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Hydrocarbon-Degrading Microbial Communities in Natural Oil Seeps

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Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

Hydrocarbons in natural oil seeps provide carbon and energy sources for extensive and diverse microbial communities. This chapter provides an introduction to sulfate-reducing, methanogenic, and methane- or alkane-oxidizing anaerobic microbial populations from hydrocarbon-rich marine habitats. Persistent enrichment and cultivation efforts and pure culture studies have greatly increased the recognized diversity of cultured, hydrocarbon-oxidizing microorganisms and the knowledge of their substrate spectra, habitat preferences, and ecophysiological function in their natural environments. This chapter highlights model ecosystems where diverse hydrocarbon-oxidizing microbial communities are sustained by fossil hydrocarbons; characteristic examples are the hydrocarbon seeps in the Gulf of Mexico, where deeply sourced hydrocarbons of Jurassic origin are rising through extensive sediment layers that are fractured by salt tectonics, and the hydrothermal Guaymas Basin in the Gulf of California, where buried organic matter of photosynthetic origin, which is undergoing thermal maturation, is transformed into young petroleum within the upper sediment layers. These examples provide surface expressions of subsurface hydrocarbon reservoirs and their microbiota. The microbial communities in hydrocarbon seeps and reservoirs reflect the spectrum of carbon substrates and electron donors and the wide range of physical conditions that characterize these habitats.

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References

  • Aeckersberg F, Bak F, Widdel F (1991) Anaerobic oxidation of saturated hydrocarbons to CO2 by a new type of sulfate-reducing bacterium. Arch Microbiol 156:5–14

    Article  CAS  Google Scholar 

  • Aeckersberg F, Rainey F, Widdel F (1998) Growth, natural relationships, cellular fatty acids and metabolic adaptation of sulfate-reducing bacteria that utilize long-chain alkanes under anoxic conditions. Arch Microbiol 170:361–369

    Article  CAS  PubMed  Google Scholar 

  • Ahn Y-B, Chae J-C, Zylstra GJ, Häggblom MM (2009) Degradation of phenol via phenylphosphate and carboxylation to 4- hydroxybenzoate by a newly isolated strain of the sulfate-reducing bacterium Desulfobacterium anilini. Appl Environ Microbiol 75:4248–4253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amend JP, Teske A (2005) Expanding frontiers in deep subsurface microbiology. Palaeogeogr Palaeoclimatol Palaeoecol 219:131–155

    Article  Google Scholar 

  • Amos S (1987) Late Triassic-Jurassic paleogeography and origin of Gulf of Mexico Basin. AAPG Bull 71(4):419–451

    Google Scholar 

  • Bahr M, Crump BC, Klepac-Ceraj V, Teske A, Sogin ML, Hobbie JE (2005) Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 7:1175–1185

    Article  CAS  PubMed  Google Scholar 

  • Bak F, Widdel F (1986) Anaerobic degradation of phenol and phenol derivatives by Desulfobacterium phenolicum. Arch Microbiol 146:177–180

    Article  CAS  Google Scholar 

  • Balk M, Altinbas M, Rijpstra WIC, Sinninghe Damste JS, Stams AJM (2008) Desulfatirhabdium butyrativorans gen nov., sp. nov., a butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic bioreactor. Int J Syst Evol Microbiol 58:110–115

    Article  CAS  PubMed  Google Scholar 

  • Bazylinski DA, Farrington JW, Jannasch HW (1988) Hydrocarbons in surface sediments from a Guaymas Basin hydrothermal vent site. Org Geochem 12:547–558

    Article  CAS  Google Scholar 

  • Beeder J, Nilsen RK, Rosnes JT, Torsvik T, Lien T (1994) Archaeoglobus fulgidus isolated from hot north sea oil field waters. Appl Environ Microbiol 60:1227–1231

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beeder J, Torsvik T, Lien T (1995) Thermodesulforhabdus norvegicus gen. nov., sp. nov., a novel thermophilic sulfate-reducing bacterium from oil field water. Arch Microbiol 164:331–336

    Article  CAS  PubMed  Google Scholar 

  • Berndt C, Hensen C, Mortera-Gutierrez C, Sarkar S, Geilert S, Schmidt M, Liebetrau V, Kipfer R, Scholz F, Doll M, Muff S, Karstens J, Planke S, Petersen S, Böttner C, Chi W-C, Moser M, Behrendt R, Fiskal A, Lever MA, Su C-C, Deng L, Brennwald MS, Lizarralde D (2016) Rifting under steam – how magmatism triggers methane venting from sedimentary basins. Geology 44:767–770

    Google Scholar 

  • Biddle JF, Lipp JS, Lever M, Lloyd K, Sørensen K, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs K-U (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci USA 103:3846–3851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biddle JF, Cardman Z, Mendlovitz H, Albert DB, Lloyd KG, Boetius A, Teske A (2012) Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J 6:1018–1031

    Article  CAS  PubMed  Google Scholar 

  • Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW, Brugère JF (2014) Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15:1–23

    Article  CAS  Google Scholar 

  • Bowles MW, Samarkin VA, Bowles K, Joye SB (2011) Weak coupling between sulfate reduction and the anaerobic oxidation of methane in methane-rich seafloor sediments during ex-situ incubation. Geochim Cosmochim Acta 75:500–519

    Article  CAS  Google Scholar 

  • Brooks JM, Kennicutt MC, Fay RR, McDonald TJ, Sassen R (1984) Thermogenic gas hydrates in the Gulf of Mexico. Science 223:696–698

    Article  Google Scholar 

  • Brooks JM, Cox HB, Bryan WR, Kennicutt MC II, Mann RG, MacDonald TJ (1986) Association of gas hydrates and oil seepage in the Gulf of Mexico. Org Geochem 10:221–234

    Article  CAS  Google Scholar 

  • Bryant RW, Bryant JR, Feeley MH, Simmons GR (1990) Physiographic and bathymetric characteristics of the continental slope, Northwest Gulf of Mexico. Geo-Mar Lett 10:182–199

    Article  Google Scholar 

  • Calvert SE (1966) Origin of diatom-rich varved sediments from the Gulf of California. J Geol 76:546–565

    Article  Google Scholar 

  • Cravo-Laureau C, Matheron R, Cayol J-L, Joulian C, Hirschler-Réa A (2004a) Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 54:77–83

    Article  CAS  PubMed  Google Scholar 

  • Cravo-Laureau C, Matheron R, Joulian C, Cayol J-L, Hirschler-Réa A (2004b) Desulfatibacillum alkenivorans sp. nov., a novel n-alkene-degrading, sulfate-reducing bacterium, and emendated description of the genus Desulfatibacillum. Int J Syst Evol Microbiol 54:1639–1642

    Article  CAS  PubMed  Google Scholar 

  • Cravo-Laureau C, Labat C, Joulian C, Matheron R, Hirschler-Réa A (2007) Desulfatiferula oiefinivorans gen. nov, sp. nov. a long-chain n-alkane-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 57:2699–2702

    Article  CAS  PubMed  Google Scholar 

  • Dahle H, Garshol F, Madsen M, Birjeland N-K (2008) Microbial community structure of produced water from a high-temperature North Sea oil-field. Antonie Van Leeuwenhoek 93:37–49

    Article  PubMed  Google Scholar 

  • Davey ME, Wood WA, Key R, Nakamura K, Stahl DA (1993) Isolation of three species of Geotoga and Petrotoga: two new genera, representing a new lineage in the bacterial line of descent distantly related to the “Thermotogales”. Syst Appl Microbiol 16:191–200

    Article  Google Scholar 

  • Davidova IA, Duncan KE, Choi OK, Suflita JM (2006) Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 56:2737–2742

    Article  CAS  PubMed  Google Scholar 

  • De la Lanza-Espino G, Soto LA (1999) Sedimentary geochemistry of hydrothermal vents in Guaymas Basin, Gulf of California, Mexico. Appl Geochem 14:499–510

    Article  Google Scholar 

  • Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML (2003) Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69:2765–2772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dhillon A, Lever M, Lloyd K, Albert DB, Sogin ML, Teske A (2005) Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes (mcrA) in hydrothermal sediments of the Guaymas Basin. Appl Environ Microbiol 71:4592–4601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Didyk BM, Simoneit BR (1989) Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms. Nature 342:65–69

    Article  CAS  Google Scholar 

  • Dojka M, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3868–3877

    Google Scholar 

  • Dombrowski N, Donaho J, Gutierrez T, Teske AP, Baker BJ (2016) Metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol 1:16057

    Article  CAS  PubMed  Google Scholar 

  • Dombrowski N, Seitz K, Teske A, Baker B (2017) Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediment communities. Microbiome 5:106. https://doi.org/10.1186/s40168-017-0322-2.

    Article  PubMed  PubMed Central  Google Scholar 

  • Dowell F, Cardman Z, Dasarathy S, Kellermann MY, McKay LJ, MacGregor BJ, Ruff SE, Biddle JF, Lloyd KG, Lipp JS, Hinrichs K-U, Albert DB, Mendlovitz H, Teske A (2016) Microbial communities in methane and short alkane-rich hydrothermal sediments of Guaymas Basin. Front Microbiol 7:17. https://doi.org/10.3389/fmicb.2016.00017

    Article  PubMed  PubMed Central  Google Scholar 

  • Edgcomb V, Kysela D, Teske A, de Vera Gomez A, Sogin ML (2002) Benthic eukaryotic diversity in the Guaymas Basin, a hydrothermal vent environment. Proc Natl Acad Sci USA 99:7658–7662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Einsele G, Gieskes JM, Curray J, Moore D, Aguayo E, Aubry MP et al (1980) Intrusion of basaltic sills into highly porous sediments and resulting hydrothermal activity. Nature 283:441–445

    Article  CAS  Google Scholar 

  • Elsgaard L, Isaksen MF, Jørgensen BB, Alayse A-M, Jannasch HW (1994) Microbial sulfate reduction in deep-sea sediments at the Guaymas Basin hydrothermal vent area: influence of temperature and substrates. Geochim Cosmochim Acta 58:3335–3343

    Article  CAS  Google Scholar 

  • Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K (2014) Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community. ISME J 8:757–767

    Article  CAS  PubMed  Google Scholar 

  • Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350:434–438

    Article  CAS  PubMed  Google Scholar 

  • Fisher AT, Becker K (1991) Heat flow, hydrothermal circulation and basalt intrusions in the Guaymas Basin, Gulf of California. Earth Planet Sci Lett 103:84–89

    Article  Google Scholar 

  • Galimov EM, Simoneit BRT (1982) Geochemistry of interstitial gases in sedimentary deposits of the Gulf of California, deep sea drilling project leg 64. In: Curray JR, Blakeslee J, Platt LW, Stout LN, Moore DG, Aguayo JE et al (eds) Initial reports of the deep sea drilling project, vol 64. U.S. Government Printing Office, Washington, DC, pp 781–787

    Google Scholar 

  • Galushko A, Minz D, Schink B, Widdel F (1999) Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Environ Microbiol 1:415–420

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Pineda O, MacDonald I, Zimmer B, Shedd B, Roberts H (2010) Remote- sensing evaluation of geophysical anomaly sites in the outer continental slope, northern Gulf of Mexico. Deep-Sea Res II Top Stud Oceanogr 57:1859–1869

    Article  Google Scholar 

  • Giebel HA, Klotz F, Voget S, Poehlein A, Grosser K, Teske A, Brinkhoff T (2016) Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. Stand Genomic Sci 11:81. https://doi.org/10.1186/s407893-016-0201-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Gieg L, Suflita JM (2002) Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers. Environ Sci Technol 36:3755–3762

    Article  CAS  PubMed  Google Scholar 

  • Gieskes JM, Kastner M, Einsele G, Kelts K, Niemitz J (1982) Hydrothermal activity in the Guaymas Basin, Gulf of California: a synthesis. In: Curray JR, Blakeslee J, Platt LW, Stout LN, Moore DG, Aguayo JE et al (eds) Initial reports of the deep sea drilling project, vol 64. U.S. Government Printing Office, Washington, DC, pp 1159–1167

    Google Scholar 

  • Götz FE, Jannasch HW (1993) Aromatic hydrocarbon-degrading bacteria in the petroleum-rich sediments of Guaymas Basin hydrothermal vent site: preference for aromatic carboxylic acids. Geomicrobiol J 11:1–18

    Article  Google Scholar 

  • Grassia GS, McLean KM, Glenat P, Bauld J, Sheehy AJ (1996) A systematic survey for thermophilic fermentative bacteria and archaea in high temperature petroleum reservoirs. FEMS Microbiol Ecol 21:47–58

    Article  CAS  Google Scholar 

  • Gray ND, Sherry A, Grant RJ, Rowan AK, Hubert CRJ, Callbeck CM, Aitken CM, Jones DM, Adams JJ, Larter SR, Head IM (2011) The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol 13:2957–2975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Greene AD, Patel BKC, Sheehy AJ (1997) Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. Int J Syst Bacteriol 47:505–509

    Article  CAS  PubMed  Google Scholar 

  • Guezennec JG, Dussauze J, Bian M, Rocchicioli F, Ringelberg D, Hedrick DB, White DC (1996) Bacterial community structure from Guaymas Basin, Gulf of California, as determined by analysis of phospholipid ester-linked fatty acids. J Mar Biotechnol 4:165–175

    CAS  Google Scholar 

  • Gundersen JK, Jørgensen BB, Larsen E, Jannasch HW (1992) Mats of giant sulfur bacteria on deep-sea sediments due to fluctuation hydrothermal flow. Nature 360:454–455

    Article  Google Scholar 

  • Gutierrez T, Singleton DR, Berry D, Yang T, Aitken MD, Teske A (2013) Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP. ISME J 7:2091–2104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hakil F, Amin-Ali O, Hirschler-Réa A, Mollex D, Grossi V, Duran R, Matheron R, Cravo-Laureau C (2014) Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments. Int J Syst Evol Microbiol 64:540–544

    Article  CAS  PubMed  Google Scholar 

  • Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457–1462

    Article  CAS  PubMed  Google Scholar 

  • Harms G, Zengler K, Rabus R, Aeckersberg F, Minz D, RosselloMora R, Widdel F (1999) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzes by new types of sulfate-reducing bacteria. Appl Environ Microbiol 65:999–1004

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hatzenpichler R, Connon S, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ (2016) Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci USA 113:E4069–E4078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hinrichs K-U, Hayes JM, Bach W, Spivack AJ, Hmelo LR, Holm NG, Johnson CG, Sylva SP (2006) Biological formation of ethane and propane in the deep marine subsurface. Proc Acad Natl Acad Sci USA 103:14684–14689

    Article  CAS  Google Scholar 

  • Holler T, Widdel F, Knittel K, Amann R, Kellermann MY, Hinrichs K-U, Teske A, Boetius A (2011) Thermophilic anaerobic oxidation of methane by marine microbial consortia. ISME J 5:1946–1956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever MA, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D'Hondt SL, Jørgensen BB (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci USA 103:2815–2820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jaekel U, Musat N, Adam B, Kuypers M, Grundmann O, Musat F (2013) Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps. ISME J 7:885–895

    Article  CAS  PubMed  Google Scholar 

  • Jannasch HW, Nelson DC, Wirsen CO (1989) Massive natural occurrence of unusually large bacteria (Beggiatoa spp.) at a hydrothermal deep-sea vent site. Nature 342:834–836

    Article  CAS  Google Scholar 

  • Jeanthon C, Reysenbach AL, L’Haridon S, Gambacorta A, Pace NR, Glénat P, Prieur D (1995) Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir. Arch Microbiol 164:91–97

    Article  CAS  PubMed  Google Scholar 

  • Jeanthon C, L’Haridon S, Pradel N, Prieur D (1999) Rapid identification of hyperthermophilic methanococci isolated from deep-sea hydrothermal vents. Int J Syst Bacteriol 49:591–594

    Article  CAS  PubMed  Google Scholar 

  • Johansen C, Todd AC, MacDonald IR (2017) Time series video analysis of bubble release processes at natural hydrocarbon seeps in the northern Gulf of Mexico. Mar Pet Geol 82:21–34

    Article  Google Scholar 

  • Jones WJ, Leigh JA, Mayer F, Woese CR, Wolfe RS (1983) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136:254–261

    Article  CAS  Google Scholar 

  • Jones WJ, Stugard CE, Jannasch HW (1989) Comparison of thermophilic methanogens from submarine hydrothermal vents. Arch Microbiol 151:314–319

    Article  CAS  Google Scholar 

  • Jones DM, Head IM, Gray ND, Adams JJ, Rowan AK, Aitken CM, Bennett B, Huang H, Brown A, Bowler BFJ, Oldenburg T, Erdmann M, Larter SR (2008) Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451:176–180

    Article  CAS  PubMed  Google Scholar 

  • Jørgensen BB, Boetius A (2007) Feast and famine – microbial life in the deep-sea bed. Nat Rev Microbiol 5:770–781

    Article  PubMed  CAS  Google Scholar 

  • Jørgensen BB, Zawacki LX, Jannasch HW (1990) Thermophilic bacterial sulfate reduction in deep-sea sediments at the Guaymas Basin hydrothermal vents (Gulf of California). Deep-Sea Res I 37:695–710

    Article  Google Scholar 

  • Jørgensen BB, Isaksen MF, Jannasch HW (1992) Bacterial sulfate reduction above 100°C in deep-sea hydrothermal vent systems. Science 258:1756–1757

    Article  PubMed  Google Scholar 

  • Joye SB, MacDonald IR, Montoya JP, Peccini M (2005) Geophysical and geochemical signatures of Gulf of Mexico seafloor brines. Biogeosciences 2:295–309

    Article  CAS  Google Scholar 

  • Joye SB, Samarkin VA, Orcutt BN, MacDonald IR, Hinrichs K-U, Elvert M, Teske A, Lloyd KG, Lever MA, Montoya JP, Meile CD (2009) Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics. Nat Geosci 2:349–354

    Article  CAS  Google Scholar 

  • Kallmeyer J, Boetius A (2004) Effects of temperature and pressure on sulfate reduction and anaerobic oxidation of methane in hydrothermal sediments of Guaymas Basin. Appl Environ Microbiol 70:1231–1233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kallmeyer J, Ferdelman TG, Jansen K-H, Jørgensen BB (2003) A high pressure thermal gradient block for investigating microbial activity in multiple deep-sea samples. J Microbiol Methods 55:165–172

    Article  CAS  PubMed  Google Scholar 

  • Kastner M (1982) Evidence for two distinct hydrothermal systems in the Guaymas Basin. In: Curray JR, Blakeslee J, Platt LW, Stout LN, Moore DG, Aguayo JE et al (eds) Initial reports of the deep sea drilling project. U.S. Government Printing Office, Washington, DC, pp 1143–1158

    Google Scholar 

  • Kawka OE, Simoneit BRT (1987) Survey of hydrothermally generated petroleums from the Guaymas Basin spreading center. Org Geochem 11:311–328

    Article  CAS  Google Scholar 

  • Kellermann MY, Wegener G, Elvert M, Yoshinaga MY, Lin Y-S, Holler T, Mollar XP, Knittel K, Hinrichs K-U (2012) Autotrophy as predominant mode of carbon fixation in thermophilic anaerobic methane-oxidizing microbial communities. Proc Natl Acad Sci USA 109:19321–19326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelley DS, Baross JA, Delaney RJ (2002) Volcanoes, fluids, and life at mid-ocean ridge spreading centers. Annu Rev Earth Planet Sci 30:385–491

    Article  CAS  Google Scholar 

  • Kennicutt MC, Brooks JM, Denoux GJ (1988) Leakage of deep, reservoired petroleum to the near surface on the Gulf of Mexico continental slope. Mar Chem 24:39–59

    Article  CAS  Google Scholar 

  • Khelifi N, Grossi V, Dolla A, Hamdi M, Tholozan JL, Ollivier B et al (2010) Anaerobic oxidation of fatty acids and alkenes by the hyperthemophilic sulfate-reducing archaeon, Archaeoglobus fulgidus. Appl Environ Microbiol 76:3057–3060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khelifi N, Ali OA, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Réa A (2014) Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus. ISME J 8:2153–2166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding BT, Drozdowska M, Hazen TC, Suflita J, Morris PJ (2013) Genomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front Microbiol 4:50. https://doi.org/10.3389/fmicb.2013.00050

    Article  PubMed  PubMed Central  Google Scholar 

  • Kleindienst S, Ramette A, Amann R, Knittel K (2012) Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments. Environ Microbiol 14:2689–2710

    Article  CAS  PubMed  Google Scholar 

  • Kleindienst S, Herbst FA, Stagars M, von Netzer F, von Bergen M, Seifert J, Peplies J, Amann R, Musat F, Lueders T, Knittel K (2014) Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps. ISME J 8:2029–2044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klepac-Ceraj V, Bahr M, Crump BC, Teske AP, Hobbie JE, Polz MF (2004) High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ Microbiol 6:386–398

    Article  CAS  Google Scholar 

  • Klotz F, Brinkhoff T, Freeze H, Wietz M, Teske A, Simon M, Giebel H-A (2018) Tritonibacter horizontis, gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Int J Syst Evol Microbiol 68:736–744

    Article  PubMed  Google Scholar 

  • Kniemeyer O, Fischer T, Wilkes H, Glöckner FO, Widdel F (2003) Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 69:760–768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kniemeyer O, Musat F, Sievert SM, Knittel K, Wilkes H, Blumenberg M, Michaelis W, Classen A, Bolm C, Joye SB, Widdel F (2007) Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 449:898–901

    Article  CAS  PubMed  Google Scholar 

  • Knittel K, Boetius A, Lemke A, Eilers H, Lochte K, Pfannkuche O, Linke P, Amann R (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, OR). Geomicrobiol J 20:269–294

    Article  CAS  Google Scholar 

  • Knittel K, Lösekann T, Boetius A, Kort R, Amann R (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71:467–479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Könneke M, Küver J, Galushko A, Jørgensen BB (2013) Desulfoconvexum algidum gen. nov., sp. nov. a psychrophilic sulfate-reducing bacterium isolated from permanently cold, marine sediment (Svalbard). Int J Syst Evol Microbiol 63:959–964

    Article  PubMed  CAS  Google Scholar 

  • Krukenberg V, Harding K, Richter M, Glöckner F-O, Gruber-Vodicka HR, Adam B, Berg J, Knittel K, Tegetmeyer HE, Boetius A, Wegener G (2016) Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane. Environ Microbiol 18:3073–3091

    Article  CAS  PubMed  Google Scholar 

  • Küver J (2014) The family Desulfobacteraceae. In: Rosenberg E et al (eds) The prokaryotes – deltaproteobacteria and epsilonproteobacteria. Springer, Berlin/Heidelberg, pp 45–73. https://doi.org/10.1007/978-3-642-39044-9_266

    Chapter  Google Scholar 

  • Küver J, Könneke M, Galushko A, Drzyzga O (2001) Reclassification of Desulfobacterium phenolicum and Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov. sp. nov. Int J Syst Evol Microbiol 51:171–177

    Article  Google Scholar 

  • L’Haridon S, Reysenbach A-L, Glenat P, Prieur D, Jeanthon C (1995) Hot subterranean biosphere in a continental oil reservoir. Nature 377:223–224

    Article  Google Scholar 

  • Lanoil BD, Sassen R, La Duc MT, Sweet ST, Nealson KH (2001) Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl Environ Microbiol 67:5143–5153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lapham LL, Chanton JP, Martens CS, Sleeper K, Woolsey JR (2008) Microbial activity in surficial sediments overlying acoustic wipeout zones at a Gulf of Mexico cold seep. Geochem Geophys Geosyst 9:Q06001. https://doi.org/10.1029/2008GC001944

    Article  Google Scholar 

  • Laso-Pérez R, Wegener G, Knittel K, Widdel F, Harding KJ, Krukenberg V, Meier DV, Richter M, Tegetmeyer HE, Riedel D, Richnow H-H, Adrian L, Reemtsma T, Lechtenfeld O, Musat F (2016) Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 539:396–401

    Article  PubMed  CAS  Google Scholar 

  • Lerche I, Petersen K (1995) Salt and sediment dynamics. CRC Press, Boca Raton, 322 pages

    Google Scholar 

  • Lever MA, Teske A (2015) Methane-cycling archaeal diversity in hydrothermal sediment investigated by general and group-specific functional gene and 16S rRNA gene PCR primers. Appl Environ Microbiol 81:1426–1441

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lin Y-S, Koch BP, Feseker T, Ziervogel K, Goldhammer T, Schmidt F, Witt M, Kellermann M, Zabel M, Teske A, Hinrichs K-U (2017) Near-surface heating of young rift sediment causes mass production and discharge of reactive dissolved organic matter. Sci Rep 7:44864. https://doi.org/10.1038/srep44864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Balkwill DL, Aldrich HC, Drake GR, Boone DR (1999) Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. Int J Syst Evol Bacteriol 49:545–556

    Article  CAS  Google Scholar 

  • Liu A, Garcia-Dominguez E, Rhine ED, Young LY (2004) A novel arsenate-respiring isolate that can utilize aromatic substrates. FEMS Microbiol Ecol 48:323–332

    Article  CAS  PubMed  Google Scholar 

  • Lizarralde D, Soule A, Seewald J, Proskurowski G (2011) Carbon release by off-axis magmatism in a young sedimented spreading centre. Nat Geosci 4:50–54

    Article  CAS  Google Scholar 

  • Lloyd KG, Lapham L, Teske A (2006) An anaerobic methane-oxidizing community of ANME-1 archaea in hypersaline Gulf of Mexico sediments. Appl Environ Microbiol 72:7218–7230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lloyd KG, Albert D, Biddle JF, Chanton L, Pizarro O, Teske A (2010) Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One 5(1):e8738. https://doi.org/10.1371/journal.pone.0008738

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lonsdale P, Becker K (1985) Hydrothermal plumes, hot springs, and conductive heat flow in the Southern Trough of Guaymas Basin. Earth Planet Sci Lett 73:211–225

    Article  CAS  Google Scholar 

  • Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 73:3348–3362

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • MacDonald IR, Peccini MB (2009) Distinct activity phases during the recent geological history of a Gulf of Mexico mud volcano. Mar Pet Geol 26:1824–1830

    Article  Google Scholar 

  • MacDonald IR, Reilly FJ, Guinasso JNL, Brooks JM, Carney RS, Bryant WA, Bright TJ (1990) Chemosynthetic mussels at a brine-filled pockmark in the northern Gulf of Mexico. Science 248:1096–1099

    Article  CAS  PubMed  Google Scholar 

  • MacDonald IR, Buthman DB, Sager WW, Peccini MB, Guinasso NL (2000) Pulsed oil discharge from a mud volcano. Geology 28:907–910

    Article  Google Scholar 

  • Magot M, Ollivier B, Patel BC (2000) Microbiology of petroleum reservoirs. Antonie Van Leeuwenhoek 77:103–116

    Article  CAS  PubMed  Google Scholar 

  • Martens CS (1990) Generation of short chain organic acid anions in hydrothermally altered sediments of the Guaymas Basin, Gulf of California. Appl Geochem 5:71–76

    Article  CAS  Google Scholar 

  • Mbadinga SM, Li K-P, Zhou L, Wang L-Y, Yang S-Z, Liu J-F et al (2012) Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir. Appl Microbiol Biotechnol 96:1–12

    Article  CAS  Google Scholar 

  • McKay LJ, MacGregor BJ, Biddle JF, Mendlovitz HP, Hoer D, Lipp JS, Lloyd KG, Teske AP (2012) Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments. Deep-Sea Res I 67:21–31

    Article  CAS  Google Scholar 

  • McKay L, Klokman V, Mendlovitz H, LaRowe D, Zabel M, Hoer D, Albert D, de Beer D, Amend J, Teske A (2016) Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin. Environ Microbiol Rep 8:150–161

    Article  CAS  PubMed  Google Scholar 

  • McKay L, Hatzenpichler R, Inskeep WP, Fields MW (2017) Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Sci Rep 7:7252. https://doi.org/10.1038/s41598-017-07354-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mills HJ, Hodges C, Wilson K, MacDonald IR, Sobecky PA (2003) Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol Ecol 46:39–52

    Article  CAS  PubMed  Google Scholar 

  • Mills HJ, Martinez RJ, Story S, Sobecky PA (2004) Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities from Gulf of Mexico cold-seep sediments. Appl Environ Microbiol 70:5447–5458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mills HJ, Martinez RJ, Story S, Sobecky PA (2005) Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries. Appl Environ Microbiol 71:3235–3247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muyzer G, van der Kraan G (2008) Bacteria from hydrocarbon seep areas growing on short-chain alkanes. Trends Microbiol 16:138–141

    Article  CAS  PubMed  Google Scholar 

  • Nelson DC, Wirsen CO, Jannasch HW (1989) Characterization of large autotrophic Beggiatoa abundant at hydrothermal vents of the Guaymas Basin. Appl Environ Microbiol 55:2909–2917

    CAS  PubMed  PubMed Central  Google Scholar 

  • Niemann H, Lösekann T, De Beer D, Elvert M, Nadalig T, Knittel K, Amann R, Sauter EJ, Schlüter M, Klages M, Foucher JP, Boetius A (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443:854–858

    Article  CAS  PubMed  Google Scholar 

  • Nobu MK, Narihiro T, Kuroda K, Mei R, Liu W-T (2016) Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J 10:2478–2487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ollivier B, Cayol JL, Patel BK, Magot M, Fardeau ML, Garcia JL (1997) Methanoplanus petrolearius sp. nov., a novel methanogenic bacterium from an oil-producing well. FEMS Microbiol Lett 147:51–56

    Article  CAS  PubMed  Google Scholar 

  • Ommedal H, Torsvik T (2007) Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column. Int J Syst Evol Microbiol 57:2865–2869

    Article  CAS  PubMed  Google Scholar 

  • Orcutt B, Boetius A, Elvert M, Samarkin V, Joye SB (2005) Molecular biogeochemistry of sulfate reduction, methanogenesis, and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta 69:4267–4281

    Article  CAS  Google Scholar 

  • Orcutt B, Joye SB, Kleindienst S, Knittel K, Ramette A, Rietz A, Samarkin V, Treude T, Boetius A (2010) Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep-Sea Res II 57:2008–2021

    Article  CAS  Google Scholar 

  • Orphan VJ, Taylor LT, Hafenbradl D, DeLong EF (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum deposits. Appl Environ Microbiol 66:7000–7111

    Article  Google Scholar 

  • Orphan VJ, Hinrichs K-U, Ussler W III, Paull CK, Taylor LT, Sylva SP, Hayes JM, DeLong EF (2001a) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67:1922–1934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orphan VJ, House CH, Hinrichs K-H, McKeegan KD, DeLong EF (2001b) Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:484–487

    Article  CAS  PubMed  Google Scholar 

  • Orphan VJ, House CH, Hinrichs K-H, McKeegan KD, DeLong EF (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99:7663–7668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parkes JR (1999) Cracking anaerobic bacteria. Nature 401:217–218

    Article  CAS  PubMed  Google Scholar 

  • Parkes JR, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8:11–28

    Article  Google Scholar 

  • Pearson A, Seewald JS, Eglinton TI (2005) Bacterial incorporation of relict carbon in the hydrothermal environment of Guaymas Basin. Geochim Cosmochim Acta 69:5477–5486

    Article  CAS  Google Scholar 

  • Pernthaler A, Dekas AE, Brown CT, Goffredi SK, Embaye T, Orphan VJ (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA 105:7052–7057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peter JM, Peltonen P, Scott SD, Simoneit BRT, Kawka OE (1991) 14C ages of hydrothermal petroleum and carbonate in Guaymas Basin, Gulf of California: implications for oil generation, expulsion, and migration. Geology 19:253–256

    Article  CAS  Google Scholar 

  • Phelps CD, Kerkhof LJ, Young LY (1998) Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol Ecol 27:269–279

    Article  CAS  Google Scholar 

  • Rabus RR, Nordhaus WL, Widdel F (1993) Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59:1444–1451

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rabus R, Fukui M, Wilkes H, Widdel F (1996) Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Appl Environ Microbiol 62:3605–3613

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ravot G, Magot M, Fardeau ML, Patel BKC, Prensier G, Egan A, Garcia JL, Ollivier B (1995) Thermotoga elfii sp. nov., a novel thermophilic bacterium from an African oil-producing well. Int J Syst Bacteriol 45:308–314

    Article  CAS  PubMed  Google Scholar 

  • Rees GN, Grassia GS, Sheehy AJ, Dwivedi PP, Patel BKC (1995) Desulfacinum infernum gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a petroleum reservoir. Int J Syst Bacteriol 45:85–89

    Article  Google Scholar 

  • Roberts HH, Aharon P, Carney R, Larkin J, Sassen R (1990) Sea floor responses to hydrocarbon seeps, Louisiana continental slope. Geo-Mar Lett 10:232–243

    Article  Google Scholar 

  • Roberts HH, McBride RA, Coleman J (1999) Outer shelf and slope geology of the Gulf of Mexico: an overview. In: Kumpf H, Steidinger K, Sherman K (eds) The Gulf of Mexico large marine ecosystems: assessment, sustainability, and management. Blackwell Science, Malden, Massachusettts, pp 93–112

    Google Scholar 

  • Roberts HH, Feng D, Joye SB (2010a) Cold-seep carbonates of the middle and lower continental slope, northern Gulf of Mexico. Deep-Sea Res II 57:2040–2054

    Article  CAS  Google Scholar 

  • Roberts HH, Shedd W, Hunt J (2010b) Dive site geology: DSV ALVIN (2006) and ROV JASON II (2007) dives to the middle-lower continental slope, northern Gulf of Mexico. Deep-Sea Res II Top Stud Oceanogr 57:1837–1858

    Article  CAS  Google Scholar 

  • Roussel EG, Cambon Bonavita M-A, Querellou J, Cragg BA, Webster G, Prieur D, Parkes RJ (2008) Extending the sub-seafloor biosphere. Science 320:1046

    Article  CAS  PubMed  Google Scholar 

  • Rozanova EP, Pivovarova TA (1988) Reclassification of Desulfovibrio thermophilus (Rozanova, Khudyakova, 1974). Microbiol (Engl Tr) 57:102–106

    Google Scholar 

  • Rubin-Blum M, Antony CP, Borowski C, Sayavedra L, Pape T, Sahling H, Bohrmann G, Kleiner M, Redmond MC, Valentine DL, Dubilier N (2017) Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps. Nat Microbiol 2:17093. https://doi.org/10.1038/nmicrobiol.2017.93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rullkötter J, von der Dick H, Welte DH (1982) Organic petrography and extractable hydrocarbons of sediment from the Gulf of California, deep sea drilling project leg 64. In: Curray JR, Blakeslee J, Platt LW, Stout LN, Moore DG, Aguayo JE et al (eds) Initial reports of the deep sea drilling project, vol 64. U.S. Government Printing Office, Washington, DC, pp 837–853

    Google Scholar 

  • Rüter P, Rabus R, Wilkes H, Aeckersberg F, Rainey FA, Jannasch HW, Widdel F (1994) Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature 372:455–458

    Article  Google Scholar 

  • Sassen R, Joye S, Sweet ST, DeFreitas DA, Milkov AV, MacDonald IR (1999) Thermogenic gas hydrates and hydrocarbon gases in complex chemosynthetic communities Gulf of Mexico continental slope. Org Geochem 30:485–497

    Article  CAS  Google Scholar 

  • Saunders A, Fornari DJ, Joron JL, Tarney J, Treuil M (1982) Geochemistry of basic igneous rocks, Gulf of California. In: Curray J, Moore D (eds) Initial reports of the deep sea drilling project, vol 64. Ocean Drilling Program, College Station, pp 595–642

    Google Scholar 

  • Schrader H (1982) Diatom biostratigraphy and laminated diatomaceous sediments from the Gulf of California, deep sea drilling project leg 64. In: Initial reports of the deep sea drilling project, vol 64. U.S. Government Printing Office, Washington, DC, pp 973–981

    Google Scholar 

  • Schreiber L, Holler T, Knittel K, Meyerdierks A, Amann R (2010) Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ Microbiol 12:2327–2340

    CAS  PubMed  Google Scholar 

  • Seewald JS, Setfried WE Jr, Shanks WC III. (1994) Variations in the chemical and stable isotope composition of carbon and sulfur species during organic-rich sediment alteration: an experimental and theoretical study of hydrothermal activity at Guaymas Basin, Gulf of California. Geochim Cosmochim Acta 58:5065–5082

    Article  CAS  Google Scholar 

  • Siddique T, Fedorak PM, MacKinnon MD, Foght JM (2007) Metabolism of BTEX and naphtha compounds to methane in oil sands tailings. Environ Sci Technol 41:2350–2356

    Article  CAS  PubMed  Google Scholar 

  • Siddique T, Penner T, Semple K, Foght JM (2011) Anaerobic biodegradation of longer-chain n-alkanes coupled to methane production in oil sands tailings. Environ Sci Technol 45:5892–5899

    Article  CAS  PubMed  Google Scholar 

  • Siddique T, Penner T, Klassen J, Nesbø C, Foght JM (2012) Microbial communities involved in methane production from hydrocarbons in oil sands tailings. Environ Sci Technol 46:9802–9810

    Article  CAS  PubMed  Google Scholar 

  • Simoneit BRT, Bode GR (1982) Appendix II: carbon/carbonate and nitrogen analysis, Leg 64, Gulf of California. In: Curray JR, Blakeslee J, Platt LW, Stout LN, Moore DG, Aguayo JE et al (eds) Initial reports of the deep sea drilling project, vol 64. U.S. Government Printing Office, Washington, DC, pp 1303–1305

    Google Scholar 

  • So CM, Young LY (1999) Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl Environ Microbiol 65:2969–2976

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stetter KO et al (1993) Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365:743–745

    Article  Google Scholar 

  • Suzuki D, Li Z, Cui X, Zhang C, Katayama A (2014) Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov. Int J Syst Evol Microbiol 64:3081–3086

    Article  CAS  PubMed  Google Scholar 

  • Tan B, Nesbø C, Foght J (2014) Re-analysis of omics data indicates Smithella may degrade alkanes by addition to fumarate under methanogenic conditions. ISME J 8:2353–2356

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tardy-Jacquenod C, Caumette P, Matheron R, Lanau C, Arnauld O, Magot M (1996) Characterization of sulfate-reducing bacteria isolated from oil-field waters. Can J Microbiol 42:259–266

    Article  CAS  PubMed  Google Scholar 

  • Teske A, Hinrichs K-U, Edgcomb V, de Vera Gomez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW (2002) Microbial diversity in hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68:1994–2007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teske A, Dhillon A, Sogin ML (2003) Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation. Biol Bull 204:186–191

    Article  CAS  PubMed  Google Scholar 

  • Teske A, de Beer D, McKay L, Tivey MK, Biddle JF, Hoer D, Lloyd KG, Lever MA, Røy H, Albert DB, Mendlovitz H, MacGregor BJ (2016) The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation. Front Microbiol 7:75. https://doi.org/10.3389/fmicb.2016.00075

    Article  PubMed  PubMed Central  Google Scholar 

  • Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 1:1–9. https://doi.org/10.1038/nmicrobiol.2016.170

    Article  CAS  Google Scholar 

  • Voordouw G, Armstrong SM, Reimer MF, Fouts B, Telang AJ, Shen Y, Gevertz D (1996) Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl Environ Microbiol 62:1623–1629

    CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe K, Watanabe K, Kodama Y, Syutsubo K, Harayama S (2000) Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl Environ Microbiol 66:4803–4809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe K, Kodama Y, Hamamura N, Kaku N (2002) Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl Environ Microbiol 68:3899–3907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe M, Higashioka Y, Kojima H, Fukui M (2017) Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment, and emended description of the genus Desulfosarcina. Int J Syst Evol Microbiol 67:2994–2997

    Article  CAS  PubMed  Google Scholar 

  • Wawrik B, Marks CR, Davidova IA, McInerney MJ, Pruitt S, Duncan KE, Suflita JM, Callaghan AV (2016) Methanogenic paraffin degradation proceeds via the alkane addition to fumarate by Smithella spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens. Environ Microbiol 18:2604–2619

    Article  CAS  PubMed  Google Scholar 

  • Weber A, Jørgensen BB (2002) Bacterial sulfate reduction in hydrothermal sediments of the Guaymas Basin, Gulf of California, Mexico. Deep-Sea Res I 149:827–841

    Article  Google Scholar 

  • Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A (2015) Intracellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature 526:587–590

    Article  CAS  PubMed  Google Scholar 

  • Welhan JA (1988) Origins of methane in hydrothermal systems. Chem Geol 71:183–1988

    Article  CAS  Google Scholar 

  • Wellsbury P, Goodman K, Barth T, Cragg BA, Barnes SP, Parkes RJ (1997) Deep bacterial biosphere fuelled by increasing organic matter availability during burial and reheating. Nature 388:573–576

    Article  CAS  Google Scholar 

  • Whelan JK, Simoneit BRT, Tarafa ME (1988) C1–C8 hydrocarbons in sediments from Guaymas Basin, Gulf of California – comparison to Peru Margin, Japan Trench, and California Borderlands. Org Geochem 12:171–194

    Article  CAS  Google Scholar 

  • Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds) The Prokaryotes, 2nd edn. Springer, New York, pp 3352–3378

    Chapter  Google Scholar 

  • Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12:259–276

    Article  CAS  PubMed  Google Scholar 

  • Yang T, Speare K, McKay L, MacGregor BJ, Joye SB, Teske A (2016) Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout. Front Microbiol 7:1384. https://doi.org/10.3389/fmicb.2016.01384

    Article  PubMed  PubMed Central  Google Scholar 

  • Zengler K, Richnow HH, Rossello-Mora R, Michaelis W, Widdel F (1999) Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401:266–269

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

Andreas Teske was supported by NSF (Biological Oceanography 0647633 and 1357238 for Guaymas Basin; Emerging Frontiers/Microbial Observatories: Microbial Interactions and Processes 0801741 for the Gulf of Mexico) and by the Gulf of Mexico Research Institute [GOMRI] through the ECOGIG [Ecological Consequences of Oil and Gas input into the Gulf of Mexico] consortium.

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Teske, A. (2019). Hydrocarbon-Degrading Microbial Communities in Natural Oil Seeps. In: McGenity, T. (eds) Microbial Communities Utilizing Hydrocarbons and Lipids: Members, Metagenomics and Ecophysiology . Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-60063-5_3-2

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  1. Latest

    Hydrocarbon-Degrading Microbial Communities in Natural Oil Seeps
    Published:
    21 March 2019

    DOI: https://doi.org/10.1007/978-3-319-60063-5_3-2

  2. Original

    Hydrocarbon-Degrading Microbial Communities in Natural Oil Seeps
    Published:
    25 September 2018

    DOI: https://doi.org/10.1007/978-3-319-60063-5_3-1