A natural species concept for prokaryotes

Current Opinion in Microbiology

Volumn 1, Issue 3, 1998, Pages 271-277

  Ward, David M ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROKARYOTA;

RIBOSOME DNA;

BACTERIUM; CLASSIFICATION; ECOLOGY; GENETICS; MOLECULAR EVOLUTION; NASA DISCIPLINE EXOBIOLOGY; NON-NASA CENTER; REVIEW;

NASA DISCIPLINE EXOBIOLOGY; NON-NASA CENTER;

BACTERIA; DNA, RIBOSOMAL; ECOLOGY; EVOLUTION, MOLECULAR;

EID: 0032082556     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(98)80029-5     Document Type: Article

References (45)

1. Goodfellow M, Manfio GP, Chun J: Towards a practical species concept for cultivable bacteria. In Species: the Units of Biodiversity. Edited by Claridge MF, Dawah HA, Wilson MR. London: Chapman and Hall; 1997:25-59. A review on the development of thinking among bacteriologists as they have attempted to conceptualize what prokaryotic species are.
2. Embley TM, Stackebrandt E: Species in practice: exploring uncultured prokaryote diversity in natural samples. In Species: the Units of Biodiversity. Edited by Claridge MF, Dawah HA, Wilson MR. London: Chapman and Hall; 1997:61-81. A review on how molecular phylogeny and direct molecular analysis of microbial communities have affected thinking about bacterial species in recent years.
3. Claridge MF, Dawah HA, Wilson MR (Eds): Species: the Units of Biodiversity. London: Chapman and Hall; 1997. A recent collection of articles on species concepts for viruses, bacteria and macroorganisms.
4. Mayr E: Species concepts and definitions. In The Species Problem. Edited by Mayr E. Washington, DC: The American Association for the Advancement of Science; 1957:1-22.
5. Simpson GG: Principles of Animal Taxonomy. New York and London: Columbia University Press; 1961.
6. Mayden RL: A hierarchy of species concepts: the denouement in the saga of the species problem. In Species: the Units of Biodiversity. Edited by Claridge MF, Dawah HA, Wilson MR. London: Chapman and Hall; 1997:381-424. A review of numerous species concepts that concludes that only one, the evolutionary species concept of Simpson (1961) [5], is natural, especially given the important philosophical ground work laid by Mayr (1957) [4] about species concepts. In Mayden's opinion "It is unfortunate that more scientists from all disciplines had not read....and bequeathed this philosophy to their academic descendants".
7. Ward DM, Ferris MJ, Nold SC, Bateson MM: Microbial biodiversity within hot spring cyanobacterial mat communities: an evolutionary ecology view. Microbiol Mol Biol Rev 1998, in press. A review of a decade of molecular study of the composition and structure of a model microbial community. The paper compares populations detected by 16S rRNA sequencing to those previously cultivated from these habitats and considers the basis for discrepancy between populations detected by such approaches. It demonstrates how the ecological and evolutionary patterns of occurrence of 16S rRNA genes permit inferences about species distributions, and how species diversity can be explained by universal principles of evolution and ecology.
8. Amann RI, Ludwig W, Schleifer KH: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169.
9. Ravin AW: Experimental approaches to the study of bacterial phylogeny. American Naturalist 1963, 97;307-318.
10. Maynard Smith J: Do bacteria have population genetics? Soc Gen Microbiol 1995, 52:1-12.
11. Roberts MS, Cohan FM: The effect of DNA sequence divergence on sexual isolation in Bacillus. Genetics 1993, 134:401-408.
12. Wilson EO: The Diversity of Life. New York: WW Norton and Company; 1992.
13. Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL: Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol 1997, 63:2330-2337 A nice example of how one can obtain historic evidence of lateral gene flow that has actually occurred among relatively closely related bacteria co-inhabiting a contaminated habitat. This can be contrasted with 'zoo mating' experiments between bacteria combined in the lab that may never co-exist in nature.
14. Stratz M, Mau M, Timmis KN: System to study horizontal gene exchange among microorganisms without cultivation of recipients. Mol Microbiol 1996, 22:207-215. A nice method that might enable detection of the frequency of genetic recombination between various bacterial donors and actual recipients without the potential bias of cultivation.
15. Cohan FM: The role of genetic exchange in bacterial evolution. Am Soc Microbiol News 1996, 62:631-636. A nice example of how an evolutionary biologist views the processes by which bacterial species form.
16. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E et al.: Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987, 37:463-464.
17. Staley JT: Biodiversity: are microbial species threatened? Curr Opin Biotechnol 1997, 8:340-345. A thoughtful review of microbial biodiversity thai points out how arbitrary our concept of bacterial species is.
18. Stackebrandt E, Goebel BM: Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J System Bacteriol 1994, 44:846-849.
19. Mallet J: A species definition for the modern synthesis. Trends Ecol Evolut 1995, 10:294-299.
20. Fox GE, Wisotzkey JD, Jurtshuk P: How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 1992, 42:166-170.
21. Palys T, Nakamura LK, Cohan FM: Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 1997, 47:1145-1156. A wonderful example of evolutionary ecology thinking applied to bacteria. Species, viewed as ecological units, are demonstrated to also equate to separate evolutionary units. There is an excellent theoretical introduction as to how bacterial species might evolve to form discreet evolutionary units, and nice discussions of DNA-DNA hybridization and 16S rRNA sequence relatedness in the context of species as units of evolution and ecology.
22. Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM: Molecular phytogeny of Archaea from soil. Proc Natl Acad Sci USA 1997, 94:277-282.
23. Borneham J, Triplett EW: Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial populations shifts associated with deforestation. Appl Environ Microbiol 1997, 63:2647-2653.
24. Borneman J, Skrock P, O'Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW: Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 1996, 62:1935-1943.
25. Gray JP, Herwig RP: Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Micrcbiol 1996, 62:4049-4059.
26. Kowalchuk GA, Stephen JR, De Boer W, Presser JI, Embley TM, Woldendorp JW: Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 1997, 63:1489-1497. A nice demonstration of how denaturing gradient gel electrophoresis can be used to simultaneously detect this occurrence of 16S rRNA genes along spatial and temporal environmental gradients.
27. Mullins TD, Britschgi TB, Krest RL, Giovannoni SJ: Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol Oceanogr 1995, 40:148-158.
28. Ohkuma M, Kudo T: Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl Environ Microbiol 1996, 62:461-468.
29. Pace NR: A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740. A nice overview on how molecular approaches are revealing diverse heretofore unknown and sometimes phylogenetically novel prokaryotes in natural habitats.
30. Barns SM, Delwiche CF, Palmer JD, Pace NR: Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 1996, 93:9188-9193.
31. Ferris MJ, Muyzer G, Ward DM: Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 1996, 62:340-346.
32. Nübel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H: Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 1996, 178:5635-5643.
33. Nold SC, Ward DM: Photosynthate partitioning and fermentation in hot spring microbial mat communities. Appl Environ Microbiol 1996, 62:4598-4607.
34. Field KG, Gordon D, Wright T, Rappe M, Urbach E, Vergin K, Giovannoni SJ: Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 1997, 63:63-70. A nice example of the ecological and evolutionary patterns of occurrence of as-yet uncultivated closely related bacteria that have been recognized through molecular analysis as inhabitants of the open ocean water column.
35. Giovannoni SJ, Rappe MS, Vergin KL, Adair NL 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proc Natl Acad Sci USA 1996, 93:7979-7984.
36. Gordon DA, Giovannoni SJ: Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific Oceans. Appl Environ Microbiol 1996, 62:1171-1177.
37. Nold SC, Zwart G: Patterns and structuring forces in aquatic microbial communities. Aquatic Microbial Ecology 1998, in press. A review on the patterns of occurrence of native bacterial populations detected in aquatic habitats by molecular analysis, considered in the context of principles of evolution and ecology.
38. Van Regenmortel MHV: Viral species. In Species: the Units of Biodiversity. Edited by Claridge MF, Dawah HA, Wilson MR. London: Chapman and Hall; 1997:17-24.
39. Streeter JG: Failure of inoculant rhizobia to overcome the dominance of indigenous strains for nodule formation. Can J Microbiol 1994, 40:513-522.
40. Tang W-C, White JC, Alexander M: Utilization of sorbed compounds by microorganism specifically isolated for that purpose. Appl Microbiol Biotechnol 1998 49:117-121. A very nice example of a new enrichment strategy that stimulates the natural microenvironmental conditions associated with sorption of contaminants to reduce their bioavailability. The species obtained by using this enrichment strategy appears more fit to degrade contaminants in situ than species obtained in more traditional but less realistic culture environments.
41. Begon M, Harper JL, Townsend CR: Ecology: Individuals, Populations and Communities, edn 3. Blackwell Science Ltd; 1996. An excellent introductory text that emphasizes the obvious link between ecology and evolutionary biology. It should be required reading for all microbial ecologists.
42. Rosenzweig ML: Species Diversity in Space and Time. Cambridge: University Press; 1995.
43. Staley JT, Castenholz RW, Colwell RR, Holt JG, Kane MD, Pace NR, Salyers AA, Tiedje JM: The microbial world: foundation of the biosphere. In Report from the American Academy of Microbiology: 1996 Jan 19-21; Palm Coast FL Washington, DC: American Society for Microbiology; 1997. A report of a recent workshop where leading microbiologists considered how to encourage biologists, politicans and people in general to develop a greater appreciation for the vast importance of microorganisms to the diversity and quality of life on Earth.
44. Claridge MF, Dawah HA, Wilson MR: Practical approaches to species concepts for living organisms. In Species: the Units of Biodiversity. Edited by Claridge MF, Dawah HA, Wilson MR. London: Chapman and Hall; 1997:1-15.
45. Ferris MJ, Ward DM: Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl Environ Microbiol 1997, 63:1375-1381. A nice demonstration of how denaturing gradient gel electrophoresis can be used to simultaneously detect the occurrence of 16S rRNA genes along spatial and temporal environmental gradients.