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Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

  • 1.

    Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 1997;61:262–80.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 2.

    Vignais PM, Billoud B. Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 2007;107:4206–72.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 3.

    Wolf PG, Biswas A, Morales SE, Greening C, Gaskins HR. H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes. 2016;7:235–45.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 4.

    Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK, Steen JA, et al. Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature. 2017;552:400–3.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 5.

    Islam ZF, Welsh C, Bayly K, Grinter R, Southam G, Gagen EJ, et al. A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth. ISME J. 2020;14:2649–58.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 6.

    Greening C, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, et al. Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. ISME J. 2016;10:761–77.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 7.

    Amend JP, McCollom TM, Hentscher M, Bach W. Catabolic and anabolic energy for chemolithoautotrophs in deep-sea hydrothermal systems hosted in different rock types. Geochim Cosmochim Acta. 2011;75:5736–48.

    CAS 
    Article 

    Google Scholar 

  • 8.

    Reveillaud J, Reddington E, McDermott J, Algar C, Meyer JL, Sylva S, et al. Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Environ Microbiol. 2016;18:1970–87.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 9.

    Perner M, Hansen M, Seifert R, Strauss H, Koschinsky A, Petersen S. Linking geology, fluid chemistry, and microbial activity of basalt- and ultramafic-hosted deep-sea hydrothermal vent environments. Geobiology. 2013;11:340–55.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 10.

    Schubotz F, Hays LE, Meyer-Dombard D, Gillespie A, Shock EL, Summons RE. Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs. Front Microbiol. 2015;6:42.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 11.

    Fortunato CS, Huber JA. Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME J. 2016;10:1925–38.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 12.

    McNichol J, Stryhanyuk H, Sylva SP, Thomas F, Musat N, Seewald JS, et al. Primary productivity below the seafloor at deep-sea hot springs. Proc Natl Acad Sci USA. 2018;115:6756–61.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 13.

    Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, et al. Quantitative microbial ecology through stable isotope probing. Appl Environ Microbiol. 2015;81:7570–81.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 14.

    Coskun ÖK, Pichler M, Vargas S, Gilder S, Orsi WD. Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing. Appl Environ Microbiol 2018;84:e01083–18.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Tuorto SJ, Darias P, McGuinness LR, Panikov N, Zhang T, Häggblom MM, et al. Bacterial genome replication at subzero temperatures in permafrost. ISME J. 2014;8:139–49.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Maia M, Sichel S, Briais A, Brunelli D, Ligi M, Ferreira N, et al. Extreme mantle uplift and exhumation along a transpressive transform fault. Nat Geosci. 2016;9:619–23.

    CAS 
    Article 

    Google Scholar 

  • 17.

    Klein F, Tarnas JD, Bach W. Abiotic sources of molecular hydrogen on Earth. Elements. 2020;16:19–24.

    CAS 
    Article 

    Google Scholar 

  • 18.

    Seewald JS, Doherty KW, Hammar TR, Liberatore SP. A new gas-tight isobaric sampler for hydrothermal fluids. Deep Sea Res Part I. 2002;49:189–96.

    CAS 
    Article 

    Google Scholar 

  • 19.

    Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, et al. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. ISME J. 2016;10:2158–73.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    Vuillemin A, Wankel SD, Coskun OK, Magritsch T, Vargas S, Estes ER, et al. Archaea dominate oxic subseafloor communities over multimillion-year time scales. Sci Adv. 2019;5:eaaw4108.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Oremland RS, Miller LG, Whiticar MJ. Sources and flux of natural gases from Mono Lake, California. Geochim Cosmochim Acta. 1987;51:2915–29.

    CAS 
    Article 

    Google Scholar 

  • 22.

    Lang SQ, Butterfield DA, Schulte M, Kelley DS, Lilley MD. Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field. Geochim Cosmochim Acta. 2010;74:941–52.

    CAS 
    Article 

    Google Scholar 

  • 23.

    Butler IB, Schoonen MA, Rickard DT. Removal of dissolved oxygen from water: a comparison of four common techniques. Talanta. 1994;41:211–5.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Ortega-Arbulu AS, Pichler M, Vuillemin A, Orsi WD. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ Microbiol. 2019;21:374–88.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 25.

    Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol 2016;18:1403–14.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 26.

    Coskun ÖK, Özen V, SD Wankel SD, Orsi WD. Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O. ISME J. 2019;13:1546–59.

  • 27.

    Pichler M, Coskun ÖK, Ortega-Arbulú A-S, Conci N, Wörheide G, Vargas S, et al. A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform. Microbiologyopen 2018:7;e00611.

  • 28.

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    CAS 
    Article 

    Google Scholar 

  • 29.

    Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.

    CAS 
    Article 

    Google Scholar 

  • 30.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 32.

    Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, et al. Phylogenetic organization of bacterial activity. ISME J. 2016;10:2336.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 34.

    Youngblut ND, Barnett SE, Buckley DH. HTSSIP: an R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS ONE. 2018;13:e0189616.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 35.

    R. Team. Others, RStudio: integrated development for R. vol. 42. Boston, MA: RStudio, Inc; 2015. P. 14.

    Google Scholar 

  • 36.

    Blomberg SP, Garland T Jr, Ives AR. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution. 2003;57:717–45.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 37.

    Pagel M. Inferring the historical patterns of biological evolution. Nature. 1999;401:877–84.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Orsi WD, Morard R, Vuillemin A, Eitel M, Worheide G, Milucka J, et al. Anaerobic metabolism of Foraminifera thriving below the seafloor. ISME J. 2020;14:2580–94.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38:e191.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 40.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 41.

    Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12:e1001889.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 42.

    Sieradzki ET, Koch BJ, Greenlon A, Sachdeva R, Malmstrom RR, Mau RL, et al. Measurement error and resolution in quantitative stable isotope probing: implications for experimental design. mSystems. 2020;5:e00151–20.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 43.

    Youngblut ND, Barnett SE, Buckley DH. SIPSim: a modeling toolkit to predict accuracy and aid design of DNA-SIP experiments. Front Microbiol 2018;9:570.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 44.

    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 45.

    Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010;27:221–4.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 46.

    Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232–235.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 48.

    Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 49.

    Keck F, Rimet F, Bouchez A, Franc A. phylosignal: an R package to measure, test, and explore the phylogenetic signal. Ecol Evol 2016;6:2774–80.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 50.

    Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–90.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 51.

    Meier DV, Pjevac P, Bach W, Markert S, Schweder T, Jamieson J, et al. Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environ Microbiol. 2019;21:682–701.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 52.

    Lecoeuvre A, Menez B, Cannat M, Chavagnac V, Gerard E. Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge). ISME J. 2021;15:818–32.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 53.

    Mason OU, Di Meo-Savoie CA, Van Nostrand JD, Zhou J, Fisk MR, Giovannoni SJ. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J. 2009;3:231–42.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 54.

    Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lucker S, et al. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science. 2014;345:1052–4.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 55.

    Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL, Sogin ML, et al. Abundance and diversity of microbial life in ocean crust. Nature. 2008;453:653–7.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 56.

    Schrenk MO, Brazelton WJ, Lang SQ. Serpentinization, carbon, and deep life. Rev Mineral Geochem 2013;75:575–606.

    CAS 
    Article 

    Google Scholar 

  • 57.

    Klein F, Bach W, Humphris SE, Kahl W-A, Jöns N, Moskowitz B, et al. Magnetite in seafloor serpentinite—some like it hot. Geology. 2014;42:135–8.

    CAS 
    Article 

    Google Scholar 

  • 58.

    Kelley DS, Karson JA, Früh-Green GL, Yoerger DR, Shank TM, Butterfield DA, et al. A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science. 2005;307:1428–34.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 59.

    Wankel SD, Germanovich LN, Lilley MD, Genc G, DiPerna CJ, Bradley AS, et al. Influence of subsurface biosphere on geochemical fluxes from diffuse hydrothermal fluids. Nat Geosci. 2011;4:461–8.

    CAS 
    Article 

    Google Scholar 

  • 60.

    McDowall JS, Murphy BJ, Haumann M, Palmer T, Armstrong FA, Sargent F. Bacterial formate hydrogenlyase complex. Proc Natl Acad Sci USA. 2014;111:E3948–3956.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 61.

    Fones EM, Colman DR, Kraus EA, Stepanauskas R, Templeton AS, Spear JR, et al. Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation. ISME J. 2021;15:1121–35.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 62.

    Carr SA, Orcutt BN, Mandernack KW, Spear JR. Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica. Front Microbiol 2015;6:872.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 63.

    Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, et al. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME J. 2016;10:273–86.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 64.

    Schuchmann K, Müller V. Energetics and application of heterotrophy in acetogenic bacteria. Appl Environ Microbiol 2016;82:4056–69.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 65.

    Vuillemin A, Vargas S, Coskun OK, Pockalny R, Murray RW, Smith DC, et al. Atribacteria reproducing over millions of years in the Atlantic Abyssal subseafloor. mBio. 2020;11:e01937–20.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 66.

    Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499:431–7.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 67.

    Bryant FO, Adams MW. Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J Biol Chem 1989;264:5070–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 68.

    Berney M, Greening C, Conrad R, Jacobs WR Jr, Cook GM. An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia. Proc Natl Acad Sci USA 2014;111:11479–84.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 69.

    Kwan P, McIntosh CL, Jennings DP, Hopkins RC, Chandrayan SK, Wu C-H, et al. The [NiFe]-hydrogenase of Pyrococcus furiosus exhibits a new type of oxygen tolerance. J Am Chem Soc. 2015;137:13556–65.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 70.

    Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, et al. Cultivation and genomic analysis of “Candidatus Nitrosocaldus islandicus,” an obligately thermophilic, ammonia-oxidizing Thaumarchaeon from a hot spring biofilm in Graendalur Valley, Iceland. Front Microbiol. 2018;9:193.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    W Qin W, Amin SA, Martens-Habbena W, Walker CB, Urakawa H, Devol AH, et al. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. Proc Natl Acad Sci USA. 2014;111:12504–9.

    Article 
    CAS 

    Google Scholar 

  • 72.

    Seyler LM, McGuinness LR, Gilbert JA, Biddle JF, Gong D, Kerkhof LJ. Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic. FEMS Microbiol Ecol 2018;94:fiy014.

  • 73.

    Bristow LA, Dalsgaard T, Tiano L, Mills DB, Bertagnolli AD, Wright JJ, et al. Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters. Proc Natl Acad Sci USA. 2016;113:10601–6.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 74.

    Diaz R, Rosenberg R. Marine benthic hypoxia: a review of its ecological effects and the behavioural response of benthic macrofauna. Oceanogr Mar Biol. 1995;33:245–303.

    Google Scholar 

  • 75.

    Jenkins MC, Kemp WM. The coupling of nitrification and denitrification in two estuarine sediments. Limnol Oceanogr. 1984;29:609–19.

    CAS 
    Article 

    Google Scholar 

  • 76.

    Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM, Kelemen P, et al. Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman. Front Microbiol. 2017;8:56.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 77.

    Ragsdale SW. Life with carbon monoxide. Crit Rev Biochem Mol Biol. 2004;39:165–95.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 78.

    Fones EM, Colman DR, Kraus EA, Nothaft DB, Poudel S, Rempfert KR, et al. Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. ISME J. 2019;13:1750–62.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 79.

    Morrill PL, Brazelton WJ, Kohl L, Rietze A, Miles SM, Kavanagh H, et al. Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN. Front Microbiol. 2014;5:613.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 80.

    Wilcoxen J, Zhang B, Hille R. Reaction of the molybdenum- and copper-containing carbon monoxide dehydrogenase from Oligotropha carboxydovorans with quinones. Biochemistry. 2011;50:1910–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 81.

    Cordero PRF, Bayly K, Man Leung P, Huang C, Islam ZF, Schittenhelm RB, et al. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J. 2019;13:2868–81.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 82.

    Seewald JS, Zolotov MY, McCollom T. Experimental investigation of single carbon compounds under hydrothermal conditions. Geochim Cosmochim Acta. 2006;70:446–60.

    CAS 
    Article 

    Google Scholar 

  • 83.

    Can M, Armstrong FA, Ragsdale SW. Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase. Chem Rev. 2014;114:4149–74.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 84.

    Gudasz C, Bastviken D, Steger K, Premke K, Sobek S, Tranvik LJ. Temperature-controlled organic carbon mineralization in lake sediments. Nature. 2010;466:478–81.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 85.

    Katayama T, Nobu MK, Kusada H, Meng XY, Hosogi N, Uematsu K, et al. Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure. Nat Commun. 2020;11:6381.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 86.

    Brisbarre N, Fardeau M-L, Cueff V, Cayol J-L, Barbier G, Cilia V, et al. Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney. Int J Syst Evol Microbiol. 2003;53:1043–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 87.

    Roslev P, Larsen MB, Jørgensen D, Hesselsoe M. Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria. J Microbiol Methods. 2004;59:381–93.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 88.

    Spona-Friedl M, Braun A, Huber C, Eisenreich W, Griebler C, Kappler A, et al. Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling. FEMS Microbiol Ecol 2020;96:fiaa080.

  • 89.

    Jansen K, Thauer RK, Widdel F, Fuchs G. Carbon assimilation pathways in sulfate reducing bacteria. Formate, carbon dioxide, carbon monoxide, and acetate assimilation by Desulfovibrio baarsii. Arch Microbiol. 1984;138:257–62.

    CAS 
    Article 

    Google Scholar 

  • 90.

    Braun A, Spona-Friedl M, Avramov M, Elsner M, Baltar F, Reinthaler T, et al. Reviews and syntheses: heterotrophic fixation of inorganic carbon—significant but invisible flux in global carbon cycling. Biogeosciences 2020;18:3689–3700.

  • 91.

    Russell MJ, Hall AJ, Martin W. Serpentinization as a source of energy at the origin of life. Geobiology. 2010;8:355–71. https://doi.org/10.1111/j.1472-4669.2010.00249.x

  • 92.

    Martin W, Baross J, Kelley D, Russell MJ. Hydrothermal vents and the origin of life. Nat Rev Microbiol. 2008;6:805–14. 10.1038/nrmicro1991.


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