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

References

• Böltner D, Moreno-Morillas S, Ramos JL. (2005). 16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains. Environ Microbiol, 7, 1329–1338.
   PubMed Web of Science ®Google Scholar
• Bramucci M, Chen M, Nagarajan V. (2006). Genetic organization of a plasmid from an industrial wastewater bioreactor. Appl Microbiol Biotechnol, 71, 67–74.
   Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• Chatterjee DK, Chakrabarty AM. (1983). Genetic homology between independently isolated chlorobenzoate-degradative plasmids. J Bacteriol, 153, 532–534.
   Google Scholar
• 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.
   Google Scholar
• Copley SD. (2000). Evolution of a metabolic pathway for degradation of a toxic xenobiotic: The patchwork approach. Trends Biochem Sci, 25, 261–265.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Demerec M. (1960). Frequency of deletions among spontaneous and induced mutations in salmonella. Proc Natl Acad Sci USA, 46, 1075–1079.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Devers M, Rouard N, Martin-Laurent F. (2008). Fitness drift of an atrazine-degrading population under atrazine selection pressure. Environ Microbiol, 10, 676–684.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Don RH, Pemberton JM. (1981). Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol, 145, 681–686.
   PubMed Web of Science ®Google Scholar
• Dutta C, Pan A. (2002). Horizontal gene transfer and bacterial diversity. J Biosci, 27, 27–33.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Firsova JE, Doronina NV, Trotsenko YA. (2010). Analysis of the key functional genes in new aerobic degraders of dichloromethane. Microbiology, 79, 66–72.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fulthorpe RR, Wyndham RC. (1992). Involvement of a chlorobenzoate-catabolic transposon, Tn5271, in community adaptation to chlorobiphenyl, chloroaniline, and 2,4-dichlorophenoxyacetic acid in a freshwater ecosystem. Appl Environ Microbiol, 58, 314–325.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Holliger C, Wohlfarth G, Diekert G. (1999). Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol Rev, 22, 383–398.
   Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205. Arch Microbiol, 188, 313–325.
   PubMedGoogle Scholar
• Jacob F, Monod J. (1962). On the regulation of gene activity. Cold Spring Harbor Symp Quant Biol, 26, 193–211.
   Google Scholar
• Janssen DB, Pries F, van der Ploeg JR. (1994). Genetics and biochemistry of dehalogenating enzymes. Annu Rev Microbiol, 48, 163–191.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Koonin EV, Makarova KS, Aravind L. (2001). Horizontal gene transfer in prokaryotes: Quantification and classification. Annu Rev Microbiol, 55, 709–742.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• Kulakova AN, Larkin MJ, Kulakov LA. (1997). The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143 (Pt 1), 109–115.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Lawrence JG, Roth JR. (1996). Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics, 143, 1843–1860.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Lal R, Dogra C, Malhotra S, Sharma P, Pal R. (2006). Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. Trends Biotechnol, 24, 121–130.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• Leveau JH, van der Meer JR. (1997). Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134. Gene, 202, 103–114.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Maymó-Gatell X, Chien Y, Gossett JM, Zinder SH. (1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science, 276, 1568–1571.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   Google Scholar
• Muller EE, Bringel F, Vuilleumier S. (2011). Dichloromethane-degrading bacteria in the genomic age. Res Microbiol. doi:10.1016/j.resmic.2011.01.008
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Ochman H, Lawrence JG, Groisman EA. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299–304.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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-trichlorobenzene-degrading bacterium Pseudomonas sp. strain P51, confers the ability to grow on 3-chlorobenzoate. Appl Environ Microbiol, 65, 724–731.
   PubMed Web of Science ®Google Scholar
• Oltmanns RH, Rast HG, Reineke W. (1988). Degradation of 1, 4-dichlorobenzene by enriched and constructed bacteria. Appl Microbiol Biotechnol, 28, 609–616.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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-dibromoethane-degradative pathways. J Bacteriol, 182, 2191–2199.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Potrawfke T, Armengaud J, Wittich RM. (2001). Chlorocatechols substituted at positions 4 and 5 are substrates of the broad-spectrum chlorocatechol 1,2-dioxygenase of Pseudomonas chlororaphis RW71. J Bacteriol, 183, 997–1011.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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 laboratory-scale activated-sludge microcosms. Appl Environ Microbiol, 64, 2126–2132.
   PubMed Web of Science ®Google Scholar
• Reams AB, Neidle EL. (2004). Selection for gene clustering by tandem duplication. Annu Rev Microbiol, 58, 119–142.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• Schlömann M. (1994). Evolution of chlorocatechol catabolic pathways. Conclusions to be drawn from comparisons of lactone hydrolases. Biodegradation, 5, 301–321.
   PubMedGoogle Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Slater J, Bull A, Hardman D. (1995). Microbial dehalogenation. Biodegradation, 6, 181–189.
   Web of Science ®Google Scholar
• 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.
   Google Scholar
• Sota M, Kawasaki H, Tsuda M. (2003). Structure of haloacetate-catabolic IncP-1β plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon. J Bacteriol, 185, 6741–6745.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Top EM, Springael D. (2003). The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol, 14, 262–269.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Tsuda M, Tan HM, Nishi A, Furukawa K. (1999). Mobile catabolic genes in bacteria. J Biosci Bioeng, 87, 401–410.
   PubMed Web of Science ®Google Scholar
• Udikovic-Kolic N, Hršak D, Devers M, Klepac-Ceraj V, Petric I, Martin-Laurent F. (2010). Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil. J Appl Microbiol, 109, 355–367.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Villemur R, Lanthier M, Beaudet R, Lépine F. (2006). The Desulfitobacterium genus. FEMS Microbiol Rev, 30, 706–733.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Wang G, Li R, Li S, Jiang J. (2010). A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil. J Bacteriol, 192, 2737–2745.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Wyndham RC, Cashore AE, Nakatsu CH, Peel MC. (1994a). Catabolic transposons. Biodegradation, 5, 323–342.
   Google Scholar
• 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.
   Google Scholar
• 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.
   PubMedGoogle Scholar
• Zhou JZ, Tiedje JM. (1995). Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol Ecol, 4, 613–618.
   Google Scholar