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Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1

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Abstract

Nitrate-reducing bacteria of the recently recognized Azoarcus/Thauera group within the Betaproteobacteria contribute significantly to the biodegradation of aromatic and other refractory compounds in anoxic waters and soils. Strain EbN1 belongs to a distinct cluster (new genus) and is the first member of this phylogenetic group, the genome of which has been determined (4.7 Mb; one chromosome, two plasmids) by [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]. Ten anaerobic and four aerobic aromatic-degradation pathways were recognized on the chromosome, with the coding genes mostly forming clusters. Presence of paralogous gene clusters (e.g. for anaerobic ethylbenzene degradation) suggests an even broader degradation spectrum than previously known. Metabolic versatility is also reflected by the presence of multiple respiratory complexes and is apparently controlled by an extensive regulatory network. Strain EbN1 is unique for its capacity to degrade toluene and ethylbenzene anaerobically via completely different pathways. Bioinformatical analysis of their genetic blueprints and global expression analysis (DNA-microarray and proteomics) of substrate-adapted cells [Kühner S, Wöhlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493–1503] indicated coordinated vs sequential modes of regulation for the toluene and ethylbenzene pathways, respectively.

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References

  • Anders HJ, Kaetzke A, Kämpfer P, Ludwig W, Fuchs G (1995) Taxonomic position of aromatic-degrading denitrifying pseudomonad strains K 172 and KB 740 and description as new members of the genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., respectively, members of the beta subclass of the Proteobacteria. Int J Syst Bacteriol 45:327–333

    PubMed  CAS  Google Scholar 

  • Barragán MJL, Blázquez B, Zamarro MT, Mancheño JM, García JL, Díaz E, Carmona M (2005) BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators. J Biol Chem 280:10683–10694

    Article  PubMed  CAS  Google Scholar 

  • Boll M, Fuchs G, Heider J (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr Opin Chem Biol 6:604–611

    Article  PubMed  CAS  Google Scholar 

  • Breinig S, Schiltz E, Fuchs G (2000) Genes involved in anaerobic metabolism of phenol in the bacterium Thauera aromatica. J Bacteriol 182:5849–5863

    Article  PubMed  CAS  Google Scholar 

  • Champion KM, Zengler K, Rabus R (1999) Anaerobic degradation of ethylbenzene and toluene in denitrifying strain EbN1 proceeds via independent substrate-induced pathways. J Mol Microbiol Biotechnol 1:157–164

    PubMed  CAS  Google Scholar 

  • Coschigano PW, Bishop BJ (2004) Role of benzylsuccinate in the induction of the tutE tutFDGH gene complex of T. aromatica strain T1. FEMS Microbiol Lett 231:261–266

    Article  PubMed  CAS  Google Scholar 

  • Cunningham JA, Rahme H, Hopkins GD, Lebron C, Reinhard M (2001) Enhanced in situ bioremediation of BTEX-contaminated groundwater by combined injection of nitrate and sulfate. Environ Sci Technol 35:1663–1670

    Article  PubMed  CAS  Google Scholar 

  • Dejonghe W, Boon N, Seghers D, Top EM, Verstraete W (2001) Bioaugmentation of soils by increasing microbial richness: missing links. Environ Microbiol 3:649–657

    Article  PubMed  CAS  Google Scholar 

  • Dörr J, Hurek T, Reinhold-Hurek B (1998) Type IV pili are involved in plant-microbe and fungus-microbe interactions. Mol Microbiol 30:7–17

    Article  PubMed  Google Scholar 

  • Egland PG, Pelletier DA, Dispensa M, Gibson J, Harwood CS (1997) A cluster of bacterial genes for anaerobic benzene ring biodegradation. Proc Natl Acad Sci U S A 94:6484–6489

    Article  PubMed  CAS  Google Scholar 

  • Gersberg RM, Dawsey WJ, Bradley MD (1993) Nitrate enhancement of in situ bioremediation of monoaromatic compounds in groundwater. Remediation 3:233–245

    Article  Google Scholar 

  • Gibson J, Harwood CS (2002) Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu Rev Microbiol 56:345–369

    Article  PubMed  CAS  Google Scholar 

  • Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236–243

    Article  PubMed  CAS  Google Scholar 

  • Greated A, Lambertsen L, Williams PA, Thomas CM (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4:856–871

    Article  PubMed  CAS  Google Scholar 

  • Harayama S, Kok M, Neidle EL (1992) Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol 46:565–601

    Article  PubMed  CAS  Google Scholar 

  • Harwood CS, Burchhardt G, Hermann H, Fuchs G (1999) Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol Rev 22:439–458

    Article  Google Scholar 

  • Hayes F (2003) Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496–1499

    Article  PubMed  CAS  Google Scholar 

  • Heider J, Fuchs G (1997) Anaerobic metabolism of aromatic compounds. Eur J Biochem 243:577–596

    Article  PubMed  CAS  Google Scholar 

  • Heider J, Boll M, Breese K, Breinig S, Ebenau-Jehle C, Feil U, Gadón N, Laempe D, Leuthner B, Mohamed ME, Schneider S, Burchhardt G, Fuchs G (1998) Differential induction of enzymes involved in anaerobic metabolism of aromatic compounds in the denitrifying bacterium Thauera aromatica. Arch Microbiol 170:120–131

    Article  PubMed  CAS  Google Scholar 

  • Hess A, Zarda B, Hahn D, Häner A, Stax D, Höhener P, Zeyer J (1997) In situ analysis of denitrifying toluene- and m-xylene-degrading bacteria in a diesel fuel-contaminated laboratory aquifer column. Appl Environ Microbiol 63:2136–2141

    PubMed  CAS  Google Scholar 

  • Hurek T, Reinhold-Hurek B (2003) Azoarcus sp. strain BH72 as a model for nitrogen-fixing grass endophytes. J Biotechnol 106:169–178

    Article  PubMed  CAS  Google Scholar 

  • Jiménez JI, Miñambres B, García JL, Díaz E (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4:824–841

    Article  PubMed  Google Scholar 

  • Johnson HA, Pelletier DA, Spormann AM (2001) Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol 183:4536–4542

    Article  PubMed  CAS  Google Scholar 

  • Kniemeyer O, Heider J (2001a) Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J Biol Chem 276:21381–21386

    Article  PubMed  CAS  Google Scholar 

  • Kniemeyer O, Heider J (2001b) (S)-1-Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch Microbiol 176:129–135

    Article  PubMed  CAS  Google Scholar 

  • Körner H, Sofia HJ, Zumft WG (2003) Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol Rev 27:559–592

    Article  PubMed  CAS  Google Scholar 

  • Kube M, Heider J, Amann J, Hufnagel P, Kühner S, Beck A, Reinhardt R, Rabus R (2004) Genes involved in the anaerobic degradation of toluene in a denitrifying bacterium, strain EbN1. Arch Microbiol 181:182–194

    Article  PubMed  CAS  Google Scholar 

  • Kube M, Beck A, Meyerdierks A, Amann R, Reinhardt R, Rabus R (2005) A catabolic gene cluster for anaerobic benzoate degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol 28:287–294

    Article  PubMed  CAS  Google Scholar 

  • Kuhn EP, Zeyer J, Eicher P, Schwarzenbach RP (1985) Anaerobic degradation of alkylated benzenes in denitrifying laboratory aquifer columns. Appl Environ Microbiol 54:490–496

    Google Scholar 

  • Kühner S, Wöhlbrand L, Fritz I, Wruck W, Hultschig C, Hufnagel P, Kube M, Reinhardt R, Rabus R (2005) Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1. J Bacteriol 187:1493–1503

    Article  PubMed  CAS  Google Scholar 

  • Kumagai H, Fujiwara T, Matsubara H, Saeki K (1997) Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases. Biochemistry 36:5509–5521

    Article  PubMed  CAS  Google Scholar 

  • Laempe D, Jahn M, Breese K, Schägger H, Fuchs G (2001) Anaerobic metabolism of 3-hydroxybenzoate by the denitrifying bacterium Thauera aromatica. J Bacteriol 183:968–979

    Article  PubMed  CAS  Google Scholar 

  • Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres y Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22:55–61

    Article  PubMed  CAS  Google Scholar 

  • Leuthner B, Leutwein C, Schulz H, Hörth P, Haehnel W, Schiltz E, Schägger H, Heider J (1998) Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol Microbiol 28:615–628

    Article  PubMed  CAS  Google Scholar 

  • Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, Madupu R, Nelson W, White O, Peterson J, Khouri H, Hance I, Chris Lee P, Holtzapple E, Scanlan D, Tran K, Moazzez A, Utterback T, Rizzo M, Lee K, Kosack D, Moestl D, Wedler H, Lauber J, Stjepandic D, Hoheisel J, Straetz M, Heim S, Kiewitz C, Eisen J, Timmis KN, Düsterhöft A, Tümmler B, Fraser CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799–808

    Article  PubMed  CAS  Google Scholar 

  • Pelz O, Chatzinotas A, Andersen N, Bernasconi SM, Hesse C, Abraham W-R, Zeyer J (2001) Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations. Arch Microbiol 175:270–281

    Article  PubMed  CAS  Google Scholar 

  • Pitcher RS, Cheesman MR, Watmough NJ (2002) Molecular and spectroscopic analysis of the cytochrome cbb 3 oxidase from Pseudomonas stutzeri. J Biol Chem 277:31474–31483

    Article  PubMed  CAS  Google Scholar 

  • Rabus R (2005) Biodegradation of hydrocarbons under anoxic conditions. In: Ollivier B, Magot M (eds) Petroleum microbiology. ASM, Washington DC, pp 277–299

    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) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96–103

    Article  PubMed  CAS  Google Scholar 

  • Rabus R, Widdel F (1996) Utilization of alkylbenzenes during anaerobic growth of pure cultures of denitrifying bacteria on crude oil. Appl Environ Microbiol 62:1238–1241

    CAS  Google Scholar 

  • Rabus R, Wilkes H, Schramm A, Harms G, Behrends A, Amann R, Widdel F (1999) Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the β-subclass of Proteobacteria. Environ Microbiol 1:145–157

    Article  PubMed  CAS  Google Scholar 

  • Rabus R, Kube M, Beck A, Widdel F, Reinhardt R (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 178:506–516

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Ramos JL, Marqués S, Timmis KN (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Ann Rev Microbiol 51:341–372

    Article  CAS  Google Scholar 

  • Reinhold-Hurek B, Hurek T (2000) Reassessment of the taxonomic structure of the diazotrophic genus Azoarcus sensu lato and description of three new genera and new species, Azovibrio restrictus gen. nov., sp. nov., Azospira oryzae gen. nov., sp. nov. and Azonexus fungiphilus gen. nov., sp. nov. Int J Syst Evol Microbiol 50:649–659

    PubMed  CAS  Google Scholar 

  • Schmeling S, Narmandakh A, Schmitt O, Gad'on N, Schuhle K, Fuchs G (2004) Phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in Thauera aromatica. J Bacteriol 186:8044–8057

    Article  PubMed  CAS  Google Scholar 

  • Schmid A, Dordick JS, Hauer B, Kiener A, Wubbolts M, Witholt B (2001) Industrial biocatalysis today and tomorrow. Nature 409:258–268

    Article  PubMed  CAS  Google Scholar 

  • Sluis MK, Larsen RA, Krum JG, Anderson R, Metcalf WW, Ensign SA (2002) Biochemical, molecular, and genetic analyses of the acetone carboxylase from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10. J Bacteriol 184:2969–2977

    Article  PubMed  CAS  Google Scholar 

  • Smolenski WJ, Suflita JM (1987) Biodegradation of cresol isomers in anoxic aquifers. Appl Environ Microbiol 53:710–716

    PubMed  CAS  Google Scholar 

  • Song B, Häggblom MM, Zhou J, Tiedje JM, Palleroni NJ (1999) Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov. Int J Syst Bacteriol 49:1129–1140

    Article  PubMed  CAS  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed  Google Scholar 

  • Unden G, Achebach S, Holighaus G, Tran HG, Wackwitz B, Zeuner Y (2002) Control of FNR function of Escherichia coli by O2 and reducing conditions. J Mol Microbiol Biotechnol 4:263–268

    PubMed  CAS  Google Scholar 

  • Wackett LP, Hershberger CD (2001) Biocatalysis and biodegradation: microbial transformation of organic compounds. ASM, Washington DC

    Google Scholar 

  • Weinel C, Nelson KE, Tümmler B (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4:809–818

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Williams PA, Murray K (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120:416–423

    PubMed  CAS  Google Scholar 

  • Zaar A, Gescher J, Eisenreich W, Bacher A, Fuchs G (2004) New enzymes involved in aerobic benzoate metabolism in Azoarcus evansii. Mol Microbiol 54:223–238

    Article  PubMed  CAS  Google Scholar 

  • Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM (1995) Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 45:500–506

    PubMed  CAS  Google Scholar 

  • Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533–616

    PubMed  CAS  Google Scholar 

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Acknowledgements

R. Reinhardt, A. Beck and M. Kube (Berlin) are greatly acknowledged for genome sequencing and fruitful collaboration. J. heider (Darmstadt) is thanked for expert participation in annotation.

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  1. Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359, Bremen, Germany

    Ralf Rabus

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Rabus, R. Functional genomics of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Appl Microbiol Biotechnol 68, 580–587 (2005). https://doi.org/10.1007/s00253-005-0030-x

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