1887

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

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Phylogeny and Functionality: Taxonomy as a Roadmap to Genes, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap28-1.gif /docserver/preview/fulltext/10.1128/9781555817770/9781555812676_Chap28-2.gif

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

Key Concept Ranking

High-Performance Liquid Chromatography
0.4323079
Elongation Factor Tu
0.43097767
16s rRNA Sequencing
0.41552266
0.4323079
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
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
Permissions and Reprints Request Permissions
Download as Powerpoint

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. 49:961967.
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. 243:593599.
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. 77:834846.
4. Altaha, R.,, T. Fojo,, E. Reed,, and J. Abraham. 2002. Epothilones: a novel class of nontaxane microtubule-stabilizing agents. Curr. Pharm. Des. 8:17071712.
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. 49:13951402.
6. Andersson, J. O.,, W. F. Doolittle,, and C. L. Nesbs. 2001. Genomics—are there bugs in our genome? Science 292:18481850.
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. 7:207216.
8. Bansal, A. K.,, and T. E. Meyer. 2002. Evolutionary analysis by whole genome comparisons. J. Bacteriol. 184:22602272.
9. Beadle, G. W.,, and E. L. Tatum. 1941. Genetic control of biochemical reactions in Neurospora. Proc. Natl. Acad. Sci. USA 27:499506.
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. 13:236243.
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 417:141147.
12. Bérdy, J. 1995. Are actinomycetes exhausted as a source of secondary metabolites? Biotechnologia 7-8:1314.
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. 52:10491070.
14. Bishop, P. E.,, and R. Premakumar,. 1992. Alternative nitrogen fixation systems, p. 736762. 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. 55:23252333.
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. 37:703716.
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. 18:13781388.
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. 3:19811984.
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. 18:15.
23. Broun, P.,, S. Gettner,, and C. Somerville. 1999. Genetic engineering of plant lipids. Annu. Rev. Nutr. 19:197216.
24. Bull, A. T.,, A. C. Ward,, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64:573606.
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. 12:583611.
27. Castresana, J.,, and D. Moreira. 1999. Respiratory chains in the last common ancestor of living organisms. J. Mol. Evol. 49:453460.
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: 120.
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. 187:111114.
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. 185:553563.
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. 178:143148.
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. 176:65096598.
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. 14:15841586.
34. Collins, M. D., 1994. Isoprenoid quinones, p. 265309. 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 77:359367.
36. Colwell, R. R. 1970. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J. Bacteriol. 104:410433.
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. 3:103112.
39. Curtis, T. P.,, W. T. Sloan,, and J. W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99:1049410499.
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. 262:957964.
41. Davies, J. 1996. Origins and evolution of antibiotic resistance. Microbiologia 12:916.
42. Dawid, W. 2000. Biology and global distribution of myxobacteria in soils. FEMS Microbiol. Rev. 24:403427.
43. De Boer, C.,, P. A. Meulman,, R. J. Wnuk,, and D. H. Peterson. 1970. Geldanamycin, a new antibiotic. J. Antibiot. 23:442447.
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: 17691773.
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. 51:730737.
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. 333:381388.
47. Dobzhansky, T. 1967. Looking back at Mendel's discovery. Science 156:15881589.
48. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:21242129.
49. Doolittle, W. F.,, and J. M. Logsdon, Jr. 1998. Archaeal genomics: do archaea have a mixed heritage? Curr. Biol. 8:R209R211.
50. Drews, J. 2000. Drug discovery: a historical perspective. Science 287:19601964.
51. Drews, G. 2000. The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. FEMS Microbiol. Rev. 24:225249.
52. Dykhuizen, D. E.,, and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:72577268.
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 79:127133.
54. Embley, T. M.,, and E. Stackebrandt,. 1997. Species in practice: exploring uncultured prokaryotic diversity in natural samples, p. 6181. 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. 121161. 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. 53:158162.
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 98:182187.
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 98:88218826.
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. 49:489502.
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 99:44544458.
61. Gill, I.,, and R. Valivety. 1997. Polyunsaturated fatty acids. Part I. Occurrence, biological activities and applications. Trends Biotechnol. 15:401409.
62. Goldfine, H. 1972. Comparative aspects of bacterial lipids. Adv. Microbiol. Physiol. 8:158.
63. Goodfellow, M. 1985. Staphylococcal systematics: past, present and future. Zbl. Bakt. Suppl. 14:6981.
64. Goodfellow, M.,, and T. Cross,. 1983. Classifications, p. 7164. 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. 171. 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. 354. 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. 87104. 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. 2560. 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 74:320.
72. Goodfellow, M.,, K. Isik,, and E. Yates. 1999. Actinomycetes systematics: an unfinished synthesis. Nova Ada Leopold. 312: 4782.
73. Gordon, R. E., 1968. The taxonomy of soil bacteria, p. 293321. 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. 28:605607.
75. Green, R.,, and H. F. Noller. 1997. Ribosomes and translation. Annu. Rev. Biochem. 66:679716.
76. Gribaldo, S.,, and H. Philippe. 2002. Ancient phylogenetic relationships. Theor. Pop. Biol. 61:391408.
77. Grimont, P. A. D. 1988. Use of DNA re-association in bacterial classification. Can. J. Microbiol. 34:541546.
78. Guezennec, J.,, and A. Fiala-Medioni. 1996. Bacterial abundance and diversity in the Barbados Trench determined by phospho-lipids analysis. FEMS Microbiol. Ecol. 19:8393.
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. 50:16551663.
80. Harvey, A. 2000. Strategies for discovering drugs from previously unexplored natural products. Drug Discovery Today 5:294300.
81. Helm, D.,, H. Labischinski,, G. Schallehn,, and D. Naumann. 1991. Classification and identification of bacteria by Fourier-transform infrared spectroscopy. J. Gen. Microbiol. 137:6979.
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 278:609614.
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. 142:342348.
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. 59:75121.
85. Hille, R. 1996. The mononuclear molybdenum enzymes. Chem. Rev. 96:27572816.
86. Hopwood, D. A. 1997. Genetic contributions to understanding polyketide synthases. Chem. Rev. 97:24652498.
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. 15:31833192.
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. 63:12881297.
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. 180:366376.
90. Hurek, T.,, T. Egener, and B. Reinhold-Hurek. 1997. Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the β subclass. J. Bacteriol. 179:41724178.
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 56:15.
93. Jain, R.,, M. C. Rivera,, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:38013806.
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 51:364376.
95. Johns, R. B.,, and G. J. Perry. 1977. Lipids of the marine bacterium Flexibacter polymorphus. Arch. Microbiol. 114:267271.
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:295298.
97. Kandler, O., 1985. Evolution of systematics of bacteria, p. 335361. 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. 61:367390.
99. Katz, L. A. 2002. Lateral gene transfers and the evolution of eukaryotes: theories and data. Int. J. Syst. Evol. Microbiol. 52:18931900.
100. Keddie, R. M.,, and I. J. Bousfield,. 1980. Cell wall composition in the classification and identification of coryneform bacteria, p. 167188. 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. 4783. 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: 21982203.
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. 183:60286035.
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. 168:303311.
106. Koch, R. 1877. Die Ätiologie der Milzbrandkrankheit, begriidet auf die Entwicklungsgeschiichte des Bacillus anthracts. Beitr. Biol. Pflanz. 2:277310.
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 39:116.
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 390:249256.
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. 41:398401.
111. Lan, R.,, and P. R. Reeves. 2000. Intraspecies variation in bacterial genomes: the need for a species concept. Trends Microbiol. 8:396401.
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. 9:419424.
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: 1317213177.
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 3:6370.
115. Lawrence, J. G. 1999. Selfish opérons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9:642648.
116. Lawrence, J. G. 2002. Gene transfer in bacteria: speciation without species? Theor. Pop. Biol. 61:449460.
117. Lawrence, J. G.,, and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383397.
118. Lawrence, J. G.,, and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 94139417.
119. Lawrence, J. G.,, and J. R. Roth,. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263289. 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 79:399405.
121. Lechevalier, M. P., 1976. The taxonomy of the genus Nocardia: some light at the end of the tunnel? p. 138. 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. 20:435443.
123. Lechevalier, H. A.,, and M. P. Lechevalier,. 1988. Chemotaxonomic use of lipids—an overview, p. 869902. 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. 5:249260.
125. Li, S. M.,, S. Hennig,, and L. Heide. 1998. Biosynthesis of the dimethylallyl moiety of novobiocin via the non-mevalonate pathway. Tetrahedron Lett. 39:27172720.
126. Ludwick, W.,, and K. H. Schleifer. 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol. Rev. 15:155173.
127. Ludwick, W.,, and H.-P. Klenk,. 2001. Overview: a phylogenetic backbone and taxonomie framework for prokaryotic systematics, p. 4965. 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 152:12991305.
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. 29:173174.
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 95:31403145.
131. Mazel, D.,, and J. Davies. 1999. Antibiotic resistance in microbes. Cell Mol. Life Sci. 56:742754.
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. 28:49744986.
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. 68:44724479.
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 293:290293.
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. 68:50055011.
137. Minnikin, D. E.,, and M. Goodfellow,. 1980. Lipid composition in the classification and identification of acid fast bacteria, p. 189256. 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. 337388. 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. 85160. 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 169:17.
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:S925S931.
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. 42:419429.
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. 181:65736584.
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. 52:573586.
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 130:399410.
147. Nakagawa, Y.,, and K. Yamasato. 1993. Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J. Gen. Microbiol. 139:11551161.
148. Napier, J. A. 2002. Plumbing the depths of PUFA biosynthesis: a novel polyketide synthase-like pathway from marine organisms. Trends Plant Sci. 7:5154.
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. 2:123127.
150. Napier, J. A.,, O. Sayanova,, P. Sperling,, and E. Heinz. 1999b. A growing family of cytochrome bs-doman fusion proteins. Trends Plant Sci. 4:24.
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 399:323329.
152. Nichols, D. S.,, and T. A. McMeekin. 2002. Biomarker techniques to screen for bacteria that produce polyunsaturated fatty acids. J. Microbiol. Methods 48:161170.
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. 8:157178.
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. 34:25312536.
155. Normand, P.,, and J. Bousquet. 1989. Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing organisms. J. Mol. Biol. 29:15991602.
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. 177:139149.
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. 52:91100.
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 98:1221512220.
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) 51:676678.
160. Pennisi, E. 1998. Genome data shake the tree of life. Science 280:672674.
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. 23:4757.
162. Ponting, C. P. 2001. Plagiarized bacterial genes in the human book of life. Trends Genet. 17:235237.
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. 162:177184.
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. 28:13971406.
167. Reeves, P. R. 1995. Role of O-antigen variation in the immune response. Trends Microbiol. 3:381386.
168. Reichenbach, H. 2001. Myxobacteria, producers of novel bioac-tive substances. J. Ind. Microbiol. Biotech. 27:149156.
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. 8:12171224.
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. 66:25412547.
171. Rosselló-Mora, R.,, and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol Rev. 25:3967.
172. Roszak, D. B., and R. R. Colwell. 1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev. 51:365379.
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. 63:47044712.
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. 4:654666.
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 415:497502.
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. 36:407477.
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 78:353366.
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. 37:79797982.
183. Sneath, P. H. A., 1988. The phenetic and cladistic approaches, p. 252273. 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. 264:213221.
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. 29:18.
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. 44:846849.
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. 822. 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. 52:10431047.
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. 45:13791384.
194. Staley, J. T.,, and J. J. Gosink. 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53:189215.
195. Stanier, R. Y.,, and C. B. van Niel. 1962. The concept of a bacterium. Arch. Mikrobiol. 42:1735.
196. Stoiz, J. F.,, and P. Basu. 2002. Evolution of nitrate reductase: molecular and structural variations on a common function. ChemBioChem 3:198206.
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 406:959964.
198. Strohl, W. R.,, M. L. Dickens,, V. B. Rajgarhia,, A. J. Woo,, and N. D. Priestley,. 1997. Anthracyclines, p. 577657. 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. 195250. 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. 28:43174331.
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. 176:66236630.
202. Thampapillai, G.,, R. T. Lan,, and P. R. Reeves. 1994. Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11:813828.
203. Tischner, R. 2000. Nitrate uptake and reduction in higher and lower plants. Plant Cell Environ. 23:10051024.
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. 42:269276.
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. 21:8190.
206. Tsoi, C. J.,, and C. Khosla. 1995. Combinatorial biosynthesis of unnatural natural products—the polyketide example. Chem. Biol. 2:355362.
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. 25:169183.
208. Ueda, K.,, T. Seki,, T. Kudo,, T. Yoshida,, and M. Kataoka. 1999. Two distinct mechanisms cause heterogeneity of 16S rRNA. J. Bacteriol. 181:7882.
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. 73:41344144.
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. 60:407443.
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. 19:43994403.
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. 28:721726.
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. 42:315323.
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: 29752982.
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. 1:99134.
217. Walsh, C. T. 2002. Combinatorial biosynthesis of antibiotics: challenges and opportunities. ChemBioChem 3:124134.
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) 146:28452854.
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. 179:32703276.
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. 1:271277.
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. 122:467473.
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. 176:386390.
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. 37:463464.
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 95:65786583.
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. 51:221271.
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. 181:52015209.
231. Yates, M. G., 1992. The enzymology of molybdenum-dependent nitrogen fixation, p. 685735. 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:S297S300.
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. 50:11931201.
234. Young, J. P. W., 1992. Phylogenetic classification of nitrogen-fixing organisms, p. 4386. 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. 67:377386.
236. Zuckerlandl, E.,, and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357366.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error