Helgeson, H. C., Owens, C. E., Knox, A. M. & Richard, L. Calculation of the standard molal thermodynamic properties of crystalline, liquid, and gas organic molecules at high temperatures and pressures. Geochim. Cosmochim. Acta 62, 985–1081 (1998).
Article ADS CAS Google Scholar
Amend, J. P. & Shock, E. L. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol. Rev. 25, 175–243 (2001).
Article CAS PubMed Google Scholar
Liu, Y.-F. et al. Genomic and transcriptomic evidence supports methane metabolism in Archaeoglobi. mSystems 5, e00653–00620 (2020).
Article Google Scholar
Wang, J. et al. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. Sci. Adv. 9, eadg6004 (2023).
Article CAS PubMed PubMed Central Google Scholar
Zhou, Z. et al. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature 601, 257–262 (2022).
Article ADS CAS PubMed Google Scholar
Yu, T. et al. Evidence of direct methane production from long-chain fatty acids by thermophilic Archaeoglobi. Nat. Microbiol. https://doi.org/10.1038/s41564-026-02490-5 (2026).
Falkowski, P. et al. The global carbon cycle: a test of our knowledge of earth as a system. Science 290, 291–296 (2000).
Article ADS CAS PubMed Google Scholar
Ferry, J. G. & Lessner, D. J. Methanogenesis in marine sediments. Ann. N. Y. Acad. Sci. 1125, 147–157 (2008).
Article ADS CAS PubMed Google Scholar
Rice, D. D. & Claypool, G. E. Generation, accumulation, and resource potential of biogenic gas. AAPG Bull. 65, 5–25 (1981).
Article CAS Google Scholar
Huang, Y. et al. Methanol transfer supports metabolic syntrophy between bacteria and archaea. Nature 639, 190–195 (2025).
Article ADS CAS PubMed Google Scholar
Dolfing, J., Larter, S. R. & Head, I. M. Thermodynamic constraints on methanogenic crude oil biodegradation. ISME J. 2, 442–452 (2008).
Article CAS PubMed Google Scholar
Mayumi, D. et al. Methane production from coal by a single methanogen. Science 354, 222–225 (2016).
Article ADS CAS PubMed Google Scholar
Evans, P. N. et al. An evolving view of methane metabolism in the archaea. Nat. Rev. Microbiol. 17, 219–232 (2019).
Article CAS PubMed Google Scholar
Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).
CAS PubMed PubMed Central Google Scholar
Borrel, G. et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat. Microbiol. 4, 603–613 (2019).
Article CAS PubMed PubMed Central Google Scholar
Laso-Pérez, R. et al. Anaerobic degradation of non-methane alkanes by ‘Candidatus Methanoliparia’ in hydrocarbon seeps of the Gulf of Mexico. mBio 10, e01128–01119 (2019).
Article Google Scholar
Evans, P. N. et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350, 434–438 (2015).
Article ADS CAS PubMed Google Scholar
Hua, Z.-S. et al. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring archaea. Nat. Commun. 10, 4574 (2019).
Article ADS PubMed PubMed Central Google Scholar
Berghuis, B. A. et al. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc. Natl Acad. Sci. USA 116, 5037–5044 (2019).
Article ADS CAS PubMed PubMed Central Google Scholar
Wu, K. et al. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature 632, 1124–1130 (2024).
Article ADS CAS PubMed Google Scholar
Kohtz, A. J. et al. Cultivation and visualization of a methanogen of the phylum Thermoproteota. Nature 632, 1118–1123 (2024).
Article ADS CAS PubMed Google Scholar
Wu, K., Ma, S., Li, J., Sousa, D. Z. & Cheng, L. Culturing the uncultured anaerobes from the perspective of microbial growth curves. Trends Microbiol. 34, 89–97 (2026).
Article CAS PubMed Google Scholar
Wu, K. et al. Targeted isolation of H2-dependent methylotrophic methanogens by a cocktail approach. Nat. Protoc. 21, 959–986 (2026).
Article CAS PubMed Google Scholar
Sauer, D. B. & Wang, D.-N. Predicting the optimal growth temperatures of prokaryotes using only genome derived features. Bioinformatics 35, 3224–3231 (2019).
Article CAS PubMed PubMed Central Google Scholar
Bashiri, G. et al. A revised biosynthetic pathway for the cofactor F420 in prokaryotes. Nat. Commun. 10, 1558 (2019).
Article ADS PubMed PubMed Central Google Scholar
Sousa, D. Z., Smidt, H., Alves, M. M. & Stams, A. J. Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids. FEMS Microbiol. Ecol. 68, 257–272 (2009).
Article CAS PubMed Google Scholar
Schäfer, T., Selig, M. & Schönheit, P. Acetyl-CoA synthetase (ADP forming) in archaea, a novel enzyme involved in acetate formation and ATP synthesis. Arch. Microbiol. 159, 72–83 (1993).
Article Google Scholar
Chen, D., Wu, R., Bryan, T. L. & Dunaway-Mariano, D. In vitro kinetic analysis of substrate specificity in enterobactin biosynthetic lower pathway enzymes provides insight into the biochemical function of the hot dog-fold thioesterase EntH. Biochemistry 48, 511–513 (2009).
Article CAS PubMed PubMed Central Google Scholar
Ragsdale, S. W. & Kumar, M. Nickel-containing carbon monoxide dehydrogenase/acetyl-CoA synthase. Chem. Rev. 96, 2515–2540 (1996).
Article CAS PubMed Google Scholar
Welte, C. & Deppenmeier, U. Re-evaluation of the function of the F420 dehydrogenase in electron transport of Methanosarcina mazei. FEBS J. 278, 1277–1287 (2011).
Article CAS PubMed Google Scholar
Brüggemann, H., Falinski, F. & Deppenmeier, U. Structure of the F420H2: quinone oxidoreductase of Archaeoglobus fulgidus: identification and overproduction of the F420H2-oxidizing subunit. Eur. J. Biochem. 267, 5810–5814 (2000).
Article PubMed Google Scholar
Ge, X. et al. Characterization of the membrane-associated electron-bifurcating flavoenzyme EtfABCX from the hyperthermophilic bacterium Thermotoga maritima. Biochemistry 62, 3554–3567 (2023).
Article CAS PubMed PubMed Central Google Scholar
Courbon, G. M. et al. Structural basis for EtfD-mediated coupling of β-oxidation and the respiratory chain in Mycobacteria. EMBO J. 45, 2785–2807 (2026).
Article CAS PubMed PubMed Central Google Scholar
Buessecker, S. et al. Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring. ISME J. 17, 1649–1659 (2023).
Article CAS PubMed PubMed Central Google Scholar
Lynes, M. M., Jay, Z. J., Kohtz, A. J. & Hatzenpichler, R. Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring. ISME J. 18, wrae026 (2024).
Article CAS PubMed PubMed Central Google Scholar
Meyerdierks, A. et al. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12, 422–439 (2010).
Article CAS PubMed Google Scholar
Welander, P. V. & Metcalf, W. W. Mutagenesis of the C1 oxidation pathway in Methanosarcina barkeri: new insights into the Mtr/Mer bypass pathway. J. Bacteriol. 190, 1928–1936 (2008).
Article CAS PubMed PubMed Central Google Scholar
Crable, B. R. et al. Membrane complexes of Syntrophomonas wolfei involved in syntrophic butyrate degradation and hydrogen formation. Front. Microbiol. 7, 1795 (2016).
Article PubMed PubMed Central Google Scholar
Johnson, E. F. & Mukhopadhyay, B. A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the Methanarchaeon Methanocaldococcus jannaschii. J. Biol. Chem. 280, 38776–38786 (2005).
Article CAS PubMed Google Scholar
Krzycki, J. A., Kenealy, W. R., DeNiro, M. J. & Zeikus, J. G. Stable carbon isotope fractionation by Methanosarcina barkeri during methanogenesis from acetate, methanol, or carbon dioxide-hydrogen. Appl. Environ. Microbiol. 53, 2597–2599 (1987).
Article ADS CAS PubMed PubMed Central Google Scholar
Conrad, R. Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal. Org. Geochem. 36, 739–752 (2005).
Article ADS CAS Google Scholar
Gropp, J., Bill, M., Stolper Daniel, A. & Nayak Dipti, D. Methanol-specific methyltransferase isozymes have large carbon kinetic isotope effects that impact methane isotopic signatures. Appl. Environ. Microbiol. 0, e00664–00626 (2026).
Google Scholar
Penger, J., Conrad, R. & Blaser, M. Stable carbon isotope fractionation by methylotrophic methanogenic archaea. Appl. Environ. Microbiol. 78, 7596–7602 (2012).
Article ADS CAS PubMed PubMed Central Google Scholar
Grabowski, A., Blanchet, D. & Jeanthon, C. Characterization of long-chain fatty-acid-degrading syntrophic associations from a biodegraded oil reservoir. Res. Microbiol. 156, 814–821 (2005).
Article CAS PubMed Google Scholar
Pérez Castro, S. et al. Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. ISME J. 15, 3480–3497 (2021).
Article PubMed PubMed Central Google Scholar
Jay, Z. J., Kellom, M., Eloe-Fadrosh, E. & Hatzenpichler, R. Ecology of methyl-coenzyme M reductase encoding Thermoproteota. Curr. Opin. Microbiol. 89, 102699 (2026).
Article CAS PubMed Google Scholar
Davis, J. B. & Squires, R. M. Detection of microbially produced gaseous hydrocarbons other than methane. Science 119, 381–382 (1954).
Article ADS CAS PubMed Google Scholar
Milkov, A. V. & Etiope, G. Revised genetic diagrams for natural gases based on a global dataset of >20,000 samples. Org. Geochem. 125, 109–120 (2018).
Article ADS CAS Google Scholar
Defratyka, S. M. et al. Global inventory of doubly substituted isotopologues of methane (Δ13CH3D and Δ12CH2D2). Earth Syst. Sci. Data 17, 6889–6910 (2025).
Article ADS Google Scholar
Grosskopf, R., Janssen, P. H. & Liesack, W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64, 960–969 (1998).
Article ADS CAS PubMed PubMed Central Google Scholar
Takada Hoshino, Y. et al. Effect of soil type and fertilizer management on archaeal community in upland field soils. Microbes Environ. 26, 307–316 (2011).
Article Google Scholar
Hou, Q. et al. Design of primers for evaluation of lactic acid bacteria populations in complex biological samples. Front. Microbiol. 9, 2045 (2018).
Article PubMed PubMed Central Google Scholar
Jing, X. et al. The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate. Nat. Commun. 6, 8159 (2015).
Article ADS PubMed PubMed Central Google Scholar
Wu, K. et al. Gudongella oleilytica gen. nov., sp. nov., an aerotorelant bacterium isolated from Shengli oilfield and validation of family Tissierellaceae. Int. J. Syst. Evol. Microbiol. 70, 951–957 (2020).
Article CAS PubMed Google Scholar
Chen, Y. et al. The production of diverse brGDGTs by an Acidobacterium providing a physiological basis for paleoclimate proxies. Geochim. Cosmochim. Acta 337, 155–165 (2022).
Article ADS CAS Google Scholar
Zheng, F. et al. A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry. Nat. Commun. 17, 588 (2025).
Article ADS PubMed PubMed Central Google Scholar
Cheng, L. et al. DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLoS ONE 8, e66784 (2013).
Article ADS CAS PubMed PubMed Central Google Scholar
Cheng, L., Rui, J., Li, Q., Zhang, H. & Lu, Y. Enrichment and dynamics of novel syntrophs in a methanogenic hexadecane-degrading culture from a Chinese oilfield. FEMS Microbiol. Ecol. 83, 757–766 (2013).
Article CAS PubMed Google Scholar
Dissanayake, T. T. et al. Comparison of methods for the preparation of fatty acid methyl esters for the analysis of omega-3 rich oils by gas chromatography. J. Am. Oil Chem. Soc. 102, 1351–1361 (2025).
Article CAS Google Scholar
Hayes, J. M. Factors controlling 13C contents of sedimentary organic compounds: principles and evidence. Mar. Geol. 113, 111–125 (1993).
Article ADS CAS Google Scholar
Chi, Y. et al. Determination of carbonyl compounds in the atmosphere by DNPH derivatization and LC–ESI-MS/MS detection. Talanta 72, 539–545 (2007).
Article CAS PubMed Google Scholar
Peng, J., Lü, Z., Rui, J. & Lu, Y. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl. Environ. Microbiol. 74, 2894–2901 (2008).
Article ADS CAS PubMed PubMed Central Google Scholar
Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 13, 134 (2012).
Article CAS Google Scholar
Lane, D. J. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics (eds Stackebrandt, E. & Goodfellow, M.) 115–175 (John Wiley & Sons, 1991).
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. USA 108, 4516–4522 (2011).
Article ADS CAS PubMed Google Scholar
Chen, S. Fastp 1.0: an ultra-fast all-round tool for FASTQ data quality control and preprocessing. iMeta 4, e70078 (2025).
Article CAS PubMed PubMed Central Google Scholar
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Article ADS CAS PubMed PubMed Central Google Scholar
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Article CAS PubMed PubMed Central Google Scholar
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Article CAS PubMed Google Scholar
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Article CAS PubMed PubMed Central Google Scholar
Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203–1212 (2023).
Article CAS PubMed Google Scholar
Aramaki, T. et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).
Article CAS PubMed PubMed Central Google Scholar
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Article CAS PubMed PubMed Central Google Scholar
Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).
Article ADS CAS PubMed PubMed Central Google Scholar
Olson, S. A. EMBOSS opens up sequence analysis. Brief. Bioinform. 3, 87–91 (2002).
Article PubMed Google Scholar
Bushnell, B. BBMap: a fast, accurate, splice-aware aligner https://www.osti.gov/biblio/1241166 (OSTI, 2014).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Article CAS PubMed PubMed Central Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Article PubMed PubMed Central Google Scholar
Quinlan, A. R. BEDTools: the Swiss-army tool for genome feature analysis. Curr. Protoc. Bioinform. 47, 11.12.11–11.12.34 (2014).
Article Google Scholar
Wagner, G. P., Kin, K. & Lynch, V. J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131, 281–285 (2012).
Article CAS PubMed Google Scholar
Baker, B. A. et al. Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors. Nat. Microbiol. 10, 1593–1604 (2025).
Article CAS PubMed Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
Article Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Article CAS PubMed Google Scholar
Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).
Article CAS PubMed PubMed Central Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Article ADS PubMed PubMed Central Google Scholar
Thalén, F. PhyloPyPruner: Tree-Based Orthology Inference for Phylogenomics with New Methods for Identifying and Excluding Contamination. MSc. Thesis, Lund Univ. (2018).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Article CAS PubMed PubMed Central Google Scholar
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Article PubMed PubMed Central Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Article CAS PubMed PubMed Central Google Scholar
Tanizawa, Y., Fujisawa, T. & Nakamura, Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34, 1037–1039 (2018).
Article CAS PubMed PubMed Central Google Scholar
Wilkinson, L. ggplot2: elegant graphics for data analysis. Biometrics 67, 678–679 (2011).
Article Google Scholar