Discovery and classification of ecological diversity in the bacterial world: The role of DNA sequence data

International Journal of Systematic Bacteriology

Volumn 47, Issue 4, 1997, Pages 1145-1156

  Palys, Thomas ^a   Nakamura, L K ^b   Cohan, Frederick M ^a  

^a WESLEYAN UNIVERSITY   (United States)

^b NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIUM; BIODIVERSITY; DNA SEQUENCE; ECOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL;

EID: 0030870289     PISSN: 00207713     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-47-4-1145     Document Type: Article

References (91)

1. Ambler, R. P. 1996. The distance between bacterial species in sequence space. J. Mol. Evol. 42:617-630.
2. Ash, C., J. A. E. Farrow, M. Dorsch, E. Stackebrandt, and M. D. Collins. 1991. Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int. J. Syst. Bacteriol. 41:343-346.
3. Ash, C., J. A. E. Farrow, S. Wallbanks, and M. D. Collins. 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA sequences. Lett. Appl. Microbiol. 13:202-206.
4. Atwood, K. C., L. K. Schneider, and F. J. Ryan. 1951. Periodic selection in Escherichia coli. Proc. Natl. Acad. Sci. USA 37:146-155.
5. Avise, J. C. 1994. Molecular markers, natural history and evolution, p. 104. Chapman and Hall, New York, N.Y.
6. Baess, I. 1983. Deoxyribonucleic acid relationships between different serovars of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum. Acta Pathol. Microbiol. Immunol. Scand. Sect. B 91:201-203.
7. Balmelli, T., and J. Piffaretti. 1996. Analysis of the genetic polymorphism of Borrelia burgdorferi sensu lato by multilocus enzyme electrophoresis. Int. J. Syst. Bacteriol. 46:167-172.
8. Baranton, G., D. Postic, I. Saint Girons, P. Boerlin, J. C. Piffaretti, M. Assous, and P. A. Grimont. 1992. Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis. Int. J. Syst. Bacteriol. 42:378-383.
9. Boddinghaus, B., J. Wolters, W. Heikens, and E. C. Bottger. 1990. Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level. FEMS Microbiol. Lett. 70:197-204.
10. Bonnet, F., C. Saillard, J. M. Bové, R. H. Leach, D. L. Rose, G. S. Cottew, and J. G. Tulley. 1993. DNA relatedness between field isolates of mycoplasma F38 group, the agent of contagious caprine pleuropneumonia, and strains of Mycoplasma capricolum. Int. J. Syst. Bacteriol. 43:597-602.
11. Boyd, E. F., K. Nelson, F. Wang, T. S. Whittam, and R. K. Selander. 1994. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 91:1280-1284.
12. Boyd, E. F., F. Wang, T. S. Whittam, and R. K. Selander. 1996. Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62:804-808.
13. Britschgi, T. B., and S. J. Giovannoni. 1991. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1707-1713.
14. Cohan, F. M. 1994. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143:965-986.
15. Cohan, F. M. 1994. Genetic exchange and evolutionary divergence in prokaryotes. Trends Ecol. Evol. 9:175-180.
16. Cohan, F. M. 1995. Does recombination constrain neutral divergence among bacterial taxa? Evolution 49:164-175.
17. Cohan, F. M. 1996. The role of genetic exchange in bacterial evolution. ASM News 62:631-636.
18. Cohan, F. M. Genetic structure of bacterial populations. In R. Singh and C. Krimbas (ed.), Evolutionary genetics from molecules to morphology, in press. Cambridge University Press, Cambridge, England.
19. Cohan, F. M., M. S. Roberts, and E. C. King. 1991. The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45:1393-1421.
20. Collins, M. D., A. M. Williams, and S. Wallbanks. 1990. The phytogeny of Aerococcus and Pediococcus as determined by 16S rRNA sequence analysis: description of Tetragenococcus gen. nov. FEMS Microbiol. Lett. 70:255-262.
21. Darrasse, A., S. Priou, A. Kotoujansky, and Y. Bertheau. 1994. PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato diseases. Appl. Environ. Microbiol. 60:1437-1443.
22. Dobson, S. J., T. A. McMeekin, and P. D. Franzmann. 1993. Phylogenetic relationships between some members of the genera Deleya, Halomonas, and Halovibrio. Int. J. Syst. Bacteriol. 43:665-673.
23. Dolina, M., and R. Peduzzi. 1993. Population genetics of human, animal and environmental Yersinia strains. Appl. Environ. Microbiol. 59:442-450.
24. Drake, J. W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88:7160-7164.
25. Forsman, M., G. Sandstrom, and A. Sjostedt. 1994. Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR. Int. J. Syst. Bacteriol. 44:38-46.
26. Fox, G. E., J. D. Wisotzkey, and P. Jurtshuk, Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166-170.
27. Fukunaga, M., and Y. Koreki. 1996. A phylogenetic analysis of Borrelia burgdorferi sensu lato isolates associated with Lyme disease in Japan by flagellin gene sequence determination. Int. J. Syst. Bacteriol. 46:416-421.
28. Gordon, R. E., W. C. Haynes, and C. H.-N. Pang. 1973. The genus Bacillus. Agricultural handbook no. 427. U.S. Department of Agriculture, Washington, D.C.
29. Guibourdenche, M., M. Y. Popoff, and J. Y. Riou. 1986. Deoxyribonucleic acid relatedness among Neisseria gonorrhoeas, N. meningitidis, N. lactamica, N. cinerea and "Neisseria polysaccharea." Ann. Inst. Pasteur Microbiol. 137B(2):177-185.
30. Gundersen, D. E., I.-M. Lee, D. A. Schaff, N. A. Harrison, C. J. Chang, R. E. Davis, and D. T. Kingsbury. 1996. Genomic diversity and differentiation among phytoplasma strains in 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int. J. Syst. Bacteriol. 46:64-75.
31. Guttman, D. S., and D. E. Dykhuizen. 1994. Clonal divergence in Escherichia coli is a result of recombination, not mutation. Science 266:1380-1383.
32. Henderson, I., C. J. Duggleby, and P. C. Turnbull. 1994. Differentiation of Bacillus anthracis from other Bacillus cereus group bacteria with the PCR. Int. J. Syst. Bacteriol. 44:99-105.
33. Heyndrickx, M., K. Vandemeulebroecke, B. Hoste, P. Janssen, K. Kersters, P. De Vos, N. A. Logan, N. Ali, and R. C. W. Berkeley. 1996. Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens. Int. J. Syst. Bacteriol. 46:270-279.
34. Hudson, R. R. 1987. Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50:242-250.
35. Ichige, A., and G. C. Walker. 1997. Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants. J. Bacteriol. 179:209-216.
36. Johnson, J. L. 1986. Nucleic acids in bacterial classification, p. 972-975. In P. H. A. Sneath, N. S. Mair, N. E. Sharpe, and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 2. Williams & Wilkins, Baltimore, Md.
37. Kapur, V., L. L. Li, M. R. Hamrick, B. B. Plikaytis, T. M. Shinnick, A. Telenti, W. R. Jacobs, Jr., A. Banerjee, S. Cole, and K. Y. Yuen. 1995. Rapid Mycobacterium species assignment and unambiguous identification of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis by automated DNA sequencing. Arch. Pathol. Lab. Med. 119:131-138.
38. Karaolis, D. K. R., R. Lan, and P. K. Reeves. 1995. The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae. J. Bacteriol. 177:3191-3198.
39. Keis, S., C. F. Bennet, V. K. Ward, and D. T. Jones. 1995. Taxonomy and phylogeny of industrial solvent-producing clostridia. Int. J. Syst. Bacteriol. 45:693-705.
40. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, England.
41. Knight, I. T., W. E. Holben, J. M. Tiedje, and R. R. Colwell. 1992. Nucleic acid hybridization techniques for detection, identification, and enumeration of microorganisms in the environment, p. 65-91. In M. A. Levin, R. J. Seidler, and M. Rogul (ed.), Microbial ecology: principles, methods, and applications, McGraw-Hill, New York, N.Y.
42. Koch, A. L. 1974. The pertinence of the periodic selection phenomenon to prokaryotic evolution. Genetics 77:127-142.
43. Lan, R., and P. R. Reeves. 1996. Gene transfer is a major factor in bacterial evolution. Mol. Biol. Evol. 13:47-55.
44. Larkin, J. M., and J. L. Stokes. 1967. Taxonomy of psychrophilic strains of Bacillus. J. Bacteriol. 94:889-895.
45. Legard, D. E., C. F. Aquadro, and J. E. Hunter. 1993. DNA sequence variation and phylogenetic relationships among strains of Pseudomonas syringae pv. syringae inferred from restriction site maps and restriction fragment length polymorphism. Appl. Environ. Microbiol. 59:4180-4188.
46. Levin, B. R. 1981. Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99:1-23.
47. Love, D. N. 1995. Porphyromonas macacae comb. nov., a consequence of Bacteroides macacae being a senior synonym of Porphyromonas salivosa. Int. J. Syst. Bacteriol. 45:90-92.
48. Mallet, J. 1995. A species definition for the modern synthesis. Trends Ecol. Evol. 10:294-299.
49. Martinez, E., D. Romero, and P. Palacios. 1990. The Rhizobium genome. Crit. Rev. Plant Sci. 9:17-19.
50. Maynard Smith, J., N. H. Smith, M. O'Rourke, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
51. Mikulskis, A. V., and G. R. Cornelis. 1994. A new class of proteins regulating gene expression in enterobacteria. Mol. Microbiol. 11:77-86.
52. Milkman, R., and M. M. Bridges. 1993. Molecular evolution of the Escherichia coli chromosome. Genetics 133:455-468.
53. Murray, R. G. E., and E. Stackebrandt. 1995. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45:186-187.
54. Nakamura, L. K. 1984. Bacillus psychrophilus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 34:121-123.
55. Nakamura, L. K. 1990. Bacillus thiaminolyticus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 40:242-246.
56. Nakamura, L. K. 1994. DNA relatedness among Bacillus thuringiensis serovars. Int. J. Syst. Bacteriol. 44:125-129.
57. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York, N.Y.
58. Nelson, K., and R. K. Selander. 1992. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J. Bacteriol. 174: 6886-6895.
59. Nelson, K., and R. K. Selander. 1994. Intergenic transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc. Natl. Acad. Sci. USA 91:10227-10231.
60. Nelson, K., T. S. Whittam, and R. K. Selander. 1991. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA 88:6667-6671.
61. Nicholson, L. A., C. J. Morrow, L. A. Corner, and A. L. M. Hodgson. 1994. Phylogenetic relationship of Fusobacterium necrophorum A, AB, and B biotypes based upon 16S rRNA gene sequence analysis. Int. J. Syst. Bacteriol. 44:315-319.
62. Normand, P., S. Orso, B. Cournoyer, P. Jeannin, C. Chapelon, J. Dawson, L. Evtushenko, and A. K. Misra. 1996. Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int. J. Syst. Bacteriol. 46:1-9.
63. Osuna, R., S. A. Boylan, and R. A. Bender. 1991. In vitro transcription of the histidine utilization (hutUH) operon from Klebsiella aerogenes. J. Bacteriol. 173:116-123.
64. Palys, T., E. Berger, L. K. Nakamura, and F. M. Cohan. Unpublished data.
65. Poveda, J. B., J. Giebel, J. Flossdorf, J. Meier, and H. Kirchhoff. 1994. Mycoplasma buteonis sp. nov., Mycoplasma falconis sp. nov., and Mycoplasma gypis sp. nov., three species from birds of prey. Int. J. Syst. Bacteriol. 44:94-98.
66. Rainey, F. A., N. Weiss, and E. Stackebrandt. 1995. Phylogenetic analysis of the genera Cellulomonas, Promicromonospora, and Jonesia and the proposal to exclude the genus Jonesia from the family Cellulomonadaceae. Int. J. Syst. Bacteriol. 45:649-652.
67. Rasmussen, F. O., P. Skouboe, L. Dons, L. Rossen, and J. E. Olson. 1995. Listeria monocytogenes exists in at least three evolutionary lines: evidence from flagellin, invasive associated protein and listeriolysin O genes. Microbiology 141:2053-2061.
68. Rayssiguier, C., D. S. Thaler, and M. Radman. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396-401.
69. Roberts, M. S., and F. M. Cohan. 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49:1081-1094.
70. Roberts, M. S., L. K. Nakamura, and F. M. Cohan. 1994. Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition. Int. J. Syst. Bacteriol. 44:256-264.
71. Roberts, M. S., L. K. Nakamura, and F. M. Cohan. 1996. Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California. Int. J. Syst. Bacteriol. 46:470-475.
72. Ros, C., and K. Belak. 1996. Detection and identification of mycobacteria in formalin-fixed, paraffin-embedded tissues by nested PCR and restriction enzyme analysis. J. Clin. Microbiol. 34:2351-2355.
73. Sedgwick, S. G., D. Lodwick, N. Doyle, H. Crowne, and P. Strike. 1991. Functional complementation between chromosomal and plasmid mutagenic DNA repair genes in bacteria. Mol. Gen. Genet. 229:428-436.
74. Segovia, L., D. Piñero, R. Palacios, and E. Martinez-Romero. 1991. Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum. Appl. Environ. Microbiol. 57:426-433.
75. Selander, R. K., and J. M. Musser. 1990. Population genetics of bacterial pathogenesis, p. 11-36. In B. H. Iglewski and V. L. Clark (ed.), molecular basis of bacterial pathogenesis. Academic Press, San Diego, Calif.
76. Sharp, P. M., N. C. Nolan, N. N. Cholmain, and K. M. Devine. 1992. DNA sequence variability at the rplX locus of Bacillus subtilis. J. Gen. Microbiol. 138:39-45.
77. Smart, C. D., B. Schneider, C. L. Blomquist, L. J. Guerra, N. A. Harrison, U. Ahrens, K. H. Lorenz, E. Seemuller, and B. C. Kirkpatrick. 1996. Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region. Appl. Environ. Microbiol. 62:2988-2993.
78. Soini, H., E. C. Bottger, and M. K. Viljanen. 1994. Identification of mycobacteria by PCR-based sequence determination of the 32-kilodalton protein gene. J. Clin. Microbiol. 32:2944-2947.
79. Soria, G., J. Barbe, and I. Gibert. 1994. Molecular fingerprinting of Salmonella typhimurium by IS200-typing as a tool for epidemiological and evolutionary studies. Microbiologia 10:57-68.
80. Taghavi, M., C. Hayward, L. I. Sly, and M. Fegan. 1996. Analysis of the phylogenetic relationships of the strains of Burkholderia solanacearum, Pseudomonas syzygii, the blood disease bacterium of banana based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 46:10-15.
81. Thampapillai, R. Lan, and P. R. Reeves. 1994. Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11:813-828.
82. Vandamme, P., B. Pot, M. Gillis, P. De Vos, K. Kersters, and J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407-438.
83. Vauterin, L., B. Hoste, K. Kersters, and J. Swings. 1995. Reclassification of Xanthomonas. Int. J. Syst. Bacteriol. 45:472-489.
84. Vazquez, J. A., L. de la Fuente, S. Berron, M. O'Rourke, N. H. Smith, J. Zhou, and B. G. Spratt. 1993. Ecological separation and genetic isolation of Neisseria gonorrhoeae and Neisseria meningitidis. Curr. Biol. 3:567-572.
85. 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.
86. Whittam, T. S., and S. E. Ake. 1993. Genetic polymorphisms and recombination in natural populations of Escherichia coli, p. 223-245. In N. Takahata and A. G. Clark (ed.), Molecular paleopopulation biology. Japan Scientific Society Press, Tokyo, Japan.
87. Williams, A. M., U. M. Rodriguez, and M. D. Collins. 1991. Intrageneric relationships of Enterococci as determined by reverse transcriptase sequenc-ing of small-subunit rRNA. Res. Microbiol. 142:67-74.
88. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
89. E and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. J. Bacteriol. 177:3259-3268.
90. Zawadzki, P., M. S. Roberts, and F. M. Cohan. 1995. The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140:917-932.
91. Zhou, J., and B. G. Spratt. 1992. Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argF gene. Mol. Microbiol. 6:2135-2146.