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Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site

  • 1.

    Macdonald IR, Guinasso NL, Sassen R, Brooks JM, Lee L, Scott KT. Gas hydrate that breaches the sea-floor on the continental-slope of the Gulf-of-Mexico. Geology. 1994;22:699–702.

    CAS 

    Google Scholar 

  • 2.

    Kvenvolden KA. A review of the geochemistry of methane in natural gas hydrate. Org Geochem. 1995;23:997–1008.

    CAS 

    Google Scholar 

  • 3.

    Milkov AV. Molecular and stable isotope compositions of natural gas hydrates: a revised global dataset and basic interpretations in the context of geological settings. Org Geochem. 2005;36:681–702.

    CAS 

    Google Scholar 

  • 4.

    Cragg BA, Parkes RJ, Fry JC, Weightman AJ, Rochelle PA, Maxwell JR. Bacterial populations and processes in sediments containing gas hydrates (ODP Leg 146: Cascadia Margin). Earth Planet Sc Lett. 1996;139:497–507.

    CAS 

    Google Scholar 

  • 5.

    Yoshioka H, Maruyama A, Nakamura T, Higashi Y, Fuse H, Sakata S, et al. Activities and distribution of methanogenic and methane-oxidizing microbes in marine sediments from the Cascadia Margin. Geobiology. 2010;8:223–33.

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    Yoshioka H, Sakata S, Cragg BA, Parkes RJ, Fujii T. Microbial methane production rates in gas hydrate-bearing sediments from the eastern Nankai Trough, off central Japan. Geochem J. 2009;43:315–21.

    CAS 

    Google Scholar 

  • 7.

    Heuer VB, Inagaki F, Morono Y, Kubo Y, Spivack AJ, Viehweger B, et al. Temperature limits to deep subseafloor life in the Nankai Trough subduction zone. Science. 2020;370:1230–4.

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Wellsbury P, Goodman K, Cragg BA, Parkes RJ. The geomicrobiology of deep marine sediments from Blake Ridge containing methane hydrate (sites 994, 995 and 997). Proc Ocean Drill Program Sci results. 2000;164:379–91.

    Google Scholar 

  • 9.

    Bidle KA, Kastner M, Bartlett DH. A phylogenetic analysis of microbial communities associated with methane hydrate containing marine fluids and sediments in the Cascadia margin (ODP site 892B). Fems Microbiol Lett. 1999;177:101–8.

    CAS 
    PubMed 

    Google Scholar 

  • 10.

    Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, et al. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol. 2002;68:3759–70.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Briggs BR, Inagaki F, Morono Y, Futagami T, Huguet C, Rosell-Mele A, et al. Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol Ecol. 2012;81:88–98.

    CAS 
    PubMed 

    Google Scholar 

  • 12.

    Kendall MM, Boone DR. Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon. Archaea. 2006;2:31–38.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol. 2008;66:181–96.

    CAS 
    PubMed 

    Google Scholar 

  • 14.

    Nunoura T, Takaki Y, Shimamura S, Kakuta J, Kazama H, Hirai M, et al. Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan. Environ Microbiol. 2016;18:1889–906.

    CAS 
    PubMed 

    Google Scholar 

  • 15.

    Mikucki JA, Liu Y, Delwiche M, Colwell FS, Boone DR. Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl Environ Microbiol. 2003;69:3311–6.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 16.

    Weng C-Y, Chen S-C, Lai M-C, Wu S-Y, Lin S, Yang TF, et al. Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan. Int J Syst Evol Micr. 2015;65:1044–9.

    CAS 

    Google Scholar 

  • 17.

    Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB, Boone DR. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol. 2006;56:1525–9.

    CAS 
    PubMed 

    Google Scholar 

  • 18.

    Strąpoć D, Ashby M, Wood L, Levinson R, Huizinga B. Significant contribution of methyl/methanol-utilising methanogenic pathway in a subsurface biogas environment. In: Skovhus T, Whitby C, editors. Applied microbiology and molecular biology in oilfield systems. Dordrecht: Springer; 2010. p. 211–6.

  • 19.

    Guo H, Liu R, Yu Z, Zhang H, Yun J, Li Y, et al. Pyrosequencing reveals the dominance of methylotrophic methanogenesis in a coal bed methane reservoir associated with Eastern Ordos Basin in China. Int J Coal Geol. 2012;93:56–61.

    CAS 

    Google Scholar 

  • 20.

    Katayama T, Yoshioka H, Muramoto Y, Usami J, Fujiwara K, Yoshida S, et al. Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers. ISME J. 2015;9:436–46.

    CAS 
    PubMed 

    Google Scholar 

  • 21.

    Yanagawa K, Tani A, Yamamoto N, Hachikubo A, Kano A, Matsumoto R, et al. Biogeochemical cycle of methanol in anoxic deep-sea sediments. Microbes Environ. 2016;31:190–3.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 22.

    Colwell F, Matsumoto R, Reed D. A review of the gas hydrates, geology, and biology of the Nankai Trough. Chem Geol. 2004;205:391–404.

    CAS 

    Google Scholar 

  • 23.

    Uchida T, Waseda A, Namikawa T. Methane accumulation and high concentration of gas hydrate in marine and terrestrial sandy sediments. In: Collett T, Johnson A, Knapp C, Boswell R, editors. Natural gas hydrates: energy resource potential and associated geologic hazards. Tulsa: American Association of Petroleum Geologists Memoir 89; 2009. p. 401–13.

  • 24.

    Katayama T, Yoshioka H, Takahashi HA, Amo M, Fujii T, Sakata S. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough. FEMS Microbiol Ecol. 2016;92:fiw093.

    PubMed 

    Google Scholar 

  • 25.

    Oba M, Sakata S, Fujii T. Archaeal polar lipids in subseafloor sediments from the Nankai Trough: Implications for the distribution of methanogens in the deep marine subsurface. Org Geochem. 2015;78:153–60.

    CAS 

    Google Scholar 

  • 26.

    Noguchi S, Shimoda N, Takano O, Oikawa N, Inamori T, Saeki T, et al. 3-D internal architecture of methane hydrate-bearing turbidite channels in the eastern Nankai Trough, Japan. Mar Pet Geol. 2011;28:1817–28.

    Google Scholar 

  • 27.

    Fujii T, Suzuki K, Takayama T, Tamaki M, Komatsu Y, Konno Y, et al. Geological setting and characterization of a methane hydrate reservoir distributed at the first offshore production test site on the Daini-Atsumi Knoll in the eastern Nankai Trough, Japan. Mar Pet Geol. 2015;66:310–22.

    CAS 

    Google Scholar 

  • 28.

    Kanno T, Fukuhara M, Osawa O, Chee S, Takekoshi M, Wang X, et al. Estimation of geothermal gradient in marine gas-hydrate-bearing formation in the Eastern Nankai Trough. Beijing, China: Proceedings of the 8th International Conference on Gas Hydrates (ICGH8–2014); 2014.

  • 29.

    Kaneko M, Takano Y, Ogawa NO, Sato Y, Yoshida N, Ohkouchi N. Estimation of methanogenesis by quantification of coenzyme F430 in marine sediments. Geochem J. 2016;50:453–60.

    CAS 

    Google Scholar 

  • 30.

    Kaneko M, Takano Y, Chikaraishi Y, Ogawa NO, Asakawa S, Watanabe T, et al. Quantitative analysis of coenzyme F430 in environmental samples: a new diagnostic tool for methanogenesis and anaerobic methane oxidation. Anal Chem. 2014;86:3633–8.

    CAS 
    PubMed 

    Google Scholar 

  • 31.

    Katayama T, Kamagata Y Cultivation of Methanogens. Hydrocarbon and lipid microbiology protocols. In: McGenity T, Timmis K, Nogales B, editors. Springer protocols handbooks. Berlin, Heidelberg: Springer; 2016. p. 177–95.

  • 32.

    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–96.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 34.

    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Jobb G, von Haeseler A, Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 2004;4:18.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Whiticar MJ. Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem Geol. 1999;161:291–314.

    CAS 

    Google Scholar 

  • 37.

    Scheller S, Goenrich M, Thauer RK, Jaun B. Methyl-coenzyme M reductase from methanogenic archaea: Isotope effects on the formation and anaerobic oxidation of methane. J Am Chem Soc. 2013;135:14975–84.

    CAS 
    PubMed 

    Google Scholar 

  • 38.

    Diekert G, Konheiser U, Piechulla K, Thauer RK. Nickel requirement and factor F430 content of methanogenic bacteria. J Bacteriol. 1981;148:459–64.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Mayr S, Latkoczy C, Krüger M, Günther D, Shima S, Thauer RK, et al. Structure of an F430 variant from archaea associated with anaerobic oxidation of methane. J Am Chem Soc. 2008;130:10758–67.

    CAS 
    PubMed 

    Google Scholar 

  • 40.

    House CH, Orphan VJ, Turk KA, Thomas B, Pernthaler A, Vrentas JM, et al. Extensive carbon isotopic heterogeneity among methane seep microbiota. Environ Microbiol. 2009;11:2207–15.

    CAS 
    PubMed 

    Google Scholar 

  • 41.

    Lloyd KG, Alperin MJ, Teske A. Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea. Environ Microbiol. 2011;13:2548–64.

    CAS 
    PubMed 

    Google Scholar 

  • 42.

    Laso-Pérez R, Wegener G, Knittel K, Widdel F, Harding KJ, Krukenberg V, et al. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature. 2016;539:396–401.

    PubMed 

    Google Scholar 

  • 43.

    Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, et al. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA. 2006;103:2815–20.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 44.

    Marchesi JR, Weightman AJ, Cragg BA, Parkes RJ, Fry JC. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol Ecol. 2001;34:221–8.

    CAS 
    PubMed 

    Google Scholar 

  • 45.

    Nunoura T, Inagaki F, Delwiche ME, Colwell FS, Takai K. Subseafloor microbial communities in methane hydrate-bearing sediment at two distinct locations (ODP Leg 204) in the Cascadia Margin. Microbes Environ. 2008;23:317–25.

    PubMed 

    Google Scholar 

  • 46.

    Cord-Ruwisch R, Ollivier B. Interspecific hydrogen transfer during methanol degradation by Sporomusa acidovorans and hydrogenophilic anaerobes. Arch Microbiol. 1986;144:163–5.

    CAS 

    Google Scholar 

  • 47.

    Heijthuijsen JHFG, Hansen TA. Interspecies hydrogen transfer in co-cultures of methanol-utilizing acidogens and sulfate-reducing or methanogenic bacteria. FEMS Microbiol Ecol. 1986;2:57–64.

    Google Scholar 

  • 48.

    Eichler B, Schink B. Oxidation of primary aliphatic alcohols by Acetobacterium carbinolicum sp. nov., a homoacetogenic anaerobe. Arch Microbiol. 1984;140:147–52.

    CAS 

    Google Scholar 

  • 49.

    Parkes RJ, Cragg B, Roussel E, Webster G, Weightman A, Sass H. A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere: geosphere interactions. Mar Geol. 2014;352:409–25.

    CAS 

    Google Scholar 

  • 50.

    Imachi H, Aoi K, Tasumi E, Saito Y, Yamanaka Y, Saito Y, et al. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J. 2011;5:1913–25.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 51.

    Newberry CJ, Webster G, Cragg BA, Parkes RJ, Weightman AJ, Fry JC. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ Microbiol. 2004;6:274–87.

    PubMed 

    Google Scholar 

  • 52.

    Orsi WD, Edgcomb VP, Christman GD, Biddle JF. Gene expression in the deep biosphere. Nature 2013;499:205–8.

    CAS 
    PubMed 

    Google Scholar 

  • 53.

    Vigneron A, L’Haridon S, Godfroy A, Roussel EG, Cragg BA, Parkes RJ, et al. Evidence of active methanogen communities in shallow sediments of the sonora margin cold seeps. Appl Environ Microbiol. 2015;81:3451–9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 


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