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
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
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
Amend JP, Teske A (2005) Expanding frontiers in deep subsurface microbiology. Palaeogeogr Palaeoclimatol Palaeoecol 219:131–155
Amos S (1987) Late Triassic-Jurassic paleogeography and origin of Gulf of Mexico Basin. AAPG Bull 71(4):419–451
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
Bak F, Widdel F (1986) Anaerobic degradation of phenol and phenol derivatives by Desulfobacterium phenolicum. Arch Microbiol 146:177–180
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
Bazylinski DA, Farrington JW, Jannasch HW (1988) Hydrocarbons in surface sediments from a Guaymas Basin hydrothermal vent site. Org Geochem 12:547–558
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
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
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
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
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
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
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
Brooks JM, Kennicutt MC, Fay RR, McDonald TJ, Sassen R (1984) Thermogenic gas hydrates in the Gulf of Mexico. Science 223:696–698
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
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
Calvert SE (1966) Origin of diatom-rich varved sediments from the Gulf of California. J Geol 76:546–565
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
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
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
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
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
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
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
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
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
Didyk BM, Simoneit BR (1989) Hydrothermal oil of Guaymas Basin and implications for petroleum formation mechanisms. Nature 342:65–69
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
Gieg L, Suflita JM (2002) Detection of anaerobic metabolites of saturated and aromatic hydrocarbons in petroleum-contaminated aquifers. Environ Sci Technol 36:3755–3762
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Jones WJ, Stugard CE, Jannasch HW (1989) Comparison of thermophilic methanogens from submarine hydrothermal vents. Arch Microbiol 151:314–319
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
Jørgensen BB, Boetius A (2007) Feast and famine – microbial life in the deep-sea bed. Nat Rev Microbiol 5:770–781
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
Jørgensen BB, Isaksen MF, Jannasch HW (1992) Bacterial sulfate reduction above 100°C in deep-sea hydrothermal vent systems. Science 258:1756–1757
Joye SB, MacDonald IR, Montoya JP, Peccini M (2005) Geophysical and geochemical signatures of Gulf of Mexico seafloor brines. Biogeosciences 2:295–309
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
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
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
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
Kawka OE, Simoneit BRT (1987) Survey of hydrothermally generated petroleums from the Guaymas Basin spreading center. Org Geochem 11:311–328
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Lerche I, Petersen K (1995) Salt and sediment dynamics. CRC Press, Boca Raton, 322 pages
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
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
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
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
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
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
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
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
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
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
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
MacDonald IR, Buthman DB, Sager WW, Peccini MB, Guinasso NL (2000) Pulsed oil discharge from a mud volcano. Geology 28:907–910
Magot M, Ollivier B, Patel BC (2000) Microbiology of petroleum reservoirs. Antonie Van Leeuwenhoek 77:103–116
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
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
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
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
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
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
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
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
Muyzer G, van der Kraan G (2008) Bacteria from hydrocarbon seep areas growing on short-chain alkanes. Trends Microbiol 16:138–141
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
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
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
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
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
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
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
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
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
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
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
Parkes JR (1999) Cracking anaerobic bacteria. Nature 401:217–218
Parkes JR, Cragg BA, Wellsbury P (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8:11–28
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
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
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
Phelps CD, Kerkhof LJ, Young LY (1998) Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol Ecol 27:269–279
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
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
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
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
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
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
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
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
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
Rozanova EP, Pivovarova TA (1988) Reclassification of Desulfovibrio thermophilus (Rozanova, Khudyakova, 1974). Microbiol (Engl Tr) 57:102–106
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
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
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
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
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
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
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
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
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
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
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
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
So CM, Young LY (1999) Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl Environ Microbiol 65:2969–2976
Stetter KO et al (1993) Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365:743–745
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Welhan JA (1988) Origins of methane in hydrothermal systems. Chem Geol 71:183–1988
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
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
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
Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12:259–276
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
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
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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Hydrocarbon-Degrading Microbial Communities in Natural Oil Seeps- Published:
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DOI: https://doi.org/10.1007/978-3-319-60063-5_3-2
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