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PubMed2026

An integrated culturomic and genomic database and analysis platform for methanogenic archaea.

Methanogenic archaea research is challenged by limited strain resources, fragmented genomic data, inconsistent genome quality, substantial uncultured lineages, and difficulties in laboratory culturing, hindering advances in biogas production, climate mitigation, and microbial ecology. These archaea play crucial roles in global carbon cycling and anaerobic environments, yet scattered data and unculturable strains limit systematic studies and applications. To address this, we created MethArDB (Methanogenic Archaeal Genome Database), a specialized database for methanogenic archaea, compiling 3919 genomes, 87 host-associated plasmids, and 42 phages, with standardized quality classifications (complete, scaffold, draft), protein sequences, and metadata on geography, habitats, metabolism, and inheritable elements. Integrated MethArCT (Methanogenic Archaeal Culturomics Toolkit) employs a dual-threshold orthologous/paralogous protein analysis to evaluate metabolic pathway completeness, predicting cultivation parameters and suggesting candidate cultivation strategies, including potential medium formulations and conditions, to support strain isolation. Overall, MethArDB and MethArCT form an integrated platform combining genomics and culturomics to facilitate methanogenic archaea research. Database URL:  http://methardb.cn.

Genome, Archaeal↗

PubMed2026

Up-to-date, and taxonomy-curated mcrA reference databases for methanogen community profiling.

The methyl-coenzyme M reductase subunit alpha gene (mcrA) is an important phylogenetic marker for high throughput ecological profiling of methanogenic archaea, central to industrial biological methane production and greenhouse gas emissions. Yet, dedicated reference databases predate current relevant NCBI sequence accumulation and archaeal taxonomic revision. We present three updated mcrA reference databases: (i) one derived from NCBI-catalogued methanogen genomes (1572 sequences); (ii) a database built by expansion of a previously published reference dataset, leveraging the NCBI nucleotide collection (27,942 sequences); (iii) a curated-taxonomy version of the latter. The updated amplicon databases provide a ∼ 3.5-fold sequence richness expansion, extend genus-level richness from 31 to 83 taxa, more than 4-fold species-level richness, and incorporate novel lineages compared with the previous reference dataset (e.g. Thermoplasmatota-encompassed). All databases were formatted to support analysis with relevant contemporary software pipelines and packages. Overall, the generated databases facilitate a highly improved characterization of methanogen diversity and ecology.

Archaea↗

PubMed2025

ModE Regulates Alternative Nitrogenase Expression in the Methanogen Methanosarcina acetivorans.

All methanogens that can fix nitrogen use molybdenum (Mo) nitrogenase. Some methanogens, including Methanosarcina acetivorans , also contain alternative vanadium- and iron-nitrogenases, encoded by the vnf and anf operons, respectively. These nitrogenases are produced when there is insufficient Mo to support Mo-nitrogenase activity. The factors that control the expression of the alternative nitrogenases in response to Mo availability are unknown in methanogens. Here we show that ModE is the regulator that represses transcription of the vnf and anf operons in M. acetivorans when cells are grown with Mo. CRISPRi repression of modE results in a significant increase in the transcription of the vnf and anf operons as well as the detection of Fe-nitrogenase during nitrogen fixation in the presence of Mo. Gel shift assays with recombinant ModE demonstrated that ModE binds a specific sequence motif upstream of the vnf and anf operons, as well as other genes and operons related to nitrogen fixation and Mo transport. However, purified ModE does not contain Mo, and the addition of Mo does not alter the affinity of ModE for DNA, indicating M. acetivorans ModE may not directly bind Mo. This study shows that ModE is the primary Mo-responsive regulator of alternative nitrogenase expression in M. acetivorans , but other factor(s) are likely involved in directly sensing Mo.

Methanosarcina↗

PubMed2026

Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.

Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.

Manure↗

PubMed2026

Lithosyntrophy: Obligate syntrophy in a phosphite-oxidizing, methanogenic culture.

The anaerobic conversion of organic matter to methane and carbon dioxide typically relies on obligate syntrophic interactions between bacteria and methanogenic archaea, where interspecies electron transfer enables thermodynamically constrained reactions to proceed near equilibrium. Syntrophs often couple the oxidation of fermentation products such as fatty acids and alcohols to the reduction of protons to form hydrogen (H2). These reactions can only proceed if low H2 concentrations are maintained by H2-consuming syntrophic partners. Here, we describe "lithosyntrophy," a mode of syntrophic interaction in which electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (HPO32-, oxidation state +3) to phosphate coupled to hydrogenogenesis in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Physiology experiments, thermodynamic calculations, genomic annotation, and metaproteomics analysis collectively revealed a mechanism for syntrophic phosphite oxidation in Phox-21. In this pathway, electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase. Unlike previously characterized acetogenic phosphite oxidizers, Phox-21 is a mixotroph that assimilates acetate to form biomass. Lithosyntrophic phosphite oxidizers may play important roles both in transferring reducing equivalents as well as biologically available phosphorus to other members of their surrounding microbial communities, establishing a previously unrecognized metabolic and biogeochemical link between the phosphorus and carbon redox cycles in anoxic ecosystems.

Oxidation-Reduction↗

PubMed2026

Metagenome-resolved evidence that soluble factors in granular activated carbon-amended reactor effluent reprogram propionate metabolism and methanogenic pathways.

Granular activated carbon (GAC) enhances anaerobic digestion performance, yet the mechanisms underlying reactor-scale improvements remain incompletely understood, particularly how GAC affects biomass not attached to its surface. Here, sludge from a non-GAC up-flow anaerobic sludge blanket reactor was incubated with 0.45-μm-filtered effluents from non-GAC and GAC-amended reactors under repeated propionate loading, followed by genome-resolved metagenomics. GAC-reactor effluent increased methane yield from 64 ± 3% to 76 ± 3% (p < 0.01) in the absence of GAC particles. A non-redundant catalog of 170 quality-filtered metagenome-assembled genomes (MAGs) was recovered, enabling pathway- and gene-set quantification. Genomic potential for both major propionate-oxidation routes increased in the GAC-effluent group relative to the non-GAC group, with a larger increase for the methylmalonyl-CoA (MMC) route than for the dismutation route (1.289- versus 1.221-fold). Accordingly, the MMC-to-dismutation preference ratio was 5.60% higher in the GAC-effluent group, alongside a broader carrier base. Cobamide potential shifted toward remodeling and cobamide-dependent use rather than increased de novo corrin-ring synthesis. Candidate electron-transfer architectures were also rebalanced: PilA-associated carriers became less prominent, whereas maturation-supported multiheme cytochrome carriers increased from 22.96% to 34.90% of community abundance, although H2/formate-module carriers remained prevalent. Quorum-sensing systems underwent pathway- and carrier-specific redistribution, while all eight curated extracellular-polysaccharide modules showed higher mean gene abundance in the GAC-effluent composite. These findings show that a filter-passing effluent fraction can extend GAC-associated effects beyond direct particle contact and link enhanced methanogenesis to a broader, redistributed network of metabolic, redox, and coordination capacities. This expands the mechanistic framework of conductive-material-assisted anaerobic digestion and provides a basis for harnessing GAC-derived functions throughout the reactor.

Extracellular polymeric substances (EPS)↗

PubMed2026

Genome-resolved assessment of archaeal diversity in full-scale anaerobic digesters reveals variability in mcrA primer coverage.

AIMS: Methanogenic archaea are key players in anaerobic digestion, driving methane production in biogas reactors. This study aimed to assess the diversity of methanogenic archaea in full-scale anaerobic digesters using genome-resolved metagenomics and to systematically evaluate the taxonomic coverage of commonly used mcrA-targeted qPCR primer sets against this genomic framework. METHODS AND RESULTS: Methanogenic diversity was assessed using 113 dereplicated archaeal metagenome-assembled genomes (MAGs) recovered from 109 full-scale anaerobic digesters treating diverse substrates. Genome-resolved analyses revealed a diverse archaeal community spanning multiple phyla, dominated by Halobacteriota and Methanobacteriota, with additional representatives from Methanobacteriota_B, Thermoplasmatota, and Thermoproteota. The presence of the mcrA gene was identified in a subset 55 MAGs, which were subsequently used as the genomic framework to evaluate six commonly used mcrA qPCR primer sets in silico. This subset clustered into nine phylogenetic groups and formed the basis for the primer coverage analysis. The evaluation revealed marked differences in taxonomic coverage among primer sets. Most primers preferentially detected Methanobacteriales and Methanosarcinales, while underrepresenting or excluding other methanogenic lineages, including H₂-dependent methylotrophic Methanomassiliicoccaceae. CONCLUSIONS: Commonly used mcrA primer sets differ substantially in their ability to capture methanogenic diversity, with some showing broad representation of reactor-associated methanogens and others exhibiting strong lineage-specific biases. Genome-resolved metagenomics provides an effective framework for benchmarking primer performance and supports the selection and improvement of molecular tools for more accurate monitoring of anaerobic digestion systems.

Archaea↗

PubMed2026

Evidence of direct methane production from long-chain fatty acids by thermophilic Archaeoglobi.

Methanogenic degradation of long-chain fatty acids has traditionally been thought to occur through syntrophic partnerships between fatty acid-degrading bacteria and methanogenic archaea. However, recent genomic evidence suggests that certain archaea may independently carry out the entire process. Here we report the enrichment of an archaeon from the class Archaeoglobi, Candidatus Methanoglobus sphaerolipidus DLY3, from hot spring sediments in Tengchong, China. The results of selective enrichment, growth experiments, microscopy, stable isotope tracing, metagenomics and metatranscriptomics suggest that Ca. M. sphaerolipidus directly converts long-chain fatty acids to methane. This transformation involves the beta-oxidation pathway, the Wood-Ljungdahl pathway and methanogenic methyl-coenzyme M reductase and methyltransferase complexes-a process we term liparotrophy. In addition to oleic acid, Ca. M. sphaerolipidus is also capable of utilizing methanol as a substrate for methanogenesis. Our findings expand the known substrate range for methanogenic archaea beyond carbon dioxide reduction, acetoclastic methanogenesis, methylotrophy, methyl reduction, methoxydotrophy and the recently reported alkylotrophy.

Journal Article↗

PubMed2026

Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.

Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900 °C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2 % compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5 %), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55 %. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.

Sewage↗

PubMed2026

Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.

Enteric methane emission from dairy cattle is an environmental challenge. The most efficient mitigation strategies nowadays include the use of methanogenesis inhibitors that specifically target the rumen methanogens. Specific inhibitors, such as 3-nitrooxypropanol (3-NOP), reduce methane emissions without negative effects on the products of fermentation that serve as energy metabolites for the host. However, the concomitant effects of methanogenesis inhibition on rumen microbiota and host metabolism are poorly characterized. Thus, the objective of this study was to explore the association between rumen microbiota and host metabolism when methanogenesis is inhibited. Thirteen dairy cows were used as controls, and 12 were supplemented with 3-NOP for 6 weeks. Rumen microbiota composition and activity were characterized using metagenomics and metatranscriptomics. The host metabolism was assessed in a previous publication by a metabolomic analysis of the plasma. Microbiota data were used as explanatory variables of the metabolome data in a multiblock sparse partial least squares analysis. Overall, the association between rumen microbiota and host metabolism was moderate. Notwithstanding this, a few downregulated transcripts related to glycolysis, hydrogen transfer, and protein synthesis, together with a decrease in the proportion of taxa of the Oscillospirales order, showed a correlation with host one-carbon metabolites (|r| > 0.6). These associations raised novel hypotheses that remain to be elucidated, especially with regard to the effects of dihydrogen on the accumulation of microbial glycolysis and methanogenesis metabolite intermediates.IMPORTANCEDairy cattle produce a substantial amount of methane, a potent greenhouse gas. Several strategies have been designed to reduce methane production by targeting the rumen microbiota. One such strategy specifically inhibits methanogens with a molecule called 3-nitrooxypropanol. This study uses an integrative data analysis approach, combining rumen microbiota and host metabolome information, to explore the consequences of inhibiting methanogenesis on the holobiont. This provides additional holistic insight into the effect of methane mitigation strategies on dairy cattle.

Animals↗

PubMed2026

Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.

BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics. RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.

Metagenome↗

PubMed2026

Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams.

BACKGROUND: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia. RESULTS: We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions. CONCLUSIONS: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.

Animals↗

PubMed2026

Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?

PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes. RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.

Humans↗

PubMed2026

Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.

Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.

Hydrogen↗

PubMed2026

Host-virus dynamics in anaerobic digesters facing abiotic inhibition.

Viruses play a major role in controlling the structure and dynamics of microbial communities in anaerobic digesters, ecosystems sensitive to disturbances that inhibit methane production. Here, we studied the interplay between abiotic disturbances, microbiome and virome composition, and process performance, to assess whether provirus induction can be triggered by abiotic stresses known to inhibit anaerobic digestion (ammonium, phenol and sodium chloride). We monitored viral dynamics in batch mesophilic anaerobic digesters fed with biowaste through shotgun metavirome sequencing. The diversity of both prokaryotes and viruses was high, with Clostridiales dominating the prokaryotic community and Caudoviricetes dominating the viromes. We identified 132 viral contigs and 19 host genera that were differentially abundant under disturbed conditions. No significant impact of the tested abiotic stresses on provirus induction was observed under the current experimental and analytical framework. The results were consistent with viruses exerting steady, background-level predation through a putative combination of kill-the-winner dynamics at the sub-genus level and piggyback-the-winner dynamics, rather than stress-triggered, synchronous lytic bursts. A few auxiliary metabolic genes were detected, potentially targeting carbon, sulfur and cofactor metabolism in anaerobic digestion. Temperate viruses were dominant, representing up to 71% of the viral genomes confirmed as complete across all conditions. Electron microscopy analysis revealed diverse virus-like particles, including head-tailed particles typical of Caudoviricetes, but also spherical, rod-shaped and spindle-shaped particles typical of archaeal viruses. Notably, we present a new virus family, Eurekaviridae, of spindle-shaped viruses associated with methanogenic archaea.

Anaerobiosis↗

PubMed2024

Metagenome reveals the possible mechanism that microbial strains promote methanogenesis during anaerobic digestion of food waste.

For better understanding the mechanism of microbial strains promoting methane production, four strains Hungatella xylanolytica A5, Bacillus licheniformis B1, Paraclostridium benzoelyticum C2 and Advenella faeciporci E1 were inoculated into anaerobic digestion systems. After bioaugmentation, the cumulative methane production of A5, B1, C2 and E1 groups elevated by 11.68%, 8.20%, 18.21% and 15.67% compared to CK group, respectively. The metagenomic analysis revealed that the species diversity and uniformity of the experimental groups was improved, and hydrolytic acidifying bacteria, represented by Clostridiaceae, Anaerolineaceae and Oscillospiraceae, and methanogens, such as Methanotrichaceae and Methanobacteriaceae, were enriched. Meanwhile, the abundance of key genes in carbohydrate, pyruvate and methane metabolism was increased in the inoculated groups, providing reasonable reasons for more methane production. The strengthening mechanism of microbial strains in this study offered a theoretical foundation for selecting a suitable bioaugmentation strategy to solve the problems of slow start-up and low methane production in anaerobic digestion.

Methane↗

PubMed2026

Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.

Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.

Ammonia↗

PubMed2026

Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.

Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.

Fermentation↗