Amplified rDNA restriction analysis and further genotypic characterisation of metal-resistant soil bacteria and related facultative hydrogenotrophs

Systematic and Applied Microbiology

Volumn 22, Issue 2, 1999, Pages 258-268

  Brim, Hassan ^a,b   Heyndrickx, Marc ^d   De Vos, Paul ^f   Wilmotte, Annick ^e   Springael, Dirk ^b   Schlegel, Hans G ^c   Mergeay, Max ^a,b  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b FLEMISH INSTITUTE FOR TECHNOLOGICAL RESEARCH VITO   (Belgium)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

^d Centrum voor Landbouwkundig Onderzoek Gent CLO / Centre de Recherches Agronomiques Gand   (Belgium)

^e UNIVERSITY OF LIÈGE   (Belgium)

^f VITO Bœretang ^*

Author keywords

Alcaligenes; ARDRA; czc; Hydrogenotrophs; Metal resistance; Mutator phenotype; ncc; Ralstonia; Taxonomy

Indexed keywords

CADMIUM; COBALT; HEAVY METAL; METAL; NICKEL; RIBOSOME DNA; ZINC;

ALCALIGENES; ARTICLE; BACTERIAL GROWTH; BURKHOLDERIA; CONTROLLED STUDY; GENOTYPE; HYBRIDIZATION; NONHUMAN; OPERON; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RALSTONIA; RESTRICTION MAPPING; SEDIMENT; SOIL; SOIL MICROFLORA; WASTE; WAUTERSIA EUTROPHA;

ACHROMOBACTER XYLOSOXIDANS; ALCALIGENES; ALCALIGENES XYLOSOXIDANS; BACTERIA (MICROORGANISMS); BURKHOLDERIA; NEGIBACTERIA; RALSTONIA; RALSTONIA EUTROPHA; RALSTONIA PICKETTII; RALSTONIA SOLANACEARUM; WAUTERSIA EUTROPHA;

EID: 0032999894     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0723-2020(99)80073-3     Document Type: Article

References (53)

1. BUSSE, H. J., AULING, G.: The genera Alcaligenes and Achromobacter, pp. 2544-2555. In: A. BALOWS, H. G. TRÜPER, M. DWORKIN, W. HARDER & K.-H. SCHLEIFER (eds.): The Prokaryotes. Vol. III. Springer Verlag New York (1991).
2. COLLARD, J. M., CORBISIER, P., DIELS, L., DONG, Q., JEANTHON, C., MERGEAY, M., TAGHAVI, S., VAN DER LELIE, D., WILMOTTE, A., WUERTZ, S.: Plasmids for heavy metal resistance in Alcaligenes eutrophus CH34: Mechanisms and Applications. FEMS Microbiol Reviews 14, 405-414 (1994).
3. CORBISIER, P., THIRY, E., MASOLIJN, A., DIELS, L.: Cosntruction and Development of Metal Ion Biosensors, pp. 151-155. In: Bioluminescence and Chemiluminescence: Fundamental and Applied Aspects. Proceedings of the Eighth International Symposium on Bioluminescence and Chemiluminescence, Cambridge, September 1994. Edited by A. K. CAMPBELL, L. J. KRICKA & P. E. STANLEY. Chichester, UK: John Wiley & Sons (1994).
4. DIELS, L., SADOUK, A., MERGEAY, M.: Large plasmids governing multiple resistances to heavy metals: a genetic approach. Toxicol. Environ. Chem. 23, 79-89 (1988).
5. DIELS, L., MERGEAY, M.: DNA probe-mediated detection of resistant bacteria from soils highly polluted by heavy metals. Appl. Environ. Microbiol. 56, 1485-1491 (1990).
6. DIELS, L., DONG, Q., VAN DER LELIE, D., BAEYENS, W., MERGEAY, M.: The czc operon of Alcaligenes eutrophus CH34: from resistance mechanism to the removal of heavy metals. J. Ind. Microbiol. 14, 142-153 (1995).
7. DON, R. H., PEMBERTON, J. M.: Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J. Bacteriol. 145, 681-686 (1981).
8. FELSENSTEIN, J.: Confidences limits on phytogenies: an approach using the bootstrap. Evaluation 39, 783-791 (1985).
9. FRIEDRICH, B., HOGREFE, C., SCHLEGEL, H. G.: Naturally occuring genetic transfer of hydrogen-oxidizing ability between strains of Alcaligenes eutrophus. J. Bacteriol. 147, 198-205 (1981).
10. GERSTENBERG, C., FRIEDRICH, B., SCHLEGEL, H. G.: Physical evidence for plasmids in autotrophic, especially hydrogen-oxidizing bacteria. Arch. Microbiol. 133, 90-96 (1982).
11. GURTLER, V., WILSON, V. A., MAYALL, B. C.: Classification of medically important Clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J. Gen. Microbiol. 137, 2673-2679 (1991).
12. HEYNDRICKX, M., VANDEMEULENBROECKE, K., SCHELDEMAN, P., KERSTERS, K., DE VOS, P., LOGAN, N. A., AZIZ, A. M., ALI, N., BERKELEY, R. C. W.: A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (NAKAMURA 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae. Int. J. Syst. Bacteriol. 46, 988-1003 (1996a).
13. HEYNDRICKX, M., VAUTERIN, L., VANDAMME, P., KERSTERS, K., DE VOS, P.: Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. K. Microbiological Methods 26, 247-259 (1996b).
14. 2-lithotrophic, oxalate-oxidizing bacteria related to Alcaligenes eutrophus. Syst. Appl. Microbiol. 10, 126-133 (1988).
15. KAUR, P., ROSS, K., SIDDIQUI, R. A., SCHLEGEL, H. G.: Nickel resistance of Alcaligenes denitrificans strain 4a-2 is chromosomally coded. Arch. Microbiol. 154, 133-138 (1990).
16. LAGUERRE, G., RIGOTTIER-GOIS, L., LEMANCKAU, P.: Fluorescent Pseudomonas species categorized by using Polymerase chain Reaction (PCR)/restriction fragment analysis of 16S rDNA. Molecular Ecology 3, 479-487 (1994a).
17. LAGUERRE, G., ALLARD, M., REVOY, F., AMARGER, N.: Rapid identification of Rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 60, 56-63 (1994b).
18. LEJEUNE, P., MERGEAY, M., VAN GIJSEGEM, E, FAELEN, M., GERITS, J., TOUSSANT, A.: Chromosome transfer and R-prime plasmid formation mediated by plasmid pULB113 (RP4;:Mini-Mu) in Alcaligenes eutrophus CH34 and Pseudomonas fluorescens 6.2. J. Bacteriol. 155, 1015-1026 (1983).
19. LIESEGANG, H., SIDDIQUI, R. A., SCHLEGEL, H. G.: Characterization of the inducible nickel and cobalt resistance determinant cm from pMOL28 of Alcaligenes eutrophus CH34. J. Bacteriol 175, 767-778 (1993).
20. MARTIN, C., AIT ICHOU, M., MASSICOT, P., GOUDEAU, A., QUENTIN, R.: Genetic Diversity of Pseudomonas aeruginosa isolated from patients with cystic fibrosis revealed by restriction fragment length polymorphism of the 16S rRNA gene region. J. Clin. Microbiol. 33, 1461-1466 (1995).
21. MERGEAY, M., HOUBA, C:, GERITS, J.: Extrachromosomal inheritance controlling resistance to cadmium, cobalt and zinc ions: evidence from curing in a Pseudomonas. Arch. Int. Physiol. Biochim. 86, 440-441 (1978).
22. MERGEAY, M., NIES, D., SCHLEGEL, H. G., GERITS, J., CHARLES, P., VAN GIJSEGEM, E: Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J. Bacteriol. 162, 328-334 (1985).
23. MERGEAY, M., SPRINGAEL, D., TOP, E.: Gene transfer in polluted soils. In: Bacterial Genetics in Natural Environment, pp. 152-171. Edited by J. C. C. FRY & M. DAY. London, UK: Chapman & Hall (1990).
24. NIES, D. H.: The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J. Bacteriol. 177, 2707-2712 (1995).
25. NIES, D., MERGFAY, M., FRIEDRICH, B., SCHLEGEL, H. G.: Cloning of plasmid genes encoding resistances to cadmium, zinc and cobalt in Alcaligenes eutrophus CH34. J. Bacteriol. 169, 4865-4868 (1987).
26. NIES, A., NIES, D. H., CHU, L., SILVER, S.: Expression and nucleotide sequence of a plasmid-determined divalent cation efflux system from Alcaligenes eutropha. Proc. Natl. Acad. sci. USA 86, 7351-7355 (1989).
27. ROBERTS, S. J., EDEN-GREEN, S. J., JONES, P., AMBLER, D. J.: Pseudomonas syzygii, sp. nov. the cause of Sumatra disease of cloves. System. Appl. Microbiol. 13, 34-43 (1990).
28. SADOUK, A., MERGEAY, M.: Chromosome mapping in Alcaligenes eutrophus CH34. Mol. Gen. Genet. 240, 181-187 (1993).
29. SAITOU, N., NEI, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987).
30. SCHLEGEL, H. G., COSSON, J. P., BAKER, A. J. M.: Nickel-hyper-accumulating plants provide a niche for nickel-resistant bacteria. Bot. Acta 104, 18-25 (1991).
31. SCHMIDT, T., STOPPEL, R. D., SCHLEGEL, H. G.: High-level nickel resistance in Alcaligenes xylosoxydans 31A and Alcaligenes eutrophus KT02. Appl. Environ. Microbiol. 57, 3301-3309 (1991).
32. SCHMIDT, T., SCHLEGEL, H. G.: Combined nickel-resistance encoded by the ncc locus of Alcaligenes xylosoxidans 31A. J. Bacteriol. 176, 7045-7054 (1994).
33. SHIELDS, M. S., HOOPER, S. W., SAYLER, G. S.: Plasmid-mediated mineralization of 4-chlorobiphenyl. J. Bacteriol. 163, 882-889 (1985).
34. SIDDIQUI, R. A., BENTHIN, K., SCHLEGEL, H. G.: Cloning of pMOL28-encoded nickel resistance genes and expression of the genes in Alcaligenes eutrophus and Pseudomonas spp. J. Bacteriol. 171, 5071-5078 (1989).
35. SPRINGAEL, D.: Genetics of PCB-degrading bacteria: identification of a new catabolic transposon Tn4371. Ph.D. Thesis, Vrije Universiteit Brussel (1990).
36. 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. 175, 1674-1681 (1993).
37. STOPPEL, R. D., SCHLEGEL, H. G.: Nickel-resistant bacteria from anthropogenically nickel-polluted and naturally nickel-percolated ecosystems. Appl. Environ. Microbiol. 61, 2276-2285 (1995).
38. TAGHAVI, S., MERGEAY, M., VAN DER LELIE, D.: Genetic and physical maps of the Alcaligenes eutrophus CH34 megaplasmid pMOL28 and its derivate pMOL50 obtained after Temperature Induced Mutagenesis and Mortality (TIMM). Plasmid. 37, 22-34 (1997).
39. TIMOTIUS, K., SCHLEGEL, H. G.: Aus Abwässern isolierte nickelresistente Bakterien. Nachrichten der Akademie der Wissenschaften Göttingen. II. Math.-Physik. Klasse 3, 15-23 (1987).
40. TOP, E., MERGEAY, M., SPRINGAEL, D., VERSTRAETE, W.: Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples. Appl. Environ. Microbiol. 56, 2471-2479 (1990).
41. VANDAMME, P., POT, B., GILLIS, M., DE VOS, P., KERSTERS, K., SWINGS, J.: Polyphasic Taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60, 407-438 (1996).
42. VAN DE PEER, Y., DE WACHTER, R.: TREECON: a software package for the construction and drawing of evolutionary trees. Compact Applic. Biosci. 9, 177-182 (1993).
43. VAN DER LELIE, D., SADOUK, A., FERHAT, A., TACHAVI, S., TOUS-SAINT, A., MERGEAY, M.: Stress and survival in Alcaligenes eutropbus CH34: effects of temperature and genetic rearrangements. In: Gene Transfer and Environment, pp. 27-32. Edited by M. J. GAUTHIER, Heidelberg, Germany: Springer verlag (1992).
44. VAN DER LELIE, D., SCHWUCHOW, T., SCHWIDETZKY, U., WUERTZ, S., BEYENS, W., MERGEAY, M., NIES, D. H.:Two-component regulatory system involved in transcriptional control of heavy-metal homoeostasis in Alcaligenes eutrophus. Molecular Microbiology 23, 493-503 (1997).
45. VANEECHOUTTE, M., ROSSAU, R., DE VOS, P., GILLIS, M., JANSSENS, D., PAEPE, N., DE ROUCK, A., FIERS, T., CLAEYS, G., KERSTERS, K.: Rapid identification of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol. Letters 93, 227-234 (1992).
46. VANEECHOUTTE, M., CARTWRIGHT, C. P., WILLIAMS, E. C., JAGER, B., TICHY, H. V., DE BAERE, T., DE ROUCK, A., VERSCHRAEGEN, G.: Evaluation of 16S rRNA gene restriction analysis for the identification of cultured organisms of clinically important Clostridium species. Anaerobe 2, 249-256 (1996).
47. VIGALYS, R., HESTER, M.: Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172, 4238-4246 (1990).
48. WEUNDER, S., ARNOLD, W., PUHLER, A.: Diversity of uncultured microorganisms associated with the seagras Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 62, 766-771 (1996).
49. WILDMOTTE, A., VAN DER AUWERA, G., DE WACHTER, R.: Structure of the 16S ribosomal thermophilic cyanobacterium Chlorogloeopsis HTF (,Mastigocladus laminosus HTF;) strain pCC7518, and phylogenetic analysis. FEBS Letters 317, 96-100 (1993).
50. WILSON, M. J., WADE, W. G., WEIGHTMAN, A. J.: Restriction fragment length polymorphism of PCR-ampligied 16S ribosomal DNA of human Capnocytophaga. J. Appl. Bacteriol. 78, 394-401 (1995).
51. WYNDHAM, R. C., STRAUS, N. A.: Chlorobenzoate catabolism and interaction between Alcaligenes and Pseudomonas species from Bloody Run Creek. Arch. Microbiol. 150, 230-236 (1988).
52. YABUUCHI, E., KOSAKO, Y., YANO, I., HOTTA, H., NISHIUCHI, Y.: Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni & Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) Comb. Nov. and Ralstonia eutropha (Davis 1969) comb. nov. Microbiol. Immunol. 39, 897-904 (1995).
53. ZELLER, K. A., LEVY, M.: Intraspecies differenciation in the powdery mildew Erysiphe cichoracearum determined with rDNA FRLPs. Molecular Ecology 4, 277-283 (1995).