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Anaerobic Utilization of Hydrocarbons, Oils, and Lipids pp 225–232Cite as

Functional Genomics of Sulfate-Reducing Bacteria Degrading Hydrocarbons

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

Abstract

Sulfate-reducing bacteria (SRB) are well known for their significance in the carbon and sulfur cycles of marine sediments. Despite their general energetic restriction, some SRB are capable of anaerobic degradation of aromatic hydrocarbons in the marine environments, such as deep sea sediments characterized by recent oil formation. Proteogenomics has allowed hitherto unknown insights into the physiology of SRB from single catabolic reactions to complex metabolic networks. Best studied aromatic compound-degrading SRB at present are toluene-degrading Desulfobacula toluolica Tol2 and the naphthalene-degrading enrichment culture N47.

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References

  • Annweiler E, Materna A, Safinowski M, Kappler A, Richnow HH, Michaelis W, Meckenstock RU (2000) Anaerobic degradation of 2-methylnaphthalene by a sulfate-reducing enrichment culture. Appl Environ Microbiol 66:5329–5333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bergmann FD, Selesi D, Meckenstock RU (2011a) Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47. Arch Microbiol 193:241–250

    Article  CAS  PubMed  Google Scholar 

  • Bergmann F, Selesi D, Weinmaier T, Tischler P, Rattei T, Meckenstock RU (2011b) Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47. Environ Microbiol 13:1125–1137

    Article  CAS  PubMed  Google Scholar 

  • Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, Gieseke A, Amann R, Jørgensen BB, Witte U, Pfannkuche O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626

    Article  CAS  PubMed  Google Scholar 

  • Bowles MW, Mogollón JM, Kasten S, Zable M, Hinrichs K-U (2014) Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities. Science 344:889–891

    Article  CAS  PubMed  Google Scholar 

  • DiDonato RJ Jr, Young ND, Butler JE, Chin K-J, Hixson KK, Mouser P, Lipton MS, DeBoy R, Methé BA (2010) Genome sequence of the deltaproteobacterial strain NaphS2 and analysis of differential gene expression during anaerobic growth on naphthalene. PLoS One 5:e14072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding B, Schmeling S, Fuchs G (2008) Anaerobic metabolism of catechol by the denitrifying bacterium Thauera aromatica – a result of promiscuous enzymes and regulators? J Bacteriol 190:1620–1630

    Article  CAS  PubMed  Google Scholar 

  • Dörries M, Wöhlbrand L, Kube M, Reinhardt R, Rabus R (2016) Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059. BMC Genomics 17:918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eberlein C, Estelmann S, Seifert J, von Bergen M, Müller M, Meckenstock RU, Boll M (2013) Identification and characterization of 2-naphthoyl-coenzyme A reductase, the prototype of a novel class of dearomatizing reductases. Mol Microbiol 88:1032–1039

    Article  CAS  PubMed  Google Scholar 

  • Enning D, Garrelfs J (2014) Corrosion of iron by sulfate-reducing bacteria: new views of an old problem. Appl Environ Microbiol 80:1226–1236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Estelmann S, Blank I, Feldmann A, Boll M (2015) Two distinct old yellow enzymes are involved in naphthyl ring reduction during anaerobic naphthalene degradation. Mol Microbiol 95:162–172

    Article  CAS  PubMed  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 

  • Gittel A, Mußmann M, Sass H, Cypionka H, Könneke M (2008) Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments by direct cultivation and CARD-FISH analysis. Environ Microbiol 10:2645–2658

    Article  CAS  PubMed  Google Scholar 

  • Griebler C, Safinowski M, Vieth A, Richnow HH, Meckenstock RU (2004) Combined application of stable carbon isotope analysis and specific metabolites determination for assessing in situ degradation of aromatic hydrocarbons in a tar oil-contaminated aquifer. Environ Sci Technol 38:617–631

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Head IM, Gray ND, Larter SR (2014) Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management. Front Microbiol 5:566

    Article  PubMed  PubMed Central  Google Scholar 

  • Jørgensen BB (1982) Mineralization of organic matter in the sea bed – the role of sulphate reduction. Nature 296:643–645

    Article  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Kim S-J, Park S-J, Jung M-Y, Kim J-G, Min U-G, Hong H-J, Rhee S-K (2014) Draft genome sequence of an aromatic compound-degrading bacterium, Desulfobacula sp. TS, belonging to the Deltaproteobacteria. FEMS Microbiol Lett 360:9–12

    Article  CAS  PubMed  Google Scholar 

  • Kimes NE, Callaghan AV, Suflita JM, Morris PJ (2014) Microbial transformation of the Deepwater Horizon oil spill – past, present, and future perspectives. Front Microbiol 5:603

    Article  PubMed  PubMed Central  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 

  • Kuever J, Kulmer J, Jannsen S, Fischer U, Blotevogel K-H (1993) Isolation and characterization of a new spore-forming sulfate-reducing bacterium growing by complete oxidation of catechol. Arch Microbiol 159:282–288

    Article  CAS  PubMed  Google Scholar 

  • Kuever J, Rainey FA, Hippe H (1999) Description of Desulfotomaculum sp. Groll as Desulfotomaculum gibsoniae sp. nov. Int J Syst Bacteriol 49:1801–1808

    Article  CAS  PubMed  Google Scholar 

  • Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IAC, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, Chain P, Davenport KW, Rhode M, Spring S, Klenk H-P, Stams AJM (2014) Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 9:821–839

    Article  PubMed  PubMed Central  Google Scholar 

  • Kung JW, Löffler C, Dörner K, Heintz D, Gallien S, Van Dorsselaer A, Friedrich T, Boll M (2009) Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases. PNAS 106:17687–17692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meckenstock RU, Annweiler E, Michaelis W, Richnow HH, Schink B (2000) Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Appl Environ Microbiol 66:2743–2747

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A (2017) More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. Microbiome 5:118

    Article  PubMed  PubMed Central  Google Scholar 

  • Miralles G, Grossi V, Acquaviva M, Duran R, Claude Bertrand J, Cuny P (2007) Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil. Chemosphere 68:1327–1334

    Article  CAS  PubMed  Google Scholar 

  • Mouttaki H, Johannes J, Meckenstock RU (2012) Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons. Environ Microbiol 14:2770–2774

    Article  CAS  PubMed  Google Scholar 

  • Musat F, Galushko A, Jacob J, Widdel F, Kube M, Reinhardt R, Wilkes H, Schink B, Rabus R (2009) Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environ Microbiol 11:209–219

    Article  CAS  PubMed  Google Scholar 

  • Mußmann M, Ishii K, Rabus R, Amann R (2005) Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol 7:405–418

    Article  PubMed  Google Scholar 

  • Muyzer G, Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6:441–454

    Article  CAS  PubMed  Google Scholar 

  • Rabus R, Heider J (1998) Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria. Arch Microbiol 170:377–384

    Article  CAS  Google Scholar 

  • Rabus R, Widdel F (1995) Conversion studies with substrate analogues of toluene in a sulfate-reducing bacterium, strain Tol2. Arch Microbiol 164:448–451

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F, Reinhardt R (2005) The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27–36

    Article  CAS  PubMed  Google Scholar 

  • Rabus R, Venceslau SS, Wöhlbrand L, Voordouw G, Wall JD, Pereira IAC (2015) A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulphate-reducing prokaryotes. In: Advances in microbial physiology, vol 66. Academic Press, Oxford, pp 55–321

    Google Scholar 

  • Ravenschlag K, Sahm K, Knoblauch C, Jørgensen BB, Amann R (2000) Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl Environ Microbiol 66:3592–3602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rueter 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  CAS  PubMed  Google Scholar 

  • Safinowski M, Meckenstock RU (2006) Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Environ Microbiol 8:347–352

    Article  CAS  PubMed  Google Scholar 

  • Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU (2010) Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol 192:295–306

    Article  CAS  PubMed  Google Scholar 

  • Sinkko H, Lukkari K, Sihvonen LM, Sivonen K, Leivuori M, Rantanen M, Paulin L, Lyra C (2013) Bacteria contribute to sediment nutrient release and reflect progressed eutrophication-driven hypoxia in an organic-rich continental sea. PLoS One 8:e67061

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stagars MH, Mishra S, Treude T, Amann R, Knittel K (2017) Microbial community response to simulated petroleum seepage in Caspian Sea sediments. Front Microbiol 8:764

    Article  PubMed  PubMed Central  Google Scholar 

  • Stetter KO, Huber R, Blöchl E, Kurr M, Eden RD, Fielder M, Cash H, Vance I (1993) Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365:743–745

    Article  Google Scholar 

  • Townsend GT, Prince RC, Suflita JM (2003) Anaerobic oxidation of crude oil hydrocarbons by the resident microorganisms of a contaminated anoxic aquifer. Environ Sci Technol 37:5213–5218

    Article  CAS  PubMed  Google Scholar 

  • Widdel (1980) Anaerober Abbau von Fettsäuren und Benzoesäure durch neu isolierte Arten Sulfat-reduzierender Bakterien. PhD thesis. Georg-August Universität zu Göttingen, Göttingen

    Google Scholar 

  • Wilkes H, Boreham C, Harms G, Zengler K, Rabus R (2000) Anaerobic degradation and carbon isotopic fractionation of alkylbenzenes in crude oil by sulphate-reducing bacteria. Org Geochem 31:101–115

    Article  CAS  Google Scholar 

  • Wöhlbrand L, Jacob JH, Kube M, Mussmann M, Jarling R, Beck A, Amann R, Wilkes H, Reinhardt R, Rabus R (2013) Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium. Environ Microbiol 15:1334–1355

    Article  CAS  PubMed  Google Scholar 

  • Wöhlbrand L, Ruppersberg HS, Feenders C, Blasius B, Braun H-P, Rabus R (2016) Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1 D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE. Proteomics 16:973–988

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany

    Ralf Rabus

  2. Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany

    Heinz Wilkes

Authors
  1. Ralf Rabus
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  2. Heinz Wilkes
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Correspondence to Ralf Rabus .

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Editors and Affiliations

  1. Microbiology, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

    Matthias Boll

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Rabus, R., Wilkes, H. (2020). Functional Genomics of Sulfate-Reducing Bacteria Degrading Hydrocarbons. In: Boll, M. (eds) Anaerobic Utilization of Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50391-2_12

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