Horizontal transfer of dehalogenase genes involved in the catalysis of chlorinated compounds: Evidence and ecological role

Critical Reviews in Microbiology

Volumn 38, Issue 2, 2012, Pages 95-110

  Liang, Bin ^a,b   Jiang, Jiandong ^a   Zhang, Jun ^a   Zhao, Yanfu ^a   Li, Shunpeng ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Chlorinated compounds; Community adaptation; Dehalogenase genes; Horizontal gene transfer (HGT); Mobile genetic elements (MGEs)

Indexed keywords

1,2 DIBROMOETHANE; 1,2 DICHLOROETHANE; ALKANE DERIVATIVE; AROMATIC COMPOUND; ATRAZINE; BACTERIAL ENZYME; CHLORINE DERIVATIVE; CHLOROBENZENE; CHLOROTHALONIL; DICHLOROMETHANE; HEXACHLOROCYCLOHEXANE; PENTACHLOROPHENOL; TETRACHLOROETHYLENE; TRICHLOROETHYLENE; VINYL CHLORIDE;

ADAPTATION; BACTERIAL GENE; CATALYSIS; DEHALOGENASE GENE; DEHALOGENATION; ENZYME ACTIVITY; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; POLLUTION; PRIORITY JOURNAL; REVIEW;

EID: 84859704736     PISSN: 1040841X     EISSN: 15497828     Source Type: Journal    
DOI: 10.3109/1040841X.2011.618114     Document Type: Review

References (143)

1. Böltner D, Moreno-Morillas S, Ramos JL. (2005). 16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexanedegrading Sphingomonas strains. Environ Microbiol, 7, 1329-1338. (Pubitemid 41204927)
2. Bramucci M, Chen M, Nagarajan V. (2006). Genetic organization of a plasmid from an industrial wastewater bioreactor. Appl Microbiol Biotechnol, 71, 67-74. (Pubitemid 43807464)
3. Brokamp A, Schmidt FRJ. (1991). Survival of Alcaligenes xylosoxidans degrading 2,2-dichloropropionate and horizontal transfer of its halidohydrolase gene in a soil microcosm. Curr Microbiol, 22, 299-306.
4. Cai B, Han Y, Liu B, Ren Y, Jiang S. (2003). Isolation and characterization of an atrazine-degrading bacterium from industrial wastewater in China. Lett Appl Microbiol, 36, 272-276. (Pubitemid 36532506)
5. Caux P, Kent R, Fan G, Stephenson G. (1996). Environmental fate and effects of chlorothalonil: A Canadian perspective. Crit Rev Environ Sci Technol, 26, 45-93. (Pubitemid 26039795)
6. Chatterjee DK, Chakrabarty AM. (1983). Genetic homology between independently isolated chlorobenzoate-degradative plasmids. J Bacteriol, 153, 532-534. (Pubitemid 13119583)
7. Clément P, Pieper DH, González B. (2001). Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid. Microbiology 147, 2141-2148. (Pubitemid 32785494)
8. Copley SD. (2000). Evolution of a metabolic pathway for degradation of a toxic xenobiotic: The patchwork approach. Trends Biochem Sci, 25, 261-265. (Pubitemid 30333381)
9. Crawford RL, Jung CM, Strap JL. (2007). The recent evolution of pentachlorophenol (PCP)-4-monooxygenase (PcpB) and associated pathways for bacterial degradation of PCP. Biodegradation, 18, 525-539. (Pubitemid 47305474)
10. Dai XZ, Jiang JD, Gu LF, Li R, Li SP. (2007). Isolation and characterization of an atrazine-degrading bacterium strain SA1. Wei Sheng Wu Xue Bao, 47, 544-547.
11. de Souza ML, Sadowsky MJ, Wackett LP. (1996). Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: Gene sequence, enzyme purification, and protein characterization. J Bacteriol, 178, 4894-4900. (Pubitemid 26321290)
12. de Souza ML, Seffernick J, Martinez B, Sadowsky MJ, Wackett LP. (1998a). The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol, 180, 1951-1954. (Pubitemid 28173080)
13. de Souza ML, Wackett LP, Sadowsky MJ. (1998b). The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl Environ Microbiol, 64, 2323-2326. (Pubitemid 28252812)
14. Demerec M. (1960). Frequency of deletions among spontaneous and induced mutations in salmonella. Proc Natl Acad Sci USA, 46, 1075-1079.
15. Devers M, El Azhari N, Kolic NU, Martin-Laurent F. (2007a). Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions. FEMS Microbiol Lett, 273, 78-86. (Pubitemid 47024900)
16. Devers M, Henry S, Hartmann A, Martin-Laurent F. (2005). Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil. Pest Manag Sci, 61, 870-880. (Pubitemid 41290932)
17. Devers M, Rouard N, Martin-Laurent F. (2007b). Genetic rearrangement of the atzAB atrazine-degrading gene cassette from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2. Gene, 392, 1-6. (Pubitemid 46482830)
18. Devers M, Rouard N, Martin-Laurent F. (2008). Fitness drift of an atrazine-degrading population under atrazine selection pressure. Environ Microbiol, 10, 676-684. (Pubitemid 351160908)
19. Di Gioia D, Peel M, Fava F, Wyndham RC. (1998). Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl Environ Microbiol, 64, 1940-1946. (Pubitemid 28234810)
20. Dogra C, Raina V, Pal R, Suar M, Lal S, Gartemann KH, Holliger C, van der Meer JR, Lal R. (2004). Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: Evidence for horizontal gene transfer. J Bacteriol, 186, 2225-2235. (Pubitemid 38451824)
21. Don RH, Pemberton JM. (1981). Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol, 145, 681-686. (Pubitemid 11140391)
22. Dutta C, Pan A. (2002). Horizontal gene transfer and bacterial diversity. J Biosci, 27, 27-33. (Pubitemid 34285617)
23. Emanuelsson MA, Osuna MB, Ferreira Jorge RM, Castro PM. (2009). Isolation of a Xanthobacter sp. degrading dichloromethane and characterization of the gene involved in the degradation. Biodegradation, 20, 235-244.
24. Firsova JE, Doronina NV, Trotsenko YA. (2010). Analysis of the key functional genes in new aerobic degraders of dichloromethane. Microbiology, 79, 66-72.
25. Friedrich B, Meyer M, Schlegel HG. (1983). Transfer and expression of the herbicide-degrading plasmid pJP4 in aerobic autotrophic bacteria. Arch Microbiol, 134, 92-97. (Pubitemid 13080849)
26. Fulthorpe RR, Wyndham RC. (1992). Involvement of a chlorobenzoatecatabolic transposon, Tn5271, in community adaptation to chlorobiphenyl, chloroaniline, and 2,4-dichlorophenoxyacetic acid in a freshwater ecosystem. Appl Environ Microbiol, 58, 314-325.
27. Futagami T, Tsuboi Y, Suyama A, Goto M, Furukawa K. (2006). Emergence of two types of nondechlorinating variants in the tetrachloroethene-halorespiring Desulfitobacterium sp. strain Y51. Appl Microbiol Biotechnol, 70, 720-728. (Pubitemid 43760509)
28. Gaillard M, Pernet N, Vogne C, Hagenbüchle O, van der Meer JR. (2008). Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1. Proc Natl Acad Sci USA, 105, 7058-7063. (Pubitemid 351754529)
29. Gaillard M, Pradervand N, Minoia M, Sentchilo V, Johnson DR, van der Meer JR. (2010). Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiol, 10, 153.
30. Gartemann KH, Eichenlaub R. (2001). Isolation and characterization of IS1409, an insertion element of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1, and development of a system for transposon mutagenesis. J Bacteriol, 183, 3729-3736. (Pubitemid 32536651)
31. Gerritse J, Drzyzga O, Kloetstra G, Keijmel M, Wiersum LP, Hutson R, Collins MD, Gottschal JC. (1999). Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1. Appl Environ Microbiol, 65, 5212-5221. (Pubitemid 129520600)
32. Ghosal D, You IS, Chatterjee DK, Chakrabarty AM. (1985). Genes specifying degradation of 3-chlorobenzoic acid in plasmids pAC27 and pJP4. Proc Natl Acad Sci USA, 82, 1638-1642. (Pubitemid 15079448)
33. Ghosh D, Roy K, Williamson KE, White DC, Wommack KE, Sublette KL, Radosevich M. (2008). Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA. Appl Environ Microbiol, 74, 495-502.
34. Hill KE, Weightman AJ. (2003). Horizontal transfer of dehalogenase genes on IncP1β plasmids during bacterial adaptation to degrade α-halocarboxylic acids. FEMS Microbiol Ecol, 45, 273-282. (Pubitemid 36959926)
35. Hirkala DL, Germida JJ. (2004). Field and soil microcosm studies on the survival and conjugation of a Pseudomonas putida strain bearing a recombinant plasmid, pADPTel. Can J Microbiol, 50, 595-604. (Pubitemid 39506789)
36. Hoffmann D, Kleinsteuber S, Müller RH, Babel W. (2003). A transposon encoding the complete 2,4-dichlorophenoxyacetic acid degradation pathway in the alkalitolerant strain Delftia acidovorans P4a. Microbiology (Reading, Engl), 149, 2545-2556. (Pubitemid 37160729)
37. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJ. (1998). Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra-and trichloroethene in an anaerobic respiration. Arch Microbiol, 169, 313-321. (Pubitemid 28189535)
38. Holliger C, Wohlfarth G, Diekert G. (1999). Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol Rev, 22, 383-398.
39. Hughes K, Meek M, Caldwell I. (1994). 1, 2-Dichloroethane: Evaluation of risks and health from environmental exposure in Canada. J Environ Sci Health Part C Environ Carcinog Rev, 12, 293-303. (Pubitemid 24354933)
40. Ito M, Prokop Z, Klvana M, Otsubo Y, Tsuda M, Damborský J, Nagata Y. (2007). Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexaneutilizing bacterium Sphingobium sp. MI1205. Arch Microbiol, 188, 313-325. (Pubitemid 47415687)
41. Jacob F, Monod J. (1962). On the regulation of gene activity. Cold Spring Harbor Symp Quant Biol, 26, 193-211.
42. Janssen DB, Pries F, van der Ploeg JR. (1994). Genetics and biochemistry of dehalogenating enzymes. Annu Rev Microbiol, 48, 163-191. (Pubitemid 24334095)
43. Jencova V, Strnad H, Chodora Z, Ulbrich P, Hickey WJ, Paces V. (2004). Chlorocatechol catabolic enzymes from Achromobacter xylosoxidans A8. Int Biodeterior Biodegrad, 54, 175-181. (Pubitemid 39122981)
44. Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L. (2008). Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl Environ Microbiol, 74, 2864-2872. (Pubitemid 351632617)
45. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW. (2009). Genomic islands: Tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev, 33, 376-393.
46. Kaschabek SR, Kasberg T, Müller D, Mars AE, Janssen DB, Reineke W. (1998). Degradation of chloroaromatics: Purification and characterization of a novel type of chlorocatechol 2,3-dioxygenase of Pseudomonas putida GJ31. J Bacteriol, 180, 296-302. (Pubitemid 28100295)
47. Kiesel B, Müller RH, Kleinsteuber R. (2007). Adaptative potential of alkaliphilic bacteria towards chloroaromatic substrates assessed by a gfp-tagged 2,4-D degradation plasmid. Eng Life Sci, 7, 361-372. (Pubitemid 47162082)
48. Kleinsteuber S, Müller RH, Babel W. (2001). Expression of the 2,4-D degradative pathway of pJP4 in an alkaliphilic, moderately halophilic soda lake isolate, Halomonas sp. EF43. Extremophiles, 5, 375-384. (Pubitemid 33737387)
49. Koonin EV, Makarova KS, Aravind L. (2001). Horizontal gene transfer in prokaryotes: Quantification and classification. Annu Rev Microbiol, 55, 709-742. (Pubitemid 32978121)
50. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE. (2004). Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol, 70, 6347-6351. (Pubitemid 39471893)
51. Krajmalnik-Brown R, Sung Y, Ritalahti KM, Saunders FM, Löffler FE. (2007). Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiol Ecol, 59, 206-214. (Pubitemid 44952423)
52. Jason Krutz L, Shaner DL, Weaver MA, Webb RM, Zablotowicz RM, Reddy KN, Huang Y, Thomson SJ. (2010). Agronomic and environmental implications of enhanced s-triazine degradation. Pest Manag Sci, 66, 461-481.
53. Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L. (2005). Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol, 23, 1269-1273. (Pubitemid 41486854)
54. Kulakov LA, Poelarends GJ, Janssen DB, Larkin MJ. (1999). Characterization of IS2112, a new insertion sequence from Rhodococcus, and its relationship with mobile elements belonging to the IS110 family. Microbiology (Reading, Engl), 145 (Pt 3), 561-568. (Pubitemid 29127035)
55. Kulakova AN, Larkin MJ, Kulakov LA. (1997). The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143 (Pt 1), 109-115. (Pubitemid 27072965)
56. Kumari R, Subudhi S, Suar M, Dhingra G, Raina V, Dogra C, Lal S, van der Meer JR, Holliger C, Lal R. (2002). Cloning and characterization of lin genes responsible for the degradation of Hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90. Appl Environ Microbiol, 68, 6021-6028. (Pubitemid 36342436)
57. Lal R, Pandey G, Sharma P, Kumari K, Malhotra S, Pandey R, Raina V, Kohler HP, Holliger C, Jackson C, Oakeshott JG. (2010). Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev, 74, 58-80.
58. Lawrence JG, Roth JR. (1996). Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics, 143, 1843-1860. (Pubitemid 26286959)
59. Kunze M, Zerlin KF, Retzlaff A, Pohl JO, Schmidt E, Janssen DB, Vilchez-Vargas R, Pieper DH, Reineke W. (2009). Degradation of chloroaromatics by Pseudomonas putida GJ31: Assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome. Microbiology 155, 4069-4083.
60. Lal R, Dogra C, Malhotra S, Sharma P, Pal R. (2006). Diversity, distribution and divergence of lin genes in hexachlorocyclohexanedegrading sphingomonads. Trends Biotechnol, 24, 121-130.
61. Lee JS, Lee K, Ka JO, Chae JC, Kim CK. (2003). Structural analysis of the fcbABC gene cluster responsible for hydrolytic dechlorination of 4-chlorobenzoate from pJS1 plasmid of Comamonas sp P08. J Microbiol, 41, 89-94. (Pubitemid 36890806)
62. Leveau JH, van der Meer JR. (1997). Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134. Gene, 202, 103-114. (Pubitemid 27523709)
63. Liang B, Li R, Jiang D, Sun J, Qiu J, Zhao Y, Li S, Jiang J. (2010). Hydrolytic dechlorination of chlorothalonil by Ochrobactrum sp. CTN-11 isolated from a chlorothalonil-contaminated soil. Curr Microbiol, 61, 226-233.
64. Liang B, Wang G, Zhao Y, Chen K, Li S, Jiang J. (2011). Facilitation of bacterial adaptation to chlorothalonil-contaminated sites by horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene. Appl Environ Microbiol, 77, 4268-4272.
65. Loessner I, Dietrich K, Dittrich D, Hacker J, Ziebuhr W. (2002). Transposase-dependent formation of circular IS256 derivatives in Staphylococcus epidermidis and Staphylococcus aureus. J Bacteriol, 184, 4709-4714.
66. Müller JA, Rosner BM, Von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM. (2004). Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol, 70, 4880-4888. (Pubitemid 39095517)
67. Müller TA, Werlen C, Spain J, Van Der Meer JR. (2003). Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia. Environ Microbiol, 5, 163-173. (Pubitemid 36352436)
68. Maillard J, Regeard C, Holliger C. (2005). Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1. Environ Microbiol, 7, 107-117.
69. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ. (2001). Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol, 183, 5684-5697. (Pubitemid 32898616)
70. Marzorati M, de Ferra F, Van Raemdonck H, Borin S, Allifranchini E, Carpani G, Serbolisca L, Verstraete W, Boon N, Daffonchio D. (2007). A novel reductive dehalogenase, identified in a contaminated groundwater enrichment culture and in Desulfitobacterium dichloroeliminans strain DCA1, is linked to dehalogenation of 1,2-dichloroethane. Appl Environ Microbiol, 73, 2990-2999. (Pubitemid 46718583)
71. 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, 6405-6416.
72. Maymó-Gatell X, Chien Y, Gossett JM, Zinder SH. (1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science, 276, 1568-1571. (Pubitemid 27255322)
73. McMurdie PJ, Behrens SF, Holmes S, Spormann AM. (2007). Unusual codon bias in vinyl chloride reductase genes of Dehalococcoides species. Appl Environ Microbiol, 73, 2744-2747. (Pubitemid 46668769)
74. McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM. (2009). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet, 5, e1000714.
75. Mehrabi R, Bahkali AH, Abd-Elsalam KA, Moslem M, Ben M'barek S, Gohari AM, Jashni MK, Stergiopoulos I, Kema GH, de Wit PJ. (2011). Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range. FEMS Microbiol Rev, 35, 542-554.
76. Miller E, Wohlfarth G, Diekert G. (1997). Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S. Arch Microbiol, 168, 513-519. (Pubitemid 27522521)
77. Miyauchi K, Lee HS, Fukuda M, Takagi M, Nagata Y. (2002). Cloning and characterization of linR, involved in regulation of the downstream pathway for gamma-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol, 68, 1803-1807. (Pubitemid 34279988)
78. Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M. (2006). Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol, 72, 6923-6933. (Pubitemid 44748402)
79. Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. (2006). Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet, 2, e214.
80. Mulbry WW, Zhu H, Nour SM, Topp E. (2002). The triazine hydrolase gene trzN from Nocardioides sp. strain C190: Cloning and construction of gene-specific primers. FEMS Microbiol Lett, 206, 75-79. (Pubitemid 34084941)
81. Muller EE, Bringel F, Vuilleumier S. (2011). Dichloromethanedegrading bacteria in the genomic age. Res Microbiol. doi:10.1016/j. resmic.2011.01.008
82. Nakatsu C, Ng J, Singh R, Straus N, Wyndham C. (1991). Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc Natl Acad Sci USA, 88, 8312-8316. (Pubitemid 21915346)
83. Nakatsu CH, Fulthorpe RR, Holland BA, Peel MC, Wyndham RC. (1995). The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed. Mol Ecol, 4, 593-603.
84. Neilson JW, Josephson KL, Pepper IL, Arnold RB, Di Giovanni GD, Sinclair NA. (1994). Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl Environ Microbiol, 60, 4053-4058. (Pubitemid 24335859)
85. Nikolausz M, Kappelmeyer U, Nijenhuis I, Ziller K, Kästner M. (2005). Molecular characterization of dichloromethane-degrading Hyphomicrobium strains using 16S rDNA and DCM dehalogenase gene sequences. Syst Appl Microbiol, 28, 582-587. (Pubitemid 41073489)
86. Ochman H, Lawrence JG, Groisman EA. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304. (Pubitemid 30337055)
87. Ogawa N, Miyashita K. (1995a). Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements. Appl Environ Microbiol, 61, 3788-3795.
88. Ogawa N, Miyashita K. (1995b). A transposon-like structure carrying genes for the catabolism of 3-chlorobenzoate on a plasmid from Alcaligenes eutrophus strain NH9. Appl Environ Microbiol, 61, 3788-3795.
89. Ogawa N, Miyashita K. (1999). The chlorocatechol-catabolic transposon Tn5707 of Alcaligenes eutrophus NH9, carrying a gene cluster highly homologous to that in the 1,2,4-trichlorobenzenedegrading bacterium Pseudomonas sp. strain P51, confers the ability to grow on 3-chlorobenzoate. Appl Environ Microbiol, 65, 724-731. (Pubitemid 29075122)
90. Oltmanns RH, Rast HG, Reineke W. (1988). Degradation of 1, 4-dichlorobenzene by enriched and constructed bacteria. Appl Microbiol Biotechnol, 28, 609-616.
91. Pérez-Pantoja D, Guzmán L, Manzano M, Pieper DH, González B. (2000). Role of tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II) F(II) gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134(pJP4). Appl Environ Microbiol, 66, 1602-1608. (Pubitemid 30185638)
92. Peel MC, Wyndham RC. (1999). Selection of clc, cba, and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the Hyde park, Niagara Falls, chemical landfill. Appl Environ Microbiol, 65, 1627-1635. (Pubitemid 29173694)
93. Poelarends GJ, Kulakov LA, Larkin MJ, van Hylckama Vlieg JE, Janssen DB. (2000a). Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene-and 1,2-dibromoethanedegradative pathways. J Bacteriol, 182, 2191-2199. (Pubitemid 30183538)
94. Poelarends GJ, Zandstra M, Bosma T, Kulakov LA, Larkin MJ, Marchesi JR, Weightman AJ, Janssen DB. (2000b). Haloalkane-utilizing Rhodococcus strains isolated from geographically distinct locations possess a highly conserved gene cluster encoding haloalkane catabolism. J Bacteriol, 182, 2725-2731. (Pubitemid 30246901)
95. Poh RP, Smith AR, Bruce IJ. (2002). Complete characterisation of Tn5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4- dichlorophenoxyacetate uptake by the organism. Plasmid, 48, 1-12.
96. Potrawfke T, Armengaud J, Wittich RM. (2001). Chlorocatechols substituted at positions 4 and 5 are substrates of the broadspectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71. J Bacteriol, 183, 997-1011. (Pubitemid 32095310)
97. Radice F, Orlandi V, Massa V, Battini V, Bertoni G, Reineke W, Barbieri P. (2007). Cloning of the Arthrobacter sp. FG1 dehalogenase genes and construction of hybrid pathways in Pseudomonas putida strains. Appl Microbiol Biotechnol, 75, 1111-1118. (Pubitemid 46944531)
98. Ravatn R, Studer S, Springael D, Zehnder AJ, van der Meer JR. (1998a). Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. Strain B13. J Bacteriol, 180, 4360-4369. (Pubitemid 28405556)
99. Ravatn R, Zehnder AJ, van der Meer JR. (1998b). Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratoryscale activated-sludge microcosms. Appl Environ Microbiol, 64, 2126-2132. (Pubitemid 28252774)
100. Reams AB, Neidle EL. (2004). Selection for gene clustering by tandem duplication. Annu Rev Microbiol, 58, 119-142. (Pubitemid 39551981)
101. Regeard C, Maillard J, Dufraigne C, Deschavanne P, Holliger C. (2005). Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195. Appl Environ Microbiol, 71, 2955-2961. (Pubitemid 40807199)
102. Reineke W, Wessels SW, Rubio MA, Latorre J, Schwien U, Schmidt E, Schlömann M, Knackmuss HJ. (1982). Degradation of monochlorinated aromatics following transfer of genes encoding chlorocatechol catabolism. FEMS Microbiol Lett, 14, 291-294. (Pubitemid 12033586)
103. Ren X, Li H, Chen S. (2011). Cloning of the chlorothalonil-degrading gene cluster and evidence of its horizontal transfer. Curr Microbiol, 62, 1068-1073.
104. Rousseaux S, Soulas G, Hartmann A. (2002). Plasmid localisation of atrazine-degrading genes in newly described Chelatobacter and Arthrobacter strains. FEMS Microbiol Ecol, 41, 69-75. (Pubitemid 34671191)
105. Sajjaphan K, Shapir N, Wackett LP, Palmer M, Blackmon B, Tomkins J, Sadowsky MJ. (2004). Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl Environ Microbiol, 70, 4402-4407. (Pubitemid 38969793)
106. Schlömann M. (1994). Evolution of chlorocatechol catabolic pathways. Conclusions to be drawn from comparisons of lactone hydrolases. Biodegradation, 5, 301-321.
107. Schmid-Appert M, Zoller K, Traber H, Vuilleumier S, Leisinger T. (1997). Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria. Microbiology 143 (Pt 8), 2557-2567. (Pubitemid 27389941)
108. Sentchilo V, Czechowska K, Pradervand N, Minoia M, Miyazaki R, van der Meer JR. (2009). Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol Microbiol, 72, 1293-1306.
109. Sentchilo V, Ravatn R, Werlen C, Zehnder AJ, van der Meer JR. (2003). Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13. J Bacteriol, 185, 4530-4538. (Pubitemid 36890500)
110. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF. (2005). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science, 307, 105-108. (Pubitemid 40093488)
111. Slater J, Bull A, Hardman D. (1995). Microbial dehalogenation. Biodegradation, 6, 181-189.
112. Sota M, Endo M, Nitta K, Kawasaki H, Tsuda M. (2002). Characterization of a class II defective transposon carrying two haloacetate dehalogenase genes from Delftia acidovorans plasmid pUO1. Appl Environ Microbiol, 68, 2307-2315. (Pubitemid 34477826)
113. Sota M, Kawasaki H, Tsuda M. (2003). Structure of haloacetatecatabolic IncP-1β plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon. J Bacteriol, 185, 6741-6745. (Pubitemid 37385899)
114. Springael D, Peys K, Ryngaert A, Van Roy S, Hooyberghs L, Ravatn R, Heyndrickx M, van der Meer JR, Vandecasteele C, Mergeay M, Diels L. (2002). Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: Indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Environ Microbiol, 4, 70-80. (Pubitemid 34305749)
115. Springael D, Top EM. (2004). Horizontal gene transfer and microbial adaptation to xenobiotics: New types of mobile genetic elements and lessons from ecological studies. Trends Microbiol, 12, 53-58. (Pubitemid 38167335)
116. Suyama A, Yamashita M, Yoshino S, Furukawa K. (2002). Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. J Bacteriol, 184, 3419-3425. (Pubitemid 34625648)
117. Thiel M, Kaschabek SR, Gröning J, Mau M, Schlömann M. (2005). Two unusual chlorocatechol catabolic gene clusters in Sphingomonas sp. TFD44. Arch Microbiol, 183, 80-94. (Pubitemid 40248272)
118. Thiem SM, Krumme ML, Smith RL, Tiedje JM. (1994). Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer. Appl Environ Microbiol, 60, 1059-1067. (Pubitemid 24113917)
119. Thomas AW, Slater JH, Weightman AJ. (1992). The dehalogenase gene dehI from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated DEH. J Bacteriol, 174, 1932-1940.
120. Tiirola MA, Wang H, Paulin L, Kulomaa MS. (2002). Evidence for natural horizontal transfer of the pcpB gene in the evolution of polychlorophenol- degrading sphingomonads. Appl Environ Microbiol, 68, 4495-4501. (Pubitemid 34988133)
121. Top EM, Springael D. (2003). The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol, 14, 262-269. (Pubitemid 36782654)
122. Topp E, Zhu H, Nour SM, Houot S, Lewis M, Cuppels D. (2000). Characterization of an atrazine-degrading Pseudaminobacter sp. isolated from Canadian and French agricultural soils. Appl Environ Microbiol, 66, 2773-2782. (Pubitemid 30497580)
123. Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Pérez-Pantoja D, Sánchez MA, Stuardo M, González B. (2004). Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol, 6, 655-668. (Pubitemid 38847730)
124. Tsuda M, Tan HM, Nishi A, Furukawa K. (1999). Mobile catabolic genes in bacteria. J Biosci Bioeng, 87, 401-410. (Pubitemid 29238999)
125. Udikovic-Kolic N, Hršak D, Devers M, Klepac-Ceraj V, Petric I, Martin-Laurent F. (2010). Taxonomic and functional diversity of atrazinedegrading bacterial communities enriched from agrochemical factory soil. J Appl Microbiol, 109, 355-367.
126. Udikovic Kolic N, Martin-Laurent F, Devers M, Petric I, Begonja Kolar A, Hrsak D. (2008). Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent. J Appl Microbiol, 105, 1334-1343.
127. Vaishampayan PA, Kanekar PP, Dhakephalkar PK. (2007). Isolation and characterization of Arthrobacter sp. strain MCM B-436, an atrazine-degrading bacterium, from rhizospheric soil. Internat Biodet Biodeg, 60, 273-278. (Pubitemid 350101220)
128. van der Meer JR, de Vos WM, Harayama S, Zehnder AJ. (1992). Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev, 56, 677-694.
129. van der Meer JR, Eggen RI, Zehnder AJ, de Vos WM. (1991a). Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: Evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J Bacteriol, 173, 2425-2434.
130. van der Meer JR, Ravatn R, Sentchilo V. (2001). The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases. Arch Microbiol, 175, 79-85. (Pubitemid 32200302)
131. van der Meer JR, van Neerven AR, de Vries EJ, de Vos WM, Zehnder AJ. (1991b). Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51. J Bacteriol, 173, 6-15.
132. van der Meer JR, Zehnder AJ, de Vos WM. (1991c). Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J Bacteriol, 173, 7077-7083.
133. Vedler E, Kõiv V, Heinaru A. (2000). Analysis of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011 of Achromobacter xylosoxidans subsp. denitrificans strain EST4002. Gene, 255, 281-288.
134. Vedler E, Vahter M, Heinaru A. (2004). The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol, 186, 7161-7174. (Pubitemid 39383100)
135. Villemur R, Lanthier M, Beaudet R, Lépine F. (2006). The Desulfitobacterium genus. FEMS Microbiol Rev, 30, 706-733. (Pubitemid 44199347)
136. Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Médigue C, Lidstrom ME. (2009). Methylobacterium genome sequences: A reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS ONE, 4, e5584.
137. Wang G, Li R, Li S, Jiang J. (2010). A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil. J Bacteriol, 192, 2737-2745.
138. Wang GL, Wang L, Chen HH, Shen B, Li SP, Jiang JD. (2011). Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil. Int J Syst Evol Microbiol, 61, 674-679.
139. Weightman AJ, Topping AW, Hill KE, Lee LL, Sakai K, Slater JH, Thomas AW. (2002). Transposition of DEH, a broad-host-range transposon flanked by ISPpu12, in Pseudomonas putida is associated with genomic rearrangements and dehalogenase gene silencing. J Bacteriol, 184, 6581-6591. (Pubitemid 35332563)
140. Wyndham RC, Cashore AE, Nakatsu CH, Peel MC. (1994a). Catabolic transposons. Biodegradation, 5, 323-342.
141. Wyndham RC, Nakatsu C, Peel M, Cashore A, Ng J, Szilagyi F. (1994b). Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system. Appl Environ Microbiol, 60, 86-93. (Pubitemid 24019922)
142. Xia XS, Aathithan S, Oswiecimska K, Smith AR, Bruce IJ. (1998). A novel plasmid pIJB1 possessing a putative 2,4-dichlorophenoxyacetate degradative transposon Tn5530 in Burkholderia cepacia strain 2a. Plasmid, 39, 154-159. (Pubitemid 28145076)
143. Zhou JZ, Tiedje JM. (1995). Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol Ecol, 4, 613-618.