Bacterial species and evolution: Theoretical and practical perspectives

Journal of Industrial Microbiology and Biotechnology

Volumn 17, Issue 3-4, 1996, Pages 137-150

  Istock, C A ^a   Bell, J A ^b   Ferguson, N ^a   Istock, N L ^a  

^a The University of Arizona   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Bacteria; Diversity; Evolution; Genetics; Species concepts

Indexed keywords

BACTERIUM; BIODIVERSITY; EVOLUTION; GENETIC VARIABILITY; MOLECULAR GENETICS; NONHUMAN; REVIEW; SPECIES; TAXONOMY;

EID: 0030497908     PISSN: 13675435     EISSN: None     Source Type: Journal    
DOI: 10.1007/bf01574687     Document Type: Review

References (63)

1. Arbige MV, BA Balthuis, J Schultz and D Crabb. 1993. Fermentation of Bacillus. In: Bacillus subtilis and Other Gram-Positive Bacteria (Sonenshein AL, JA Hoch and R Losick, eds), pp 872-895, Am Soc Microbiology, Washington, DC.
2. Barns SM, RE Fundyga, MW Jeffries and NR Pace. 1994. Remarkable archael diversity detected in a Yellowstone National Park hot-spring environment. Proc Natl Acad Sci USA 91: 1609-1613.
3. Bell JA and SB Friedman. 1995. Genetic structure and diversity within local populations of Bacillus mycoides. Evolution 48: 1678-1714.
4. Berdy J, A Aszalos, M Bostain and KL McNitt. 1980. CRC Handbook of Antibiotic Compounds vol 1; vol 4, part 1. CRC Press, Boca Raton, Florida.
5. Bostin DA and PR Reeves. 1995. Sequence and analysis of the O-antigen gene (rfb) cluster of Escherichia coli 111. Gene 164: 17-23.
6. Brock TD, MT Madigan, JM Martinko and J Parker. 1994. Biology of Microorganisms. Prentice Hall, Englewood Cliffs.
7. Caugant DA, BR Levin and RK Selander. 1981. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics 98: 467-490.
8. Cohan FM, MS Roberts and EC King. 1991. The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45: 1383-1421.
9. Cracraft J. 1989. Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. In: Speciation and its Consequences (Otte D and J Endler, eds), pp 28-59, Sinauer Associates, Sunderland.
10. de Bruijn FJ. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium melilloti and other soil bacteria. Appl Environ Microbiol 58: 2180-2187.
11. Dobzhansky T. 1937. Genetics and the Origin of Species. Columbia University Press, New York.
12. Duncan KE, N Ferguson, K Kimura, X Zhou and CA Istock. 1994. Fine-scale genetic and phenotypic structure in natural populations of Bacillus subtilis and Bacillus licheniformis: implications for bacterial evolution and speciation. Evolution 48: 2002-2025.
13. Duncan KE, CA Istock, JB Graham and N Ferguson. 1989. Genetic exchange between Bacillus subtilis and Bacillus licheniformis: variable hybrid stability and the nature of bacterial species. Evolution 43: 1585-1609.
14. Dykhuizen D and L Green. 1991. Recombination in Escherichia coli and the nature of bacterial species. J Bacteriol 173: 7257-17268.
15. Eldredge N. 1985. Unfinished Synthesis: Biological Hierarchies and Modern Evolutionary Thought. Oxford University Press, Oxford.
16. Ferrari E, AS Jarnigan and BF Schmidt. 1993. In: Bacillus subtilis and Other Gram-Positive Bacteria (Sonenshein AL, JA Hoch and R Losick, eds), pp 917-937, Am Soc Microbiology, Washington, DC.
17. Fleischmann RD, MD Adams, O White, RA Clayton, EF Kirkness, AR Kerlavage, CJ Bult, J Tomb, BA Dougherty, JM Merrick, K McKenney, G Sutton, W Fitshugh, C Fields, JD Gocayne, J Scott, R Shirley, L Liu, A Glodek, JM Kelley, JF Weidmann, CA Phillips, T Spriggs, E Hedblom, MD Cotton, TR Utterback, MC Hanna, DT Nguyen, DM Saudek, RC Brandon, LD Fine, JL Fritchman, JC Fuhrmann, NMS Geoghagen, CL Gnehm, LA McDonald, KV Small, CM Fraser, HO Smith and JC Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
18. Gould SJ. 1980. Is a new and general theory of evolution emerging? Paleobiology 6: 119-130.
19. Grant V. 1981. Plant Speciation, 2nd edn. Columbia University Press, NY.
20. Howard DJ. 1988. The species problem. Evolution 42: 1111-1112.
21. Huxley J. 1942. Evolution: The Modern Synthesis. Allen and Unwin, London.
22. Istock CA, KE Duncan, N Ferguson and X Zhou. 1992. Sexuality in a natural population of bacteria - Bacillus subtilis challenges the clonal paradigm. Mol Ecol 1: 95-103.
23. Reference deleted in proof.
24. Istock CA. 1990. Genetic exchange and genetic stability in bacterial populations. In: Ecological Risks of Biotechnology (Ginzburg LR, ed), pp 123-147, Butterworths, London.
25. Judd AK, M Schneider, M Sadowsky and FJ de Bruijn. 1993. Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. Appl Environ Microbiol 59: 1702-1708.
26. Lan R and PR Reeves. 1996. Gene transfer is a major factor in bacterial evolution. J Molec Biol Evol 13: 47-55.
27. Lorenz NA, BW Ardema and W Wackernagel. 1988. Highly efficient genetic transformation of Bacillus subtilis attached to sand grains. J Gen Microbiol 134: 107-112.
28. Lorenz MG and W Wackernagel. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58: 563-602.
29. Lynch M and BG Milligan. 1994. Analysis of population genetic structure with RAPD markers. Mol Ecol 3: 91-99.
30. Maiden MCJ. 1993. Population genetics of a transformable bacterium: the influence of horizontal gene exchange on the biology of Neisseria meningitidis. FEMS Microbiol Lett 112: 243-250.
31. Maynard Smith J. 1995. Do bacteria have population genetics? In: Population Genetics of Bacteria (Baumberg S, JPW Young, EMH Wellington and JR Saunders, eds), pp 1-12, Cambridge University Press, Cambridge.
32. Maynard Smith J, NH Smith, M O'Rourke and BG Spratt. 1993. How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384-4388.
33. Mayr E. 1988. Toward a New Philosophy of Biology. Harvard University Press, Cambridge.
34. Mayr E. 1991. One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought. Harvard University Press, Cambridge, MA, pp 26-34.
35. Mayr E. 1942. Systematics and the Origin of Species. Columbia University Press, New York.
36. Mayr E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge.
37. Milkman R and A Stoltzfus. 1988. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics 120: 359-366.
38. Milkman R and MM Bridges. 1990. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126: 505-517.
39. Mischler BD and MJ Donoghue. 1982. Species concepts: a case for pluralism. System Zool 31: 491-503.
40. Nelson G. 1989. Species and taxa: systematics and evolution. In: Speciation and its Consequences (Otte D and J Endler, eds), pp 60-81, Sinauer Associates, Sunderland.
41. O'Donnell AG, M Goodfellow and DL Hawksworth. 1994. Theoretical and practical aspects of the quantification of biodiversity among microorganisms. Phil Trans R Soc Lond B 345: 65-73.
42. Otte D and J Endler. 1989. Speciation and its Consequences. Sinauer Associates, Sunderland.
43. Paterson HEH. 1985. The recognition species concept. In: Species and Speciation (Vrba ES, ed), pp 21-29, Transvaal Museum Monograph No. 4, Pretoria.
44. Pennington TH. 1994. Molecular systematics and traditional medical microbiologists - problems and solutions. J Med Microbiol 41: 371-373.
45. Ravin AW. 1960. The origin of bacterial species: genetic recombination and factors limiting it between bacterial populations. Bacteriol Rev 24: 201-220.
46. Roberts MS, LK Nakamura and FM Cohan. 1994. Bacillus mojavensis sp nov, distinguishable from B. subtilis by sexual isolation, divergence in DNA sequence and differences in fatty acid composition. Int J Syst Bacteriol 44: 256-264.
47. Selander RK, DA Caugant and TS Whittam. 1987. Genetic structure and variation in natural populations of Escherichia coli. In: Cellular and Molecular Biology, Vol 2: Escherichia coli and Salmonella typhimurium (Neidhardt FC, JL Ingraham, KB Low, B Megasanik, M Schaechter and HE Umbarger, eds), pp 1625-1648, American Society of Microbiology, Washington, DC.
48. Selander RK, DA Caugant, H Ochman, JM Musser, MN Glimour and TS Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol 51: 873-884.
49. Sneath PHA. 1989. Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. Syst Appl Microbiol 12: 15-31.
50. Sneath PHA and RR Sokal. 1973. Numerical Taxonomy. WH Freeman, San Francisco.
51. Sokal RR and TJ Crovello. 1970. The biological species concept: a critical evaluation. Am Nat 104: 104-127.
52. Souza V, L Eguiarte, G Avila, R Capello, C Gallardo, J Montoya and D Pinero. 1994. Genetic structure of Rhizobium etli biovar phasioli associated with wild and cultivated beans (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico. Appl Environ Microbiol 60: 1260-1268.
53. Sullivan JT, HN Patrick, WL Lowther, DB Scott and CW Ronson. 1995. Nodulating strains of Rhizobium loti arise through chromosomal gene transfer in the environment. Proc Natl Acad Sci USA 92: 8985-8989.
54. Templeton AR. 1989. The meaning of species and speciation: a genetic perspective. In: Speciation and its Consequences (Otte D and J Endler, eds), pp 3-27, Sinauer Associates, Sunderland.
55. 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.
56. Vary P. 1992. Development of genetic engineering in Bacillus megaterium. In: Biology of the Bacilli: Applications to Industry (Doi RH and M McGloughlin, eds), pp 251-310, Butterworth-Heinemann, Boston.
57. Vrba ES. 1980. Macroevolutionary trends: new perspectives on the roles of adaptation and incidental effect. Science 221: 387-389.
58. Wayne LG, DJ Brenner, RR Colwell, PAD Grimont, O Kandler, MI Krichevsky, LH Moore, WEC Moore, RGE Murray, E Stackebrandt, MP Starr and HG Truper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Intl J Syst Bact 37: 463-464.
59. Welsh J and M McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucl Acid Res 18: 7213-7218.
60. Welsh J, C Pretzman, D Postic, I Saint Girons, G Baranton and M McClelland. 1993. Genomic fingerprinting by arbitrarily primed polymerase chain reaction resolves Borrelia burgdorferi into three distinct phyletic groups. Int J Syst Bacteriol 42: 370-375.
61. Whittam TS and RA Wilson. 1988. Genetic relationships among pathogenic strains of avian Escherichia coli. Infect Immun 56: 2458-2466.
62. Williams JGK, AR Kubelik, KJ Livak, JA Rifelski and SV Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acid Res 18: 6531-6535.
63. Zuber P, MM Nakano and MA Marahiel. 1993. Peptide antibiotics. In: Bacillus subtilis and Other Gram-Positive Bacteria (Sonenshein AL, JA Hoch and R Losick, eds), pp 897-916, Am Soc Microbiology, Washington, DC.