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Hydrocarbon Degradation by Betaproteobacteria

  • Watumesa A. Tan
  • Rebecca E. ParalesEmail author
Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Members of the Betaproteobacteria are widespread in soil environments. Many isolates are capable of aerobic degradation of aromatic hydrocarbons, as well as chloroaromatic, nitroaromatic, and aminoaromatic compounds. Anaerobic aromatic hydrocarbon degradation under nitrate-reducing or (per)chlorate-reducing conditions appears to be a process that is carried out mainly by Betaproteobacteria. Less is known about the distribution of Betaproteobacteria that are capable of utilizing alkanes as carbon and energy sources, but both aerobic and anaerobic alkane-degrading Betaproteobacteria have been isolated.

Notes

Acknowledgments

Research in the Parales laboratory is supported by the National Science Foundation (award MCB 1716833).

References

  1. Ahmad D, Masse R, Sylvestre M (1990) Cloning and expression of genes involved in 4-chlorobiphenyl transformation by Pseudomonas testosteroni: homology to polychlorobiphenyl-degrading genes in other bacteria. Gene 86:53–61CrossRefPubMedGoogle Scholar
  2. Alfreider A, Vogt C (2007) Bacterial diversity and aerobic biodegradation potential in a BTEX-contaminated aquifer. Water Air Soil Pollut 183:415–426CrossRefGoogle Scholar
  3. Anders HJ, Kaetzke A, Kampfer P, Ludwig W, Fuchs G (1995) Taxonomic position of aromatic-degrading denitrifying pseudomonad strains K172 and KB740 and their 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 45:327–333CrossRefPubMedGoogle Scholar
  4. Anzai Y, Kim HS, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589CrossRefPubMedGoogle Scholar
  5. Bedard DL, Wagner RE, Brennan MJ, Haberl ML, Brown JF (1987) Extensive degradation of Aroclors and environmentally transformed polychlorinated biphenyls by Alcaligenes eutrophus H850. Appl Environ Microbiol 53:1094–1102PubMedPubMedCentralGoogle Scholar
  6. Beil S, Happe B, Timmis KN, Pieper DH (1997) Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12 – dechlorination of 1,2,4,5-tetrachlorobenzene. Eur J Biochem 247:190–199CrossRefPubMedGoogle Scholar
  7. Boon N, Goris J, De Vos P, Verstraete W, Top EM (2000) Bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading Comamonas testosteroni strain, I2gfp. Appl Environ Microbiol 66:2906–2913CrossRefPubMedPubMedCentralGoogle Scholar
  8. Boon N, Goris J, De Vos P, Verstraete W, Top EM (2001) Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae. Appl Environ Microbiol 67:1107–1115CrossRefPubMedPubMedCentralGoogle Scholar
  9. Bopp LH (1986) Degradation of highly chlorinated PCB’s by Pseudomonas strain LB400. J Ind Microbiol 1:23–29CrossRefGoogle Scholar
  10. Brunsbach FR, Reineke W (1993) Degradation of chloroanilines in soil slurry by specialized organisms. Appl Microbiol Biotechnol 40:402–407CrossRefGoogle Scholar
  11. Chain PS et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103:15280–15287CrossRefPubMedGoogle Scholar
  12. Chakraborty R, Coates JD (2005) Hydroxylation and carboxylation – two crucial steps of anaerobic benzene degradation by Dechloromonas strain RCB. Appl Environ Microbiol 71:5427–5432CrossRefPubMedPubMedCentralGoogle Scholar
  13. Chakraborty R, O’Connor SM, Chan E, Coates JD (2005) Anaerobic degradation of benzene, toluene, ethylbenzene, and xylene compounds by Dechloromonas strain RCB. Appl Environ Microbiol 71:8649–8655CrossRefPubMedPubMedCentralGoogle Scholar
  14. Coates JD, Chakraborty R, Lack JG, O'Connor SM, Cole KA, Bender KS, Achenbach LA (2001) Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature 411:1039–1043CrossRefPubMedGoogle Scholar
  15. Coleman NV, Mattes TE, Gossett JM, Spain JC (2002) Biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium. Appl Environ Microbiol 68:2726–2730CrossRefPubMedPubMedCentralGoogle Scholar
  16. Cooley RB, Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ (2009) Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly “Pseudomonas butanovora”. Microbiology 155:2086–2096CrossRefPubMedPubMedCentralGoogle Scholar
  17. Dejonghe W et al. (2002) Diversity of 3-chloroaniline and 3,4-dichloroaniline degrading bacteria isolated from three different soils and involvement of their plasmids in chorloaniline degradation. FEMS Microbiol Ecol 42:315–325CrossRefPubMedGoogle Scholar
  18. Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ (2009) Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as “Pseudomonas butanovora”. Int J Syst Evol Microbiol 59:1576–1578CrossRefPubMedPubMedCentralGoogle Scholar
  19. Ehrenreich P, Behrends A, Harder J, Widdel F (2000) Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria. Arch Microbiol 173:58–64CrossRefPubMedGoogle Scholar
  20. Evans PJ, Mang DT, Kim KS, Young LY (1991) Anaerobic degradation of toluene by a denitrifying bacterium. Appl Environ Microbiol 57:1139–1145PubMedPubMedCentralGoogle Scholar
  21. Fahy A, McGenity TJ, Timmis KN, Ball AS (2006) Heterogeneous aerobic benzene-degrading communities in oxygen-depleted groundwaters. FEMS Microbiol Ecol 58:260–270CrossRefPubMedGoogle Scholar
  22. Fahy A, Ball AS, Lethbridge G, Timmis KN, McGenity TJ (2008) Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer. Lett Appl Microbiol 47:60–66CrossRefPubMedGoogle Scholar
  23. Fernández H, Prandoni N, Fernández-Pascual M, Fajardo S, Morcillo C, Díaz E, Carmona M (2014) Azoarcus sp. CIB, an anaerobic biodegrader of aromatic compounds shows an endophytic lifestyle. PLoS One 9:e110771CrossRefPubMedPubMedCentralGoogle Scholar
  24. Fuenmayor SL, Rodriguez-Lemoine V (1992) Characterization of polycyclic aromatic hydrocarbons degradative soil Pseudomonas. Acta Cient Venez 43:349–354PubMedGoogle Scholar
  25. Fuenmayor SL, Wild M, Boyles AL, Williams PA (1998) A gene cluster encoding steps in the conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J Bacteriol 180:2522–2530PubMedPubMedCentralGoogle Scholar
  26. Fujii T, Takeo M, Maeda Y (1997) Plasmid-encoded genes specifying aniline oxidation from Acinetobacter sp. strain YAA. Microbiology 143:93–99CrossRefPubMedGoogle Scholar
  27. Fukumori F, Saint C (1997) Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1). J Bacteriol 179:399–408CrossRefPubMedPubMedCentralGoogle Scholar
  28. Goyal AK, Zylstra GJ (1996) Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl Environ Microbiol 62:230–236PubMedPubMedCentralGoogle Scholar
  29. Goyal AK, Zylstra GJ (1997) Genetics of naphthalene and phenanthrene degradation by Comamonas testosteroni. J Ind Microbiol Biotechnol 19:401–407CrossRefPubMedGoogle Scholar
  30. Haigler BE, Pettigrew CA, Spain JC (1992) Biodegradation of mixtures of substituted benzenes by Pseudomonas sp. strain JS150. Appl Environ Microbiol 58:2237–2244PubMedPubMedCentralGoogle Scholar
  31. Haigler BE, Wallace WH, Spain JC (1994) Biodegradation of 2-nitrotoluene by Pseudomonas sp. strain JS42. Appl Environ Microbiol 60:3466–3469PubMedPubMedCentralGoogle Scholar
  32. Halsey KH, Doughty DM, Sayavedra-Soto LA, Bottomley PJ, Arp DJ (2007) Evidence for modified mechanisms of chloroethene oxidation in Pseudomonas butanovora mutants containing single amino acid substitutions in the hydroxylase alpha-subunit of butane monooxygenase. J Bacteriol 189:5068–5074CrossRefPubMedPubMedCentralGoogle Scholar
  33. Harms G, Rabus R, Widdel F (1999) Anaerobic oxidation of the aromatic plant hydrocarbon p-cymene by newly isolated denitrifying bacteria. Arch Microbiol 172:303–312CrossRefPubMedGoogle Scholar
  34. Hinteregger C, Streichsbier F (2001) Isolation and characterization of Achromobacter xylosoxidans T7 capable of degrading toluidine isomers. J Basic Microbiol 41:159–170CrossRefPubMedGoogle Scholar
  35. Irie S, Doi S, Yorifuji T, Takagi M, Yano K (1987) Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida. J Bacteriol 169:5174–5179CrossRefPubMedPubMedCentralGoogle Scholar
  36. Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL (2003) Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci USA 100:13591–13596CrossRefPubMedGoogle Scholar
  37. Jeon CO, Park W, Ghiorse WC, Madsen EL (2004) Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst Evol Microbiol 54:93–97CrossRefPubMedGoogle Scholar
  38. Jeon CO, Park M, Ro HS, Park W, Madsen EL (2006) The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: evolutionary implications for two gene clusters and novel regulatory control. Appl Environ Microbiol 72:086–1095Google Scholar
  39. Jiang XW, Liu H, Xu Y, Wang S, Leak DJ, Zhou NY (2009) Genetic and biochemical analyses of chlorobenzene degradation gene clusters in Pandoraea sp. strain MCB032. Arch Microbiol 191:485–492CrossRefPubMedGoogle Scholar
  40. Jiang B, Zhou Z, Dong Y, Tao W, Wang B, Jiang J, Guan X (2015) Biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Comamonas sp. JB. Appl Biochem Biotechnol 176:1700–1708CrossRefPubMedGoogle Scholar
  41. Johnson HA, Spormann AM (1999) In vitro studies on the initial reactions of anaerobic ethylbenzene mineralization. J Bacteriol 181:5662–5668PubMedPubMedCentralGoogle Scholar
  42. Johnson GR, Jain RK, Spain JC (2000) Properties of the trihydroxytoluene oxygenase from Burkholderia cepacia R34: an extradiol dioxygenase from the 2,4-dinitrotoluene pathway. Arch Microbiol 173:86–90CrossRefPubMedGoogle Scholar
  43. Juárez JF, Zamarro MT, Eberlein C, Boll M, Carmona M, Díaz E (2013) Characterization of the mbd cluster encoding the anaerobic 3-methylbenzoyl-CoA central pathway. Environ Microbiol 15:148–166CrossRefPubMedGoogle Scholar
  44. Kang H et al. (2003) Degradation of phenanthrene and naphthalene by a Burkholderia species strain. Can J Microbiol 49:139–144CrossRefPubMedGoogle Scholar
  45. Kerstens K, Ludwig W, Vancanneyt M, de Vos P, Gillis M, Schleifer K-H (1996) Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 19:465–477CrossRefGoogle Scholar
  46. Kimbara K, Hashimoto T, Fukuda M, Koana T, Takagi M, Oishi M, Yano K (1989) Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. J Bacteriol 171:2740–2747CrossRefPubMedPubMedCentralGoogle Scholar
  47. Kiyohara H, Nagao K, Kouno K, Yano K (1982) Phenanthrene-degrading phenotype of Alcaligenes faecalis AFK2. Appl Environ Microbiol 43:458–461PubMedPubMedCentralGoogle Scholar
  48. Klankeo P, Nopcharoenkul W, Pinyakong O (2009) Two novel pyrene-degrading Diaphorobacter sp. and Pseudoxanthomonas sp. isolated from soil. J Biosci Bioeng 108:488–495CrossRefPubMedGoogle Scholar
  49. Kniemeyer O, Heider J (2001) Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J Biol Chem 276:21381–21386CrossRefPubMedGoogle Scholar
  50. Krieger CJ, Beller HR, Reinhard M, Spormann AM (1999) Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T. J Bacteriol 181:6403–6410PubMedPubMedCentralGoogle Scholar
  51. Kukor JJ (1990) Diversity of toluene degradation following long term exposure to BTEX in situ. In: Kamely D, Chakrabarty A, Omenn GS (eds) Biotechnology and biodegradation. Portfolio Publishing Co, The Woodlands, pp 405–421Google Scholar
  52. Laurie AD, Lloyd-Jones G (1999) The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181:531–540PubMedPubMedCentralGoogle Scholar
  53. Lee SK, Lee SB (2001) Isolation and characterization of a thermotolerant bacterium Ralstonia sp. strain PHS1 that degrades benzene, toluene, ethylbenzene, and o-xylene. Appl Microbiol Biotechnol 56:270–275CrossRefPubMedGoogle Scholar
  54. Lessner DJ, Johnson GR, Parales RE, Spain JC, Gibson DT (2002) Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl Environ Microbiol 68:634–641CrossRefPubMedPubMedCentralGoogle Scholar
  55. Lessner DJ, Parales RE, Narayan S, Gibson DT (2003) Expression of nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 185:3895–3904CrossRefPubMedPubMedCentralGoogle Scholar
  56. Liu Z, Yang H, Huang Z, Zhou P, Liu SJ. (2002) Degradation of aniline by newly isolated, extremely aniline-tolerant Delftia sp. AN3. Appl Microbiol Biotechnol 58:679–682Google Scholar
  57. Loidl M, Hinteregger C, Ditzelmüller G, Ferschl A, Streichsbier F (1990) Degradation of aniline and monochlorinated anilines by soil-born Pseudomonas acidovorans strains. Arch Microbiol 155:56–61CrossRefGoogle Scholar
  58. López Barragán MJ et al. (2004) The bzd gene cluster, coding for anaerobic benzoate catabolism, in Azoarcus sp. strain CIB. J Bacteriol 186:5762–5774CrossRefPubMedGoogle Scholar
  59. Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, Coleman NV (2008) The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol 74:6405–6416CrossRefPubMedPubMedCentralGoogle Scholar
  60. Miyachi N, Tanaka T, Suzuki T, Hotta Y, Omori T (1993) Microbial oxidation of dimethylnaphthalene isomers. Appl Environ Microbiol 59:1504–1506PubMedPubMedCentralGoogle Scholar
  61. Monferrán MV, Echenique JR, Wunderlin DA (2005) Degradation of chlorobenzenes by a strain of Acidovorax avenae isolated from a polluted aquifer. Chemosphere 61:98–106CrossRefPubMedGoogle Scholar
  62. Mukerjee-Dhar G, Hatta T, Shimura M, Kimbara K (1998) Analysis of changes in congener selectivity during PCB degradation by Burkholderia sp. strain TSN101 with increasing concentrations of PCB and characterization of the bphBCD genes and gene products. Arch Microbiol 169:61–70Google Scholar
  63. Nelson MJK, Montgomery SO, Mahaffey WR, Pritchard PH (1987) Biodegradation of trichloroethylene and involvement of an aromatic biodegradative pathway. Appl Environ Microbiol 53:949–954PubMedPubMedCentralGoogle Scholar
  64. Nishino SF, Spain JC (1995) Oxidative pathway for the biodegradation of nitrobenzene by Comamonas sp. strain JS765. Appl Environ Microbiol 61:2308–2313PubMedPubMedCentralGoogle Scholar
  65. Nishino SF, Paoli GC, Spain JC (2000) Aerobic degradation of dinitrotoluenes and the pathway for bacterial degradation of 2,6-dinitrotoluene. Appl Environ Microbiol 66:2139–2147CrossRefPubMedPubMedCentralGoogle Scholar
  66. Nishino SF, Shin KA, Gossett JM, Spain JC (2013) Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666. Appl Environ Microbiol 79:2263–2272CrossRefPubMedPubMedCentralGoogle Scholar
  67. Ohtsubo Y, Goto H, Nagata Y, Kudo T, Tsuda M (2006) Dentification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102. Mol Microbiol 60:1563–1575CrossRefPubMedGoogle Scholar
  68. Oosterkamp MJ et al (2013) Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.). PLoS One 8:e66971CrossRefPubMedPubMedCentralGoogle Scholar
  69. Palleroni NJ (1984) Family I. Pseudomonadaceae. In: Krieg NR (ed) Bergey’s manual of systematic bacteriology, vol 1. The Williams & Wilkens Co, Baltimore, pp 141–199Google Scholar
  70. Palleroni NJ (2003) Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: a personal view. Microbiology 149:1–7CrossRefPubMedGoogle Scholar
  71. Palleroni NJ, Kunisawa R, Contopoulou R, Doudoroff M (1973) Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23:333–339CrossRefGoogle Scholar
  72. Parales RE (2000) Molecular biology of nitroarene degradation. In: Spain JC, Hughes JB, Knackmuss H-J (eds) Biodegradation of nitroaromatic compounds and explosives. CRC Press, Boca Raton, pp 63–89Google Scholar
  73. Pollmann K, Beil S, Pieper DH (2001) Transformation of chlorinated benzenes and toluenes by Ralstonia sp. strain PS12 tecA (tetrachlorobenzene dioxygenase) and tecB (chlorobenzene dihydrodiol dehydrogenase) gene products. Appl Environ Microbiol 67:4057–4063CrossRefPubMedPubMedCentralGoogle Scholar
  74. Posman KM, DeRito CM, Madsen EL (2017) Benzene degradation by a Variovorax species within a coal tar-contaminated groundwater microbial community. Appl Environ Microbiol 83:e02658–e02616CrossRefPubMedPubMedCentralGoogle Scholar
  75. Rabus R, Widdel F (1995) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96–103CrossRefPubMedGoogle Scholar
  76. Rabus R et al. (2001) Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. J Bacteriol 183:1707–1715Google Scholar
  77. 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 183:27–36CrossRefPubMedGoogle Scholar
  78. Rabus R, Jarling R, Lahme S, Kühner S, Heider J, Widdel F, Wilkes H (2011) Co-metabolic conversion of toluene in anaerobic n-alkane-degrading bacteria. Environ Microbiol 13:2576–2586CrossRefPubMedGoogle Scholar
  79. Rabus R et al (2016) Anaerobic microbial degradation of hydrocarbons: from enzymatic reactions to the environment. J Mol Microbiol Biotechnol 26:5–28CrossRefPubMedGoogle Scholar
  80. Rapp P, Timmis KN (1999) Degradation of chlorobenzenes at nanomolar concentrations by Burkholderia sp. strain PS14 in liquid cultures and in soil. Appl Environ Microbiol 65:2547–2552PubMedPubMedCentralGoogle Scholar
  81. Salamanca D, Engesser KH (2014) Isolation and characterization of two novel strains capable of using cyclohexane as carbon source. Environ Sci Pollut Res Int 21:12757–12766CrossRefPubMedGoogle Scholar
  82. Salamanca D, Karande R, Schmid A, Dobslaw D (2015) Novel cyclohexane monooxygenase from Acidovorax sp. CHX100. Appl Microbiol Biotechnol 99:6889–6887CrossRefPubMedGoogle Scholar
  83. Salinero KK, Keller K, Feil W, Feil H, Trong S, Di Bartolo G, Lapidus A (2009) Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation. BMC Genomics 10:351CrossRefPubMedPubMedCentralGoogle Scholar
  84. Samanta SK, Chakraborti AK, Jain RK (1999) Degradation of phenanthrene by different bacteria: evidence for novel transformation sequences involving the formation of 1-naphthol. Appl Microbiol Biotechnol 53:98–107CrossRefPubMedGoogle Scholar
  85. Sander P, Wittich R-M, Fortnagel P, Wilkes H, Francke W (1991) Degradation of 1,2,4-trichloro- and 1,2,4,5-tetrachlorobenzene by Pseudomonas strains. Appl Environ Microbiol 57:1430–1440PubMedPubMedCentralGoogle Scholar
  86. Shinoda Y et al (2004) Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1. Appl Environ Microbiol 70:1385–1392CrossRefPubMedPubMedCentralGoogle Scholar
  87. Shuttleworth KL, Cerniglia CE (1996) Bacterial degradation of low concentrations of phenanthrene and inhibition by naphthalene. Microb Ecol 31:305–317CrossRefGoogle Scholar
  88. Singh D, Ramanathan G (2013) Biomineralization of 3-nitrotoluene by Diaphorobacter species. Biodegradation 24:645–655CrossRefPubMedGoogle Scholar
  89. Singh D, Kumari A, Ramanathan G (2014) 3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies. Biodegradation 25:479–492CrossRefPubMedGoogle Scholar
  90. Singleton DR, Guzmán Ramirez L, Aitken MD (2009) Characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading Acidovorax strain. Appl Environ Microbiol 75:2613–2620CrossRefPubMedPubMedCentralGoogle Scholar
  91. Sluis MK, Sayavedra-Soto LA, Arp DJ (2002) Molecular analysis of the soluble butane monooxygenase from Pseudomonas butanovora. Microbiology 48:3617–3629CrossRefGoogle Scholar
  92. Song B, Young LY, Palleroni NJ (1998) Identification of denitrifier strain T1 as Thauera aromatica and proposal for emendation of the genus Thauera definition. Int J Syst Bacteriol 48:889–894CrossRefPubMedGoogle Scholar
  93. Spanggord RJ, Spain JC, Nishino SF, Mortelmans KE (1991) Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp. Appl Environ Microbiol 57:3200–3205PubMedPubMedCentralGoogle Scholar
  94. Sperfeld M, Rauschenbach C, Diekert G, Studenik S (2018) Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation. Water Res 132:146–157CrossRefPubMedGoogle Scholar
  95. Stanier RY, Palleroni NJ, Doudoroff M (1966) The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271CrossRefPubMedGoogle Scholar
  96. Strijkstra A et al (2014) Anaerobic activation of p-cymene in denitrifying Betaproteobacteria: methyl group hydroxylation versus addition to fumarate. Appl Environ Microbiol 80:7592–7603CrossRefPubMedPubMedCentralGoogle Scholar
  97. Suen W-C, Spain JC (1993) Cloning and characterization of Pseudomonas sp. strain DNT genes for 2,4-dinitrotoluene degradation. J Bacteriol 175:1831–1837CrossRefPubMedPubMedCentralGoogle Scholar
  98. Suen W-C, Haigler BE, Spain JC (1996) 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase. J Bacteriol 178:4926–4934CrossRefPubMedPubMedCentralGoogle Scholar
  99. Takahashi J, Ichikawa Y, Sagae H, Komura I, Kanou H, Yamada K (1980) Isolation and identification of n-butane-assimilating bacterium. Agric Biol Chem 44:1835–1840Google Scholar
  100. Tan HM (1993) The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene 130:33–39CrossRefPubMedGoogle Scholar
  101. Urata M, Uchida E, Nojiri H, Omori T, Obo R, Miyaura N, Ouchiyama N (2004) Genes involved in aniline degradation by Delftia acidovorans strain 7N and its distribution in the natural environment. Biosci Biotechnol Biochem 68:2457–2465CrossRefPubMedGoogle Scholar
  102. van der Meer JR, Roelofsen W, Schraa G, Zehnder A (1987) Degradation of low concentrations of dichlorobenzenes and 1,2,4-trichlorobenzene by Pseudomonas sp. strain P51. FEMS Microbiol Ecol 45:333–341CrossRefGoogle Scholar
  103. van der Meer JR, Zehnder A, de Vos WM (1991) Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J Bacteriol 173:7077–7083CrossRefPubMedPubMedCentralGoogle Scholar
  104. van der Meer JR, Werlen C, Nishino SF, Spain JC (1998) Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Appl Environ Microbiol 64:4185–4193PubMedPubMedCentralGoogle Scholar
  105. van der Zaan BM et al (2012) Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae as a dominant benzene degraders and evidence for a syntrophic process. Environ Microbiol 14:1171–1181CrossRefPubMedGoogle Scholar
  106. Vandamme P, Coenye T (2004) Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol 54:2285–2289CrossRefPubMedGoogle Scholar
  107. Vézina J, Barriault D, Sylvestre M (2008) Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit. J Mol Microbiol Biotechnol 15:139–151CrossRefPubMedGoogle Scholar
  108. Weelink SA et al (2008) Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor. Appl Environ Microbiol 74:6672–6681Google Scholar
  109. Weelink SAB, van Doesburg W, Saia FT, Rijpstra WI, Roling WF, Smidt H, Stams AJ (2009) A strictly anaerobic Betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor. FEMS Microbiol Ecol 70:575–585Google Scholar
  110. Werlen C, Kohler H-PE, van der Meer JR (1996) The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. P51 are linked evolutionary to the enzymes for benzene and toluene degradation. J Biol Chem 271:4009–4016CrossRefPubMedGoogle Scholar
  111. Wilkes H, Buckel W, Golding BT, Rabus R (2016) Metabolism of hydrocarbons in n-alkane-utilizing anaerobic bacteria. J Mol Microbiol Biotechnol 26:38–151CrossRefGoogle Scholar
  112. Wilson MS, Herrik JB, Jeon CO, Hinman DE, Madsen EL (2003) Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments. Appl Environ Microbiol 69:2172–2181CrossRefPubMedPubMedCentralGoogle Scholar
  113. Wittich RM, Wolff P (2007) Growth of the genetically engineered strain Cupriavidus necator RW112 with chlorobenzoates and technical chlorobiphenyls. Microbiology 153:186–195CrossRefPubMedGoogle Scholar
  114. Wu JF, Jiang CY, Wang BJ, Ma Y, Liu ZP, Liu SJ (2006) Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl Environ Microbiol 72:1759–1765CrossRefPubMedPubMedCentralGoogle Scholar
  115. Yuste L, Corbella ME, Turiégano MJ, Karlson U, Puyet A, Rojo F (2000) Characterization of bacterial strains able to grow on high molecular mass residues from crude oil processing. FEMS Microbiol Ecol 32:69–75CrossRefPubMedGoogle Scholar
  116. Zedelius J et al (2011) Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. Environ Microbiol Rep 3:125–135CrossRefPubMedPubMedCentralGoogle Scholar
  117. Zhang T, Zhang J, Liu S, Liu Z (2008) A novel and complete gene cluster involved in the degradation of aniline by Delftia sp. AN3. J Environ Sci 20:717–724CrossRefGoogle Scholar
  118. Zhang LL, He D, Chen JM, Liu Y (2010) Biodegradation of 2-chloroaniline, 3-chloroaniline, and 4-chloroaniline by a novel strain Delftia tsuruhatensis H1. J Hazard Mater 179:875–882CrossRefPubMedGoogle Scholar
  119. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM (1995) Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 45:500–506CrossRefPubMedGoogle Scholar
  120. Zhou N-Y, Fuenmayor SL, Williams PA (2001) nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J Bacteriol 183:700–708CrossRefPubMedPubMedCentralGoogle Scholar
  121. Zylstra GJ, Gibson DT (1989) Toluene degradation by Pseudomonas putida F1. Nucleotide sequence of the todC1C2BADE genes and their expression in Escherichia coli. J Biol Chem 264:14940–14946PubMedGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Faculty of BiotechnologyAtma Jaya Catholic University of IndonesiaJakartaIndonesia
  2. 2.Department of Microbiology and Molecular GeneticsThe University of CaliforniaDavisUSA

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