Microbial Community Compositions and Geochemistry of Sediments with Increasing Distance to the Hydrothermal Vent Outlet in the Kairei Field

References

• Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 57:289–300.
   Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120.
   PubMed Web of Science ®Google Scholar
• Bruins MR, Kapil S, Oehme FW. 2000. Microbial resistance to metals in the environment. Ecotoxicol Environ Saf 45(3):198–207.
   PubMed Web of Science ®Google Scholar
• Bryce C, Blackwell N, Schmidt C, Otte J, Huang YM, Kleindienst S, Tomaszewski E, Schad M, Warter V, Peng C, et al. 2018. Microbial anaerobic Fe(II) oxidation: ecology, mechanisms and environmental implications. Environ Microbiol 20(10):3462–3483.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data [Letter Research Support, American Recovery and Reinvestment Act Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't]. Nat Methods 7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Carr SA, Vogel SW, Dunbar RB, Brandes J, Spear JR, Levy R, Naish TR, Powell RD, Wakeham SG, Mandernack KW. 2013. Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica. Geobiology 11(4):377–395.
   PubMed Web of Science ®Google Scholar
• Cerqueira T, Pinho D, Egas C, Froufe H, Altermark B, Candeias C, Santos RS, Bettencourt R. 2015. Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge. Mar Genomics 24:343–355.
   PubMed Web of Science ®Google Scholar
• Cerqueira T, Pinho D, Froufe H, Santos R S, Bettencourt R, Egas C. 2017. Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores. Microb Ecol. 74(2):332–349. 28144700 doi:10.1007/s00248-017-0943-9.
   PubMed Web of Science ®Google Scholar
• Cheung KH, Gu J-D. 2005. Chromate reduction by Bacillus megaterium TKW3 isolated from marine sediments. World J Microbiol Biotechnol 21(3):213–219.
   Web of Science ®Google Scholar
• Chobotar'ov A, Hodiienko AS, Kurdysh IK. 2010. Influence of natural minerals on growth of Azotobacter vinelandii IMV B-7076. Mikrobiol Z 72(5):27–31.
   PubMedGoogle Scholar
• Chobotar'ov A, Hordiienko AS, Samchuk AI, Kurdysh IK. 2010. Influence of silicon dioxide and saponite on growth of Bacillus subtilis IMV B-7023. Mikrobiol Z 72(4):33–39.
   PubMedGoogle Scholar
• Coogan LA, Attar A, Mihaly SF, Jeffries M, Pope M. 2017. Near-vent chemical processes in a hydrothermal plume: insights from an integrated study of the endeavour segment. Geochem Geophys Geosyst 18(4):1641–1660.
   Web of Science ®Google Scholar
• Costa UR, Fyfe WS, Kerrich R, Nesbitt HW. 1980. Archaean hydrothermal talc evidence for high ocean temperatures. Chem Geol 30(4):341–349.
   Web of Science ®Google Scholar
• Dahl C, Friedrich CG. 2008. Microbial Sulfur Metbolism. Heidelberg: Springer.
   Google Scholar
• Ding J, Zhang Y, Wang H, Jian H, Leng H, Xiao X. 2017. Microbial community structure of deep-sea hydrothermal vents on the ultraslow spreading southwest Indian ridge. Front Microbiol 8:1012.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461.
   PubMed Web of Science ®Google Scholar
• Garbe-Schönberg C. 1993. Simultaneous determination of thirty-seven trace elements in twenty-eight international rock standards by ICP-MS. Geostand Newslett 17(1):81–97.
   Web of Science ®Google Scholar
• Geptner A, Kristmannsdottir H, Kristjansson J, Marteinsson V. 2002. Biogenic saponite from an active submarine hot spring, Iceland. Clays Clay Miner 50(2):174–185.
   Web of Science ®Google Scholar
• Gonnella G, Böhnke S, Indenbirken D, Garbe-Schönberg D, Seifert R, Mertens C, Kurtz S, Perner M. 2016. Endemic hydrothermal vent species identified in the open ocean seed bank. Nat Microbiol.1(8):16086.
   PubMed Web of Science ®Google Scholar
• Han Y, Gonnella G, Adam N, Schippers A, Burkhardt L, Kurtz S, Schwarz-Schampera U, Franke H, Perner M. 2018. Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits. Sci Rep 8(1):10386.
   PubMed Web of Science ®Google Scholar
• Hashimoto J, Ohta S, Gamo T, Chiba H, Yamaguchi T, Tsuchida S, Okudaira T, Watabe H, Yamanaka T, Kitazawa M. 2001. First hydrothermal vent communities from the Indian Ocean discovered. Zool Sci 18(5):717–721.
   Web of Science ®Google Scholar
• Heggie D, Lewis T. 1984. Cobalt in porewaters of marine sediments. Nature 311(5985):453–455.
   Web of Science ®Google Scholar
• Huber H, Stetter K. 2006. Thermoplasmatales. In: Dworkin M, Falkow S, Rosenberg E, editors. The Prokaryotes. Berlin: Springer, p101–112.
   Google Scholar
• Johnston CW, Wyatt MA, Li X, Ibrahim A, Shuster J, Southam G, Magarvey NA. 2013. Gold biomineralization by a metallophore from a gold-associated microbe. Nat Chem Biol 9(4):241.
   PubMed Web of Science ®Google Scholar
• Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D'Hondt S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA 109(40):16213–16216.
   PubMed Web of Science ®Google Scholar
• Kawaichi S, Ito N, Kamikawa R, Sugawara T, Yoshida T, Sako Y. 2013. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. Int J Syst Evol Microbiol 63(Pt 8):2992–3002.
   PubMed Web of Science ®Google Scholar
• Kelley DS, Baross JA, Delaney JR. 2002. Volcanoes, fluids, and life at mid-ocean ridge spreading centers. Annu Rev Earth Planet Sci 30(1):385–491.
   Web of Science ®Google Scholar
• Kessler D. 2006. Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes. FEMS Microbiol Rev 30(6):825–840.
   PubMed Web of Science ®Google Scholar
• Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1.
   PubMed Web of Science ®Google Scholar
• Klinkhammer GP, Heggie DT, Graham DW. 1982. Metal diagenesis in oxic marine sediments. Earth Planet Sc Lett 61(2):211–219.
   Web of Science ®Google Scholar
• Koch H, Galushko A, Albertsen M, Schintlmeister A, Gruber-Dorninger C, Lucker S, Pelletier E, Le Paslier D, Spieck E, Richter A, et al. 2014. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 345(6200):1052–1054.
   PubMed Web of Science ®Google Scholar
• Koch H, Lucker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, Nielsen PH, Wagner M, Daims H. 2015. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci USA 112(36):11371–11376.
   PubMed Web of Science ®Google Scholar
• Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437(7058):543–546.
   PubMed Web of Science ®Google Scholar
• Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ. 2017. SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. MBio 8(2):e00413–00417.
   PubMed Web of Science ®Google Scholar
• Lunau M, Lemke A, Walther K, Martens-Habbena W, Simon M. 2005. An improved method for counting bacteria from sediments and turbid environments by epifluorescence microscopy. Environ Microbiol 7(7):961–968.
   PubMed Web of Science ®Google Scholar
• Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. 2015. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 282(23):4480–4496.
   PubMed Web of Science ®Google Scholar
• Mehrshad M, Rodriguez-Valera F, Amoozegar MA, Lopez-Garcia P, Ghai R. 2018. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. ISME J 12(3):655–668.
   PubMed Web of Science ®Google Scholar
• Metz S, Trefry JH, Nelsen TA. 1988. History and geochemistry of a metalliferous sediment core from the Mid-Atlantic Ridge at 26°N. Geochim Cosmochim Acta 52(10):2369–2378.
   Web of Science ®Google Scholar
• Mills R, Elderfield H, Thomson J. 1993. A dual origin for the hydrothermal component in a metalliferous sediment core from the mid-Atlantic ridge. J Geophys Res 98(B6):9671–9681.
   Web of Science ®Google Scholar
• Møller MH, Glombitza C, Lever MA, Deng L, Morono Y, Inagaki F, Doll M, Su CC, Lomstein BA. 2018. d:l-Amino acid modeling reveals fast microbial turnover of days to months in the subsurface hydrothermal sediment of Guaymas basin. Front Microbiol 9:967.
   PubMed Web of Science ®Google Scholar
• Moussard H, L'Haridon S, Tindall BJ, Banta A, Schumann P, Stackebrandt E, Reysenbach AL, Jeanthon C. 2004. Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 54(Pt 1):227–233.
   PubMed Web of Science ®Google Scholar
• Nakagawa T, Nakagawa S, Inagaki F, Takai K, Horikoshi K. 2004. Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures. FEMS Microbiol Lett 232(2):145.
   PubMed Web of Science ®Google Scholar
• Nercessian O, Fouquet Y, Pierre C, Prieur D, Jeanthon C. 2005. Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ Microbiol 7(5):698–714.
   PubMed Web of Science ®Google Scholar
• Nunoura T, Oida H, Nakaseama M, Kosaka A, Ohkubo SB, Kikuchi T, Kazama H, Hosoi-Tanabe S, Nakamura K, Kinoshita M, et al. 2010. Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough. Appl Environ Microb 76(4):1198–1211.
   PubMed Web of Science ®Google Scholar
• Oksanen J, Blanchet F, Guillaume Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, et al. 2018. Vegan: Community Ecology Package. R package Version 2.5–3. Accessed. Available at https://CRAN.R-project.org/package=vegan.
   Google Scholar
• Peng T, Xu Y, Zhang Y. 2018. Comparative genomics of molybdenum utilization in prokaryotes and eukaryotes. BMC Genomics 19(1):691.
   PubMed Web of Science ®Google Scholar
• Pernthaler A, Pernthaler J, Amann R. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68(6):3094–3101.
   PubMed Web of Science ®Google Scholar
• Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, et al. 2014. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. Peer J 2:e545.
   PubMed Web of Science ®Google Scholar
• Sawlan JL, Murray JW. 1983. Trace metal remobilization in the interstitial waters of red clay and hemipelagic marine sediments. Earth Planet Sci Lett 64(2):213–230.
   Web of Science ®Google Scholar
• Schippers A, et al. 2016. Deep biosphere. In: Harff J, Meschede M, Petersen S, editors. Encyclopedia of Marine Geosciences. Dordrecht: Springer Science + Business Media.
   Google Scholar
• Singh Y, Ramteke PW, Tripathy A, Shukla PK. 2013. Isolation and characterization of Bacillus resistant to multiple heavy metals. Int J Curr Microbiol Appl Sci 2(11):525–530.
   Google Scholar
• Sorokin DY, Vejmelkova D, Lucker S, Streshinskaya GM, Rijpstra WI, Sinninghe Damste JS, Kleerbezem R, van Loosdrecht M, Muyzer G, Daims H. 2014. Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi. Int J Syst Evol Microbiol 64(Pt 6):1859–1865.
   PubMed Web of Science ®Google Scholar
• Suzuki Y, Inagaki F, Takai K, Nealson KH, Horikoshi K. 2004. Microbial diversity in inactive chimney structures from deep-sea hydrothermal systems. Microbial Ecol 47(2):186–196.
   PubMed Web of Science ®Google Scholar
• Takai K, Gamo T, Tsunogai U, Nakayama N, Hirayama H, Nealson KH, Horikoshi K. 2004. Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles 8(4):269–282.
   PubMed Web of Science ®Google Scholar
• Takai K, Nealson KH, Horikoshi K. 2004. Hydrogenimonas thermophila gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing chemolithoautotroph within the ε-Proteobacteria, isolated from a black smoker in a Central Indian Ridge hydrothermal field. Int J Syst Evol Microbiol 54(1):25–32.
   PubMed Web of Science ®Google Scholar
• Teske A, Callaghan AV, LaRowe DE. 2014. Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin. Front Microbiol 5:362.
   PubMed Web of Science ®Google Scholar
• Teske A, Hinrichs KU, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microb 68(4):1994–2007.
   PubMed Web of Science ®Google Scholar
• Thiel V, Hamilton TL, Tomsho LP, Burhans R, Gay SE, Schuster SC, Ward DM, Bryant DA. 2014. Draft genome sequence of a sulfide-oxidizing, autotrophic filamentous anoxygenic phototrophic bacterium. Chloroflexus Sp. strain MS-G (Chloroflexi). Genome Announce. 2(5):e00872–e00914.
   PubMedGoogle Scholar
• Van Dover CL, Humphris SE, Fornari D, Cavanaugh CM, Collier R, Goffredi SK, Hashimoto J, Lilley MD, Reysenbach AL, Shank TM, et al. 2001. Biogeography and ecological setting of Indian Ocean hydrothermal vents. Science 294(5543):818–823.
   PubMed Web of Science ®Google Scholar
• Vignais PM, Billoud B. 2007. Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 107(10):4206–4272.
   PubMed Web of Science ®Google Scholar
• Volesky B, Holan ZR. 1995. Biosorption of heavy metals. Biotechnol Prog 11(3):235–250.
   PubMed Web of Science ®Google Scholar
• Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, et al. 2018. Erratum: addendum: comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 9:772.
   PubMed Web of Science ®Google Scholar
• Wang Y, Han X, Jin X, Qiu Z, Ma Z, Yang H. 2012. Hydrothermal activiy events at Kairei Field, Central Indian Ridge 25°S. Resour Geol 62(2):208–214.
   Web of Science ®Google Scholar
• Wei M, Zhang R, Wang Y, Ji H, Zheng J, Chen X, Zhou H. 2013. Microbial community structure and diversity in deep-sea hydrothermal vent sediments along the Eastern Lau Spreading Centre. Acta Oceanol Sin 32(2):42–51.
   Web of Science ®Google Scholar
• Winter JM, Moore BS. 2009. Exploring the chemistry and biology of vanadium-dependent haloperoxidases. J Biol Chem 284(28):18577–18581.
   PubMed Web of Science ®Google Scholar
• Yilmaz EI. 2003. Metal tolerance and biosorption capacity of Bacillus circulans strain EB1. Res Microbiol 154(6):409–415.
   PubMed Web of Science ®Google Scholar
• Zhang J, Sun QL, Zeng ZG, Chen S, Sun L. 2015. Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough. Microbiol Res 177:43–52.
   PubMed Web of Science ®Google Scholar
• Zhang L, Kang M, Xu J, Xu J, Shuai Y, Zhou X, Yang Z, Ma K. 2016. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge. Sci Rep 6(1):25982.
   PubMed Web of Science ®Google Scholar
• Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DB, Martiny JB, Sogin M, Boetius A, Ramette A. 2011. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One 6(9):e24570.
   PubMed Web of Science ®Google Scholar