Methanogenesis

Keystone taxa drive the synchronous production of methane and refractory dissolved organic matter in inland waters

The production of both methane (CH4) and refractory dissolved organic matter (RDOM) depends on microbial consortia in inland waters, and it is unclear yet the link of these two processes and the underlying microbial regulation mechanisms. Therefore, a large-scale survey was conducted in China's inland waters, with the measurement of CH4 concentrations, DOM chemical composition, microbial community composition, and relative environmental parameters mainly by chromatographic, optical, mass spectrometric, and high-throughput sequencing analyses, to clarify the abovementioned questions. Here, we found a synchronous production of CH4 and RDOM linked by microbial consortia in inland waters. The increasing microbial cooperation driven by the keystone taxa (mainly Fluviicola and Polynucleobacter) could promote the transformation of labile DOM into RDOM and meanwhile benefit methanogenic microbial communities to produce CH4. As such, CH4 and RDOM showed consistent spatial differences, which were mainly influenced by total nitrogen and dissolved oxygen concentrations. This finding deepened the understanding of microbial-driven carbon transformation and will help to more accurately evaluate the carbon source-sink relationship in inland waters.

Methane cycle in subsurface environment: A review of microbial processes

Methane is a pivotal component of the global carbon cycle. It acts both as a potent greenhouse gas and a vital energy source. While the microbial cycling of methane in subsurface environments is crucial, its impact on geological settings and related engineering projects is often underestimated. This review uniquely integrates the latest findings on methane production, oxidation, and migration processes in strata, revealing novel microbial mechanisms and their implications for environmental sustainability. We address critical issues of methane leakage and engineering safety during resource extraction, underscoring the urgent need for effective methane management strategies. This work clarifies geological factors affecting methane budgets and emissions, deepening our understanding of methane dynamics. It offers practical insights for geological engineering and sustainable natural gas hydrate exploration, paving the way for future research and applications.

Insights into the catalytic mechanism of archaeal peptidoglycan endoisopeptidases from methanogenic phages

Archaeal peptidoglycan, a crucial component of the cell walls of Methanobacteria and Methanopyri, enhances the tightness of methanogenic cells and their resistance to known lytic enzymes and antibiotics. Although archaeal peptidoglycan endoisopeptidases (Pei) can reportedly degrade archaeal peptidoglycan, their biochemistry is still largely unknown. In this study, we investigated the activity and catalytic properties of the endoisopeptidases PeiW and PeiP using synthesized isopeptides identical to natural substrates. Enzymatic assays demonstrated their distinct substrate specificity and cleavage efficiency. The crystal structure of Pei revealed a catalytic mechanism resembling that of cysteine peptidases that use the 'CHD' triad to cleave isopeptide bonds. We also identified several key residues in the substrate binding site that confer recognition specificity, including Y174, V252 and C265. Based on the residues present in the active site and their influence on activity, we propose a classification of the archaeal peptidoglycan endoisopeptide family into four categories to facilitate the identification of new archaeal peptidases in the future. These insights into the structure and function of Pei suggest new strategies for use in methanogen biotechnology.

Using amino acid waste liquid as functional supplement to change microbial community in up-flow anaerobic sludge blanket treatment of methanolic wastewater

In this study, amino acid waste liquid was employed as a functional supplement (designated as amino acid-rich FS) in the up-flow anaerobic sludge blanket (UASB) treatment of methanolic wastewater. The effect of amino acid-rich FS was evaluated through repeated batch tests, showing that a 0.5% and 1% dosage increased the maximum methane production rate by 93.60% and 123.04%, respectively, by promoting faster methanol degradation. Additionally, long-term operation of the UASB reactor was conducted with increased dosages of amino acid-rich FS, resulting in improved performance. Microbial community analysis demonstrated that the addition of amino acid-rich FS enhanced microbial diversity, with the abundance of Sporomusa increasing by 47.5 times. Beyond the original cooperative relationships, an additional synergy between Sporomusa and Methanosarcina was observed. These findings could address the key challenge of limited microbial diversity in the anaerobic treatment of methanolic wastewater.

Feed additives for methane mitigation: Recommendations for identification and selection of bioactive compounds to develop antimethanogenic feed additives

Despite the increasing interest in developing antimethanogenic additives to reduce enteric methane (CH4) emissions and the extensive research conducted over the last decades, the global livestock industry has a very limited number of antimethanogenic feed additives (AMFA) available that can deliver substantial reduction, and they have generally not reached the market yet. This work provides technical recommendations and guidelines for conducting tests intended to screen the potential to reduce, directly or indirectly, enteric CH4 of compounds before they can be further assessed in in vivo conditions. The steps involved in this work cover the discovery, isolation, and identification of compounds capable of affecting CH4 production by rumen microbes, followed by in vitro laboratory testing of potential candidates. The finding of new bioactive compounds as AMFA can be based on 2 approaches: empirical and mechanistic. The empirical approach involves obtaining and screening compounds present in databases and repositories that potentially possess the desired effect but have not yet been tested, screening natural sources of secondary compounds such as plants, fungi, and algae for their antimethanogenic effects, or examining compounds with antimethanogenic effect on microbes in other research domains outside the rumen. In contrast, the mechanistic approach is the theoretical process of discovery new bioactive compounds based on existing knowledge of a biological target or process. The in vitro methodologies reviewed include examining effects at the subcellular level, in single pure cultures of methanogens and examining in more complex mixed rumen microbial populations. Simple in vitro methodologies (subcellular assessments and batch culture) allow testing a large number of compounds, whereas more complex systems simulating the rumen microbial ecosystem can test a limited number of candidates but provide better insight about the antimethanogenic efficacy. This work collated the main advantages, limitations, and technical recommendations associated with each step and methodology use during the identification and screening of AMFA candidates.

Microbial diversity and biogeochemical interactions in the seismically active and CO2- rich Eger Rift ecosystem

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2 concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2 during earthquakes may provide substrates for methanogenic and chemolithoautotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 238 m deep drill core, running across six lithostratigraphic zones. We evaluated the diversity and distribution of bacterial and archaeal communities. Our investigation revealed a distinct low-biomass community, with a surprisingly diverse archaeal population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis demonstrated that ion concentrations (mostly sodium and sulfate) were highest in sediments from 50 to 100 m depth and in weathered rock below 200 m, indicating an elevated potential for ion solution in these areas. Microbial communities were dominated by common soil and water bacteria. Together with the occurrence of freshwater cyanobacteria at specific depths, these observations emphasize the heterogenous character of the sediments and are indicators for vertical groundwater movement across the Eger Rift subsurface. Our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur-cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia-oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2 and, when available, H2, as a primary energy source.

Detecting and sourcing GHGs and atmospheric trace gases in a municipal waste treatment plant using coupled chemistry and isotope compositions

Landfill operations and waste processing facilities are important and highly heterogeneous sources of both greenhouse gases (GHGs) and non-GHG air pollutants in the atmosphere. This arises the need for detailed apportionment of waste sources in order to locate and subsequently reduce emissions from landfills. Here, a time series of in situ measurements of atmospheric trace gases and spatial allocation of specific emission source types under different processing phases and environmental conditions were conducted in and in the surroundings of a Municipal Solid Waste Treatment Plant (MSWTP) in south-western Poland. Results revealed that several individual GHG sources dominated across the waste processing facility and that GHGs concentrations displayed spatial seasonality. An increase in the ground-level CH4 concentrations, from ∼ 30.3 to 56.3 ppmv, was observed close (∼5 - 10 m) to the major emission sources within the MSWTP. While hotspot areas generally yielded elevated CH4 concentrations near the soil surface, these were relatively low (2.4 to 8.9 ppmv) along the facility's fence line. The study of the corresponding δ13C delineated the extent of dispersion plumes downwind emission hotspots, characterized by a 13C depletion (around 4.0 ‰) in the atmospheric CH4 and CO2. For CH4, emissions were isotopically discriminated between the extraction wells at active quarters/cells (δ13C = -58.3 ± 1.1 ‰) and biogas produced in the biological waste treatment installation (δ13C = -62.7 ± 0.7 ‰). Most of the trace compounds (non-methane hydrocarbons, halocarbons, oxygen-bearing organic gases, ketones, nitrogenous and sulphurous gases, and other admixture compounds) detected at the ground surface were linked to the CH4- and CO2-rich spots. Despite the relatively high variability in the concentrations of organic and inorganic compounds observed at the MSWTP active zones, our results suggest that they do not have a meaningful impact on the surrounding air quality.

Tidal control on aerobic methane oxidation and mitigation of methane emissions from coastal mangrove sediments

Mangrove forests represent important sources of methane, partly thwarting their ecosystem function as an efficient atmospheric carbon dioxide sink. Many studies have focused on the spatial and temporal variability of methane emissions from mangrove ecosystems, yet little is known about the microbial and physical controls on the release of biogenic methane from tidally influenced mangrove sediments. Here, we show that aerobic methane oxidation is a key microbial process that effectively reduces methane emissions from mangrove sediments. We further demonstrate clear links between the tidal cycle and fluctuations in methane fluxes, with contrasting methane emission rates under different tidal amplitudes. Our data suggest that both the microbial methane oxidation activity and pressure-induced advective transport modulated methane fluxes in the mangrove sediments. Methane oxidation activity is limited by the availability of oxygen in the surface sediments, which in turn is controlled by tidal dynamics, further highlighting the interactive physico-biogeochemical controls on biological methane fluxes. Although we found some molecular evidence for anaerobic methanotrophs in the deeper sediments, anaerobic methane oxidation seems to play only a minor role in the mangrove sediments, with potential rates being two orders of magnitude lower than those of aerobic methane oxidation. Our findings confirmed the importance of surface sediments as biological barrier for methane. Specifically, when sediments were exposed to the air, methane consumption increased by ∼227%, and the methane flux was reduced by ∼62%, compared to inundated conditions. Our data demonstrate how tides can orchestrate the daily rhythm of methane consumption and production within mangrove sediments, thus explaining the temporal variability of methane emissions in the tidally influenced coastal mangrove systems.

Reactivation and long-term stabilization of the [NiFe] Hox hydrogenase of Synechocystis sp. PCC6803 by glutathione after oxygen exposure

Hydrogenases are key enzymes forming or consuming hydrogen. The inactivation of these transition metal biocatalysts with oxygen limits their biotechnological applications. Oxygen-sensitive hydrogenases are distinguished from oxygen-insensitive (tolerant) ones by their initial hydrogen turnover rates influenced by oxygen. Several hydrogenases, such as the oxygen-sensitive bidirectional [NiFe] Hox hydrogenase (Hox) of the unicellular cyanobacterium Synechocystis sp. PCC6803, are reactivated after oxygen-induced deactivation by redox mechanisms. In cyanobacteria, the glutathione (GSH) redox buffer majorly controls intracellular redox potentials. The relationship between Hox turnover rates and the redox potential in its natural reaction environment is not fully understood. We thus determined hydrogen oxidation rates as activities of Hox in cell-free extracts of Synechocystis using benzyl viologen as artificial electron acceptor. We found that GSH modulates Hox hydrogen oxidation rates under oxygen-free conditions. After oxygen exposure, it influences the maximal turnover rate and aids in the reactivation of Hox. Moreover, GSH stabilizes the long-term Hox activity under anoxic conditions and attenuates oxygen-induced deactivation of Hox in a concentration dependent manner, probably by fostering reactivation. Conversely, oxidized GSH (GSSG) negatively affects Hox activity and oxygen insensitivity. Using Blue Native PAGE followed by mass spectrometry, we showed that oxygen affects Hox complex integrity. The in-silico predicted structure of the Hox complex and complexome analyses reveal the formation of various Hox subcomplexes under different conditions. Our findings refine our current classification of oxygen-hydrogenase interactions beyond sensitive and insensitive, which is particularly important for understanding hydrogenase function under physiological conditions in future.

What causes the urban river to look darker? An underestimated source of sulfide production in methanogenic metabolism

The blackening and increased smelling of waterbodies steadily affect urban aquatic ecology. Sulfide is recognized as the key substance responsible for the darkening of urban rivers. However, the pathway of sulfide production and the underling microbial mechanisms in urban rivers are not fully understood. This study executes a comprehensive approach to investigate mechanism of sulfide production within urban river sediments, integrating field survey, laboratory incubations, and metagenomic sequencing. The results reveal that both sulfide concentrations and sulfidogenic activities in darker river sediments are significantly higher than in lighter rivers. Both the sulfate-reducing bacteria (SRB) and methanogenic communities are closely related to the sulfide content in the sediments. The finding that inhibiting SRB enhanced the potential sulfide production rate suggests the importance of methanogen-derived processes as a sulfide source in sediments. Notably, the abundance of methylated thiol coenzyme M methyltransferase genes increased 53-fold upon after the continuous methionine amendment, confirming that methanogen-derived processes, rather than SRB-derived ones, dominated sulfide production when methylated sulfur compounds are abundant. Overall, this study highlights the potential significance of methanogenesis as a hitherto underestimated sulfide source in urban river sediments, providing valuable insights for optimizing strategies to prevent and mitigate the deterioration of urban aquatic ecosystems.

Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses

Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.

Microbes drive more carbon dioxide and nitrous oxide emissions from wetland under long-term nitrogen enrichment

Wetlands are frequently regarded as weak carbon dioxide (CO2) sinks, the largest natural sources of methane (CH4), and weak sources of nitrous oxide (N2O). Anthropogenic activities and climate change-induced nitrogen (N) enrichment may affect wetland carbon (C) and N cycling via soil microbes, consequently modifying the original greenhouse gas (GHG) emissions. However, the effects and mechanisms of the duration and rate of N inputs on wetland GHG emissions remain uncertain and controversial. Therefore, this study conducted an in situ field experiment to investigate the effects and driving mechanisms of long-term N enrichment on wetland GHG emissions throughout the 2023 growing season by using the static opaque chambers method. Soil microbial composition and function were also analyzed through metagenomic sequencing. The results showed that N enrichment significantly increased wetland CO2 emissions, which were associated with the abundance of microbial C-fixing functional genes and the soil C content. Although nitrogen enrichment tended to suppress CH4 emissions, the effect was not significant. High N enrichment created a powerful wetland N2O source driven by the abundance of microbial nitrification function genes and microbial species. Vegetation influenced wetland GHG emissions by altering soil carbon content. This study elucidates the response mechanism of wetland GHG emissions to long-term nitrogen enrichment, thereby furnishing a theoretical basis for wetland conservation and nitrogen management.

Rice rhizobiome engineering for climate change mitigation

The year 2023 was the warmest year since 1850. Greenhouse gases, including CO2 and methane, played a significant role in increasing global warming. Among these gases, methane has a 25-fold greater impact on global warming than CO2. Methane is emitted during rice cultivation by a group of rice rhizosphere microbes, termed methanogens, in low oxygen (hypoxic) conditions. To reduce methane emissions, it is crucial to decrease the methane production capacity of methanogens through water and fertilizer management, breeding of new rice cultivars, regulating root exudation, and manipulating rhizosphere microbiota. In this opinion article we review the recent developments in hypoxia ecology and methane emission mitigation and propose potential solutions based on the manipulation of microbiota and methanogens for the mitigation of methane emissions.

Non-thermal atmospheric pressure plasma-irradiated cysteine protects cardiac ischemia/reperfusion injury by preserving supersulfides

Ischemic heart disease is the main global cause of death in the world. Abnormal sulfide catabolism, especially hydrogen sulfide accumulation, impedes mitochondrial respiration and worsens the prognosis after ischemic insults, but the substantial therapeutic strategy has not been established. Non-thermal atmospheric pressure plasma irradiation therapy is attracted attention as it exerts beneficial effects by producing various reactive molecular species. Growing evidence has suggested that supersulfides, formed by catenation of sulfur atoms, contribute to various biological processes involving electron transfer in cells. Here, we report that non-thermal plasma-irradiated cysteine (Cys∗) protects mouse hearts against ischemia/reperfusion (I/R) injury by preventing supersulfide catabolism. Cys∗ has a weak but long-lasting supersulfide activity, and the treatment of rat cardiomyocytes with Cys∗ prevents mitochondrial dysfunction after hypoxic stress. Cys∗ increases sulfide-quinone oxidoreductase (SQOR), and silencing SQOR abolishes Cys∗-induced supersulfide formation and cytoprotection. Local administration of mouse hearts with Cys∗ significantly reduces infarct size with preserving supersulfide levels after I/R. These results suggest that maintaining supersulfide formation through SQOR underlies cardioprotection by Cys∗ against I/R injury.

Seasonal Dynamics of Methane Fluxes from Groundwater to Lakes:Hydrological and Biogeochemical Controls

Methane (CH4) inputs to lakes through lacustrine groundwater discharge (LGD-derived CH4) represent a potentially important but often overlooked source of lake methane emissions. Although great efforts have been made to quantify LGD-derived CH4 fluxes and their spatial variablity, the underlying mechanisms controlling seasonal LGD-derived CH4 fluxes and their influence on lake CH4 emissions remain poorly understood, particularly in humid inland areas. To address this gap, we applied the 222Rn mass balance model, as well as hydrological, isotopic and microbial methods to assess seasonal LGD-derived CH4 fluxes and their influence on the seasonal variability of lake methane emissions in a typical oxbow lake, central Yangtze River. The results revealed wide seasonal differences in LGD-derived CH4 fluxes, which were controlled by hydrological and biogeochemical processes. During the dry season, although more intense methane oxidation and weaker methanogenesis occurred in groundwater, the much higher LGD rate (51.71 mm/d) produced a higher LGD-derived CH4 flux (16.41 mmol/m2/d). During the wet season, methanogenesis was more active and methane oxidation was weaker, but a lower LGD rate (12.16 mm/d) led to a lower LGD-derived CH4 flux (5.33 mmol/m2/d). Furthermore, higher LGD-derived CH4 flux in the dry season resulted in higher CH4 emissions from the lake and diminished the extent of methane oxidation in the lake. In comparison to other regions, the differences in LGD-derived CH4 fluxes and their seasonal variations were found to be controlled by climatic conditions and lake types in different global regions. Higher LGD-derived CH4 fluxes and more pronounced seasonal variations could be associated with higher temperature, larger water depth and more intense water level fluctuations. This study provides a novel perspective and broader implications for the comprehension and evaluation of seasonal methane emissions and understanding the carbon cycle in global lake ecosystems in humid areas with intense water level fluctuations.

Methanothermobacter thermautotrophicus and Alternative Methanogens: Archaea-Based Production

Methanogenic archaea convert bacterial fermentation intermediates from the decomposition of organic material into methane. This process has relevance in the global carbon cycle and finds application in anthropogenic processes, such as wastewater treatment and anaerobic digestion. Furthermore, methanogenic archaea that utilize hydrogen and carbon dioxide as substrates are being employed as biocatalysts for the biomethanation step of power-to-gas technology. This technology converts hydrogen from water electrolysis and carbon dioxide into renewable natural gas (i.e., methane). The application of methanogenic archaea in bioproduction beyond methane has been demonstrated in only a few instances and is limited to mesophilic species for which genetic engineering tools are available. In this chapter, we discuss recent developments for those existing genetically tractable systems and the inclusion of novel genetic tools for thermophilic methanogenic species. We then give an overview of recombinant bioproduction with mesophilic methanogenic archaea and thermophilic non-methanogenic microbes. This is the basis for discussing putative products with thermophilic methanogenic archaea, specifically the species Methanothermobacter thermautotrophicus. We give estimates of potential conversion efficiencies for those putative products based on a genome-scale metabolic model for M. thermautotrophicus.

Highly diverse-Low abundance methanogenic communities in hypersaline microbial mats of Guerrero Negro B.C.S., assessed through microcosm experiments

Methanogenic communities of hypersaline microbial mats of Guerrero Negro, Baja California Sur, Mexico, have been recognized to be dominated by methylotrophic methanogens. However, recent studies of environmental samples have evidenced the presence of hydrogenotrophic and methyl-reducing methanogenic members, although at low relative abundances. Physical and geochemical conditions that stimulate the development of these groups in hypersaline environments, remains elusive. Thus, in this study the taxonomic diversity of methanogenic archaea of two sites of Exportadora de Sal S.A was assessed by mcrA gene high throughput sequencing from microcosm experiments with different substrates (both competitive and non-competitive). Results confirmed the dominance of the order Methanosarcinales in all treatments, but an increase in the abundance of Methanomassiliiccocales was also observed, mainly in the treatment without substrate addition. Moreover, incubations supplemented with hydrogen and carbon dioxide, as well as the mixture of hydrogen, carbon dioxide and trimethylamine, managed to stimulate the richness and abundance of other than Methanosarcinales methanogenic archaea. Several OTUs that were not assigned to known methanogens resulted phylogenetically distributed into at least nine orders. Environmental samples revealed a wide diversity of methanogenic archaea of low relative abundance that had not been previously reported for this environment, suggesting that the importance and diversity of methanogens in hypersaline ecosystems may have been overlooked. This work also provided insights into how different taxonomic groups responded to the evaluated incubation conditions.

Comparative study on the effects of anionic, cationic, and nonionic polyacrylamide surface modified magnetic micro-particles (MMP) for anaerobic digestion treatment of vegetable waste water (VWW)

Anaerobic digestion provides a solution for the treatment of vegetable waste water (VWW), but there are currently limited targeted treatment methods available. Building upon previous studies, this research investigated the effects of polyacrylamide-modified magnetic micro-particles (MMP) on anaerobic digestion (AD) of VWW. Three variations of these particles were created by grafting anionic, cationic, and non-ionic polyacrylamide (PAM) onto the MMPs' surfaces, resulting in aPAM-MMP, cPAM-MMP, and nPAM-MMP, respectively. In AD experiments, the addition of aPAM-MMP notably enhanced the degradation of chemical oxygen demand (COD) in VWW. COD decreased to 1290 mg/L in the reactor with aPAM-MMP by day 12 and remained low, while the other reactors had COD concentrations of 4137.5, 5510, and 3010 mg/L on the same day, decreasing thereafter. This modification also improved the production and utilization of hydrogen gas and volatile fatty acids (VFAs), along with the conversion of methane. When tested for bioaffinity using fluorescent GFP-E.coli bacteria, the aPAM-MMP, cPAM-MMP, and nPAM-MMP demonstrated increases in fluorescence intensity by 51.66%, 36.13%, and 37.02%, respectively, compared to unmodified MMP when attached with GFP-E.coli. Further analyses of microbial community revealed that the reactor with aPAM-MMP had the highest microbial richness and enriched bacteria capable of organic matter degradation, such as Bacteroidota, Synergistota, Chloroflexi, Halobacterota phyla, and Parabacteroides, Muribaculaceae, and Azotobacter genera. In conclusion, our experiment verifies that APAM-MMP promotes anaerobic treatment of VWW and provides a novel reference point for enhancing VWW degradation.

Integrating genome- and transcriptome-wide association studies to uncover the host-microbiome interactions in bovine rumen methanogenesis

The ruminal microbiota generates biogenic methane in ruminants. However, the role of host genetics in modifying ruminal microbiota-mediated methane emissions remains mysterious, which has severely hindered the emission control of this notorious greenhouse gas. Here, we uncover the host genetic basis of rumen microorganisms by genome- and transcriptome-wide association studies with matched genome, rumen transcriptome, and microbiome data from a cohort of 574 Holstein cattle. Heritability estimation revealed that approximately 70% of microbial taxa had significant heritability, but only 43 genetic variants with significant association with 22 microbial taxa were identified through a genome-wide association study (GWAS). In contrast, the transcriptome-wide association study (TWAS) of rumen microbiota detected 28,260 significant gene-microbe associations, involving 210 taxa and 4652 unique genes. On average, host genetic factors explained approximately 28% of the microbial abundance variance, while rumen gene expression explained 43%. In addition, we highlighted that TWAS exhibits a strong advantage in detecting gene expression and phenotypic trait associations in direct effector organs. For methanogenic archaea, only one significant signal was detected by GWAS, whereas the TWAS obtained 1703 significant associated host genes. By combining multiple correlation analyses based on these host TWAS genes, rumen microbiota, and volatile fatty acids, we observed that substrate hydrogen metabolism is an essential factor linking host-microbe interactions in methanogenesis. Overall, these findings provide valuable guidelines for mitigating methane emissions through genetic regulation and microbial management strategies in ruminants.

Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters

The efficiency of microbial fuel cells (MFCs) in industrial wastewater treatment is profoundly influenced by the microbial community, which can be disrupted by variable industrial operations. Although microbial guilds linked to MFC performance under specific conditions have been identified, comprehensive knowledge of the convergent community structure and pathways of adaptation is lacking. Here, we developed a microbe-microbe interaction genome-scale metabolic model (mmGEM) based on metabolic cross-feeding to study the adaptation of microbial communities in MFCs treating sulfide-containing wastewater from a canned-pineapple factory. The metabolic model encompassed three major microbial guilds: sulfate-reducing bacteria (SRB), methanogens (MET), and sulfide-oxidizing bacteria (SOB). Our findings revealed a shift from an SOB-dominant to MET-dominant community as organic loading rates (OLRs) increased, along with a decline in MFC performance. The mmGEM accurately predicted microbial relative abundance at low OLRs (L-OLRs) and adaptation to high OLRs (H-OLRs). The simulations revealed constraints on SOB growth under H-OLRs due to reduced sulfate-sulfide (S) cycling and acetate cross-feeding with SRB. More cross-fed metabolites from SRB were diverted to MET, facilitating their competitive dominance. Assessing cross-feeding dynamics under varying OLRs enabled the execution of practical scenario-based simulations to explore the potential impact of elevated acidity levels on SOB growth and MFC performance. This work highlights the role of metabolic cross-feeding in shaping microbial community structure in response to high OLRs. The insights gained will inform the development of effective strategies for implementing MFC technology in real-world industrial environments.

Methanobrevibacter smithii cell variants in human physiology and pathology: A review

Methanobrevibacter smithii (M. smithii), initially isolated from human feces, has been recognised as a distinct taxon within the Archaea domain following comprehensive phenotypic, genetic, and genomic analyses confirming its uniqueness among methanogens. Its diversity, encompassing 15 genotypes, mirrors that of biotic and host-associated ecosystems in which M. smithii plays a crucial role in detoxifying hydrogen from bacterial fermentations, converting it into mechanically expelled gaseous methane. In microbiota in contact with host epithelial mucosae, M. smithii centres metabolism-driven microbial networks with Bacteroides, Prevotella, Ruminococcus, Veillonella, Enterococcus, Escherichia, Enterobacter, Klebsiella, whereas symbiotic association with the nanoarchaea Candidatus Nanopusillus phoceensis determines small and large cell variants of M. smithii. The former translocate with bacteria to induce detectable inflammatory and serological responses and are co-cultured from blood, urine, and tissular abscesses with bacteria, prototyping M. smithii as a model organism for pathogenicity by association. The sources, mechanisms and dynamics of in utero and lifespan M. smithii acquisition, its diversity, and its susceptibility to molecules of environmental, veterinary, and medical interest still have to be deeply investigated, as only four strains of M. smithii are available in microbial collections, despite the pivotal role this neglected microorganism plays in microbiota physiology and pathologies.

Toward the Use of Methyl-Coenzyme M Reductase for Methane Bioconversion Applications

ConspectusAs the main component of natural gas and renewable biogas, methane is an abundant, affordable fuel. Thus, there is interest in converting these methane reserves into liquid fuels and commodity chemicals, which would contribute toward mitigating climate change, as well as provide potentially sustainable routes to chemical production. Unfortunately, specific activation of methane for conversion into other molecules is a difficult process due to the unreactive nature of methane C-H bonds. The use of methane activating enzymes, such as methyl-coenzyme M reductase (MCR), may offer a solution. MCR catalyzes the methane-forming step of methanogenesis in methanogenic archaea (methanogens), as well as the initial methane oxidation step during the anaerobic oxidation of methane (AOM) in anaerobic methanotrophic archaea (ANME). In this Account, we highlight our contributions toward understanding MCR catalysis and structure, focusing on features that may tune the catalytic activity. Additionally, we discuss some key considerations for biomanufacturing approaches to MCR-based production of useful compounds.MCR is a complex enzyme consisting of a dimer of heterotrimers with several post-translational modifications, as well as the nickel-hydrocorphin prosthetic group, known as coenzyme F430. Since MCR is difficult to study in vitro, little information is available regarding which MCRs have ideal catalytic properties. To investigate the role of the MCR active site electronic environment in promoting methane synthesis, we performed electric field calculations based on molecular dynamics simulations with a MCR from Methanosarcina acetivorans and an ANME-1 MCR. Interestingly, the ANME-1 MCR active site better optimizes the electric field with methane formation substrates, indicating that it may have enhanced catalytic efficiency. Our lab has also worked toward understanding the structures and functions of modified F430 coenzymes, some of which we have discovered in methanogens. We found that methanogens produce modified F430s under specific growth conditions, and we hypothesize that these modifications serve to fine-tune the activity of MCR.Due to the complexity of MCR, a methanogen host is likely the best near-term option for biomanufacturing platforms using methane as a C1 feedstock. M. acetivorans has well-established genetic tools and has already been used in pilot methane oxidation studies. To make methane oxidation energetically favorable, extracellular electron acceptors are employed. This electron transfer can be facilitated by carbon-based materials. Interestingly, our analyses of AOM enrichment cultures and pure methanogen cultures revealed the biogenic production of an amorphous carbon material with similar characteristics to activated carbon, thus highlighting the potential use of such materials as conductive elements to enhance extracellular electron transfer.In summary, the possibilities for sustainable MCR-based methane conversions are exciting, but there are still some challenges to tackle toward understanding and utilizing this complex enzyme in efficient methane oxidation biomanufacturing processes. Additionally, further work is necessary to optimize bioengineered MCR-containing host organisms to produce large quantities of desired chemicals.

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

The role of monoammonium glycyrrhizinate as a methane inhibitor to limit the rumen methane emissions of Karakul sheep

Methane (CH4) from ruminant production systems produces greenhouse gases that contribute to global warming. Our goal was to determine whether monoammonium glycyrrhizinate could inhibit CH4 emissions over the long term without affecting animal performance and immune indices in Karakul sheep. This study aimed to assess the effects of medium-term (60 days) addition of monoammonium glycyrrhizinate on growth performance, apparent digestibility, CH4 emissions, methanogens, fibre-degrading bacteria and blood characteristics in Karakul sheep. Twelve male Karakul sheep (40.1 ± 3.59 kg) with fistula were randomly divided into two groups (n = 6): the Control group received a basal diet + the same volume of distilled water (30 ml) and the Treatment group received a basal diet + 8.75 g/kg monoammonium glycyrrhizinate injected via fistula. The adaptation stage was 15 days, and the measurement stage was 60 days. The sampling during the measurement stage was divided into two stages, stage I (1 ∼ 30 d) and stage II (31 ∼ 60 d). The results showed that monoammonium glycyrrhizinate significantly reduced the relative abundance of Bacteroides caccae, daily CH4 emission and protozoa population, significantly increased the relative abundance of Lachnospiraceae bacterium AD3010, Lachnospiraceae bacterium FE2018, Lachnospiraceae bacterium NK3A20, Lachnospiraceae bacterium NK4A179 and Lachnospiraceae bacterium V9D3004 in stage I (P < 0.05); significantly increased the relative abundance of Lachnospiraceae bacterium AD3010, but significantly decreased the relative abundance of Lachnospiraceae bacterium NK4A179 and Lachnospiraceae bacterium C6A11 in stage II (P < 0.05). Therefore, monoammonium glycyrrhizinate could be used as a CH4 inhibitor to limit the rumen CH4 emissions of Karakul sheep in short-term period (30 days) without affecting the growth performance, fibre digestibility and blood parameters.

Bioaugmentation by enriched hydrogenotrophic methanogens into trickle bed reactors for H2/CO2 conversion

Biomethanation represents a promising approach for biomethane production, with biofilm-based processes like trickle bed reactors (TBRs) being among the most efficient solutions. However, maintaining stable performance can be challenging, and both pure and mixed culture approaches have been applied to address this. In this study, inocula enriched with hydrogenotrophic methanogens were introduced to to TBRs as bioaugmentation strategy to assess their impacts on the process performance and microbial community dynamics. Metagenomic analysis revealed a metagenome-assembled genome belonging to the hydrogenotrophic genus Methanobacterium, which became dominant during enrichment and successfully colonized the TBR biofilm after bioaugmentation. The TBRs achieved a biogas production with > 96 % methane. The bioaugmented reactor consumed additional H2. This may be due to microbial species utilizing CO2 and H2 via various CO2 reduction pathways. Overall, implementing bioaugmentation in TBRs showed potential for establishing targeted species, although challenges remain in managing H2 consumption and optimizing microbial interactions.

Carbon dioxide capture, sequestration, and utilization models for carbon management and transformation

The elevated level of carbon dioxide in the atmosphere has become a pressing concern for environmental health due to its contribution to climate change and global warming. Simultaneously, the energy crisis is a significant issue for both developed and developing nations. In response to these challenges, carbon capture, sequestration, and utilization (CCSU) have emerged as promising solutions within the carbon-neutral bioenergy sector. Numerous technologies are available for CCSU including physical, chemical, and biological routes. The aim of this study is to explore the potential of CCSU technologies, specifically focusing on the use of microorganisms based on their well-established metabolic part. By investigating these biological pathways, we aim to develop sustainable strategies for climate management and biofuel production. One of the key novelties of this study lies in the utilization of microorganisms for CO2 fixation and conversion, offering a renewable and efficient method for addressing carbon emissions. Algae, with its high growth rate and lipid contents, exhibits CO2 fixation capabilities during photosynthesis. Similarly, methanogens have shown efficiency in converting CO2 to methane by methanogenesis, offering a viable pathway for carbon sequestration and energy production. In conclusion, our study highlights the importance of exploring biological pathways, which significantly reduce carbon emissions and move towards a more environmentally friendly future. The output of this review highlights the significant potential of CCSU models for future sustainability. Furthermore, this review has been intensified in the current agenda for reduction of CO2 at considerable extends with biofuel upgrading by the microbial-shift reaction.

Chemical and biological effects of zero-valent iron (ZVI) concentration on in-situ production of H2 from ZVI and bioconversion of CO2 into CH4 under anaerobic conditions

The conversion of carbon dioxide (CO2) to methane (CH4) is a strategy for sequestering CO2. Zero-valent iron (ZVI) has been proposed as an alternative electron donor for the CO2 reduction to CH4. In this study, the effects of ZVI concentrations on the abiotic production of H2 (without the action of microorganisms) in the first part and on the biological conversion of CO2 to CH4 using ZVI as a direct electron donor in the second part were examined. In the abiotic H2 production, the increase in the ZVI concentration from 16 to 32, 64, and 96 g/L was found to have positive effects on both the amounts of H2 generated and the rates of H2 production because the extent of ZVI oxidation positively correlates with increasing surface area. Nevertheless, the increase in ZVI concentration from 96 to 224 g/L did not benefit the H2 production because the ZVI dissolution was suppressed by the increasing aqueous pH above 10. In the bioconversion of CO2 to CH4 using ZVI as an electron donor, the main methanogenesis pathway occurred via hydrogenotrophic methanogenesis at pH 8.7-9.5 driven by the genus Methanobacterium of the class Methanobacteria. At ZVI concentrations of 64 g/L and above, the production of volatile fatty acid (VFA) became clear. Acetate was the main VFA, indicating the induction of homoacetogenesis at ZVI concentrations of 64 g/L and above. In addition, the presence of propionate as the second major VFA suggests the production of propionate from CO2 and acetate under conditions with high H2 partial pressure. The results indicated that the pathway for ZVI/CO2 conversion to CH4 was competitive between hydrogenotrophic methanogenesis and homoacetogenesis.

Effect of incubation temperature on identification of key odorants of sewage sludge using headspace GC analysis

Currently, headspace gas chromatography-mass spectrometry is a widely used method to identify the key odorants of sludge. However, the effect of incubation temperature on the generation and emission of key odorants from sludge was still uncertain. Thus, in this paper, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and headspace gas chromatography-coupled ion mobility spectrometry (HS-GC-IMS) were carried out to analyze the volatiles emitted from the sludge incubated at different temperatures (30 °C, 50 °C, 60 °C, and 80 °C). The results indicated that the total volatile concentration of the sludge increased with temperatures, which affected the identified proportion of sludge key odorants to a certain extent. Differently from the aqueous solutions, the variation of volatile emission from the sludge was inconsistent with temperature changes, suggesting a multifactorial influence of incubation temperature on the identification of sludge odorants. The microbial community structure and adenosine triphosphate (ATP) metabolic activity of the sludge samples were analyzed at the initial state, 30 °C, and 80 °C. Although no significant effect of incubation temperature on the microbial community structure of the sludge, the incubation at 80 °C led to a noticeable decrease in microbial ATP metabolic activity, accompanied by a significant change in the proportion of odor-related microorganisms with low relative abundances. Changes in the composition and activity of these communities jointly contributed to the differences in odor emission from sludge at different temperatures. In summary, the incubation temperature affects the production and emission of volatiles from sludge through physicochemical and biochemical mechanisms, by which the microbial metabolism playing a crucial role. Therefore, when analyzing the key odorants of sludge, these factors should be considered.

Intertwining of the C-N-S cycle in passive and aerated constructed wetlands

The microbial processes occurring in constructed wetlands (CWs) are difficult to understand owing to the complex interactions occurring between a variety of substrates, microorganisms, and plants under the given physicochemical conditions. This frequently leads to very large unexplained nitrogen losses in these systems. In continuation of our findings on Anammox contributions, our research on full-scale field CWs has suggested the significant involvement of the sulfur cycle in the conventional C-N cycle occurring in wetlands, which might closely explain the nitrogen losses in these systems. This paper explored the possibility of the sulfur-driven autotrophic denitrification (SDAD) pathway in different types of CWs, shallow and deep and passive and aerated systems, by analyzing the metagenomic bacterial communities present within these CWs. The results indicate a higher abundance of SDAD bacteria (Paracoccus and Arcobacter) in deep passive systems compared to shallow systems and presence of a large number of SDAD genera (Paracoccus, Thiobacillus, Beggiatoa, Sulfurimonas, Arcobacter, and Sulfuricurvum) in aerated CWs. The bacteria belonging to the functional category of dark oxidation of sulfur compounds were found to be enriched in deep and aerated CWs hinting at the possible role of the SDAD pathway in total nitrogen removal in these systems. As a case study, the percentage nitrogen removal through SDAD pathway was calculated to be 15-20% in aerated wetlands. The presence of autotrophic pathways for nitrogen removal can prove highly beneficial in terms of reducing sludge generation and hence reducing clogging, making aerated CWs a sustainable wastewater treatment solution.

Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general.

IMPORTANCE

Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro, demonstrating their capability to serve as alternatives to rumen methanogens.

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.

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.

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.

Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle

Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.

Relevance of extracellular electron uptake mechanisms for electromethanogenesis applications

Electromethanogenesis has emerged as a biological branch of Power-to-X technologies that implements methanogenic microorganisms, as an alternative to chemical Power-to-X, to convert electrical power from renewable sources, and CO2 into methane. Unlike biomethanation processes where CO2 is converted via exogenously added hydrogen, electromethanogenesis occurs in a bioelectrochemical set-up that combines electrodes and microorganisms. Thereby, mixed, or pure methanogenic cultures catalyze the reduction of CO2 to methane via reducing equivalents supplied by a cathode. Recent advances in electromethanogenesis have been driven by interdisciplinary research at the intersection of microbiology, electrochemistry, and engineering. Integrating the knowledge acquired from these areas is essential to address the specific challenges presented by this relatively young biotechnology, which include electron transfer limitations, low energy and product efficiencies, and reactor design to enable upscaling. This review approaches electromethanogenesis from a multidisciplinary perspective, putting emphasis on the extracellular electron uptake mechanisms that methanogens use to obtain energy from cathodes, since understanding these mechanisms is key to optimize the electrochemical conditions for the development of these systems. This work summarizes the direct and indirect extracellular electron uptake mechanisms that have been elucidated to date in methanogens, along with the ones that remain unsolved. As the study of microbial corrosion, a similar bioelectrochemical process with Fe0 as electron source, has contributed to elucidate different mechanisms on how methanogens use solid electron donors, insights from both fields, biocorrosion and electromethanogenesis, are combined. Based on the repertoire of mechanisms and their potential to convert CO2 to methane, we conclude that for future applications, electromethanogenesis should focus on the indirect mechanism with H2 as intermediary. By summarizing and linking the general aspects and challenges of this process, we hope that this review serves as a guide for researchers working on electromethanogenesis in different areas of expertise to overcome the current limitations and continue with the optimization of this promising interdisciplinary technology.

The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon hdrBCA in Methanosarcina barkeri

Methanogenic archaea play a key role in the global carbon cycle because these microorganisms remineralize organic compounds in various anaerobic environments. The microorganism Methanosarcina barkeri is a metabolically versatile methanogen, which can utilize acetate, methanol, and H2/CO2 to synthesize methane. However, the regulatory mechanisms underlying methanogenesis for different substrates remain unknown. In this study, RNA-seq analysis was used to investigate M. barkeri growth and gene transcription under different substrate regimes. According to the results, M. barkeri showed the best growth under methanol, followed by H2/CO2 and acetate, and these findings corresponded well with the observed variations in genes transcription abundance for different substrates. In addition, we identified a novel regulator, MSBRM_RS03855 (designated as HdrR), which specifically activates the transcription of the heterodisulfide reductase hdrBCA operon in M. barkeri. HdrR was able to bind to the hdrBCA operon promoter to regulate transcription. Furthermore, the structural model analyses revealed a helix-turn-helix domain, which is likely involved in DNA binding. Taken together, HdrR serves as a model to reveal how certain regulatory factors control the expression of key enzymes in the methanogenic pathway.IMPORTANCEThe microorganism Methanosarcina barkeri has a pivotal role in the global carbon cycle and contributes to global temperature homeostasis. The consequences of biological methanogenesis are far-reaching, including impacts on atmospheric methane and CO2 concentrations, agriculture, energy production, waste treatment, and human health. As such, reducing methane emissions is crucial to meeting set climate goals. The methanogenic activity of certain microorganisms can be drastically reduced by inhibiting the transcription of the hdrBCA operon, which encodes heterodisulfide reductases. Here, we provide novel insight into the mechanisms regulating hdrBCA operon transcription in the model methanogen M. barkeri. The results clarified that HdrR serves as a regulator of heterodisulfide reductase hdrBCA operon transcription during methanogenesis, which expands our understanding of the unique regulatory mechanisms that govern methanogenesis. The findings presented in this study can further our understanding of how genetic regulation can effectively reduce the methane emissions caused by methanogens.

Systems metabolic engineering of Corynebacterium glutamicum to assimilate formic acid for biomass accumulation and succinic acid production

Formate as an ideal mediator between the physicochemical and biological realms can be obtained from electrochemical reduction of CO2 and used to produce bio-chemicals. Yet, limitations arise when employing natural formate-utilizing microorganisms due to restricted product range and low biomass yield. This study presents a breakthrough: engineered Corynebacterium glutamicum strains (L2-L4) through modular engineering. L2 incorporates the formate-tetrahydrofolate cycle and reverse glycine cleavage pathway, L3 enhances NAD(P)H regeneration, and L4 reinforces metabolic flux. Metabolic modeling elucidates C1 assimilation, guiding strain optimization for co-fermentation of formate and glucose. Strain L4 achieves an OD600 of 0.5 and produces 0.6 g/L succinic acid. 13C-labeled formate confirms C1 assimilation, and further laboratory evolution yields 1.3 g/L succinic acid. This study showcases a successful model for biologically assimilating formate in C. glutamicum that could be applied in C1-based biotechnological production, ultimately forming a formate-based bioeconomy.

Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment

BACKGROUND

Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants.

MATERIALS AND METHODS

The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes.

RESULTS

Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments.

CONCLUSION

This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.

Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers

Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.

Salinity causes differences in stratigraphic methane sources and sinks

Methane metabolism, driven by methanogenic and methanotrophic microorganisms, plays a pivotal role in the carbon cycle. As seawater intrusion and soil salinization rise due to global environmental shifts, understanding how salinity affects methane emissions, especially in deep strata, becomes imperative. Yet, insights into stratigraphic methane release under varying salinity conditions remain sparse. Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata (15-40 m depth) through in situ and microcosm simulation studies. Coastal strata, exhibiting a salinity level five times greater than terrestrial strata, manifested a 12.05% decrease in total methane production, but a staggering 687.34% surge in methane oxidation, culminating in 146.31% diminished methane emissions. Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics, impacting the methanogenic archaeal, methanotrophic archaeal, and methanotrophic bacterial communities by 16.53%, 27.25%, and 22.94%, respectively. Furthermore, microbial interactions influenced strata system methane metabolism. Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition, facilitating methane production via Methanofastidiosales. This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.

Relationship between Dairy Cow Health and Intensity of Greenhouse Gas Emissions

The dairy industry is facing criticism for its role in exacerbating global GHG emissions, as climate change becomes an increasingly pressing issue. These emissions mostly originate from methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2). An optimal strategy involves the creation of an economical monitoring device to evaluate methane emissions from dairy animals. Livestock production systems encounter difficulties because of escalating food demand and environmental concerns. Enhancing animal productivity via nutrition, feeding management, reproduction, or genetics can result in a decrease in CH4 emissions per unit of meat or milk. This CH4 unit approach allows for a more accurate comparison of emissions across different animal production systems, considering variations in productivity. Expressing methane emissions per unit allows for easier comparison between different sources of emissions. Expressing emissions per unit (e.g., per cow) highlights the relative impact of these sources on the environment. By quantifying emissions on a per unit basis, it becomes easier to identify high-emission sources and target mitigation efforts accordingly. Many environmental policies and regulations focus on reducing emissions per unit of activity or output. By focusing on emissions per unit, policymakers and producers can work together to implement practices that lower emissions without sacrificing productivity. Expressing methane emissions in this way aligns with policy goals aimed at curbing overall greenhouse gas emissions. While it is true that total emissions affect the atmosphere globally, breaking down emissions per unit helps to understand the specific contributions of different activities and sectors to overall greenhouse gas emissions. Tackling cattle health issues can increase productivity, reduce GHG emissions, and improve animal welfare. Addressing livestock health issues can also provide favourable impacts on human health by reducing the prevalence of infectious illnesses in livestock, thereby mitigating the likelihood of zoonotic infections transmitting to humans. The progress in animal health offers the potential for a future in which the likelihood of animal diseases is reduced because of improved immunity, more effective preventative techniques, earlier identification, and innovative treatments. The primary objective of veterinary medicine is to eradicate clinical infectious diseases in small groups of animals. However, as the animal population grows, the emphasis shifts towards proactive treatment to tackle subclinical diseases and enhance production. Proactive treatment encompasses the consistent monitoring and implementation of preventive measures, such as vaccination and adherence to appropriate nutrition. Through the implementation of these measures, the livestock industry may enhance both animal well-being and mitigate the release of methane and nitrous oxide, thereby fostering environmental sustainability. In addition, advocating for sustainable farming methods and providing farmers with education on the significance of mitigating GHG emissions can bolster the industry's endeavours to tackle climate change and infectious illnesses. This will result in a more robust and environmentally sustainable agriculture industry. This review seeks to conduct a thorough examination of the correlation between the health condition of cattle, the composition of milk produced, and the emissions of methane gas. It aims to identify areas where research is lacking and to provide guidance for future scientific investigations, policy making, and industry practices. The goal is to address the difficulties associated with methane emissions in the cattle industry. The primary global health challenge is to identify the causative relationship between climate change and infectious illnesses. Reducing CH4 and N2O emissions from digestive fermentation and animal manure can be achieved by improving animal well-being and limiting disease and mortality.

Bisphenol A affects microbial interactions and metabolic responses in sludge anaerobic digestion

The widespread use of bisphenol A (BPA) has resulted in the emergence of new pollutants in various environments, particularly concentrated in sewage sludge. This study investigated the effects of BPA on sludge anaerobic digestion, focusing specifically on the interaction of microbial communities and their metabolic responses. While the influence of BPA on methane accumulation is not significant, BPA still enhanced the conversion of soluble COD, protein, and polysaccharides. BPA also positively influenced the hydrolysis-acidogenesis process, leading to 17% higher concentrations of volatile fatty acids (VFAs). Lower BPA levels (0.2-0.5 mg/kg dw) led to decreased hydrolysis and acidogenesis gene abundance, indicating metabolic inhibition; conversely, higher concentrations (1-5 mg/kg dw) increased gene abundance, signifying metabolic enhancement. Diverse methane metabolism was observed and exhibited alterations under BPA exposure. The presence of BPA impacted both the diversity and composition of microbial populations. Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi dominated in BPA-treated groups and varied in abundance among different treatments. Changes of specific genera Sedimentibacter, Fervikobacterium, Blvii28, and Coprothermobacter in response to BPA, affecting hydrolysis and acetogenesis. Archaeal diversity declined while the hydrogenotrophic methanogen Methanospirillum thrived under BPA exposure. BPA exposure enabled microorganisms to form structured community interaction networks and boost their metabolic activities during anaerobic digestion. The study also observed the enrichment of BPA biodegradation pathways at high BPA concentrations, which could interact and overlap to ensure efficient BPA degradation. The study provides insights into the digestion performance and interactions of microbial communities to BPA stress and sheds light on the potential effect of BPA during anaerobic digestion.

Effect of iron sources on methane production and phosphorous transformation in an anaerobic digestion system of waste activated sludge

The iron materials are commonly employed to enhance resource recovery from waste activated sludge through anaerobic digestion (AD). The influence of different iron sources, such as Fe2O3, Fe3O4, and FeCl3 on methane production and phosphorus transformation in AD systems with thermal hydrolyzed sludge as the substrate was assessed in this study. The results indicated that iron oxides effectively promote methane yield and methane production rate in AD systems, resulting in a maximum increase in methane production by 1.6 times. Soluble FeCl3 facilitated the removal of 92.3% of phosphorus from the supernatant through the formation of recoverable precipitates in the sludge. The introduction of iron led to an increase in the abundance of bacteria responsible for hydrolysis and hydrogenotrophic methanogenesis. However, the enrichment of microbial communities varied depending on the specific irons used. This study provides support for AD systems that recover phosphorus and produce methane efficiently from waste sludge.

A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps

Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.

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.

Pyruvate-dependent growth of Methanosarcina acetivorans

Methanogenesis is a key step during anaerobic biomass degradation. Methanogenic archaea (methanogens) are the only organisms coupling methanogenic substrate conversion to energy conservation. The range of substrates utilized by methanogens is limited, with acetate and H2+CO2 being the ecologically most relevant. The only single methanogenic energy substrate containing more carbon-carbon bonds than acetate is pyruvate. Only the aggregate-forming, freshwater methanogen Methanosarcina barkeri Fusaro was shown to grow on this compound. Here, the pyruvate-utilizing capabilities of the single-celled, marine Methanosarcina acetivorans were addressed. Robust pyruvate-dependent, methanogenic, growth could be established by omitting CO2 from the growth medium. Growth rates which were independent of the pyruvate concentration indicated that M. acetivorans actively translocates pyruvate across the cytoplasmic membrane. When 2-bromoethanesulfonate (BES) inhibited methanogenesis to more than 99%, pyruvate-dependent growth was acetogenic and sustained. However, when methanogenesis was completely inhibited M. acetivorans did not grow on pyruvate. Analysis of metabolites showed that acetogenesis is used by BES-inhibited M. acetivorans as a sink for electrons derived from pyruvate oxidation and that other, thus far unidentified, metabolites are produced.IMPORTANCEThe known range of methanogenic growth substrates is very limited and M. acetivorans is only the second methanogenic species for which growth on pyruvate is demonstrated. Besides some commonalities, analysis of M. acetivorans highlights differences in pyruvate metabolism among Methanosarcina species. The observation that M. acetivorans probably imports pyruvate actively indicates that the capabilities for heterotrophic catabolism in methanogens may be underestimated. The mostly acetogenic growth of M. acetivorans on pyruvate with concomitant inhibition of methanogenesis confirms that energy conservation of methanogenic archaea can be independent of methane formation.

Geologic sources and well integrity impact methane emissions from orphaned and abandoned oil and gas wells

The 160-year history of oil and gas drilling in the United States has left a legacy of unplugged orphaned and abandoned wells, some of which are leaking methane and other hazardous chemicals into the environment. The locations of around 120,000 documented orphaned wells are currently known with the number of undocumented orphaned wells possibly ranging towards a million. The bulk of methane emissions originate from only 10 % of orphaned and abandoned wells, while the remaining wells have undetectable emissions. Understanding the sources of methane emissions from orphaned wells is key to estimating emission rates and prioritizing plugging. In this article, we identify key studies reporting methane emission measurements from orphaned and abandoned wells in the published literature and analyze previously published isotopic methane data to categorize the sources of methane emissions. Three primary geologic sources provide methane to a leaking well that can migrate from geologic formations into or along the wellbore to contaminate groundwater, the surface environment, and the atmosphere. These geologic sources of methane are petroleum (oil and gas) sourced reservoirs, coal seams, and methanogenesis occurring in and around the wellbore. Thermogenic petroleum gas reservoirs are associated with the highest emission rates measured to date. The next highest rates are from coalbed methane sources, while biogenic sources are the lowest based on the publicly available measured emissions data. Well conditions that could potentially enable methane transport include decay of the wellhead and surface infrastructure, wellbore deterioration from corrosive fluids in the subsurface, delamination of the casing and cement, damage from seismicity, and new fracture networks created by hydraulic fracturing of newly drilled neighboring wells. With an understanding of these geologic sources and well conditions, we can (1) better identify areas where high-emitting wells are likely to be present, (2) improve emission rate estimates from orphaned and abandoned wells, and (3) better prioritize wells for plugging. SYNOPSIS: Understanding the geologic sources of methane emissions from orphaned and abandoned wells and wellbore conditions that lead to methane release can significantly improve emissions estimates and aid in prioritizing which wells to plug.

Mixed culture biotechnology and its versatility in dark fermentative hydrogen production

Over the years, extensive research has gone into fermentative hydrogen production using pure and mixed cultures from waste biomass with promising results. However, for up-scaling of hydrogen production mixed cultures are more appropriate to overcome the operational difficulties such as a metabolic shift in response to environmental stress, and the need for a sterile environment. Mixed culture biotechnology (MCB) is a robust and stable alternative with efficient waste and wastewater treatment capacity along with co-generation of biohydrogen and platform chemicals. Mixed culture being a diverse group of bacteria with complex metabolic functions would offer a better response to the environmental variations encountered during biohydrogen production. The development of defined mixed cultures with desired functions would help to understand the microbial community dynamics and the keystone species for improved hydrogen production. This review aims to offer an overview of the application of MCB for biohydrogen production.

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.