Chapter 26 : Plasmid-Mediated Tolerance Toward Environmental Pollutants

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Since the Industrial Revolution, there has been an increasing pace in the production of environmentally hazardous compounds that deliberately or accidentally have reached waters and soils, polluting them. The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Some contaminants are able to disrupt the normal development of the cell, others induce mutations, and some of these can kill cells at very low concentrations. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, permitting normal cellular subsistence in polluted environments—a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids play an important role in the evolution and dissemination of the catabolic pathways and efflux pumps.

Citation: Segura A, Molina L, Ramos J. 2015. Plasmid-Mediated Tolerance Toward Environmental Pollutants, p 507-531. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0013-2013
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Figure 1

Degradation pathways of mono- and biaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are colored to indicate their role: blue for toluene degradation genes, pink for naphthalene degradation genes, and yellow for biphenyl degradation genes. In green are the genes that can function in different degradation pathways. Genes and operons are not drawn to scale. Operon organization in some cases has not been experimentally demonstrated.

Citation: Segura A, Molina L, Ramos J. 2015. Plasmid-Mediated Tolerance Toward Environmental Pollutants, p 507-531. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0013-2013
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Figure 2

Degradation pathways for heteroaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are shown in different colors. Genes and operons are not drawn to scale.

Citation: Segura A, Molina L, Ramos J. 2015. Plasmid-Mediated Tolerance Toward Environmental Pollutants, p 507-531. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0013-2013
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Image of Figure 3
Figure 3

Degradation pathways for chloroaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are shown in different colors. Genes and operons are not drawn to scale.

Citation: Segura A, Molina L, Ramos J. 2015. Plasmid-Mediated Tolerance Toward Environmental Pollutants, p 507-531. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0013-2013
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Figure 4

Schematic representation of Tn-like region (A) and second region encoding stress resistance genes in pGRT1 (B). In red are indicated transposition-related genes, in green are stress-related functions, and in blue are putative recombinases or integrases.

Citation: Segura A, Molina L, Ramos J. 2015. Plasmid-Mediated Tolerance Toward Environmental Pollutants, p 507-531. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0013-2013
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1. Segura A,, Rojas A,, Hurtado A,, Huertas MJ,, Ramos JL . 2003. Comparative genomic analysis of solvent extrusion pumps in Pseudomonas strains exhibiting different degrees of solvent tolerance. Extremophiles 7 : 371 376.[PubMed] [CrossRef]
2. Williams PA,, Jones RM,, Zysltra GJ, . 2004. Genomics of catabolic plasmids, p 165 195. In Ramos JL (ed), Pseudomonas, vol 1. Kluwer Academic, Plenum Publishers, New York. [CrossRef]
3. Ogawa N,, Chackrabarty AM,, Zaborina O, . 2004. Degradative plasmids, p 341 392. In Funnell BE,, Phillips GJ (ed), Plasmid Biology. ASM Press, Washington, DC. [CrossRef]
4. 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] [CrossRef]
5. Jones BV,, Marchesi JR . 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 4 : 55 61.[PubMed] [CrossRef]
6. Parales RE,, Parales JV,, Pelletier DA,, Ditty JL . 2008. Diversity of microbial toluene degradation pathways. Adv Appl Microbiol 64 : 1 73.[PubMed] [CrossRef]
7. Bertini L,, Calafaro V,, Proietti S,, Caporale C,, Capasso P,, Caruso C,, Di Donato A . 2013. Deepening TOL and TAU catabolic pathways of Pseudomonas sp. OX1: Cloning, sequencing and characterization of the lower pathways. Biochimie 95 : 241 250.[PubMed] [CrossRef]
8. Williams PA,, Murray K . 1974. Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120 : 416 423.[PubMed]
9. Greated A,, Lambertsen L,, Williams PA,, Thomas CM . 2002. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida . Environ Microbiol 4 : 856 871.[PubMed] [CrossRef]
10. Gallegos MT,, Williams PA,, Ramos JL . 1997. Transcriptional control of the multiple catabolic pathways encoded on the TOL plasmid pWW53 of Pseudomonas putida MT53. J Bacteriol 179 : 5024 5029.[PubMed]
11. Ramos JL,, Marques S,, Timmis KN . 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 51 : 341 371.[PubMed] [CrossRef]
12. Silva-Roche R,, de Lorenzo V . 2013. The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Env Microbiol 15 : 271 286.[PubMed] [CrossRef]
13. Bayley SA,, Duggleby CJ,, Worsey MJ,, Williams PA,, Hardy KB,, Broda P . 1977. Two modes of loss of the Tol function from Pseudomonas putida mt-2. Mol Gen Genet 154 : 203 204.[PubMed] [CrossRef]
14. Muñoz R,, Hernández M,, Segura A,, Gouveia J,, Rojas A,, Ramos JL,, Villaverde S . 2009. Continuous cultures of Pseudomonas putida mt-2 overcome catabolic function loss under real case operating conditions. Appl Microbiol Biotech 83 : 189 198.[PubMed] [CrossRef]
15. Tsuda M,, Iino T . 1987. Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWW0. Mol Gen Genet 210 : 270 276.[PubMed] [CrossRef]
16. Tsuda M,, Iino T . 1988. Identification and characterization of Tn4653, a transposon covering the toluene transposon Tn4651 on TOL plasmid pWW0. Mol Gen Genet 213 : 72 77.[PubMed] [CrossRef]
17. Williams PA,, Jones RM,, Shaw LE . 2002. A third transposable element, IS Ppu12, from the toluene-xylene catabolic plasmid pWW0 of Pseudomonas putida mt-2. J Bacteriol 184 : 6572 6580.[PubMed] [CrossRef]
18. Williams PA,, Worsey MJ . 1976. Ubiquity of plasmids in coding for toluene and xylene metabolism in soil bacteria: evidence for the existence of new TOL plasmids. J Bacteriol 125 : 818 828.[PubMed]
19. Keil H,, Keil S,, Pickup W,, Williams PA . 1985. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53. J Bacteriol 164 : 887 895.[PubMed]
20. Chatfield LK,, Williams PA . 1986. Naturally occurring TOL plasmids in Pseudomonas strains carry either two homologous or two nonhomologous catechol 2,3-oxygenase genes. J Bacteriol 168 : 878 885.[PubMed]
21. Sentchilo VS,, Perebituk AN,, Zehnder AJ,, van der Meer JR . 2000. Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus. Appl Environ Microbiol 66 : 2842 2852.[PubMed] [CrossRef]
22. Yano H,, Garruto CE,, Sota M,, Ohtsubo Y,, Nagata Y,, Zylstra GJ,, Williams PA,, Tsuda M . 2007. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements. J Mol Biol 369 : 11 26.[PubMed] [CrossRef]
23. Yano H,, Miyakoshi M,, Ohshima K,, Tabata M,, Nagata Y,, Hattori M,, Tsuda M . 2010. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol 192 : 4337 4347.[PubMed] [CrossRef]
24. Shields MS,, Reagin MJ,, Gerger RR,, Campbell R,, Somerville C . 1995. TOM, a new aromatic degradative plasmid from Burkholderia (Pseudomonas) cepacia G4. Appl Environ Microbiol 61 : 1352 1356.[PubMed]
25. Shields MS,, Montgomery SO,, Cuskey SM,, Chapman PJ,, Pritchard PH . 1991. Mutants of Pseudomonas cepacia G4 defective in catabolism of aromatic compounds and trichloroethylene. Appl Environ Microbiol 57 : 1935 1941.[PubMed]
26. Nelson MJK,, Montgomery SO,, Mahaffey WR,, Pritchard PH . 1987. Biodegradation of trichloroethylene and involvement of an aromatic biodegradative pathway. Appl Environ Microbiol 53 : 949 954.[PubMed]
27. Molina L,, Duque E,, Gómez MJ,, Krell T,, Lacal J,, García-Puente A,, García V,, Matilla MA,, Ramos JL,, Segura A . 2011. The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditions in the environment. Environ Microbiol 13 : 2315 2327.[PubMed] [CrossRef]
28. Rheinwald JG,, Chakrabarty AM,, Gunsalus IC . 1973. A transmissible plasmid controlling camphor oxidation in Pseudomonas putida . Proc Natl Acad Sci USA 70 : 885 889.[PubMed] [CrossRef]
29. Dunn NW,, Gunsalus IC . 1973. Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida . J Bacteriol 114 : 974 979.[PubMed]
30. Yen KM,, Gunsalus IC . 1982. Plasmid gene organization: naphthalene/salicylate oxidation. Proc Natl Acad Sci USA 79 : 874 879.[PubMed] [CrossRef]
31. Yen KM,, Serdar CM . 1988. Genetics of naphthalene catabolism in pseudomonads. Crit Rev Microbiol 15 : 247 268.[PubMed] [CrossRef]
32. Denome SA,, Stanley DC,, Olson ES,, Young KD . 1993. Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of upper naphthalene catabolic pathway. J Bacteriol 175 : 6890 6901.[PubMed]
33. Simon MJ,, Osslund TD,, Saunders R,, Ensley BD,, Suggs S,, Harcourt A,, Suen WC,, Cruden DL,, Gibson DT,, Zylstra GJ . 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127 : 31 37.[PubMed] [CrossRef]
34. Eaton RW . 1994. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxy-chromene-2-carboxylate isomerase and trans- o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J Bacteriol 176 : 7757 7762.[PubMed]
35. Grimm AC,, Harwood CS . 1999. NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J Bacteriol 181 : 3310 3316.[PubMed]
36. Schell MA,, Sukordhaman M . 1989. Evidence that the transcription activator encoded by the Pseudomonas putida nahR gene is evolutionarily related to the transcription activators encoded by the Rhizobium nodD genes. J Bacteriol 171 : 1952 1959.[PubMed]
37. Dennis JJ,, Zylstra GJ . 2004. Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341 : 753 768.[PubMed] [CrossRef]
38. Li W,, Shi J,, Wang X,, Han Y,, Tong W,, Ma L,, Liu B,, Cai B . 2004. Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 336 : 231 240.[PubMed] [CrossRef]
39. Sota M,, Yano H,, Ono A,, Miyazaki R,, Ishii H,, Genka H,, Top EM,, Tsuda M . 2006. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn 4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol 188 : 4057 4067.[PubMed] [CrossRef]
40. Tsuda M,, Iino T . 1990. Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol Gen Genet 223 : 33 39.[PubMed] [CrossRef]
41. Sanseverino J,, Applegate BM,, King JMH,, Sayler GS . 1993. Plasmid-mediated mineralization of naphthalene, phenanthrene and anthracene. Appl Environ Microbiol 59 : 1931 1937.[PubMed]
42. Kiyohara H,, Nagao K . 1978. The catabolism of phenanthrene and naphthalene in bacteria. J Gen Microbiol 105 : 69 75.[CrossRef]
43. 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 : 531 540.[PubMed]
44. Pinyakong O,, Habe H,, Omori T . 2003. The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49 : 1 19.[PubMed] [CrossRef]
45. Basta T,, Keck A,, Klein J,, Stolz A . 2004. Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J Bacteriol 186 : 3862 3872.[PubMed] [CrossRef]
46. Romine MF,, Stillwell LC,, Wong K-K,, Thurston SJ,, Sisk EC,, Sensen C,, Gaasterland T,, Fredrickson JK,, Saffer JD . 1999. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181 : 1585 1602.[PubMed]
47. Feng X,, Ou X-L,, Ogram A . 1997. Plasmid-mediated mineralization of carbofuran by Sphingomonas sp. CF-06. Appl Environ Microbiol 63 : 1332 1337.[PubMed]
48. Basta I,, Buerger S,, Stolz A . 2005. Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. Microbiology 151 : 2025 2037.[PubMed] [CrossRef]
49. Keck A,, Conradt D,, Mahler A,, Stolz A,, Mattes R,, Klein J . 2006. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 : 1929 1940.[PubMed] [CrossRef]
50. Maeda K,, Nojiri H,, Shintani M,, Yoshida T,, Habe H,, Omori T . 2003. Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 326 : 21 33.[PubMed] [CrossRef]
51. Takahasi Y,, Shintani M,, Yamane H,, Nojiri H . 2009. The complete nucleotide sequence of pCAR2: pCAR2 and pCAR1 were structurally identical IncP-7 carbazole degradative plasmids. Biosci Biotechnol Biochem 73 : 744 746.[PubMed] [CrossRef]
52. Shintani M,, Urata M,, Inoue K,, Eto K,, Habe H,, Omori T,, Yamane H,, Nojiri H . 2007. The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole. J Bacteriol 189 : 2007 2020.[PubMed] [CrossRef]
53. Nam J-W,, Nojiri H,, Noguchi H,, Uchimura H,, Yoshida T,, Habe H,, Yamane H,, Omori T . 2002. Purification and characterization of carbazole 1,9a-dioxigenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl Environ Microbiol 68 : 5882 5890.[CrossRef]
54. Nojiri H . 2012. Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 76 : 1 18.[PubMed] [CrossRef]
55. Ashikawa Y,, Fujimoto Z,, Usami Y,, Inoue K,, Noguchi H,, Yamane H,, Nojiri H . 2012. Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of Rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase. BMC Struct Biol 12 : 15. doi:10.1186/1472-6807-12-15. [PubMed] [CrossRef]
56. Shintani M,, Matsumoto T,, Yoshikawa H,, Yamane H,, Ohkuma M,, Nojiri H . 2011. DNA rearrangement has occurred in the carbazole-degradative plasmid pCAR1 and the chromosome of its unsuitable host, Pseudomonas fluorescens PF0-1. Microbiology 157 : 3405 3416.[PubMed] [CrossRef]
57. Solinas F,, Marconi AM,, Ruzzi M,, Zennaro E . 1995. Characterization and sequence of a novel insertion sequence, IS 1162, from Pseudomonas fluorescens . Gene 155 : 77 82.[PubMed] [CrossRef]
58. Schneiker S,, Kosier B,, Puhler A,, Selbitschka W . 1999. The Sinorhizobium meliloti insertion sequence (IS) element ISRm14 is related to a previously unrecognized IS element located adjacent to the Escherichia coli locus of enterocyte effacement (LEE) pathogenicity island. Curr Microbiol 39 : 274 281.[PubMed] [CrossRef]
59. Yao CC,, Wong DTS,, Poh CL . 1998. IS 1491 from Pseudomonas alcaligenes NCIB 9867: characterization and distribution among Pseudomonas species. Plasmid 39 : 187 195.[PubMed] [CrossRef]
60. Nojiri H,, Sekiguchi H,, Maeda K,, Urata M,, Nakai S,, Yoshida T,, Habe H,, Omori T . 2001. Genetic characterization and evolutionary implications of a car gene cluster in carbazole degrader Pseudomonas sp. strain CA10. J Bacteriol 183 : 3663 3679.[PubMed] [CrossRef]
61. Overhage J,, Sielker S,, Hombrug S,, Parschat K,, Fetzner S . 2005. Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate. Microbiology 151 : 491 500.[PubMed] [CrossRef]
62. Parschat K,, Hauer B,, Kappl R,, Kraft R,, Hüttermann J,, Fetzner S . 2003. Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate. Characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J Biol Chem 278 : 27483 27494.[PubMed] [CrossRef]
63. Parschat K,, Overhage J,, Strittmatter AW,, Henne A,, Gottschalk G,, Fetzner S . 2007. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J Bacteriol 189 : 3855 3867.[PubMed] [CrossRef]
64. Niewerth H,, Schuldes J,, Parschat K,, Kiefer P,, Vorholt JA,, Daniel R,, Fetzner S . 2012. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics 13 : 534. doi:10.1186/1471-2164-13-534. [PubMed] [CrossRef]
65. Niewerth H,, Parschat K,, Rauschenberg M,, Ravoo BJ,, Fetzner S . 2013. The PaaX-type repressor MeqR2 of Arthrobacter sp. strain Rue61a, involved in the regulation of quinaldine catabolism, binds to its own promoter and to catabolic promoters and specifically responds to anthraniloyl coenzyme A. J Bacteriol 195 : 1068 1080.[PubMed] [CrossRef]
66. Wu W,, Leblanc SKD,, Piktel J,, Jensen SE,, Roy KL . 2006. Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 in Streptomyces clavuligerus . Can J Microbiol 52 : 293 300.[PubMed] [CrossRef]
67. Don RH,, Pemberton JM . 1981. Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus . J Bacteriol 145 : 681 686.[PubMed]
68. Laemmli CM,, Leveau JHJ,, Zehnder AJB,, van der Meer JR . 2000. Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134 (pJP4). J Bacteriol 182 : 4165 4172.[PubMed] [CrossRef]
69. 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] [CrossRef]
70. Trefault N,, De la Iglesia R,, Molina AM,, Manzano M,, Ledger T,, Perez-Pantoja D,, Sánchez MA,, Stuardo M,, Gonzalez 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] [CrossRef]
71. 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] [CrossRef]
72. Poh RP-C,, Smith ARW,, Bruce IJ . 2002. Complete characterization of Tn 5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4-dichlorophenoxyacetate uptake by the organism. Plasmid 48 : 1 12.[PubMed] [CrossRef]
73. Tsoi TV,, Plotnikova EG,, Cole JR,, Guerin WF,, Bagdasarian M,, Tiedje JM . 1999. Cloning, expression and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl Environ Microbiol 65 : 2151 2162.[PubMed]
74. Hickey WJ,, Sabat G,, Yuroff AS,, Arment AR,, Perez-Lesher J . 2001. Cloning, nucleotide sequencing and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl Environ Microbiol 67 : 4603 4609.[PubMed] [CrossRef]
75. de Souza ML,, Sadowsky MJ,, Seffernick J,, Martinez B,, Wackett LP . 1998. The atrazine catabolism genes are widespread and highly conserved. J Bacteriol 180 : 1951 1954.[PubMed]
76. de Souza ML,, Wackett LP,, Sadowsky MJ . 1998. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl Environ Microbiol 64 : 2323 2326.[PubMed]
77. 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] [CrossRef]
78. Król JE,, Penrod JT,, McCaslin H,, Rogers LM,, Yano H,, Stancik AD,, Dejonghe W,, Brown CJ,, Parales RE,, Wuertz S,, Top EM . 2011. Role of IncP-1ß plasmids pWDL7 ::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses. Appl Environ Microbiol 78 : 828 838.[PubMed] [CrossRef]
79. Wu JF,, Sun CW,, Jiang CY,, Liu ZP,, Liu SJ . 2005. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1 purification, properties, genetic cloning and expression in Escherichia coli . Arch Microbiol 183 : 1 8.[PubMed] [CrossRef]
80. Wu JF,, Jiang CY,, Wang BJ,, Ma YF,, 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 1765.[PubMed] [CrossRef]
81. Liu L,, Wu JF,, Ma YF,, Wang SY,, Zhao GP,, Liu SJ . 2007. A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J Bacteriol 189 : 2677 2682.[PubMed] [CrossRef]
82. Ma YF,, Wu JF,, Wang SY,, Jiang CY,, Zhang Y,, Qi SW,, Liu L,, Zhao GP,, Liu SJ . 2007. Nucleotide sequence of plasmid pCNB1 from Comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. Appl Environ Microbiol 73 : 4477 4483.[PubMed] [CrossRef]
83. Nagata Y,, Kamakura M,, Endo R,, Miyazaki R,, Ohtsubo Y,, Tsuda M . 2006. Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol Lett 256 : 112 118.[PubMed] [CrossRef]
84. Miyazaki R,, Sato Y,, Ito M,, Ohtsubo Y,, Nagata Y,, Tsuda M . 2006. Complete nucleotide sequence of an exogenously isolated plasmid pLB1, involved in γ-hexachlorocyclohexane degradation. Appl Environ Microbiol 72 : 6923 6933.[PubMed] [CrossRef]
85. Smalla K,, Osborn AM,, Wellington EMH, . 2000. Isolation and characterization of plasmids from bacteria, p 207 248. In Thomas CM (ed), The Horizontal Gene Pool–Bacterial Plasmids and Gene Spread. Harwood Academic Publishers, Amsterdam, The Netherlands. [CrossRef]
86. Junker F,, Cook AM . 1997. Conjugative plasmids and the degradation of arylsulfonates in Comamonas testosteroni . Appl Environ Microbiol 63 : 2403 2410.[PubMed]
87. Tralau T,, Cook AM,, Ruff J . 2001. Map of the IncP1ß plasmid pTSA encoding the widespread genes ( tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2. Appl Environ Microbiol 67 : 1508 1516.[PubMed] [CrossRef]
88. Kivisaar MA,, Habicht JK,, Heinaru AL . 1989. Degradation of phenol and m-toluate in Pseudomonas sp. strain EST1001 and its Pseudomonas putida transconjugants is determined by a multiplasmid system. J Bacteriol 171 : 5111 5116.[PubMed]
89. Kivisaar M,, Hõrak R,, Kasak L,, Heinaru A,, Habicht J . 1990. Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid 24 : 25 36.[PubMed] [CrossRef]
90. Kallastu A,, Hõrak R,, Kivisaar M . 1998. Identification and characterization of IS 1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida . J Bacteriol 180 : 5306 5312.[PubMed]
91. Peters M,, Heinaru E,, Talpsep E,, Wand H,, Stottmeister U,, Heinaru A,, Nurk A . 1997. Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl Environ Microbiol 63 : 4899 4906.[PubMed]
92. Shingler V,, Franklin FC,, Tsuda M,, Holroyd D,, Bagdasarian M . 1989. Molecular analysis of a plasmid-encoded phenol hydroxylase from Pseudomonas CF600. J Gen Microbiol 135 : 1083 1092.[PubMed]
93. Powlowski J,, Shingler V . 1994. Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation 5 : 219 236.[PubMed] [CrossRef]
94. van Beilen JB,, Wubbolts MG,, Witholt B . 1994. Genetics of alkane oxidation by Pseudomonas oleovorans . Biodegradation 5 : 161 174.[PubMed] [CrossRef]
95. van Beilen JB,, Panke S,, Lucchini S,, Franchini AG,, Röthlisberger M,, Witholt B . 2001. Analysis of Pseudomonas putida alkane degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147 : 1621 1630.[PubMed]
96. Dinamarca MA,, Aranda-Olmedo I,, Puyet A,, Rojo F . 2003. Expression of the Pseudomonas putida OCT plasmid alkane degradation pathway is modulated by two different global control signals: evidence from continuous cultures. J Bacteriol 185 : 4772 4778.[PubMed] [CrossRef]
97. Sikkema J,, de Bont JA,, Poolman B . 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59 : 201 222.[PubMed]
98. Udaondo Z,, Molina L,, Daniels C,, Gómez MJ,, Molina-Henares MA,, Matilla MA,, Roca A,, Fernández M,, Duque E,, Segura A,, Ramos JL . 2013. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome. Microb Biotechnol 6 : 598 611.[PubMed] [CrossRef]
99. Ramos JL,, Duque E,, Huertas MJ,, Haïdour A . 1995. Isolation and expansion of the catabolic potential of a Pseudomonas putida strain able to grow in the presence of high concentrations of aromatic hydrocarbons. J Bacteriol 177 : 3911 3916.[PubMed]
100. Mosqueda G,, Ramos-Gonzalez MI,, Ramos JL . 1999. Toluene metabolism by the solvent tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232 : 69 76.[PubMed] [CrossRef]
101. Udaondo Z,, Duque E,, Fernández M,, Molina L,, de la Torre J,, Bernal P,, Niqui JL,, Pini C,, Roca A,, Matilla MA,, Molina-Henares MA,, Silva-Jiménez H,, Navarro-Avilés G,, Busch A,, Lacal J,, Krell T,, Segura A,, Ramos JL . 2012. Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants. FEBS Lett 586 : 2932 2938.[PubMed] [CrossRef]
102. Rodríguez-Herva JJ,, García V,, Hurtado A,, Segura A,, Ramos JL . 2007. The ttgGHI solvent efflux pump operon of Pseudomonas putida DOT-T1E is located on a large self-transmissible plasmid. Environ Microbiol 9 : 1550 1561.[PubMed] [CrossRef]
103. Segura A,, Molina L,, Fillet S,, Krell T,, Bernal P,, Muñoz-Rojas J,, Ramos JL . 2012. Solvent tolerance in Gram-negative bacteria. Curr Opin Biotechnol 23 : 415 421.[PubMed] [CrossRef]
104. Rojas A,, Duque E,, Mosqueda G,, Golden G,, Hurtado A,, Ramos JL,, Segura A . 2001. Three efflux pumps are required to provide efficient tolerance to toluene to toluene in Pseudomonas putida DOT-TIE. J Bacteriol 183 : 3967 3973.[PubMed] [CrossRef]
105. Blair JM,, Piddock LJ . 2009. Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update. Curr Opin Microbiol 5 : 512 519.[PubMed] [CrossRef]
106. Hinchliffe P,, Symmons MF,, Hughes C,, Koronakis V . 2013. Structure and operation of bacterial tripartite pumps. Annu Rev Microbiol 67 : 221 242.[PubMed] [CrossRef]
107. Murakami S,, Nakashima R,, Yamashita E,, Yamaguchi A . 2002. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419 : 587 593.[PubMed] [CrossRef]
108. Sennhauser G,, Bukowska MA,, Briand C,, Grütter MG . 2009. Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa . J Mol Biol 389 : 134 145.[PubMed] [CrossRef]
109. Koronakis V,, Sharff A,, Koronakis E,, Luisi B,, Hughes C . 2000. Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405 : 914 919.[PubMed] [CrossRef]
110. Nikaido H,, Zgurskaya HI . 2001. AcrAB and related multidrug efflux pumps of Escherichia coli . J Mol Microbiol Biotechnol 3 : 215 218.[PubMed]
111. Symmons MF,, Bokma E,, Koronakis E,, Hughes C,, Koronakis V . 2009. The assembled structure of a complete tripartite bacterial multidrug efflux pump. Proc Natl Acad SciUSA 106 : 7173 7178.[PubMed] [CrossRef]
112. Ramos JL,, Duque E,, Godoy P,, Segura A . 1998. Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E. J Bacteriol 180 : 3323 3329.[PubMed]
113. Mosqueda G,, Ramos JL . 2000. A set of genes encoding a second toluene efflux system in Pseudomonas putida DOT-T1E is linked to the tod genes for toluene metabolism. J Bacteriol 182 : 937 943.[PubMed] [CrossRef]
114. Rojas A,, Segura A,, Guazzaroni ME,, Terán W,, Hurtado A,, Gallegos MT,, Ramos JL . 2003. In vivo and in vitro evidence that TtgV is the specific regulator of the TtgGHI multidrug and solvent efflux pump of Pseudomonas putida . J Bacteriol 185 : 4755 4763.[PubMed] [CrossRef]
115. Lacal J,, Muñoz-Martínez F,, Reyes-Darías JA,, Duque E,, Matilla M,, Segura A,, Calvo JJ,, Jímenez-Sánchez C,, Krell T,, Ramos JL . 2011. Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas . Environ Microbiol 13 : 1733 1744.[PubMed] [CrossRef]
116. Miyakoshi M,, Shintani M,, Terabayashi T,, Kai S,, Yamane H,, Nojiri H . 2007. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 189 : 6849 6860.[PubMed] [CrossRef]
117. Iwaki H,, Muraki T,, Ishihara S,, Hasegawa Y,, Rankin KN,, Sulea T,, Boyd J,, Lau PC . 2007. Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis. J Bacteriol 189 : 3502 3514.[PubMed] [CrossRef]
118. Yoakum GH,, Cole RS . 1977. Role of ATP in removal of psoralen cross-links from DNA of Escherichia coli permeabilized by treatment with toluene. J Biol Chem 252 : 7023 7030.[PubMed]
119. Rahmati S,, Yang S,, Davidson AL,, Zechiedrich EL . 2002. Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA. Mol Microbiol 43 : 677 685.[PubMed] [CrossRef]
120. Nikaido E,, Yamaguchi A,, Nishino K . 2008. AcrAB multidrug efflux pump regulation in Salmonella enterica serovar Typhimurium by RamA in response to environmental signals. J Biol Chem 283 : 24245 24253.[PubMed] [CrossRef]
121. Haines AS,, Jones K,, Batt SM,, Kosheleva IA,, Thomas CM . 2007. Sequence of plasmid pBS228 and reconstruction of the IncP-1a phylogeny. Plasmid 58 : 76 83.[PubMed] [CrossRef]
122. Kvint K,, Nachin L,, Diez A,, Nyström T . 2003. The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 6 : 140 145.[PubMed] [CrossRef]
123. Nachin L,, Nannmark U,, Nyström T . 2005. Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol 187 : 6265 6272.[PubMed] [CrossRef]
124. Xiong J,, Alexander DC,, Ma JH,, Déraspe M,, Low DE,, Jamieson FB,, Roy PH . 2013. Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrob Agents Chemother 57 : 3775 3782.[PubMed] [CrossRef]
125. Kieboom J,, Dennis JJ,, de Bont JA,, Zylstra GJ . 1998. Identification and molecular characterization of an efflux pump involved in Pseudomonas putida S12 solvent tolerance. J Biol Chem 273 : 85 91.[PubMed] [CrossRef]
126. Lacal J,, Reyes-Darias JA,, García-Fontana C,, Ramos JL,, Krell T . 2013. Tactic responses to pollutants and their potential to increase biodegradation efficiency. J Appl Microbiol 114 : 923 933.[PubMed] [CrossRef]
127. Kuc J . 1995. Phytoalexins, stress metabolism, and disease resistance in plants. Annu Rev Phytopathol 33 : 275 297.[PubMed] [CrossRef]
128. Spaink HP . 1995. The molecular basis of infection and nodulation by rhizobia: the ins and outs of sympathogenesis. Annu Rev Phytopathol 33 : 345 368.[PubMed] [CrossRef]
129. Rao JR,, Cooper JE . 1994. Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J Bacteriol 176 : 5409 5413.[PubMed]
130. González-Pasayo R,, Martínez-Romero E . 2000. Multiresistance genes of Rhizobium etli CFN42. Mol Plant Microbe Interact 13 : 572 577.[PubMed] [CrossRef]
131. Gonzalez V,, Santamaria RI,, Bustos P,, Hernandez-Gonzalez I,, Medrano-Soto A,, Moreno-Hagelsieb G,, Janga SC, Ramirez MA,, Jimenez-Jacinto V,, Collado-Vides J,, Davila G . 2006. The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 103 : 3834 3839.[PubMed] [CrossRef]
132. Mann MS,, Dragovic Z,, Schirrmacher G,, Lütke-Eversloh T . 2012. Over-expression of stress protein-encoding genes helps Clostridium acetobutylicum to rapidly adapt to butanol stress. Biotechnol Lett 34 : 1643 1649.[PubMed] [CrossRef]
133. Streit WR,, Schmitz RA,, Perret X,, Staehelin C,, Deakin WJ,, Raasch C,, Liesegang H,, Broughton WJ . 2004. An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234. J Bacteriol 186 : 535 542.[CrossRef]
134. Lim JS,, Choi BS,, Choi AY,, Kim KD,, Kim DI,, Choi IY,, Ka JO . 2012. Complete genome sequence of the fenitrothion-degrading Burkholderia sp. strain YI23. J Bacteriol 194 : 896. doi:10.1128/JB.06479-11. [CrossRef]
135. Janssen PJ,, Van Houdt R,, Moors H,, Monsieurs P,, Morin N,, Michaux A,, Benotmane MA,, Leys N,, Vallaeys T,, Lapidus A,, Monchy S,, Médigue C,, Taghavi S,, McCorkle S,, Dunn J,, van der Lelie D,, Mergeay M . 2010. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 5 : e10433. doi:10.1371/journal.pone.0010433. [CrossRef]
136. Ma Z,, Jacobsen FE,, Giedroc DP . 2009. Metal transporters and metal sensors: How coordination chemistry controls bacterial metal homeostasis. Chem Rev 13 : 4644 4681.[PubMed] [CrossRef]
137. Adriano DC . 2001. Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals. Springer-Verlag, New York, NY. [CrossRef]
138. Mergeay M,, Nies D,, Schlegel HG,, Gerits J,, Charles P,, Van Gijsegem F . 1985. Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162 : 328 334.[PubMed]
139. Monchy S,, Benotmane MA,, Janssen P,, Vallaeys T,, Taghavi S,, van der Lelie D,, Mergeay M . 2007. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 189 : 7417 7425.[PubMed] [CrossRef]
140. Nies DH . 2003. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev 27 : 313 339.[PubMed] [CrossRef]
141. Paulsen IT,, Saier MH Jr . 1997. A novel family of ubiquitous heavy metal ion transport proteins. J Membr Biol 156 : 99 103.[PubMed] [CrossRef]
142. Munkelt D,, Grass G,, Nies DH . 2004. The chromosomally encoded cation diffusion facilitator proteins DmeF and FieF from Wautersia metallidurans CH34 are transporters of broad metal specificity. J Bacteriol 186 : 8036 8043.[PubMed] [CrossRef]
143. Ramírez-Díaz MI,, Díaz-Pérez C,, Vargas E,, Riveros-Rosas H,, Campos-García J,, Cervantes C . 2008. Mechanisms of bacterial resistance to chromium compounds. Biometals 21 : 321 332.[PubMed] [CrossRef]
144. Henne KL,, Nakatsu CH,, Thompson DK,, Konopka AE . 2009. High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes. BMC Microbiol 16 : 199. doi:10.1186/1471-2180-9-199. [PubMed] [CrossRef]
145. Chen YF,, Chao H,, Zhou NY . 2014. The catabolism of 2,4-xylenol and p-cresol share the enzymes for the oxidation of para-methyl group in Pseudomonas putida NCIMB 9866. Appl Microbiol Biotechnol 98 : 1349 1356.[PubMed] [CrossRef]
146. Misra TK . 1992. Bacterial resistances to inorganic mercury salts and organomercurials. Plasmid 27 : 4 16.[PubMed] [CrossRef]
147. Diels L,, Faelen M,, Mergeay M,, Nies D . 1985. Mercury transposons from plasmids governing multiple resistance to heavy metals in Alcaligenes eutrophus CH34. Arch Intern Physiol Biochem 93 : 27 28.
148. Silver S,, Phung LT . 1996. Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50 : 753 789.[PubMed] [CrossRef]
149. Nascimento AM,, Chartone-Souza E . 2003. Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments. Genet Mol Res 2 : 92 101.[PubMed]
150. 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 1115.[PubMed] [CrossRef]
151. Schwartz E,, Henne A,, Cramm R,, Eitinger T,, Friedrich B,, Gottschalk G . 2003. Complete nucleotide sequence of pHG1: a Rastonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based lithoautotrophy and anaerobiosis. J Mol Biol 332 : 369 383.[CrossRef]
152. Chen WM,, Moulin L,, Bontemps C,, Vandamme P,, Bena G,, Boivin-Masson C . 2003. Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. J Bacteriol 185 : 7266 7272.[PubMed] [CrossRef]
153. Roselli S,, Nadalig T,, Vuilleumier S,, Bringel F . 2013. The 380 Kbp pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: A proteomic and bioinformatics study. PLoS One 8 : e56598. doi:10.1371/journal.pone.0056598. [CrossRef]
154. Liesegang H,, Lemke K,, Siddiqui RA,, Schlegel HG . 1993. Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34. J Bacteriol 175 : 767 778.[PubMed]
155. Schmidt T,, Schlegel HG . 1994. Combined nickel-cobalt-cadmium resistance encoded by the ncc locus of Alcaligenes xylosoxidans 31A. J Bacteriol 176 : 7045 7054.[PubMed]
156. Silver S,, Gupta A,, Matsui K,, Lo JF . 1999. Resistance to Ag(I) Cations in bacteria: environments, genes and proteins. Met Based Drugs 6 : 315 320.[PubMed] [CrossRef]
157. Monchy S,, Benotmane MA,, Wattiez R,, van Aelst S,, Auquier V,, Borremans B,, Mergeay M,, Taghavi S,, van der Lelie D,, Vallaeys T . 2006. Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. Microbiology 152 : 1765 1776.[PubMed] [CrossRef]
158. Mealman TD,, Blackburn NJ,, McEvoy MM . 2012. Metal export by CusCFBA, the periplasmic Cu(I)/Ag(I) transport system of Escherichia coli . Curr Top Membr 69 : 163 196.[PubMed] [CrossRef]
159. Copley SD,, Rokicki J,, Turner P,, Daligault H,, Nolan M,, Land M . 2012. The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4 : 184 198.[PubMed] [CrossRef]
160. Tabata M,, Ohtsubo Y,, Ohhata S,, Tsuda M,, Nagata Y . 2013. Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1. Genome Announc 1 :pii e00247-13. doi:10.1128/genomeA.00247-13. [PubMed] [CrossRef]
161. Gómez-Sanz E,, Kadlec K,, Feßler AT,, Zaragoza M,, Torre C,, Schwarz S . 2013. Novel erm(T)-carrying multiresistance plasmids from porcine and human isolates of methicillin-resistant Staphylococcus aureus ST398 that also harbor cadmium and copper resistance determinants. Antimicrob Agents Chemother 57 : 3275 3282.[PubMed] [CrossRef]
162. Bender CL,, Cooksey DA . 1987. Molecular cloning of copper resistance genes from Pseudomonas syringae pv. tomato. J Bacteriol 169 : 470 474.[PubMed]
163. Gutiérrez-Barranquero JA,, de Vicente A,, Carrión VJ,, Sundin GW,, Cazorla FM . 2013. Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae . Appl Environ Microbiol 79 : 1028 1033.[PubMed] [CrossRef]
164. Shin SH,, Kim S,, Kim JY,, Lee S,, Um Y,, Oh MK,, Kim YR,, Lee J,, Yang KS . 2012. Complete genome sequence of the 2,3-butanediol-producing Klebsiella pneumoniae strain KCTC 2242. J Bacteriol 194 : 2736 2737.[PubMed] [CrossRef]
165. Diels L,, Mergeay M . 1990. DNA probe-mediated detection of resistance bacteria from soils highly polluted by heavy metals. Appl Environ Microbiol 56 : 1485 1491.[PubMed]
166. Slyemi D,, Bonnefoy V . 2012. How prokaryotes deal with arsenic. Environ Microbiol Reports 4 : 571 586.[PubMed]
167. Dhuldhaj UP,, Yadav IC,, Singh S,, Sharma NK . 2013. Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management. Rev Environ Cont Toxicol 224 : 1 38.[PubMed] [CrossRef]
168. Volland S,, Rachinger M,, Strittmatter A,, Daniel R,, Gottschalk G,, Meyer O . 2011. Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5. J Bacteriol 193 : 5043. doi:10.1128/JB.05619-11. [PubMed] [CrossRef]
169. Vogel TM . 1996. Bioaugmentation as a soil bioremediation approach. Curr Opin Biotechnol 7 : 311 316.[PubMed] [CrossRef]
170. Top EM,, Springael D,, Boon N . 2002. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol Ecol 42 : 199 208.[PubMed] [CrossRef]
171. Ikuma K,, Gunsch CK . 2012. Genetic bioaugmentation as an effective method for in situ bioremediation. Functionality of catabolic plasmids following conjugal transfers. Bioengineered 3 : 236 241.[PubMed] [CrossRef]
172. Jussila MM,, Zhao J,, Souminen L,, Lindström K . 2007. TOL plasmid transfer during bacterial conjugation in vitro and rhizoremediation of oil compounds in vivo . Environ Pollut 146 : 510 524.[PubMed] [CrossRef]
173. Ramos-Gonzalez MI,, Duque E,, Ramos JL . 1991. Conjugational transfer of recombinant DNA in cultures and in soils: host range of Pseudomonas putida TOL plasmids. Appl Environ Microbiol 57 : 3020 3027.[PubMed]
174. Molbak L,, Licht TR,, Kvist T,, Kroer N,, Andersen SR . 2003. Plasmid transfer from Pseudomonas putida to the indigenous bacteria on alfalfa sprouts: characterization, direct quantification and in situ location of transconjugant cells. Appl Environ Microbiol 69 : 5536 5542.[PubMed] [CrossRef]
175. Ikuma K,, Holzem RM,, Gunsch CK . 2012. Impacts of organic carbon availability and recipient bacteria characteristics on the potential for TOL plasmid genetic bioaugmentation on soil slurries. Chemosphere 89 : 158 163.[PubMed] [CrossRef]
176. Ikuma K,, Gunsch CK . 2013. Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. Appl Microbiol Biotechnol 97 : 395 408.[PubMed] [CrossRef]
177. Pinedo CA,, Smets BF . 2005. Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies. Appl Environ Microbiol 71 : 51 57.[PubMed] [CrossRef]
178. Daane LL,, Molina J,, Sadowsky MJ . 1997. Plasmid transfer between spatially separated donor and recipient bacteria en earthworm-containing soil microcosms. Appl Environ Microbiol 63 : 679 686.[PubMed]
179. Wuertz S,, Okabe S,, Hausner M . 2004. Microbial communities and their interactions in biofilm systems: an overview. Water Sci Technol 49 : 327 336.[PubMed]
180. Mohan SV,, Falkentoft C,, Nancharaiah YV,, McSwain Sturm BS,, Wattiau P,, Wilderer PA,, Wuertz S,, Hausner M . 2009. Bioaugmentation of microbial communities in laboratory and pilot scale sequencing batch biofilm reactors using the TOL plasmid. Bioresour Technol 100 : 1746 1753.[PubMed] [CrossRef]
181. 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]
182. Molina L,, Ramos C,, Duque E,, Ronchel MC,, Garcöla JM,, Wyke L,, Ramos JL . 2000. Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 32 : 315 321.[CrossRef]
183. Mackova M,, Dowling D,, Macek T (ed) . 2006. Phytoremediation and Rhizoremediation. Theoretical Background. Series: Focus on Biotechnology. Springer, New York, NY. [CrossRef]
184. Walker TS,, Bais HP,, Grotewold E,, Vivanco JM . 2003. Root exudation and rhizosphere biology. Plant Physiol 132 : 44 51.[PubMed] [CrossRef]
185. Matilla MA,, Espinosa-Urgel M,, Rodriguez-Hervá JJ,, Ramos JL,, Ramos-González MI . 2007. Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 8 : R179. doi:10.1186/gb-2007-8-9-r179. [PubMed] [CrossRef]
186. López-Guerrero MG,, Ormeño-Orrillo E,, Acosta JL,, Mendoza-Vargas A,, Rogel MA,, Ramírez MA,, Rosenblueth M,, Martínez-Romero J,, Martínez-Romero E . 2012. Rhizobial extrachromosomal replicon variability, stability and expression in natural niches. Plasmid 68 : 149 158.[PubMed] [CrossRef]
187. Barac T,, Taghavi S,, Borremans B,, Provoost A,, Oeyen L,, Colpaert JV,, Vangronsveld J,, van der Lelie D . 2004. Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotech 22 : 583 588.[PubMed] [CrossRef]
188. Taghavi S,, Barac T,, Greenberg B,, Borremans B,, Vangronsveld J,, van der Lelie D . 2005. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 71 : 8500 8505.[PubMed] [CrossRef]
189. Lilley AK,, Bailey MJ . 1997. Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of Pseudomonas fluorescens SBW25: burden and benefit. Appl Environ Microbiol 63 : 1584 1587.[PubMed]
190. Tett A,, Spiers AJ,, Crossman LC,, Ager D,, Ciric L,, Dow JM,, Fry JC,, Harris D,, Lilley A,, Oliver A,, Parkhill J,, Quail MA,, Rainey PB,, Saunders NJ,, Seeger K,, Snyder LA,, Squares R,, Thomas CM,, Turner SL,, Zhang XX,, Field D,, Bailey MJ . 2007. Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. ISME J 1 : 331 340.[PubMed]
191. Bale MJ,, Fry JC,, Day MJ . 1987. Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones. J Gen Microbiol 133 : 3099 3107.[PubMed]
192. Top EM,, Holben WE,, Forney LJ . 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol 61 : 1691 1698.[PubMed]
193. Lilley AK,, Bailey MJ . 1997. The acquisition of indigenous plasmids by a generically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 63 : 1577 1583.[PubMed]
194. Dahlberg C,, Linberg C,, Torsvik VL,, Hermansson M . 1997. Conjugative plasmids isolated from bacteria in marine environments show various degrees of homology to each other and are not closely related to well characterized plasmids. Appl Environ Microbiol 63 : 4692 4697.[PubMed]
195. Ono A,, Miyazaki R,, Sota M,, Ohtsubo Y,, Nagata Y,, Tsuda M . 2007. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 74 : 501 510.[PubMed] [CrossRef]
196. Kav AB,, Sasson G,, Jami E,, Doron-Faigenboim A,, Benhar I,, Mizrahi I . 2012. Insights into the bovine rumen plasmidome. Proc Natl Acad Sci USA 109 : 5452 5457.[PubMed] [CrossRef]
197. Nojiri H . 2013. Impact of catabolic plasmids on host cell physiology. Curr Opin Biotech 24 : 423 430.[PubMed] [CrossRef]
198. Diaz-Ricci JC,, Hernández ME . 2000. Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20 : 79 108.[PubMed] [CrossRef]
199. Miyakoshi M,, Shitani M,, Inoue K,, Terabayashi T,, Sai F,, Ohkuma M,, Nojiri H,, Nagata Y,, Tsuda M . 2012. ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids. Environ Microbiol 14 : 2946 2959.[PubMed] [CrossRef]
200. Shintani M,, Takahashi Y,, Tokumaru H,, Kadota K,, Hara H,, Miyakoshi M,, Naito K,, Yamane H,, Nishida H,, Nojiri H . 2010. Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environ Microbiol 12 : 1413 1426.[PubMed]