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Chapter 28 : Phylogeny and Functionality: Taxonomy as a Roadmap to Genes

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Abstract:

Taxonomy, the principles and practice of classification of the organisms that make up biological diversity, enables their detection and identification. The extent to which a general, phylogenetically based taxonomy can be predictive depends on the relative contributions of horizontal and vertical transmission of genes. To exploit this predictive power will depend on one's understanding of biological diversity, the distribution of genes within that diversity, and the ecology and biogeography of the organisms. Taxonomy is a key prerequisite to this understanding. The relationship between taxonomy and genes has been indirect, and views on the distribution of genes across microbial diversity based on observations of phenotypic properties and concepts of inheritance began to be challenged only with the recognition of widespread transfer of antibiotic resistance genes. Biomarkers indirectly reflect the distribution of the genes responsible for their biosynthesis, although additional complexity is often revealed when the specific genes responsible for metabolic processes and products are identified. In the context of bioprospecting, taxonomy has three roles: enabling the classification and then the detection and identification of organisms; predicting metabolic potential; and dereplicating isolates for screening. Much of the recent evidence that lateral gene transfer is extensive has come from statistical comparisons of DNA base sequence data. New high-throughput techniques for phenotypic characterization, whole-genome and multilocus sequencing, microarrays, and subtractive hybridization will define the unit of diversity for prokaryotes—the genome species concept—and provide a roadmap to help guide the new search and discovery strategies.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28

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High-Performance Liquid Chromatography
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16s rRNA Sequencing
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Figure 1

DNA-.DNA homology versus 16S rRNA similarity. Data for actinomycetes, from the literature. Adapted from J. Chun, Ph:D. thesis, University of Newcastle upon Tyne, updated by J . Ε. M. Stach and L. A. Maldonado.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 2

Distribution of PUFAs among some members of the family . Adapted from .

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 3

clade in the streptomycete phylogenetic tree.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 4

HPLC profile of secondary metabolites from a representative strain of the clade. ELSD, evaporative light-scattering detector.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 5

DNA:DNA homology of members of the clade.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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Figure 6

Comparative genomics of some members of the clade. Genes present and absent detected by microarrays.

Citation: Ward A, Goodfellow M. 2004. Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, p 288-313. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch28
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References

/content/book/10.1128/9781555817770.chap28
1. Achouak, W.,, P. Normand,, and T. Heulin. 1999. Comparative phylogeny of rrs and nifH genes in the Bacillaceae. Int. J. Syst. Bacteriol. 49: 961 967.
2. Allen, I. W.,, and D. A. Ritchie. 1994. Cloning and analysis of DNA-sequences from Streptomyces hygroscopicus encoding gel-danamycin biosynthesis. Mol. Gen. Genet. 243: 593 599.
3. Aim, R. A.,, and T. J. Trust. 1999. Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes. J. Mol. Med. 77: 834 846.
4. Altaha, R.,, T. Fojo,, E. Reed,, and J. Abraham. 2002. Epothilones: a novel class of nontaxane microtubule-stabilizing agents. Curr. Pharm. Des. 8: 1707 1712.
5. Al-Tai, A.,, B. Kim,, S. B. Kim,, G. P. Manfio,, and M. Goodfellow. 1998. Streptomyces malaysiensis sp. nov., a new streptomycete species with rugose, ornamented spores. Int. J. Syst. Bacteriol. 49: 1395 1402.
6. Andersson, J. O.,, W. F. Doolittle,, and C. L. Nesbs. 2001. Genomics—are there bugs in our genome? Science 292: 1848 1850.
7. Arcamone, F. C.,, C. Bertazzoli,, M. Ghione,, and T. Scotti. 1959. Melanosporin and elaiophylin, a new antibiotic from Streptomyces melanosporus (sive melanosporofaciens) n. sp. Giorn. Microbiol. 7: 207 216.
8. Bansal, A. K.,, and T. E. Meyer. 2002. Evolutionary analysis by whole genome comparisons. J. Bacteriol. 184: 2260 2272.
9. Beadle, G. W.,, and E. L. Tatum. 1941. Genetic control of biochemical reactions in Neurospora. Proc. Natl. Acad. Sci. USA 27: 499 506.
10. Becker, B.,, M. P. Lechevalier,, and H. A. Lechevalier. 1965. Chemical composition of cell wall preparations from strains of various form genera of aerobic actinomycetes. Appl. Microbiol. 13: 236 243.
11. Bentley, S. D.,, K. F. Chater,, A. -M. Cerdeño-Târraga,, G. L. Challis,, N. R. Thompson,, D. James,, D. E. Harris,, M. A. Quail,, H. Kieser,, D. Harper,, A. Bateman,, S. Brown,, G. Chandra,, C. W. Chen,, M. Collins,, A. Cronin,, A. Fraser,, A. Goble,, J. Hildago,, T. Hornsby,, S. Howarth,, C.-H. Huang,, T. Kieser,, L. Larke,, L. Murphy,, K. Oliver,, S. O'Neil,, E. Rabbinowitsch,, M. A. Rajandream,, K. Rutherford,, S. Rutter,, K. Seeger,, D. Saunders,, S. Sharp,, R. Squares,, S. Squares,, K. Taylor,, T. Warren,, A. Wietzorrek,, J. Woodwark,, B. G. Barrell,, J. Parkhill,, and D. A. Hopwood. 2002. Complete genome sequence of model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141 147.
12. Bérdy, J. 1995. Are actinomycetes exhausted as a source of secondary metabolites? Biotechnologia 7- 8: 13 14.
13. Bernardet, J.-F.,, Y. Nakagawa,, and B. Holmes. 2002. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int. J. Syst. Evol. Microbiol. 52: 1049 1070.
14. Bishop, P. E.,, and R. Premakumar,. 1992. Alternative nitrogen fixation systems, p. 736 762. In R. H. Burris, and H. J. Evans (ed.), Biological Nitrogen Fixation. Chapman & Hall, New York, N.Y.
15. Bollag, D. M.,, P. A. McQueney,, J. Zhu,, O. Hensens,, L. Koupal,, J. Liesch,, M. Goetz,, E. Lazarides,, and C. M. Woods. 1995. Epothilones, a new class of microtubule-stabilising agents with a taxol-like mechanism of action. Cancer Res. 55: 2325 2333.
16. Boone, D. R.,, R. W. Casterholtz,, and G. M. Garrity (ed.). 2001. Bergey's Manual of Systematic Bacteriology, 2nd éd., vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria. Springer Verlag, New York, N.Y.
17. Boucher, Y.,, and W. F. Doolittle. 2000. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol. Microbiol. 37: 703 716.
18. Boucher, Y.,, H. Huber,, S. L'Haridon,, K. O. Stetter,, and W. F. Doolittle. 2001. Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermo-plasmatales and Archaeoglobales. Mol. Biol. Evol. 18: 1378 1388.
19. Bousfield, I. J.,, and A. G. Callely. 1978. Coryneform Bacteria. Academic Press, London, United Kingdom.
20. Brady, S. F.,, C. J. Chao,, J. Handelsman,, and J. Clardy. 2001. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org. Lett. 3: 1981 1984.
21. Brochier, C.,, and H. Philippe. 2002. Phylogeny: a non-hyperther-mophilic ancestor for bacteria. Nature 417: 244.
22. Brochier, C.,, E. Bapteste,, D. Moreira,, and H. Philippe. 2002. Eu-bacterial phylogeny based on translational apparatus proteins. Trends Genet. 18: 1 5.
23. Broun, P.,, S. Gettner,, and C. Somerville. 1999. Genetic engineering of plant lipids. Annu. Rev. Nutr. 19: 197 216.
24. Bull, A. T.,, A. C. Ward,, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64: 573 606.
25. Bullock, W. 1938. The History of Bacteriology. Oxford University Press, London, United Kingdom.
26. Cardenas, M. E.,, M. C. Cruz,, M. del Poeta,, N. J. Chung,, J. R. Perfect,, and J. Heitman. 1999. Antifungal activities of antineoplas-tic agents: Saccharomyces cerevisiae as a model system to study drug action. Clin. Microbiol. Rev. 12: 583 611.
27. Castresana, J.,, and D. Moreira. 1999. Respiratory chains in the last common ancestor of living organisms. J. Mol. Evol. 49: 453 460.
28. Chalker, A. F.,, and R. D. Lunsford. 2002. Rational identification of new antibacterial drug targets that are essential for viability using a genomics-based approach. Pharmacol. Therapeut. 95: 1 20.
29. Challis, G. L.,, and J. Ravel. 2000. Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal pep-tide synthetase FEMS Microbiol. Lett. 187: 111 114.
30. Chan, K.,, S. Baker,, C. C. Kim,, C. S. Detweiler,, G. Dougan, and S. Falkow. 2000. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica Ty-phimurium DNA microarray. J. Bacteriol. 185: 553 563.
31. Chien, Y.-T.,, and S. H. Zinder. 1994. Cloning, functional organization, transcript studies and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archeon Methanosarcina barkeri 227. J. Bacteriol. 178: 143 148.
32. Chien, Y.-T.,, and S. H. Zinder. 1996. Cloning, DNA-sequencing and characterisation of a nifD-homologous gene from the archeon Methanosarcina barkeri 227 which resembles nifDl from the eubacterium Clostridum pasteurianum. J. Bacteriol. 176: 6509 6598.
33. Claydon, M. A.,, S. N. Davey,, V. Edwards-Jones,, and D. B. Gordon. 1996. The rapid identification of intact micro-organisms using mass spectrometry. Nat. Biotech. 14: 1584 1586.
34. Collins, M. D., 1994. Isoprenoid quinones, p. 265 309. In M. Goodfellow, and A. G. O'Donnell (éd.), Chemical Methods in Prokaryotic Systematics. John Wiley & Sons, Chichester, United Kingdom.
35. Colquhoun, J. A.,, J. Zulu,, M. Goodfellow,, K. Horikoshi,, A. C. Ward,, and A. T. Bull. 2000. Rapid characterisation of deep-sea actinomycetes for biotechnology screening programmes. Antonie Leeuwenhoek 77: 359 367.
36. Colwell, R. R. 1970. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J. Bacteriol. 104: 410 433.
37. Connolly, J. D.,, and R. A. Hill. 1992. Dictionary of Terpenoids. Chapman & Hall, New York, N.Y.
38. Conway, G. C.,, S. C. Smole,, D. A. Sarracino,, R. D. Arbeit,, and P. E. Leopold. 2001. Phyloproteomics: species identification of Enterobacteriaceae using matrix-assisted laser desorption/ioniza-tion time-of-flight mass spectrometry. J. Mol. Microbiol. Biotech. 3: 103 112.
39. Curtis, T. P.,, W. T. Sloan,, and J. W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99: 10494 10499.
40. Dairi, T.,, Y. Motohira,, T. Kuzuyama,, S. Takahashi,, N. Itoh,, and H. Seto. 2000. Cloning of the gene encoding 3-hydroxy-3-methylglutaryl CoA reductase from terpenoid antibiotic-producing Streptomyces strains. Mol. Gen. Genet. 262: 957 964.
41. Davies, J. 1996. Origins and evolution of antibiotic resistance. Microbiologia 12: 9 16.
42. Dawid, W. 2000. Biology and global distribution of myxobacteria in soils. FEMS Microbiol. Rev. 24: 403 427.
43. De Boer, C.,, P. A. Meulman,, R. J. Wnuk,, and D. H. Peterson. 1970. Geldanamycin, a new antibiotic. J. Antibiot. 23: 442 447.
44. De Koning, A. P.,, F. S. L. Brinkman,, S. J. M. Jones,, and P. J. Keeling. 2000. Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Mol. Biol. Evol. 17: 1769 1773.
45. DeLong, E. F.,, and A. A. Yayanos. 1986. Biochemical functional and ecological significance of novel bacterial lipids in deep-sea prokaryotes. Appl. Environ. Microbiol. 51: 730 737.
46. Disch, A.,, J. Schwender,, C. Muller,, H. K. Lichtenthaler,, and M. Rohmer. 1998. Distribution of the mevalonate and glyceralde-hydes phosphate/pyruvate pathways for isoprenoid biosynthesis in unicellular algae and the cyanobacteriuni Synechococcus PCC 6714. Biochem.J. 333: 381 388.
47. Dobzhansky, T. 1967. Looking back at Mendel's discovery. Science 156: 1588 1589.
48. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124 2129.
49. Doolittle, W. F.,, and J. M. Logsdon, Jr. 1998. Archaeal genomics: do archaea have a mixed heritage? Curr. Biol. 8: R209 R211.
50. Drews, J. 2000. Drug discovery: a historical perspective. Science 287: 1960 1964.
51. Drews, G. 2000. The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS Microbiol. Rev. 24: 225 249.
52. Dykhuizen, D. E.,, and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173: 7257 7268.
53. Egan, S.,, P. Wiener,, D. Kallifidas,, and E. M. H. Wellington. 2001. Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters. Antonie Leeuwenhoek 79: 127 133.
54. Embley, T. M.,, and E. Stackebrandt,. 1997. Species in practice: exploring uncultured prokaryotic diversity in natural samples, p. 61 81. In M. F. Claridge,, H. A. Dawah,, and M. R. Wilson (ed.), Species: the Units of Diversity. Chapman & Hall, London, United Kingdom.
55. Embley, T. M.,, and R. Wait,. 1994. Structural lipids of eubactefia, p. 121 161. In M. Goodfellow, and A. G. O'Donnell (ed.), Chemical Methods in Prokaryotic Systematics. John Wiley & Sons, Chichester, United Kingdom.
56. Fang, A. Q.,, G. K. Wong,, and A. L. Demain. 2000. Enhancement of the antifungal activity of rapamycin by the coproduced elaiophylin and nigericin. J. Antibiot. 53: 158 162.
57. Feil, E. J.,, E. C. Holmes,, D. E. Bessen,, M.-S. Chan,, N. P. J. Day,, M. C. Enright,, R. Goldstein,, D. W. Hood,, A. Kalia,, C. E. Moore,, J. Zhou,, and B. G. Spratt. 2001. Recombination within natural populations of pathogenic bacteria: short term empirical estimates and long term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98: 182 187.
58. Fitzgerald, J. R.,, D. E. Sturdevant,, S. M. Mackie,, S. R. Gill,, and J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98: 8821 8826.
59. Freney, J.,, W. E. Kloos,, V. Hajek,, J. A. Webster,, M. Bes,, Y. Brun, and C. Vernozy-Rozand. 1999. Recommended minimal standards for description of new staphylococcal species. Int. J. Systeriol. Bact. 49: 489 502.
60. Gil, R.,, B. Sabater-Munoz,, A. Latorre,, F. J. Silva,, and A. Moya. 2002. Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc. Natl. Acad. Sci. USA 99: 4454 4458.
61. Gill, I.,, and R. Valivety. 1997. Polyunsaturated fatty acids. Part I. Occurrence, biological activities and applications. Trends Biotechnol. 15: 401 409.
62. Goldfine, H. 1972. Comparative aspects of bacterial lipids. Adv. Microbiol. Physiol. 8: 1 58.
63. Goodfellow, M. 1985. Staphylococcal systematics: past, present and future. Zbl. Bakt. Suppl. 14: 69 81.
64. Goodfellow, M.,, and T. Cross,. 1983. Classifications, p. 7 164. In M. Goodfellow,, M. Mordarski,, and S. T. Williams (ed.), The Biology of Actinomycetes. Academic Press, London, United Kingdom.
65. Goodfellow, M.,, and J. G. Magee,. 1998. Taxonomy of myxobacteria, p. 1 71. In P. R. J. Gangadharan, and P. A. Jenkins (ed.), Myxobacteria I Basic Aspects. Chapman & Hall, London, United Kingdom.
66. Goodfellow, M.,, and D. E. Minnikin (éd.). 1985. Chemical Methods in Bacterial Systematics. Academic Press, London, United Kingdom.
67. Goodfellow, M.,, and A. G. O'Donnell,. 1993. Roots of bacterial systematics, p. 3 54. In M. Goodfellow, and A. G. O'Donnell (ed.), Handbook of New Bacterial Systematics. Academic Press, London, United Kingdom.
68. Goodfellow M.,, and A. G. O'Donnell (éd.). 1994. Chemical Methods in Prokaryotic Systematics. Wiley & Sons, Chichester, United Kingdom.
69. Goodfellow, M.,, J. Chun,, E. Atalan,, and J. J. Sanglier,. 1994. Curie point pyrolysis mass spectrometry and its application to bacterial systematics, p. 87 104. In F. G. Priest,, A. Ramos-Cormenzana,, and B. J. Tindall (ed.), Bacterial Diversity and Systematics. Plenum Press, New York, N.Y.
70. Goodfellow, M.,, G. P. Manfio,, and J. Chun,. 1997. Towards a practical species concept for cultivable bacteria, p. 25 60. In M. F. Claridge,, H. A. Dawah,, and M. R. Wilson (ed.), Species: the Units of Biodiversity. Chapman & Hall, London, United Kingdom.
71. Goodfellow, M.,, G. Alderson,, and J. Chun. 1998. Rhodococcal systematics: problems and developments. Antonie Leeuwenhoek 74: 3 20.
72. Goodfellow, M.,, K. Isik,, and E. Yates. 1999. Actinomycetes systematics: an unfinished synthesis. Nova Ada Leopold. 312: 47 82.
73. Gordon, R. E., 1968. The taxonomy of soil bacteria, p. 293 321. In T. R. G. Gray, and D. Parkinson (ed.), The Ecology of Soil Bacteria. Liverpool University Press, Liverpool, United Kingdom.
74. Gordon, R. E. 1978. A species definition. Int. J. Syst. Bacteriol. 28: 605 607.
75. Green, R.,, and H. F. Noller. 1997. Ribosomes and translation. Annu. Rev. Biochem. 66: 679 716.
76. Gribaldo, S.,, and H. Philippe. 2002. Ancient phylogenetic relationships. Theor. Pop. Biol. 61: 391 408.
77. Grimont, P. A. D. 1988. Use of DNA re-association in bacterial classification. Can. J. Microbiol. 34: 541 546.
78. Guezennec, J.,, and A. Fiala-Medioni. 1996. Bacterial abundance and diversity in the Barbados Trench determined by phospho-lipids analysis. FEMS Microbiol. Ecol. 19: 83 93.
79. Hansmann, S.,, and W. Martin. 2000. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50: 1655 1663.
80. Harvey, A. 2000. Strategies for discovering drugs from previously unexplored natural products. Drug Discovery Today 5: 294 300.
81. Helm, D.,, H. Labischinski,, G. Schallehn,, and D. Naumann. 1991. Classification and identification of bacteria by Fourier-transform infrared spectroscopy. J. Gen. Microbiol. 137: 69 79.
82. Henikoff, S.,, E. A. Greene,, S. Pietrokovski,, P. Bork,, T. K. Attwood,, and L. Hood. 1997. Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609 614.
83. Hennecke, H.,, K. Kaluza,, B. Thöny,, M. Fuhrmann,, W. Ludwig,, and E. Stackebrandt. 1985. Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen-fixing bacteria. Arch. Mikrobiol. 142: 342 348.
84. Hill, D. C.,, S. K. Wrigley,, and L. J. Nisbet. 1998. Novel screen methodologies for identification of new microbial metabolites with pharmacological activity. Adv. Biochem. Eng. Biotechnol. 59: 75 121.
85. Hille, R. 1996. The mononuclear molybdenum enzymes. Chem. Rev. 96: 2757 2816.
86. Hopwood, D. A. 1997. Genetic contributions to understanding polyketide synthases. Chem. Rev. 97: 2465 2498.
87. Huang, J.,, C. J. Lih,, K. H. Pan,, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev. 15: 3183 3192.
88. Huddleston, A. S.,, N. Cresswell,, M. C. Neves,, J. E. Beringer,, S. Baumberg,, D. I. Thomas,, and E. M. H. Wellington. 1997. Molecular detection of streptomycin-producing streptomycetes in Brazilian soils. Appl. Environ. Microbiol. 63: 1288 1297.
89. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366 376.
90. Hurek, T.,, T. Egener, and B. Reinhold-Hurek. 1997. Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β subclass. J. Bacteriol. 179: 4172 4178.
91. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860921.
92. Ivanova, V.,, M. Oriol,, M. J. Montes,, A. Garcia, and J. Guinea. 2001. Secondary metabolites from a Streptomyces strain isolated from Livingston Island, Antartica. Z. Naturforsch 56: 1 5.
93. Jain, R.,, M. C. Rivera,, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96: 3801 3806.
94. Jensen, H. L. 1931. Contribution to our knowledge of the Actinomycetales II. The definition and subdivision of the genus Actinomyces with a preliminary account of Australian soil actinomycetes. Proc. Linnean Soc. NSW 51: 364 376.
95. Johns, R. B.,, and G. J. Perry. 1977. Lipids of the marine bacterium Flexibacter polymorphus. Arch. Microbiol. 114: 267 271.
96. Kanazawa, A.,, S. I. Teshima,, and O. Kazuo. 1979. Relationship between essential fatty acid requirements of aquatic animals and the capacity for bioconversion of linolenic acid to highly unsaturated fatty acids. Comp. Biochem. Physiol. 63B: 295 298.
97. Kandler, O., 1985. Evolution of systematics of bacteria, p. 335 361. In K. H. Schleifer, and E. Stackebrandt (ed.), Evolution of Prokaryotes. Academic Press, London, United Kingdom.
98. Karlin, S.,, L. Brocchieri,, J. Trent,, B. E. Blaisdell,, and J. Mrázek. 2002. Heterogeneity of genome and proteome content in Bacteria, Archaea, and Eukaryotes. Theor. Pop. Biol. 61: 367 390.
99. Katz, L. A. 2002. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int. J. Syst. Evol. Microbiol. 52: 1893 1900.
100. Keddie, R. M.,, and I. J. Bousfield,. 1980. Cell wall composition in the classification and identification of coryneform bacteria, p. 167 188. In M. Goodfellow, and R. G. Board (ed.), Microbial Classification and Identification. Williams &c Wilkins, Baltimore, Md.
101. Keddie, R. M.,, and G. I. Cure,. 1978. Cell wall composition of coryneform bacteria, p. 47 83. In I. J. Bousfield, and A. G. Cal-lely (ed.), Coryneform Bacteria. Academic Press, London, United Kingdom.
102. Khodobakshian, M. 2002. Biodiversity and natural product synthesis in members of the Streptomyces violaceusniger. M.Sc. thesis. University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom.
103. Kim, E. S.,, H. J. Hong,, C. Y. Choi,, and S. N. Cohen. 2001. Modulation of actinorhodin biosynthesis in Streptomyces lividans by glucose repression afsR2 gene transcription. J. Bacteriol. 183: 2198 2203.
104. Klein, M.,, M. Friedrich,, A. J. Roger,, P. Hugenholtz,, S. Fishbain,, H. Abicht,, L. L. Blackall,, D. A. Stahl,, and M. Wagner. 2001. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol. 183: 6028 6035.
105. Klotz, M. G.,, and J. M. Norton. 1998. Multiple copies of ammonia mono-oxygenase (amo) opérons have evolved under biased AT/GC mutational pressure in ammonia-oxidising autotrophic bacteria. FEMS Microbiol. Lett. 168: 303 311.
106. Koch, R. 1877. Die Ätiologie der Milzbrandkrankheit, begriidet auf die Entwicklungsgeschiichte des Bacillus anthracts. Beitr. Biol. Pflanz. 2: 277 310.
107. Krieg, N. R.,, and J. G. Holt (éd.). 1984. Bergey's Manual of Systematic Bacteriology, vol. I. Williams & Wilkins, Baltimore, Md.
108. Krsek, M.,, and E. M. H. Wellington. 1999. Comparison of different methods for the isolation and purification of total community DNA from soil. J. Microbiol. Methods 39: 1 16.
109. Kunst, F.,, N. Ogasawara,, I. Moszer,, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessières,, A. Bolotin, et al. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 249 256.
110. Labeda, D. P.,, and A. J. Lyons. 1991. The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: emendation of the description of Streptomyces violaceusniger and Streptomyces hygroscopicus. Int. J. Syst. Bacteriol. 41: 398 401.
111. Lan, R.,, and P. R. Reeves. 2000. Intraspecies variation in bacterial genomes: the need for a species concept. Trends Microbiol. 8: 396 401.
112. Lan, R.,, and P. R. Reeves. 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9: 419 424.
113. Lange, B. M.,, T. Rujan,, W. Martin,, and R. Croteau. 2000. Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc. Natl. Acad. Sci. USA 97: 13172 13177.
114. Larsen, O.,, T. Lien,, and N. K. Birkeland. 1999. Dissimilatory sulfite reductase from Archaeoglobus profundus and Desulfotomaculum thermoeisternum: phylogenetic and structural implications from gene sequences. Extremophiles 3: 63 70.
115. Lawrence, J. G. 1999. Selfish opérons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9: 642 648.
116. Lawrence, J. G. 2002. Gene transfer in bacteria: speciation without species? Theor. Pop. Biol. 61: 449 460.
117. Lawrence, J. G.,, and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44: 383 397.
118. Lawrence, J. G.,, and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 9413 9417.
119. Lawrence, J. G.,, and J. R. Roth,. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263 289. In R. L. Charlebois (ed.), Organization of the Prokaryotic Genome. ASM Press, Washington, D.C.
120. Lazzarini, A.,, G. Cavaletti,, G. Toppo,, and F. Marinelli. 2001. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie Leeuwenhoek 79: 399 405.
121. Lechevalier, M. P., 1976. The taxonomy of the genus Nocardia: some light at the end of the tunnel? p. 1 38. In M. Goodfellow,, G. H. Brownell,, and J. A. Serrano (ed.), The Biology of the Nocardiae. Academic Press, London, United Kingdom.
122. Lechevalier, M. P.,, and H. A. Lechevalier. 1970. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 20: 435 443.
123. Lechevalier, H. A.,, and M. P. Lechevalier,. 1988. Chemotaxonomic use of lipids—an overview, p. 869 902. In C. Ratledge,, and S. G. Wilkinson (ed.), Microbial Lipids. Academic Press, London, United Kingdom.
124. Lechevalier, M. P.,, C. DeBière,, and H. Lechevalier. 1977. Chemo-taxonomy of aerobic actinomycetes: phospholipid composition. Biochem. Syst. Ecol. 5: 249 260.
125. Li, S. M.,, S. Hennig,, and L. Heide. 1998. Biosynthesis of the dimethylallyl moiety of novobiocin via the non-mevalonate pathway. Tetrahedron Lett. 39: 2717 2720.
126. Ludwick, W.,, and K. H. Schleifer. 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol. Rev. 15: 155 173.
127. Ludwick, W.,, and H.-P. Klenk,. 2001. Overview: a phylogenetic backbone and taxonomie framework for prokaryotic systematics, p. 49 65. In D. R. Boone,, R. W. Castenholtz,, and G. M. Garrity (ed.), Bergey's Manual of Systematic Bacteriology, 2nd ed. Springer, New York, N.Y.
128. Maeder, D. L.,, R. B. Weiss,, D. M. Dunn,, J. L. Cherry,, J. M. Gonzalez,, J. DiRuggiero,, and F. T. Robb. 1999. Divergence of the hyperthermophilic archaea Pyrococcus furiosus and Pyrococcus horikoshi inferred from complete genome sequences. Genetics 152: 1299 1305.
129. Maidak, B. L.,, J. R. Cole,, T. G. Lilburn,, C. T. Parker,, P. R. Sax-man,, R. J. Farris,, G. M. Garrity,, G. J. Olsen,, T. M. Schmidt,, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29: 173 174.
130. Maiden, M. C. J.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Unwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman,, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 3140 3145.
131. Mazel, D.,, and J. Davies. 1999. Antibiotic resistance in microbes. Cell Mol. Life Sci. 56: 742 754.
132. McClelland, M.,, L. Florea,, K. Sanderson,, S. W. Clifton,, J. Parkhill,, C. Churcher, G. Dougan,, R. K. Wilson,, and W. Miller. 2000. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 28: 4974 4986.
133. Metsa-Ketela, M.,, L. Halo,, E. Munukka,, J. Hakala,, P. Mântsâlâ,, and K. Ylihonko. 2002. Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species. Appl. Environ. Microbiol. 68: 4472 4479.
134. Metz, J. G.,, P. Roessler,, D. Facciotti,, C. Levering,, F. Dittrich,, M. Lassner,, R. Valentine,, K. Lardizabal,, F. Domergue,, A. Yamada,, K. Yazawa,, V. Knauf,, and J. Browse. 2001. Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes. Science 293: 290 293.
135. Migula, W. 1897. System der Bakterien. Gustav Fischer Verlag, Jena, Germany.
136. Mincer, T. J.,, P. R. Jensen,, C. A. Kaufman,, and W. Fenical. 2002. Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments Appl. Environ. Microbiol. 68: 5005 5011.
137. Minnikin, D. E.,, and M. Goodfellow,. 1980. Lipid composition in the classification and identification of acid fast bacteria, p. 189 256. In M. Goodfellow, and R. G. Board (ed.), Microbiological Classification and Identification. Academic Press, London, United Kingdom.
138. Minnikin, D. E.,, and A. G. O'Donnell,. 1984. Actinomycete envelope lipid and peptidoglycan composition, p. 337 388. In M. Goodfellow,, M. Mordarski,, and S. T. Williams (ed.), The Biology of the Actinomycetes. Academic Press, London, United Kingdom.
139. Minnikin, D. E.,, M. Goodfellow,, and M. D. Collins,. 1978. Lipid composition in the classification and identification of coryne-form and related bacteria, p. 85 160. In I. J. Bousfield,, and A. G. Callely (ed.), Coryneform Bacteria. Academic Press, London, United Kingdom.
140. Molnar, I.,, J. F. Aparicio,, S. F. Haydock,, L. E. Khaw,, T. Schwecke,, A. Konig,, J. Staunton,, and P. F. Leadlay. 1996. Organisation of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: analysis of genes flanking the polyketide synthase. Gene 169: 1 7.
141. Monaghan, R. L.,, J. D. Polshook,, V. J. Pecore,, G. F. Bills,, M. Nallin-Omstead,, and S. L. Streicher. 1995. Discovery of novel secondary metabolites from fungi—is it really a random walk through a random forest? Can. J. Bot. 73: S925 S931.
142. Monciardini, P.,, M. Sosio,, L. Cavaletti,, C. Chiocchini,, and S. Donadio. 2002. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol. Ecol. 42: 419 429.
143. Moreno-Vivian, C.,, P. Cabello,, M. Martinez-Luque,, R. Blasco,, and F. Castillo. 1999. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacteriol nitrate re-ductases. J. Bacteriol. 181: 6573 6584.
144. Mougel, C.,, J. Thioulouse,, G. Perrière,, and X. Nesme. 2002. A mathematical method for determining genome divergence and species delineation using AFLP. Int. J. Syst. Evol. Microbiol. 52: 573 586.
145. Murray, R. G. E., 1962. Time structure and taxonomy of bacteria, p. 119-144. In G. C. Ainsworth,, and P. H. A. Sneath (ed.), Microbial Classification. Cambridge University Press, Cambridge, United Kingdom.
146. Mylvaganam, S.,, and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130: 399 410.
147. Nakagawa, Y.,, and K. Yamasato. 1993. Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J. Gen. Microbiol. 139: 1155 1161.
148. Napier, J. A. 2002. Plumbing the depths of PUFA biosynthesis: a novel polyketide synthase-like pathway from marine organisms. Trends Plant Sci. 7: 51 54.
149. Napier, J. A.,, L. V. Michaelson,, and A. K. Stobart. 1999a. Plant de-saturases: harvesting the fat of the land. Curr. Opin. Plant Biol. 2: 123 127.
150. Napier, J. A.,, O. Sayanova,, P. Sperling,, and E. Heinz. 1999b. A growing family of cytochrome bs-doman fusion proteins. Trends Plant Sci. 4: 2 4.
151. Nelson, K. E.,, R. A. Clayton,, S. R. Gill,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, W. C. Nelson,, K. A. Ketchum,, L. McDonald,, T. R. Utterback,, J. A. Malek,, K. D. Lin-her,, M. M. Garrett,, A. M. Stewart,, M. D. Cotton,, M. S. Pratt,, C. A. Phillips,, D. Richardson,, J. Heidelberg,, G. G. Sutton,, R. D. Fleischmann,, J. A. Eisen,, and C. M. Fraser. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323 329.
152. Nichols, D. S.,, and T. A. McMeekin. 2002. Biomarker techniques to screen for bacteria that produce polyunsaturated fatty acids. J. Microbiol. Methods 48: 161 170.
153. Nicholson, T. P.,, B. A. M. Rudd,, M. Dawson,, C. M. Lazarus,, T. J. Simpson,, and R. J. Cox. 2001. Design and utility of oligonu-cleotide gene probes for fungal polyketide synthases. Chem. Biol. 8: 157 178.
154. Ninet, B.,, M. Monod,, S. Emler,, J. Pawlowski,, C. Metral,, P. Rohner,, R. Auckenthaler,, and B. Herschel. 1996. Two different 16S rRNA genes in a mycobacterial strain. J. Clin. Microbiol. 34: 2531 2536.
155. Normand, P.,, and J. Bousquet. 1989. Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing organisms. J. Mol. Biol. 29: 1599 1602.
156. Norton, J. M.,, J. J. Alzerreca,, Y. Suwa,, and M. G. Klotz. 2002. Diversity of ammonia mono-oxygenase operon in autotrophic ammonia-oxidising bacteria. Arch. Microbiol. 177: 139 149.
157. Oberreuter, H.,, H. Seiler,, and S. Scherer. 2002. Identification of coryneform bacteria and related taxa by Fourier-transform infrared (FT-IR) spectroscopy. Int. J. Syst. Evol. Microbiol. 52: 91 100.
158. Omura, S.,, H. Ikeda,, J. Ishikawa,, A. Hanamotto,, C. Takahashi,, M. Shinosa,, Y. Takahashi,, H. Horikawa,, H. Nakazawa,, T. Os-onoe,, H. Kikuchi,, T. Shiba,, Y. Sakaki,, and M. Hattori. 2001. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. USA 98: 12215 12220.
159. Orihara, N.,, T. Kuzuyama,, S. Takahashi,, K. Furihata,, and H. Seto. 1998. Studies on the biosynthesis of terpenoid compounds produced by actinomycetes. 3. Biosynthesis of the isoprenoid side chain of novobiocin via the non-mevalonate pathway in Streptomyces niveus. J. Antibiot. (Tokyo) 51: 676 678.
160. Pennisi, E. 1998. Genome data shake the tree of life. Science 280: 672 674.
161. Petri, R.,, and J. F. Imhoff. 2000. The relationship of nitrate reducing bacteria on the basis of narH gene sequences and comparison of narH and 16S rDNA based phylogeny. Syst. Appl. Microbiol. 23: 47 57.
162. Ponting, C. P. 2001. Plagiarized bacterial genes in the human book of life. Trends Genet. 17: 235 237.
163. Postgate, J. R. 1982. The Fundamentals of Nitrogen Fixation. Cambridge University Press, Cambridge, United Kingdom.
164. Priest, F. G.,, and M. Goodfellow (ed.) 2000. Applied Microbial Systematics. Kluwer Academic Publishers, Dordrecht, The Netherlands.
165. Ravel, J.,, M. J. Amoroso,, R. R. Colwell,, and R. T. Hill. 1998. Mercury-resistant actinomycetes from Chesapeake Bay. FEMS Microbiol. Lett. 162: 177 184.
166. Read, T. D.,, R. C. Brunham,, C. Shen,, S. R. Gill,, J. F. Heidelberg,, O. White,, E. K. Hickey,, J. Peterson,, T. Utterback,, K. Berry,, S. Bass,, K. Linher,, J. Weidman,, H. Khouri,, B. Craven,, C. Bowman,, R. Dodson,, M. Gwinn,, W. Nelson,, R. DeBoy,, J. Kolonay,, G. McClarty,, S. L. Salzberg,, J. Eisen,, and C. M. Fraser. 2000. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28: 1397 1406.
167. Reeves, P. R. 1995. Role of O-antigen variation in the immune response. Trends Microbiol. 3: 381 386.
168. Reichenbach, H. 2001. Myxobacteria, producers of novel bioac-tive substances. J. Ind. Microbiol. Biotech. 27: 149 156.
169. Robson, R. L.,, P. R. Woodey,, R. N. Pau,, and R. R. Eady. 1989. Structural genes for the vanadium nitrogenase from Azotobacter chroococcum. EMBO J. 8: 1217 1224.
170. Rondon, M. R.,, P. R. August,, A. D. Betterman,, S. F. Brady,, T. H. Grossman,, M. R. Liles,, K. A. Loiacono,, B. A. Lynch,, I. A. McNeil,, C. Minor,, C. L. Tiong,, M. Gilman,, M. S. Osburne,, J. Clardy,, J. Handelsman,, and R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541 2547.
171. Rosselló-Mora, R.,, and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol Rev. 25: 39 67.
172. Roszak, D. B., and R. R. Colwell. 1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51: 365 379.
173. Rotthauwe, J.-H.,, K.-P. Witzel,, and W. Liesack. 1997. The ammonia mono-oxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidising populations. Appl. Environ. Microbiol. 63: 4704 4712.
174. Sait, M.,, P. Hugenholtz,, and P. H. Janssen. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4: 654 666.
175. Salanoubat, M.,, S. Genin,, F. Artiguenave,, J. Gouzy,, S. Mangenot,, M. Ariat,, A. Billault,, P. Brottler,, J. C. Camus,, L. Cattolico,, M. Chandler,, N. Choisne,, C. Claudel-Renard,, S. Cunnae,, N. De-mange,, C. Gaspin,, M. Lavie,, A. Molsan,, C. Robert,, W. Saurin,, T. Schlex,, P. Siguier,, P. Thébault,, M. Whalen,, P. Wincker,, M. Levy,, J. Weissenbach,, and C. A. Boucher. 2002. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415: 497 502.
176. Salzberg, S. L.,, O. White,, J. Peterson,, and J. A. Eisen. 2001. Microbial genes in the human genome: lateral transfer or gene loss. Science 292:1903-1906.
177. Schleifer, K. H. 1998. Phylogeny of prokaryotes beyond 16S rRNA sequencing, p. 30. In Abstracts of the 98th General Meeting. American Society for Microbiology, Washington, D.C.
178. Schleifer, K. H.,, and O. Kandler. 1972. Peptidoglycan types of bacterial cell walls and their taxonomie implications. Bacteriol. Rev. 36: 407 477.
179. Sembiring, L. 2000. The selective isolation and characterization of the Streptomyces violaceusniger clade associated with the roots of paraserianthes falcataria (L) Nielson. Ph.D. thesis. University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom.
180. Sembiring, L.,, M. Goodfellow,, and A. C. Ward. 2000. The selective isolation and characterization of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria. Antonie Leeuwenhoek 78: 353 366.
181. Sembiring, L.,, M. Goodfellow,, and A. C. Ward. The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Int. J. Syst. Evol. Microbiol, in press.
182. Seto, H.,, H. Watanabe,, and K. Funihata. 1996. Simultaneous operation of the mevalonate and non-mevalonate pathways in the biosynthesis of isopentenyl diphosphate in Streptomyces aerouvifer. Tetrahedron Lett. 37: 7979 7982.
183. Sneath, P. H. A., 1988. The phenetic and cladistic approaches, p. 252 273. In D. L. Hawksworth (ed.), Propsects in Systematics. Clarendon Press, Oxford, United Kingdom.
184. Sneath, P. H. A. 1992. International Code of Nomenclature of Bacteria. American Society for Microbiology, Washington, D.C.
185. Sneath, P. H. A.,, and R. R. Sokal. 1973. Numerical Taxonomy. W. H. Freeman & Company, San Francisco, Calif.
186. Society for Actinomycetes Japan. 2000. Identification Manual for Actinomycetes. Japan Basineis Center for Academic Societies, Tokyo, Japan.
187. Sosio, M.,, E. Bossi,, A. Bianchi,, and S. Donadio. 2000. Multiple peptide synthetase gene clusters in Actinomycetes. Mol. Gen. Genet. 264: 213 221.
188. Sosio, M.,, E. Bossi,, and S. Donadio. 2001. Assembly of large ge-nomic segments in artificial chromosomes by homologous recombination in Escherichia coli. Nucleic Acids Res. 29: 1 8.
189. Stackebrandt, E.,, and B. M. Goebel. 1994. Taxonomie note: a place for DNAiDNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846 849.
190. Stackebrandt, E.,, and M. Goodfellow. 1991. Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons, Chichester, United Kingdom.
191. Stackebrandt, E.,, and J. Swiderski,. 2002. From phylogeny to systematics: the dissection of the genus Bacillus, p. 8 22. In R. Berkeley,, M. Heyndrickx,, N. Logan,, and P. de Vos (ed.), Applications and Systematics of Bacillus and Relatives. Blackwell, London, United Kingdom.
192. Stackebrandt, E.,, W. Frederiksen,, G. M. Garrity,, P. A. D. Grimont,, P. Kampfer,, M. C. J. Maiden,, X. Nesme,, R. Rosselló-Mora,, J. Swings,, H. G. Triiper,, L. Vauterin,, A. C. Ward,, and W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043 1047.
193. Stahl, D. A.,, D. J. Lane,, G. T. Olsen,, and N. R. Pace. 1985. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Appl. Environ. Microbiol. 45: 1379 1384.
194. Staley, J. T.,, and J. J. Gosink. 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53: 189 215.
195. Stanier, R. Y.,, and C. B. van Niel. 1962. The concept of a bacterium. Arch. Mikrobiol. 42: 17 35.
196. Stoiz, J. F.,, and P. Basu. 2002. Evolution of nitrate reductase: molecular and structural variations on a common function. ChemBioChem 3: 198 206.
197. Stover, C. K.,, X. Q. Pham,, A. L. Erwin,, S. D. Mizoguchi,, P. War-rener,, M. J. Hickey,, F. S. L. Brinkman,, W. O. Hufnagle,, D. J. Kowalik,, M. Lagrou,, R. L. Garber,, L. Goltry,, E. Tolentino,, S. Westbrock-Wadman,, Y. Yuan,, L. L. Brody,, S. N. Coulter,, K. R. Folger,, A. Kas,, K. Larbig,, R. Lim,, K. Smith,, D. Spencer,, G. K.-S. Wong,, Z. Wu,, I. T. Paulsen,, J. Reizer,, M. H. Saier,, R. E. W. Hancock,, S. Lory,, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PAOl, an opportunistic pathogen. Nature 406: 959 964.
198. Strohl, W. R.,, M. L. Dickens,, V. B. Rajgarhia,, A. J. Woo,, and N. D. Priestley,. 1997. Anthracyclines, p. 577 657. In W. R. Strohl (ed.), Biotechnology of Antibiotics, 2nd ed. Marcel Dekker Publishers, New York, N.Y.
199. Suzuki, K.,, M. Goodfellow,, and A. G. O'Donnell,. 1983. Cell envelopes and classification, p. 195 250. In M. Goodfellow, and A. G. O'Donnell (ed.), Handbook of New Bacterial Systematics. Academic Press, London, United Kingdom.
200. Takami, H.,, K. Nakasone,, Y. Takaki,, G. Maeno,, R. Sasaki,, N. Masui,, F. Fuji,, C. Hirama,, Y. Nakamura,, N. Ogasawara,, S. Kuhara,, and K. Horikoshi. 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparisons with Bacillus subtilis. Nucleic Acids Res. 28: 4317 4331.
201. Teske, A.,, E. Aim,, J. M. Regan,, S. Toze,, B. E. Ritmann,, and D. A. Stahl. 1994. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176: 6623 6630.
202. Thampapillai, G.,, R. T. Lan,, and P. R. Reeves. 1994. Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11: 813 828.
203. Tischner, R. 2000. Nitrate uptake and reduction in higher and lower plants. Plant Cell Environ. 23: 1005 1024.
204. Tolba, S.,, S. Egan,, D. Kallifidas,, and E. M. H. Wellington. 2002. Distribution of streptomycin resistance and biosynthesis genes in streptomycetes recovered from different soil sites. FEMS Microbiol. Ecol. 42: 269 276.
205. Trejo-Estrada, S. R.,, A. Paszczynski,, and D. L. Crawford. 1998. Antibiotics and enzymes produced by the biocontrol agent Streptomyces violaceusniger YCED-9. J. Ind. Microbiol. Biotech. 21: 81 90.
206. Tsoi, C. J.,, and C. Khosla. 1995. Combinatorial biosynthesis of unnatural natural products—the polyketide example. Chem. Biol. 2: 355 362.
207. Uchida, K.,, and K. Aida. 1979. Taxonomie significance of cell wall acyl type in Corynebacterium-Mycobacterium-Nocardia group by glycolate test. J. Gen. Appl. Microbiol. 25: 169 183.
208. Ueda, K.,, T. Seki,, T. Kudo,, T. Yoshida,, and M. Kataoka. 1999. Two distinct mechanisms cause heterogeneity of 16S rRNA. J. Bacteriol. 181: 78 82.
209. Vaidyanathan, S.,, J. J. Rowland,, D. B. Kell,, and R. Goodacre. 2001. Discrimination of aerobic endospore-forming bacteria via electrospray mass spectrometry of whole cell suspensions. Anal. Chem. 73: 4134 4144.
210. 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: 407 443.
211. van Wezel, G. P.,, E. Vijgenboom,, and L. Bosch. 1991. A comparative study of the ribosomal RNA opérons of Streptomyces coelicolor A3(2) and sequence analysis of rrnA. Nucleic Acids Res. 19: 4399 4403.
212. Vezina, C.,, A. Kudelski,, and S. Sehgal. 1975. Rapamycin (AY-22,989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle. J. Antibiot. 28: 721 726.
213. Vincent Lévy-Frébault, V.,, and F. Portaels. 1992. Proposed minimal standards for the genus Mycobacterium and for the description of new slowly growing Mycobacterium species. Int. J. Syst. Bacteriol. 42: 315 323.
214. Wagner, M.,, A. J. Roger,, J. L. Flax,, G. A. Brusseau,, and D. A. Stahl. 1998. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J. Bacteriol. 180: 2975 2982.
215. Waksman, S. A. 1961. The Actinomycetes, vol. II: Classification, Identification and Descriptions of Genera and Species. Bailliére, Tindall and Cox Ltd., London, United Kingdom.
216. Waksman, S. A.,, and R. E. Curtis. 1916. The Actinomyces of the soil. Soil Sci. 1: 99 134.
217. Walsh, C. T. 2002. Combinatorial biosynthesis of antibiotics: challenges and opportunities. ChemBioChem 3: 124 134.
218. Wang, Y.,, and Z. Zhang. 2000. Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology (UK) 146: 2845 2854.
219. Wang, Y.,, Z. S. Zhang,, and N. Ramanan. 1997. The actinomycete Thermobispora bispora contains two distinct types of transcrip-tionally active 16S rRNA genes. J. Bacteriol. 179: 3270 3276.
220. Ward, A. C.,, E. Rashidian,, L. Sembiring,, E. Lacey,, S. W. Robinson,, J. H. Gill,, J. H. Tennont,, B. A. Boyleson,, and M. Goodfellow. 2001. Mapping metabolites to streptomycete taxonomy. In 12th International Symposium Biological Actinomycetes, Vancouver, Canada.
221. Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1: 271 277.
222. Watanabe, K.,, K. Yazawa,, K. Kondo,, and A. Kawaguchi. 1997. Fatty acid synthesis of an eicosapentaenoic acid-producing bacterium: de novo synthesis, chain elongation and desaturation systems. J. Biochem. 122: 467 473.
223. Watve, M. G.,, R. Tickoo,, M. M. Jog,, and B. D. Bhole. 2001. How many antibiotics are produced by the genus Streptomyces? Arch. Microbiol. 176: 386 390.
224. Wayne L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. L. 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.
225. Williams, S. T.,, M. E. Sharpe,, and J. G. Holt (ed.) 1989. Bergey's Manual of Systematic Bacteriology, vol. 4. Williams & Wilkins, Baltimore, Md.
226. Whitman, W. B.,, D. C. Coleman,, and W. T. Wiese. 1998. Prokary-otes: the unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578 6583.
227. Wolf, Y. I.,, I. B. Rogozin,, N. V. Grishin,, R. L. Tatusov,, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1: 8.
228. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221 271.
229. Woese, C. R., 2002. Perspective: microbiology in transition, p. xvi- xxxii. In J. T. Staley, and A.-L. Reysenbach (ed.), Biodiversity of Microbial Life: Foundation of Earth's Biosphere. John Wiley & Sons, Inc., New York, N. Y.
230. Yap, W. H.,, Z. S. Zhang,, and Y. Wang. 1999. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181: 5201 5209.
231. Yates, M. G., 1992. The enzymology of molybdenum-dependent nitrogen fixation, p. 685 735. In R. H. Burris, and H. J. Evans (ed.), Biological Nitrogen Fixation. Chapman & Hall, New York, N. Y.
232. Yazawa, K. 1996. Production of eicosapentaenoic acid from marine bacteria. Lipids 31: S297 S300.
233. Yoon, J.-H.,, Y. G. Cho,, S. S. Kang,, S. B. Kim,, S. T. Lee,, and Y. H. Park. 2000. Rhodococcus koreensis sp. nov., a 2,4-dinitrophenol-degrading bacterium. Int. J. Syst. Evol. Microbiol. 50: 1193 1201.
234. Young, J. P. W., 1992. Phylogenetic classification of nitrogen-fixing organisms, p. 43 86. In G. Stacey,, R. H. Burris,, and H. J. Evans (ed.), Biological Nitrogen Fixation. Chapman & Hall, New York, N. Y.
235. Zahn, J. A.,, R. E. Higgs,, and M. D. Hilton. 2001. Use of direct-infusion electro-spray mass spectrometry to guide empirical development of improved conditions for expression of secondary metabolites from actinomycetes. Appl. Environ. Microbiol. 67: 377 386.
236. Zuckerlandl, E.,, and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357 366.

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