Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses

International Journal of Systematic Bacteriology

Volumn 46, Issue 1, 1996, Pages 173-182

  Siering, Patricia L ^a   Ghiorse, William C ^a  

^a Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; DNA SEQUENCE; EVOLUTION; GENE AMPLIFICATION; GENOME IMPRINTING; GRAM NEGATIVE BACTERIUM; LEPTOTHRIX; NONHUMAN; PHASE CONTRAST MICROSCOPY; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TAXONOMY;

BACTERIA (MICROORGANISMS); DISCOPHORA; ENTEROBACTERIACEAE; LEPTOTHRIX; LEPTOTHRIX CHOLODNII; LEPTOTHRIX DISCOPHORA; NEGIBACTERIA; PROTEOBACTERIA; RUBRIVIVAX; SPHAEROTILUS; SPHAEROTILUS NATANS;

EID: 0030071266     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-46-1-173     Document Type: Article

References (58)

1. Adams, L. F., and W. C. Ghiorse. 1986. Physiology and ultrastructure of Leptothrix discophora SS-1. Arch. Microbiol. 145:126-135.
2. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1992. Short protocols in molecular biology, 2nd ed. John Wiley & Sons, New York.
3. Avgustin, G., F. Wright, and H. J. Flint. 1994. Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminocola from the rumen. Int. J. Syst. Bacteriol. 44:246-255.
4. Brosius, J., H. L. Palmer, J. P. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805.
5. Busse, H. J., T. El-Banna, H. Oyaizu, and G. Auling. 1992. Identification of xenobiotic-degrading isolates from the beta subclass of the Proteobacteria by a polyphasic approach including 16S rRNA partial sequencing. Int. J. Syst. Bacteriol. 42:19-26.
6. Chung, C. T., S. L. Niemal, and R. H. Miller. 1989. One-step transformation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. USA 86:2172-2175.
7. Colwell, R. R. 1970. Polyphasic taxonomy of bacteria, p. 421-436. In H. Iizuka and T. Hasegawa (ed.), Culture collections of microorganisms. University of Tokyo Press, Tokyo.
8. Corstjens, P., and G. Muyzer. 1993. Phylogenetic analysis of the metal-oxidizing bacteria Leptothrix discophora and Sphaerotilus natans using 16S rDNA sequence data. Syst. Appl. Microbiol. 16:219-223.
9. Corstjens, P. L. 1993. Bacterial oxidation of iron and manganese - a molecular biological approach. Ph.D. thesis. Leiden University, Leiden, The Netherlands.
10. Corstjens, P. L. Personal communication.
11. de Bruijn, F. J. 1992. 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. 58:2180-2187.
12. Devereux, J. P., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
13. Emerson, D., and W. C. Ghiorse. 1992. Isolation, cultural maintenance, and taxonomy of a sheath-forming strain of Leptothrix discophora and characterization of manganese-oxidizing activity associated with the sheath. Appl. Environ. Microbiol. 58:4001-4010.
14. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
15. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
16. Felsenstein, J. 1993. PHYLIP (phylogenetic inference package), version 3.5c. Department of Genetics, University of Washington, Seattle.
17. Fitch, W. M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20:406-416.
18. Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
19. Gherna, R., and P. Pienta (ed.). 1992. American Type Culture Collection catalogue of bacteria and bacteriophages, 18th ed. American Type Culture Collection, Rockville, Md.
20. Gherna, R., and C. R. Woese. 1992. A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic reconstructuring. Syst. Appl. Microbiol. 15:513-521.
21. Ghiorse, W. C. 1984. Biology of iron- and manganese-depositing bacteria. Annu. Rev. Microbiol. 38:515-550.
22. Ghiorse, W. C., and S. D. Chapnick. 1983. Metal-depositing bacteria and the distribution of manganese and iron in swamp waters. Environmental biogeochemistry. Ecol. Bull. (Stockholm) 35:367-376.
23. Ghiorse, W. C., and H. L. Ehrlich. 1992. Microbial biomineralization of iron and manganese, p. 75-101. In R. W. Fitzpatrick and H. C. W. Skinner (ed.), Biomineralization processes of iron and manganese: modern and ancient environments. Catena Verlag, Cremlingen-Destedt, Germany.
24. Herrick, J. B. Personal communication.
25. Herrick, J. B., E. L. Madsen, C. A. Batt, and W. C. Ghiorse. 1993. Polymerase chain reaction amplification of naphthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59:687-694.
26. Hillis, D. M., J. J. Bull, M. R. White, and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.
27. Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
28. Hulton, C. S. J., C. F. Higgins, and P. M. Sharp. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5:825-834.
29. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York.
30. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
31. Lane, D. J., A. P. Harrison, Jr., D. Stahl, B. Pace, S. J. Giovannoni, G. J. Olsen, and N. R. Pace. 1992. Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J. Bacteriol. 174:269-278.
32. Lane, D. J., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, and N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenctic analyses. Proc. Natl. Acad. Sci. USA 82:6955-6959.
33. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The Ribosomal Database Project. Nucleic Acids Res. 21:3021-3023.
34. Louws, F. J., D. W. Fulbright, C. T. Stephens, and F. J. de Bruijn. 1994. Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl. Environ. Microbiol. 60:2286-2295.
35. Mulder, E. G. 1989. Sheathed bacteria - genus Haliscomenobacter, p. 2003-2004. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins, Baltimore.
36. Mulder, E. G. 1989. Sheathed bacteria-genus Leptothrix, p. 1998-2003. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins, Baltimore.
37. Mulder, E. G. 1989. Sheathed bacteria - genus Sphaerotilus, p. 1994-1998. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins, Baltimore.
38. Mulder, E. G., and P. Hirsch. 1989. Sheathed bacteria, p. 1994-2008. In J. T. Staley, M. P. Bryant, N. Pfennig, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 3. William and Wilkins, Baltimore.
39. Murray, R. G. E., D. J. Brenner, R. R. Colwell, P. De Vos, M. Goodfellow, P. A. D. Grimont, N. Pfennig, E. Stackebrandt, and G. A. Zavarzin. 1990. Report of the Ad Hoc Committee on Approaches to Taxonomy within the Proteobacteria. Int. J. Syst. Bacteriol. 40:213-215.
40. Olsen, G. J. 1988. Phylogenetic analysis using ribosomal RNA. Methods Enzymol. 164:793-812.
41. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
42. Pringsheim, E. G. 1949. Iron bacteria. Biol. Rev. Camb. Philos. Soc. 24:200-245.
43. Saitou, N., and T. Imanishi. 1989. Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum likelihood, minimum evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol. Evol. 6:514-525.
44. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
45. Sanger, F. S., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
46. Siering, P. L., and W. C. Ghiorse. 1994. Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples, abstr. N-154, p. 342. In Abstracts of the 94th General Meeting of the American Society for Microbiology 1994. American Society for Microbiology, Washington, D.C.
47. Sourdis, J., and M. Nei. 1988. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol. Biol. Evol. 5:298-311.
48. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
49. Swofford, D. L. 1991. PAUP: phylogenetic analysis using parsimony, version 3.0s. Illinois Natural History Survey, Champaign.
50. Swofford, D. L., and G. J. Olsen. 1990. Phylogeny reconstruction, p. 411-515. In D. M. Hillis and C. Moritz (ed.), Molecular systematics. Sinauer Associates, Inc., Sunderland, Mass.
51. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting in bacterial genomes. Nucleic Acids Res. 19:6823-6831.
52. Ward, D. M., M. M. Bateson, R. Weller, and A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature, p. 219-286. In K. C. Marshall (ed.), Advances in microbial ecology. Plenum Press, New York.
53. Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 1987. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int. J. Syst. Bacteriol. 37:463-464.
54. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. Lane. 1991. 16S ribosomal DNA for phylogenetic study. J. Bacteriol. 173:697-703.
55. Willems, A., M. Gillis, and J. De Ley. 1991. Transfer of Rhodocychus gelatinosus to Rubrivivax gelatinosus gen. nov., comb, nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans, Pseudomonas saccharophila, and Alcaligenes latus. Int. J. Syst. Bacteriol. 41:65-73.
56. Wilson, K. H., R. B. Blitchington, and R. C. Greene. 1990. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28:1942-1946.
57. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
58. Wong, F. Y. K., E. Stackebrandt, J. K. Ladha, D. E. Fleischman, R. A. Date, and J. A. Fuerst. 1994. Phylogenetic analysis of Bradyrhizobium japonicum and photosynthetic stem-nodulating bacteria from Aeschynomene species grown in separated geographical regions. Appl. Environ. Microbiol. 60:940-946.