in marine sediments and freshwater environments, respectively. This study shows that simultaneous sulfate- and nitrate-dependent AOM can be mediated by a clade of ANME archaea, which may occur in estuaries and coastal zones, at the interface of marine and freshwater environments enriched with sulfate and nitrate. Long-term (~1,200 days) performance data of a bioreactor, metagenomic analysis and batch experiments demonstrated that ANME-2d not only conducted AOM coupled to reduction of nitrate to nitrite, but also coupled to the conversion of sulfate to sulfide, in collaboration with sulfate-reducing bacteria (SRB). Sulfide was oxidized back to sulfate by sulfide-oxidizing autotrophic denitrifiers with nitrate or nitrite as electron acceptors, in turn alleviating sulfide accumulation. In addition, dissimilatory nitrate reduction to ammonium performed by ANME-2d was detected, providing substrates to Anammox. Metatranscriptomic analysis revealed significant upregulation of flaB in ANME-2d and pilA in Desulfococcus, which likely resulted in the formation of unique nanonets connecting cells and expanding within the biofilm, and putatively providing structural links between ANME-2d and SRB for electron transfer. Simultaneous nitrate- and sulfate-dependent AOM as observed in this study could be an important link between the carbon, nitrogen and sulfur cycles in natural environments, such as nearshore environments.

Innovations to culturing the uncultured microbial majority

Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.

Dynamic modeling of anaerobic methane oxidation coupled to sulfate reduction: role of elemental sulfur as intermediate

The process dynamics of anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR), and the potential role of elemental sulfur as intermediate are presented in this paper. Thermodynamic screening and experimental evidence from the literature conclude that a prominent model to describe AOM-SR is based on the concept that anaerobic methane oxidation proceeds through the production of the intermediate elemental sulfur. Two microbial groups are involved in the process: (a) anaerobic methanotrophs (ANME-2) and (b) Desulfosarcina/Desulfococcus sulfur reducers cluster (DSS). In this work, a dynamic model was developed to explore the interactions between biotic and abiotic processes to simulate the microbial activity, the chemical composition and speciation of the liquid phase, and the gas phase composition in the reactor headspace. The model includes the microbial kinetics for the symbiotic growth of ANME-2 and DSS, mass transfer phenomena between the gas and liquid phase for methane, hydrogen sulfide, and carbon dioxide and acid-base reactions for bicarbonate, sulfide, and ammonium. A data set from batch experiments, running for 250 days in artificial seawater inoculated with sediment from Marine Lake Grevelingen (The Netherlands) was used to calibrate the model. The inherent characteristics of AOM-SR make the identification of the kinetic parameters difficult due to the high correlation between them. However, by meaningfully selecting a set of kinetic parameters, the model simulates successfully the experimental data for sulfate reduction and sulfide production. The model can be considered as the basic structure for simulating continuous flow three-phase engineered systems based on AOM-SR.

The role of humic substances in mitigating greenhouse gases emissions: Current knowledge and research gaps

Humic substances (HS) constitute a highly transformed fraction of natural organic matter (NOM) with a heterogeneous structure, which is rich in electron-transferring functional moieties. Because of this feature, HS display a versatile reactivity with a diversity of environmentally relevant organic and inorganic compounds either by abiotic or microbial processes. Consequently, extensive research has been conducted related to the potential of HS to drive relevant processes in bio-engineered systems, as well as in the biogeochemical cycling of key elements in natural environments. Nevertheless, the increase in the number of reports examining the relationship between HS and the microorganisms related to the production and consumption of greenhouse gases (GHG), the main drivers of global warming, has just emerged in the last years. In this paper, we discuss the importance of HS, and their analogous redox-active organic molecules (RAOM), on controlling the emission of three of the most relevant GHG due to their tight relationship with microbial activity, their abundance on the Earth's atmosphere, and their important global warming potentials: carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). The current knowledge gaps concerning the microbial component, on-site occurrence, and environmental constraints affecting these HS-mediated processes are provided. Furthermore, strategies involving the metabolic traits that GHG-consuming/HS-reducing and -oxidizing microbes display for the development of environmental engineered processes are also discussed.