Liang, B. et al. Different diversity and distribution of archaeal community in the aqueous and oil phases of production fluid from high-temperature petroleum reservoirs. Front. Microbiol. 9, 841 (2018).
Li, X. X. et al. Diversity and composition of sulfate-reducing microbial communities based on genomic DNA and RNA transcription in production water of high temperature and corrosive oil reservoir. Front. Microbiol. 8, 1011 (2017).
Xu, D. et al. Simulation of in situ oil reservoir conditions in a laboratory bioreactor testing for methanogenic conversion of crude oil and analysis of the microbial community. Int. Biodeterior. Biodegrad. 136, 24–33 (2019).
Gao, P. et al. Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China. Sci. Rep. 6, 20174 (2016).
Mesle, M., Dromart, G. & Oger, P. Microbial methanogenesis in subsurface oil and coal. Res. Microbiol. 164, 959–972 (2013).
Sousa, D. Z. et al. The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways. Nat. Commun. 9, 239 (2018).
Lv, X. M. et al. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int. J. Syst. Evol. Microbiol. 70, 3361–3373 (2020).
Rotaru, A.-E. et al. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energy Environ. Sci. 7, 408–415 (2014).
Dong, X., Cheng, G. & Stams, A. J. M. Butyrate oxidation by Syntrophospora bryantii in co-culture with different methanogens and in pure culture with pentenoate as electron acceptor. Appl. Microbiol. Biotechnol. 42, 647–652 (1994).
Bryant, M. P., Wolin, E. A., Wolin, M. J. & Wolfe, R. S. Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch. Mikrobiol. 59, 20–31 (1967).
Fischer, P. Q., Sanchez-Andrea, I., Stams, A. J. M., Villanueva, L. & Sousa, D. Z. Anaerobic microbial methanol conversion in marine sediments. Environ. Microbiol. 23, 1348–1362 (2021).
Zhuang, G. C., Pena-Montenegro, T. D., Montgomery, A., Hunter, K. S. & Joye, S. B. Microbial metabolism of methanol and methylamine in the Gulf of Mexico: insight into marine carbon and nitrogen cycling. Environ. Microbiol. 20, 4543–4554 (2018).
Lomans, B. P. et al. Microbial populations involved in cycling of dimethyl sulfide and methanethiol in freshwater sediments. Appl. Environ. Microbiol. 67, 1044–1051 (2001).
Stacheter, A. et al. Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs. ISME J. 7, 1051–1064 (2013).
Sperfeld, M. et al. Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria. Nat. Microbiol. 9, 2006–2021 (2024).
Yang, G. C. et al. Formate-dependent microbial conversion of CO2 and the dominant pathways of methanogenesis in production water of high-temperature oil reservoirs amended with bicarbonate. Front. Microbiol. 7, 365 (2016).
Dong, X. & Stams, A. J. Evidence for H2 and formate formation during syntrophic butyrate and propionate degradation. Anaerobe 1, 35–39 (1995).
Nobu, M. K. et al. Thermodynamically diverse syntrophic aromatic compound catabolism. Environ. Microbiol. 19, 4576–4586 (2017).
McInerney, M. J. et al. Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann. N. Y. Acad. Sci. 1125, 58–72 (2008).
Schink, B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 61, 262–280 (1997).
Morris, B. E., Henneberger, R., Huber, H. & Moissl-Eichinger, C. Microbial syntrophy: interaction for the common good. FEMS Microbiol. Rev. 37, 384–406 (2013).
McInerney, M. J., Sieber, J. R. & Gunsalus, R. P. Syntrophy in anaerobic global carbon cycles. Curr. Opin. Biotechnol. 20, 623–632 (2009).
Boone, D. R., Johnson, R. L. & Liu, Y. Diffusion of the interspecies electron carriers H2 and formate in methanogenic ecosystems and its implications in the measurement of Km for H2 or formate uptake. Appl. Environ. Microbiol. 55, 1735–1741 (1989).
Thiele, J. H. & Zeikus, J. G. Control of interspecies electron flow during anaerobic digestion: significance of formate transfer versus hydrogen transfer during syntrophic methanogenesis in flocs. Appl. Environ. Microbiol. 54, 20–29 (1988).
Dong, X., Plugge, C. M. & Stams, A. J. Anaerobic degradation of propionate by a mesophilic acetogenic bacterium in coculture and triculture with different methanogens. Appl. Environ. Microbiol. 60, 2834–2838 (1994).
Rotaru, A. E. et al. Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri. Appl. Environ. Microbiol. 80, 4599–4605 (2014).
Cheng, L. et al. Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int. J. Syst. Evol. Microbiol. 57, 2964–2969 (2007).
Mayumi, D. et al. Methane production from coal by a single methanogen. Science 354, 222–225 (2016).
Worm, P., Müller, N., Plugge, C. M., Stams, A. J. M. & Schink, B. in (Endo)symbiotic Methanogenic Archaea Vol. 19 Microbiology Monographs (ed. Hackstein, J. H. P.) Ch. 9, 143–173 (Springer, 2010).
Ahring, B. K. & Westermann, P. Product inhibition of butyrate metabolism by acetate and hydrogen in a thermophilic coculture. Appl. Environ. Microbiol. 54, 2393–2397 (1988).
Lovley, D. R. & Holmes, D. E. Protein nanowires: the electrification of the microbial world and maybe our own. J. Bacteriol. 202, e00331-20 (2020).
Lovley, D. R. Syntrophy goes electric: direct interspecies electron transfer. Annu. Rev. Microbiol. 71, 643–664 (2017).
Kurth, J. M. et al. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. 15, 3549–3565 (2021).
Kleerebezem, R. & Stams, A. J. Kinetics of syntrophic cultures: a theoretical treatise on butyrate fermentation. Biotechnol. Bioeng. 67, 529–543 (2000).
Frock, A. D., Notey, J. S. & Kelly, R. M. The genus Thermotoga: recent developments. Environ. Technol. 31, 1169–1181 (2010).
Ying, X., Wang, Y., Badiei, H. R., Karanassios, V. & Ma, K. Purification and characterization of an iron-containing alcohol dehydrogenase in extremely thermophilic bacterium Thermotoga hypogea. Arch. Microbiol. 187, 499–510 (2007).
Nissen, L. S. & Basen, M. The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J. Biotechnol. 306, 105–117 (2019).
Hattori, S., Kamagata, Y., Hanada, S. & Shoun, H. Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 50, 1601–1609 (2000).
Guyot, J. P. & Brauman, A. Methane production from formate by syntrophic association of Methanobacterium bryantii and Desulfovibrio vulgaris JJ. Appl. Environ. Microbiol. 52, 1436–1437 (1986).
Dolfing, J., Jiang, B., Henstra, A. M., Stams, A. J. & Plugge, C. M. Syntrophic growth on formate: a new microbial niche in anoxic environments. Appl. Environ. Microbiol. 74, 6126–6131 (2008).
Kim, Y. J. et al. Formate-driven growth coupled with H2 production. Nature 467, 352–355 (2010).
Kallen, R. G. & Jencks, W. P. The mechanism of the condensation of formaldehyde with tetrahydrofolic acid. J. Biol. Chem. 241, 5851–5863 (1966).
Hanson, R. S. & Hanson, T. E. Methanotrophic bacteria. Microbiol. Rev. 60, 439–471 (1996).
Nobu, M. K. et al. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. 9, 1710–1722 (2015).
Podpora, B., Świderski, F., Sadowska, A., Rakowska, R. & Wasiak-Zys, G. Spent brewer’s yeast extracts as a new component of functional food. Czech J. Food Sci. 34, 554–563 (2016).
Nobu, M. K. et al. Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome 8, 111 (2020).
Schoelmerich, M. C., Katsyv, A., Donig, J., Hackmann, T. J. & Muller, V. Energy conservation involving 2 respiratory circuits. Proc. Natl Acad. Sci. USA 117, 1167–1173 (2020).
Kato, S., Sasaki, K., Watanabe, K., Yumoto, I. & Kamagata, Y. Physiological and transcriptomic analyses of the thermophilic, aceticlastic methanogen Methanosaeta thermophila responding to ammonia stress. Microbes Environ. 29, 162–167 (2014).
Kato, S., Yumoto, I. & Kamagata, Y. Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor. Appl. Environ. Microbiol. 81, 67–73 (2015).
Igarashi, K., Miyako, E. & Kato, S. Direct interspecies electron transfer mediated by graphene oxide-based materials. Front. Microbiol. 10, 3068 (2019).
Cheng, L. et al. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. PLoS ONE 9, e113253 (2014).
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36, 2253–2255 (2020).
Hunt, M. et al. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294 (2015).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).
Lowe, T. M. & Chan, P. P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44, W54–W57 (2016).
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108 (2007).
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Lu, S. et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 48, D265–D268 (2020).
Almagro Armenteros, J. J. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).
Hallgren, J. et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. Preprint at bioRxiv https://doi.org/10.1101/2022.04.08.487609 (2022).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Zhou, Z. et al. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature 601, 257–262 (2022).
Hanselmann, K. W. Microbial energetics applied to waste repositories. Experientia 47, 645–687 (1991).
Janssen, P. H. et al. Lactosphaera gen. nov., a new genus of lactic acid bacteria, and transfer of Ruminococcus pasteurii Schink 1984 to Lactosphaera pasteurii comb. nov. Int. J. Syst. Bacteriol. 45, 565–571 (1995).