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. 1997 Jun;63(6):2330–2337. doi: 10.1128/aem.63.6.2330-2337.1997

Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site.

J B Herrick 1, K G Stuart-Keil 1, W C Ghiorse 1, E L Madsen 1
PMCID: PMC168525  PMID: 9172352

Abstract

Horizontal transfer of genes responsible for pollutant biodegradation may play a key role in the evolution of bacterial populations and the adaptation of microbial communities to environmental contaminants. However, field evidence for horizontal gene transfer between microorganisms has traditionally been very difficult to obtain. In this study, the sequences of the 16S rRNA and naphthalene dioxygenase iron-sulfur protein (nahAc) genes of nine naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site, as well as a naphthalene-degrading bacterium from a contaminated site in Washington state and two archetypal naphthalene-degrading strains, were compared. Seven strains from the study site had a single nahAc allele, whereas the 16S rRNA gene sequences of the strains differed by as much as 7.9%. No nahAc alleles from the site were identical to those of the archetypal strains, although the predominant allele was closely related to that of Pseudomonas putida NCIB 9816-4, isolated in the British Isles. However, one site-derived nahAc allele was identical to that of the Washington state strain. Lack of phylogenetic congruence of the nahAc and 16S rRNA genes indicates that relatively recent in situ horizontal transfer of the nahAc gene has occurred, possibly as a direct or indirect consequence of pollutant contamination. Alkaline lysis plasmid preparations and pulsed-field gel electrophoresis have revealed the presence of plasmids ranging in size from 70 to 88 kb in all site isolates. Southern hybridizations with a 407-bp nahAc probe have suggested that the nahAc gene is plasmid borne in all the site isolates but one, a strain isolated from subsurface sediment 400 m upstream from the source of the other site isolates. In this strain and in the naphthalene-degrading strain from Washington state, nahAc appears to be chromosomally located. In addition, one site isolate may carry nahAc on both chromosome and plasmid. Within the group of bacteria with identical nahAc sequences the Southern hybridizations showed that the gene was distributed between plasmids of different sizes and a chromosome. This suggests that plasmid modification after transfer may have been effected by transposons. Horizontal transfer of catabolic genes may play a significant role in the acclimation of microbial communities to pollutants.

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Selected References

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  1. Amábile-Cuevas C. F., Chicurel M. E. Bacterial plasmids and gene flux. Cell. 1992 Jul 24;70(2):189–199. doi: 10.1016/0092-8674(92)90095-t. [DOI] [PubMed] [Google Scholar]
  2. Anderson D. G., McKay L. L. Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl Environ Microbiol. 1983 Sep;46(3):549–552. doi: 10.1128/aem.46.3.549-552.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Asturias J. A., Díaz E., Timmis K. N. The evolutionary relationship of biphenyl dioxygenase from gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from gram-negative bacteria. Gene. 1995 Apr 14;156(1):11–18. doi: 10.1016/0378-1119(94)00530-6. [DOI] [PubMed] [Google Scholar]
  4. Balkwill D. L., Ghiorse W. C. Characterization of subsurface bacteria associated with two shallow aquifers in oklahoma. Appl Environ Microbiol. 1985 Sep;50(3):580–588. doi: 10.1128/aem.50.3.580-588.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Baur B., Hanselmann K., Schlimme W., Jenni B. Genetic transformation in freshwater: Escherichia coli is able to develop natural competence. Appl Environ Microbiol. 1996 Oct;62(10):3673–3678. doi: 10.1128/aem.62.10.3673-3678.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. doi: 10.1073/pnas.75.10.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cohen M. L. Epidemiology of drug resistance: implications for a post-antimicrobial era. Science. 1992 Aug 21;257(5073):1050–1055. doi: 10.1126/science.257.5073.1050. [DOI] [PubMed] [Google Scholar]
  8. Davies J. Inactivation of antibiotics and the dissemination of resistance genes. Science. 1994 Apr 15;264(5157):375–382. doi: 10.1126/science.8153624. [DOI] [PubMed] [Google Scholar]
  9. Dowson C. G., Hutchison A., Woodford N., Johnson A. P., George R. C., Spratt B. G. Penicillin-resistant viridans streptococci have obtained altered penicillin-binding protein genes from penicillin-resistant strains of Streptococcus pneumoniae. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5858–5862. doi: 10.1073/pnas.87.15.5858. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dunn N. W., Gunsalus I. C. Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J Bacteriol. 1973 Jun;114(3):974–979. doi: 10.1128/jb.114.3.974-979.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. EVANS W. C., FERNLEY H. N., GRIFFITHS E. OXIDATIVE METABOLISM OF PHENANTHRENE AND ANTHRACENE BY SOIL PSEUDOMONADS. THE RING-FISSION MECHANISM. Biochem J. 1965 Jun;95:819–831. doi: 10.1042/bj0950819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Eardly B. D., Wang F. S., Whittam T. S., Selander R. K. Species limits in Rhizobium populations that nodulate the common bean (Phaseolus vulgaris). Appl Environ Microbiol. 1995 Feb;61(2):507–512. doi: 10.1128/aem.61.2.507-512.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. doi: 10.1007/BF01734359. [DOI] [PubMed] [Google Scholar]
  14. Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
  15. Focht D. D., Searles D. B., Koh S. C. Genetic exchange in soil between introduced chlorobenzoate degraders and indigenous biphenyl degraders. Appl Environ Microbiol. 1996 Oct;62(10):3910–3913. doi: 10.1128/aem.62.10.3910-3913.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gutell R. R., Larsen N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. doi: 10.1128/mr.58.1.10-26.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Guttman D. S., Dykhuizen D. E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science. 1994 Nov 25;266(5189):1380–1383. doi: 10.1126/science.7973728. [DOI] [PubMed] [Google Scholar]
  18. Harayama S., Kok M., Neidle E. L. Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol. 1992;46:565–601. doi: 10.1146/annurev.mi.46.100192.003025. [DOI] [PubMed] [Google Scholar]
  19. Haugland R. A., Sangodkar U. M., Chakrabarty A. M. Repeated sequences including RS1100 from Pseudomonas cepacia AC1100 function as IS elements. Mol Gen Genet. 1990 Jan;220(2):222–228. doi: 10.1007/BF00260485. [DOI] [PubMed] [Google Scholar]
  20. Herrick J. B., Madsen E. L., Batt C. A., Ghiorse W. C. Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl Environ Microbiol. 1993 Mar;59(3):687–694. doi: 10.1128/aem.59.3.687-694.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Ka J. O., Tiedje J. M. Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer. J Bacteriol. 1994 Sep;176(17):5284–5289. doi: 10.1128/jb.176.17.5284-5289.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kapur V., Nelson K., Schlievert P. M., Selander R. K., Musser J. M. Molecular population genetic evidence of horizontal spread of two alleles of the pyrogenic exotoxin C gene (speC) among pathogenic clones of Streptococcus pyogenes. Infect Immun. 1992 Sep;60(9):3513–3517. doi: 10.1128/iai.60.9.3513-3517.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kim E., Aversano P. J., Romine M. F., Schneider R. P., Zylstra G. J. Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains. Appl Environ Microbiol. 1996 Apr;62(4):1467–1470. doi: 10.1128/aem.62.4.1467-1470.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
  25. Kinkle B. K., Sadowsky M. J., Schmidt E. L., Koskinen W. C. Plasmids pJP4 and r68.45 Can Be Transferred between Populations of Bradyrhizobia in Nonsterile Soil. Appl Environ Microbiol. 1993 Jun;59(6):1762–1766. doi: 10.1128/aem.59.6.1762-1766.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. The ribosomal database project. Nucleic Acids Res. 1993 Jul 1;21(13):3021–3023. doi: 10.1093/nar/21.13.3021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Leahy J. G., Colwell R. R. Microbial degradation of hydrocarbons in the environment. Microbiol Rev. 1990 Sep;54(3):305–315. doi: 10.1128/mr.54.3.305-315.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lehrbach P. R., McGregor I., Ward J. M., Broda P. Molecular relationships between pseudomonas INC P-9 degradative plasmids TOL, NAH, and SAL. Plasmid. 1983 Sep;10(2):164–174. doi: 10.1016/0147-619x(83)90069-0. [DOI] [PubMed] [Google Scholar]
  29. Lorenz M. G., Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev. 1994 Sep;58(3):563–602. doi: 10.1128/mr.58.3.563-602.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Madsen E. L., Sinclair J. L., Ghiorse W. C. In situ biodegradation: microbiological patterns in a contaminated aquifer. Science. 1991 May 10;252(5007):830–833. doi: 10.1126/science.2028258. [DOI] [PubMed] [Google Scholar]
  31. Matheson V. G., Forney L. J., Suwa Y., Nakatsu C. H., Sexstone A. J., Holben W. E. Evidence for Acquisition in Nature of a Chromosomal 2,4-Dichlorophenoxyacetic Acid/(alpha)-Ketoglutarate Dioxygenase Gene by Different Burkholderia spp. Appl Environ Microbiol. 1996 Jul;62(7):2457–2463. doi: 10.1128/aem.62.7.2457-2463.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Neilson J. W., Josephson K. L., Pepper I. L., Arnold R. B., Di Giovanni G. D., Sinclair N. A. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl Environ Microbiol. 1994 Nov;60(11):4053–4058. doi: 10.1128/aem.60.11.4053-4058.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Neu H. C. The crisis in antibiotic resistance. Science. 1992 Aug 21;257(5073):1064–1073. doi: 10.1126/science.257.5073.1064. [DOI] [PubMed] [Google Scholar]
  34. Nikolich M. P., Hong G., Shoemaker N. B., Salyers A. A. Evidence for natural horizontal transfer of tetQ between bacteria that normally colonize humans and bacteria that normally colonize livestock. Appl Environ Microbiol. 1994 Sep;60(9):3255–3260. doi: 10.1128/aem.60.9.3255-3260.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. O'Morchoe S. B., Ogunseitan O., Sayler G. S., Miller R. V. Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment. Appl Environ Microbiol. 1988 Aug;54(8):1923–1929. doi: 10.1128/aem.54.8.1923-1929.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Paul J. H., Frischer M. E., Thurmond J. M. Gene transfer in marine water column and sediment microcosms by natural plasmid transformation. Appl Environ Microbiol. 1991 May;57(5):1509–1515. doi: 10.1128/aem.57.5.1509-1515.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rogers K. B. Concentrating Malaria Parasites in Thin Films. Br Med J. 1946 Jan 5;1(4435):11–12. [PMC free article] [PubMed] [Google Scholar]
  38. Rosselló-Mora R. A., Lalucat J., García-Valdés E. Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl Environ Microbiol. 1994 Mar;60(3):966–972. doi: 10.1128/aem.60.3.966-972.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Salyers A. A., Shoemaker N. B., Stevens A. M., Li L. Y. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol Rev. 1995 Dec;59(4):579–590. doi: 10.1128/mr.59.4.579-590.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sandaa R. A., Enger O. Transfer in Marine Sediments of the Naturally Occurring Plasmid pRAS1 Encoding Multiple Antibiotic Resistance. Appl Environ Microbiol. 1994 Dec;60(12):4234–4238. doi: 10.1128/aem.60.12.4234-4238.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Simon M. J., Osslund T. D., Saunders R., Ensley B. D., Suggs S., Harcourt A., Suen W. C., Cruden D. L., Gibson D. T., Zylstra G. J. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene. 1993 May 15;127(1):31–37. doi: 10.1016/0378-1119(93)90613-8. [DOI] [PubMed] [Google Scholar]
  42. Sneath P. H. Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol. 1993 Jul;43(3):626–629. doi: 10.1099/00207713-43-3-626. [DOI] [PubMed] [Google Scholar]
  43. Springael D., Kreps S., Mergeay M. Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5. J Bacteriol. 1993 Mar;175(6):1674–1681. doi: 10.1128/jb.175.6.1674-1681.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stanier R. Y., Palleroni N. J., Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol. 1966 May;43(2):159–271. doi: 10.1099/00221287-43-2-159. [DOI] [PubMed] [Google Scholar]
  45. Sullivan J. T., Patrick H. N., Lowther W. L., Scott D. B., Ronson C. W. Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8985–8989. doi: 10.1073/pnas.92.19.8985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Syvanen M. Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet. 1994;28:237–261. doi: 10.1146/annurev.ge.28.120194.001321. [DOI] [PubMed] [Google Scholar]
  47. Top E. M., Holben W. E., Forney L. J. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol. 1995 May;61(5):1691–1698. doi: 10.1128/aem.61.5.1691-1698.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Tsuda M., Iino T. Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol Gen Genet. 1990 Aug;223(1):33–39. doi: 10.1007/BF00315794. [DOI] [PubMed] [Google Scholar]
  49. Tsuda M., Minegishi K., Iino T. Toluene transposons Tn4651 and Tn4653 are class II transposons. J Bacteriol. 1989 Mar;171(3):1386–1393. doi: 10.1128/jb.171.3.1386-1393.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Versalovic J., Koeuth T., Lupski J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991 Dec 25;19(24):6823–6831. doi: 10.1093/nar/19.24.6823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Williams H. G., Day M. J., Fry J. C., Stewart G. J. Natural transformation in river epilithon. Appl Environ Microbiol. 1996 Aug;62(8):2994–2998. doi: 10.1128/aem.62.8.2994-2998.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Williams P. A., Sayers J. R. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation. 1994 Dec;5(3-4):195–217. doi: 10.1007/BF00696460. [DOI] [PubMed] [Google Scholar]
  53. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Wyndham R. C., Nakatsu C., Peel M., Cashore A., Ng J., Szilagyi F. Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system. Appl Environ Microbiol. 1994 Jan;60(1):86–93. doi: 10.1128/aem.60.1.86-93.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Zhou J. Z., Tiedje J. M. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol Ecol. 1995 Oct;4(5):613–618. doi: 10.1111/j.1365-294x.1995.tb00261.x. [DOI] [PubMed] [Google Scholar]
  56. de Bruijn F. J. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol. 1992 Jul;58(7):2180–2187. doi: 10.1128/aem.58.7.2180-2187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. van der Meer J. R., Zehnder A. J., de Vos W. M. Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J Bacteriol. 1991 Nov;173(22):7077–7083. doi: 10.1128/jb.173.22.7077-7083.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. van der Meer J. R., de Vos W. M., Harayama S., Zehnder A. J. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev. 1992 Dec;56(4):677–694. doi: 10.1128/mr.56.4.677-694.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]

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