Methanogenesis pathways of methanogens and their responses to substrates and temperature in sediments from the South Yellow Sea

Advancing anaerobic microbial studies with in situ Raman spectroscopy: Methanogenic archaea as a model

Methanogenic archaea play a critical role in methane (CH4) production and the global carbon cycle, yet accurately monitoring their gas metabolism under anaerobic conditions remains a technical challenge. In this study, we developed a Raman spectroscopy-based gas quantification model, achieving high-precision monitoring of CO2-N2-CH4 ternary gas mixtures over a temperature range of 12-52 °C. The model exhibited strong linear correlations between the Raman peak area ratios and gas molar ratios, which were further validated against gas chromatography, revealing no significant differences (p > 0.05). This confirms the reliability and accuracy of the approach.. Building upon this model, we conducted real-time monitoring of the gas metabolism of methylotrophic methanogenic archaea under anaerobic conditions. The results demonstrated that methanol concentration significantly influenced the gas production kinetics. At a methanol concentration of 10 μL/mL, the highest CH4 yield (59.97 %) was achieved, along with stable metabolic activity. In contrast, higher concentrations caused substrate saturation effects, leading to decreased metabolic efficiency. Furthermore, by integrating Raman spectroscopy with high-precision pressure monitoring, this study successfully achieved real-time molar quantification of CH4 and CO2 during methanogen cultivation. This approach provided detailed insights into gas production dynamics and substrate utilization patterns. Compared to traditional methods, this non-destructive, real-time monitoring platform offers a novel tool for anaerobic metabolism research and lays a solid foundation for applications in biogas optimization, industrial fermentation, and renewable energy development.

Structure and metabolic function of spatiotemporal pit mud microbiome

BACKGROUND

Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

RESULTS

Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

CONCLUSION

Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.

Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation

Biomethanation is a crucial process occurring in natural and engineered systems which can reduce carbon dioxide to methane impacting the global carbon cycle. However, little is known about the effect of on-and-off gaseous provision and micronutrients on bioconversion. Here, anaerobic microbiomes underwent intermittent feeding with incremental starvations and selective metal supplementation to assess the impact of hydrogen and carbon dioxide availability on microbial physiology. Resilience was tested under differential cultivations in basal medium supplemented with either nickel or cobalt. Nickel-augmented cultures exhibited faster recovery upon starvation, suggesting a beneficial effect. Dominant Methanothermobacter thermautotrophicus demonstrated robust growth, genetic stability and transcriptional downregulation when starved. Conversely, bacteria were plastic and prone to genetic fluctuations, accumulating mutations on genes encoding for ABC-transporters and C-metabolism enzymes. This study pioneers cellular resilience and response to micronutrient supplementation in anaerobic carbon dioxide-fixating microbiomes, offering valuable insights into microbial activity recovery after carbon and electron donor deprivation.

Methane emission fluxes and associated microbial community characteristics in a temperate seagrass meadow

Seagrass meadows are acknowledged as blue carbon ecosystems, yet they are also ideal habitats for methane (CH4) release, offsetting their ability to mitigate climate change. The global CH4 fluxes in seagrass meadows remain highly uncertain due to regional and species biases, and the microbial mechanisms driving methane release are poorly understood. Here, we investigated CH4 air-sea fluxes, sediment CH4 emission potential and microbes involved in CH4 release using geochemical techniques combined with qPCR and Illumina sequencing in a temperate Zostera japonica and Zostera marina mixed meadow. The CH4 air-sea fluxes fluctuated from -0.42 to 11.42 μmol·m-2·d-1, showing a strong seasonal variation. CH4 emission potential was significantly higher in seagrass vegetated sediments (10.34 ± 2.72 nmol·g-1·d-1) than in the adjacent bare sediments (1.55 ± 1.15 nmol·g-1·d-1), primarily attributed to variations in sediment organic matter content. Diverse methanogens occurred in the seagrass meadow, with Methanolobus dominating in seagrass sediments, while Methanococcoides, Methanosarcina, and Methanoculleus being prevalent in bare sediments. Meanwhile, a variety of methylotrophic groups were detected, including aerobic Gammaproteobacteria, anaerobic Desulfobacterota and Methylomirabilota, as well as archaea Candidatus Methanoperedens. The co-occurrence of these functional groups implied the presence of complex CH4 production and oxidation pathways, which regulated the CH4 budget in the seagrass ecosystems. Taken together, our findings enhance the comprehension of the methane emission process and driving mechanism in seagrass ecosystems.

Diversity and Distribution of Methane Functional Microorganisms in Sedimentary Columns of Hongfeng Reservoir in Different Seasons

Freshwater ecosystem is a significant natural source of CH4 emission in the atmosphere. To fully understand the dynamics of methane emissions in reservoirs, it is essential to grasp the temporal and vertical distribution patterns, as well as the factors that influence the methanogenic bacterial communities within the sediments. This study investigates the methane dynamics, carbon isotope fractionation (δ13CH4), and abundance of functional microorganisms along the geochemical gradient in the in situ sedimentary column of Hongfeng Reservoir (China). Notably, the methane concentration in sediment in summer ranged in 15.39-127.22 µmol/L, which is twice as high as wintertime concentrations in the surface layer near the sediment-water interface (0-10 cm depth). Illumina sequencing of the sediments identified 11 genera affiliated with methanogenic archaea, with dominant genus Methanosaeta reaching a relative abundance of 34.95% in summer. The total carbon (TOC) content in sedimentary columns in different seasons is positively correlated with Methanosarcina (P < 0.05). In addition, seasonal discrepancies are observed in the sediment profiles for total nitrogen (TN), sulfate (SO42-), and ferrous iron (Fe2+) concentrations. The concentration of total nitrogen (TN) is higher in summer than in winter. In summer, sulfate accumulates in the middle layer of the sedimentary column, while in winter, the maximum concentration of sulfate in the surface layer reaches 0.65 mmol/L. These geochemical gradients drive the biological transformation of nitrogen, sulfur, and iron, may also be linked to the consumption of methane. Thus, it is established that the temporal and spatial dynamics of methanogenic communities in sediments significantly influence the fluctuations in methane release fluxes within reservoirs, highlighting the necessity to account for seasonal biological variations when assessing greenhouse gas emissions from reservoirs.

Methanogens dominate methanotrophs and act as a methane source in aquaculture pond sediments

Aquaculture pond sediments act as hotspots for methane (CH4) emissions; however, knowledge gaps on the regulation of microorganisms hinder our further understanding of methane dynamics in aquaculture pond sediment. Using field sampling and molecular analysis, we examined CH4 fluxes, the methanogenic community composition, and their interaction with methanotrophs to comprehensively understand the methane cycling in sediments of aquaculture ponds in northern China. Compared with a fishing pond without feed inputs, the abundances of methanogens mcrA and methanotrophs pmoA genes increased significantly in aquaculture ponds sediments. The dominant methanogens were Methanothrix, Methanoregula, and Methanolinea, and the α-diversity indices of methanogens demonstrated higher levels in 0-5 cm surface sediment. The methanotrophs were dominated by Methylocystis, Methylocaldum, and Methylobacter, and the α-diversity indices of methanotrophs showed no significant difference. The total organic carbon (TOC) contents and oxidation reduction potential (ORP) were the key factors driving methanogenic and methanotrophic communities on methane cycle in aquaculture sediment. The inter-domain ecological network (IDEN) analysis revealed that total number of network nodes, links, connectances, and links per species in the aquaculture sediments presented relatively higher levels, whereas the IDEN modules were fewer. The methanogens dominated in the networks and the interaction of methanogens and methanotrophs was more competitive and complex in aquaculture sediments. These findings highlight the marked methane production in aquaculture sediment, primarily due to the abundance, diversity, and competitive advantage of methanogens over methanotrophic communities.

Biohythane production via anaerobic digestion process: fundamentals, scale-up challenges, and techno-economic and environmental aspects

Biohythane, a balanced mixture comprising bioH2 (biohydrogen) and bioCH4 (biomethane) produced through anaerobic digestion, is gaining recognition as a promising energy source for the future. This article provides a comprehensive overview of biohythane production, covering production mechanisms, microbial diversity, and process parameters. It also explores different feedstock options, bioreactor designs, and scalability challenges, along with techno-economic and environmental assessments. Additionally, the article discusses the integration of biohythane into waste management systems and examines future prospects for enhancing production efficiency and applicability. This review serves as a valuable resource for researchers, engineers, and policymakers interested in advancing biohythane production as a sustainable and renewable energy solution.

Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production

Coastal seas contribute the majority of human methylmercury (MeHg) exposure via marine fisheries. The terrestrial area surrounding the Bohai Sea and Yellow Sea (BS and YS) is one of the mercury (Hg) emission "hot spots" in the world, resulting in high concentrations of Hg in BS and YS seawater in comparison to other marine systems. However, comparable or even lower Hg levels were detected in seafood from the BS and YS than other coastal regions around the word, suggesting a low system bioaccumulation of Hg. Reasoning a low system efficiency of MeHg production (represented by MeHg/THg (total Hg) in seawater) may be present in these two systems, seven cruises were conducted in the BS and YS to test this hypothesis. MeHg/THg ratios in BS and YS seawater were found to be lower than that in most coastal systems, indicating that the system efficiency of MeHg production is relatively lower in the BS and YS. The low system efficiency of MeHg production reduces the risk of Hg in the BS and YS with high Hg discharge intensity. By measuring in situ production and degradation of MeHg using double stable isotope addition method, and MeHg discharge flux from various sources and its exchange at various interfaces, the budgets of MeHg in the BS and YS were estimated. The results indicate that in situ methylation and demethylation are the major source and sink of MeHg in the BS and YS. By comparing the potential controlling processes and environmental parameters for MeHg/THg in the BS and YS with the other coastal seas, estuaries and bays, lower transport efficiency of inorganic Hg from water column to the sediment, slower methylation of Hg, and rapid demethylation of MeHg were identified to be major reasons for the low system efficiency of MeHg production in the BS and YS. This study highlights the necessity of monitoring the system efficiency of MeHg production, associated processes, and controlling parameters to evaluate the efficiency of reducing Hg emissions in China as well as the other countries.

Stochastic processes drive the diversity and composition of methanogenic community in a natural mangrove ecosystem

Methanogens are considered to be crucial components of mangrove ecosystems with ecological significance. However, understanding the assembly processes of methanogenic communities in mangrove ecosystems is relatively insufficient. In the current study, a natural mangrove in a protection zone was employed to investigate the diversity and assembly processes of methanogenic community by using amplicon high-throughput sequencing, a null model as well as a neutral community model. The results showed that methanogenic community in mangrove sediments were highly diverse, with the predominance of methylotrophic Methanolobus, and hydrogenotrophic Methanogenium, Methanospirillum. The diversity, composition, and gene abundance varied obviously across the mangrove sampling sites, whereas the measured environmental variables exhibited a negligible effect. Null model showed that the values of beta nearest-taxon index were mostly between -2 and 2, indicating that stochastic processes contributed more than deterministic processes driving the methanogenic community assembly in mangrove sediments. Neutral community model revealed a high estimated migration rate of methanogenic community, further substantiating the significance of stochastic processes. Among the keystone species identified in network analysis, methanogens affiliated to hydrogenotrophic Methanospirillum may have a crucial role in maintaining the structure and function of methanogenic community. Notably, these keystone species were almost unaffected by measured environmental factors, indicating that the methanogenic community in mangrove sediments is more likely to be affected by stochastic processes. This study deepens the understanding of the diversity and assembly of methanogenic community in mangrove sediments, and provides clues to maintain mangrove ecosystem functioning.

Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau

Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH4-oxidizing bacteria (MOB) and CH4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH4 fluxes in grazed and nongrazed plots were -34.10 and -22.82 μg‧m-2‧h-1, respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (-0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH4 sink. However, GE reduces the CH4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.

Untapped talents: insight into the ecological significance of methanotrophs and its prospects

The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.

Variable promotion of algae and macrophyte organic matter on methanogenesis in anaerobic lake sediment

Shallow lakes are an important natural source of atmospheric methane (CH4), and the input of autochthonous organic matter (OM) into their sediments encourages methanogenesis. Although algal- and macrophytic-originated OM in these lakes are expected to have different impacts on methanogenesis and methanogenic archaeal communities in lake sediments owing to their various properties, their specific influence and role in sediment remain unclear. In this study, a 148-day incubation was carried out by adding algal- and macrophytic-OM to the sediments of shallow eutrophic Lake Chaohu and Lake Taihu in China. CH4 was periodically monitored, while the methanogens were examined via qPCR and high-throughput sequencing at the end of incubation. Algal-OM stimulated CH4 production more than macrophytic-OM in both sediments, with the rates initially increasing and then decreasing before reaching a relative constant. Macrophytic-OM promoted CH4 production to a comparable extent in both lakes, while algal-OM promoted greater CH4 in Lake Chaohu than in Lake Taihu. However, algal-OM did not significantly increase mcrA gene copies, while macrophytic-OM did by 17.0-20.1-fold. Algal-OM potentially promoted the methylotrophic pathway in Lake Taihu but did not change the methanogenic structure in Lake Chaohu. Comparatively, macrophytic-OM promoted CH4 production mainly by acetoclastic methanogen proliferation in both lakes. More CH4 release with algal-OM compared to macrophytic-OM deserves further attention owing to the prevailing increasing algal blooms and the declining macrophyte population in lakes.

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

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

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

Deeper insight into the effect of salinity on the relationship of enzymatic activity, microbial community and key metabolic pathway during the anaerobic digestion of high strength organic wastewater

The threshold salt concentration to inhibit the anaerobic digestion (AD) has been intensively investigated, but its insight mechanism is not fully revealed. Therefore, this study systematically investigated the effect of salinity on acidogenesis and methanogenesis and its mechanism. Results showed that low salinity level (i.e. 0.6%) had stimulatory effect on volatile fatty acids (VFA) and methane production, while significant inhibition was observed with further increased salinity. Moreover, high salinity limited the butyric acid degradation at acidogenesis process. The decreases of enzymes (AK and PTA) activity and functional genes (ackA, pta and ACOX) expression that related to β-oxidation explained the butyric acid accumulation at high salinity levels. Microbial community analysis revealed high salinity levels significantly inhibited the proliferation of Syntrophomonas sp., which are known to be associated with butyric acid degradation. Similarly, the relative abundance of acetoclastic methanogen (Methanothrix sp.) and methylotrophic methanogen (Methanolinea sp.) significantly decreased at salinity condition.