Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae

International Journal of Systematic and Evolutionary Microbiology

Volumn 55, Issue 5, 2005, Pages 1759-1766

  Maldonado, Luis A ^a,c   Fenical, William ^b   Jensen, Paul R ^b   Kauffman, Christopher A ^b   Mincer, Tracy J ^b,d   Ward, Alan C ^a   Bull, Alan T ^a   Goodfellow, Michael ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^d Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; DNA 23S; DOUBLE STRANDED DNA; RNA 16S; SPACER DNA;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIOPLANKTON; BACTERIUM CULTURE; DNA BASE COMPOSITION; GENE ASSIGNMENT; GENOTYPE PHENOTYPE CORRELATION; MICROMONOSPORACEAE; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SALINISPORA ARENICOLA; SALINISPORA TROPICA; SPECIES DIFFERENTIATION; SPECIES IDENTIFICATION; TAXONOMY;

DNA, BACTERIAL; DNA, RIBOSOMAL SPACER; GENES, RRNA; MICROMONOSPORACEAE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHENOTYPE; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEAWATER;

ACTINOBACTERIA (CLASS); ARENICOLA; MICROMONOSPORACEAE; SALINOSPORA;

EID: 20444459450     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63625-0     Document Type: Article

References (73)

1. Asano, K. & Kawamoto, I. (1986). Catellatospora, a new genus of the Actinomycetales. Int J Syst Bacteriol 36, 512-517.
2. Asano, K. & Kawamoto, I. (1988). Catellatospora citrea subsp. methionotrophica subsp. nov., a methionine-deficient auxotroph of the Actinomycetales. Int J Syst Bacteriol 38, 326-327.
3. Asano, K., Masunaga, I. & Kawamoto, I. (1989). Catellatospora matsumotoense sp. nov. and C. tsunoense sp. nov., actinomycetes found in woodland soils. Int J Syst Bacteriol 39, 309-313.
4. Buchanan, R. E. (1917). Studies in the nomenclature and classification of the bacteria. II. The primary subdivisions of the schizomycetes. J Bacteriol 2, 155-164.
5. Bull, A. T., Ward, A. C. & Goodfellow, M. (2000). Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Mol Biol Rev 64, 573-606.
6. Collins, M. D. (1994). Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics, pp. 265-309. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
7. Colquhoun, J. A., Mexson, J., Goodfellow, M., Ward, A. C., Horikoshi, K. & Bull, A. T. (1998). Novel rhodococci and other mycolate actinomycetes from the deep sea. Antonie van Leeuwenhoek 74, 27-40.
8. Feling, R. H., Buchanan, G. O., Mincer, T. J., Kaufman, C. A., Jensen, P. R. & Fenical, W. (2003). Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. Angew Chem Int Ed Engl 42, 355-357.
9. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376.
10. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
11. Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.
12. Fiedler, H.-P., Bruntner, C., Bull, A. T., Ward, A. C., Goodfellow, M. & Mihm, G. (2005). Marine actinomycetes as a source of novel secondary metabolites. Antonie van Leeuwenhoek 87, 37-42.
13. Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees. Science 155, 279-284.
14. García-Martínez, J., Bescos, I., Rodríguez-Sala, J. J. & Valera, F. R. (2001). RISSC: a novel database for ribosomal 16S-23S RNA gene spacer regions. Nucleic Acids Res 29, 178-180.
15. Goodfellow, M. (1989). The actinomycetes. I. Suprageneric classification of actinomycetes. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2333-2339. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
16. Goodfellow, M. & Haynes, J. A. (1984). Actinomycetes in marine sediments. In Biological, Biochemical and Biomedical Aspects of Actinomycetes, pp. 453-472. Edited by L. Ortiz-Ortiz, L. F. Bojalil & V. Yakoleff. Orlando: Academic Press.
17. Goodfellow, M., Stanton, L. J., Simpson, K. E. & Minnikin, D. E. (1990). Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 136, 19-36.
18. Gordon, R. E. (1967). The taxonomy of soil bacteria. In The Ecology of Soil Bacteria, pp. 293-321. Edited by T. R. G. Gray & D. Parkinson. Liverpool: Liverpool University Press.
19. Groth, I., Rodríguez, C., Schütze, B., Schmitz, P., Leistner, E. & Goodfellow, M. (2004). Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov., and K. terrestris sp. nov. Int J Syst Evol Microbiol 54, 2121-2129.
20. Gürtler, V. & Stanisich, V. A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
21. Han, S. K., Nedashkovszkaya, O. I., Mikhailov, V. V., Kim, S. B. & Bae, K. S. (2003). Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53, 2061-2066.
22. Helmke, E. & Weyland, H. (1984). Rhodococcus marinonascens sp. nov., an actinomycete from the sea. Int J Syst Bacteriol 34, 127-138.
23. Jensen, P. R., Dwight, R. & Fenical, W. (1991). Distribution of actinomycetes in near-shore tropical marine sediments. Appl Environ Microbiol 57, 1102-1108.
24. Jones, K. L. (1949). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57, 141-145.
25. Jones, A. L., Brown, J. M., Mishra, V., Perry, J. D., Steigerwalt, A. G. & Goodfellow, M. (2004). Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil. Int J Syst Evol Microbiol 54, 407-411.
26. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
27. Kim, S. B., Falconer, C., Williams, E. & Goodfellow, M. (1998). Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol 48, 59-68.
28. Kim, S. B., Brown, R., Oldfield, C., Gilbert, S. C. & Goodfellow, M. (1999). Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. Int J Syst Bacteriol 49, 1845-1851.
29. Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1-32.
30. Koch, C., Kroppenstedt, R. M., Rainey, F. A. & Stackebrandt, E. (1996). 16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae. Int J Syst Bacteriol 46, 765-768.
31. Komagata, K. & Suzuki, K. (1987). Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19, 161-207.
32. Krasil'nikov, N. A. (1938). Ray Fungi and Related Organisms - Actinomycetales. Moscow: Akademii Nauk SSSR (in Russian).
33. Kroppenstedt, R. M. (1985). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics, pp. 173-199. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
34. Kudo, T., Nakajima, Y. & Suzuki, K. (1999). Catenuloplanes crispus (Petrolini et al. 1993) comb. nov.: incorporation of the genus Planopolyspora Petrolini 1993 into the genus Catenuloplanes Yokota et al. 1993 with an emended description of the genus Catenuloplanes. Int J Syst Bacteriol 49, 1853-1860.
35. Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115-175. Edited by E. Stackebrandt & M. Goodfellow. New York: Wiley.
36. Lechevalier, M. P. & Lechevalier, H. (1970). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20, 435-443.
37. Lechevalier, M. P., de Bièvre, C. & Lechevalier, H. A. (1977). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249-260.
38. Lee, S. D. & Hah, Y. C. (2002). Proposal to transfer Catellatospora ferruginea and 'Catellatospora ishikariense' to Asanoa gen. nov. as Asanoa ferruginea comb. nov. and Asanoa ishikariensis sp. nov., with emended description of the genus Catellatospora. Int J Syst Evol Microbiol 52, 967-972.
39. Lee, S. D., Kang, S.-O. & Hah, Y. C. (2000). Catellatospora koreensis sp. nov., a novel actinomycete isolated from a gold-mine cave. Int J Syst Evol Microbiol 50, 1103-1111.
40. Maldonado, L. A., Stach, J. E. M., Pathom-aree, W., Ward, A. C., Bull, A. T. & Goodfellow, M. (2005). Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87, 11-18.
41. Matsumoto, A., Takahashi, Y., Shinose, M., Seino, A., Iwai, Y. & Ömura, S. (2003). Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae. Int J Syst Evol Microbiol 53, 1553-1559.
42. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
43. Mincer, T. J., Jensen, P. R., Kauffman, C. A. & Fenical, W. (2002). Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 68, 5005-5011.
44. Moran, M. A., Rutherford, L. T. & Hodson, R. E. (1995). Evidence for indigenous Streptomyces populations in a marine environment determined with a 16S rRNA probe. Appl Environ Microbiol 61, 3695-3700.
45. Nam, S.-W., Chun, J., Kim, S., Kim, W., Zakrzewska-Czerwinska, J. & Goodfellow, M. (2003). Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants. Syst Appl Microbiol 26, 367-375.
46. Nesterenko, O. A., Nogina, T. M., Kasumova, S. A., Kvasnikov, E. I. & Batrakov, S. G. (1982). Rhodococcus luteus nom. nov. and Rhodococcus maris nom. nov. Int J Syst Bacteriol 32, 1-14.
47. Pitcher, D. G., Saunders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151-156.
48. Piza, F. F., Prado, P. I. & Manfio, G. P. (2004). Investigation of bacterial diversity in Brazilian tropical estuarine sediments reveals high actinobacterial diversity. Antonie van Leeuwenhoek 86, 317-328.
49. Pridham, T. G. & Gottlieb, D. (1948). The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 56, 107-114.
50. Rainey, F. A., Klatte, S., Kroppenstedt, R. M. & Stackebrandt, E. (1995). Dietzia, a new genus including Dietzia maris comb. nov., formerly Rhodococcus maris. Int J Syst Bacteriol 45, 32-36.
51. Rheims, H., Schumann, P., Rohde, M. & Stackebrandt, E. (1998). Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae. Int J Syst Bacteriol 48, 1119-1127.
52. Riedlinger, J., Reicke, A., Zähner, H. & 9 other authors (2004). Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032. J Antibiot 57, 271-279.
53. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
54. Schaal, K. P. (1985). Identification of clinically significant actinomycetes and related bacteria using chemical techniques. In Chemical Methods in Bacterial Systematics, pp. 359-381. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
55. Shirling, E. B. & Gottlieb, D. (1966). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313-340.
56. Society of American Bacteriologists (1957). Manual of Microbiological Methods. New York: McGraw-Hill.
57. Stach, J. E. M., Maldonado, L. A., Ward, A. C., Goodfellow, M. & Bull, A. T. (2003a). New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ Microbiol 5, 828-841.
58. Stach, J. E. M., Maldonado, L. A., Masson, D. G., Ward, A. C., Goodfellow, M. & Bull, A. T. (2003b). Statistical approaches to estimating actinobacterial diversity in marine sediments. Appl Environ Microbiol 69, 6189-6200.
59. Stach, J. E. M., Maldonado, L. A., Ward, A. C., Bull, A. T. & Goodfellow, M. (2004). Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan. Int J Syst Evol Microbiol 54, 191-194.
60. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. (1997). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479-491.
61. Staneck, J. L. & Roberts, G. D. (1974). Simplified approach to the identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226-231.
62. Takami, H., Kobata, K., Nagahama, T., Kobayashi, H., Inoue, A. & Horikoshi, K. (1999). Biodiversity in deep-sea sites located near the south part of Japan. Extremophiles 3, 97-102.
63. Takizawa, M., Colwell, R. R. & Hill, R. T. (1993). Isolation and diversity of actinomycetes in the Chesapeake Bay. Appl Environ Microbiol 59, 997-1002.
64. Tamaoka, J. (1994). Determination of DNA base composition. In Chemical Methods in Prokaryotic Systematics, pp. 463-470. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
65. Tamura, T., Nakagaito, Y., Nishii, T., Hasegawa, T., Stackebrandt, E. & Yokota, A. (1994). A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov. Int J Syst Bacteriol 44, 193-203.
66. Tamura, T., Yokota, A., Huang, L. H., Hasegawa, T. & Hatano, K. (1995). Five new species of the genus Catenuloplanes: Catenuloplanes niger sp. nov., Catenuloplanes indicus sp. nov., Catenuloplanes atrovinosus sp. nov., Catenuloplanes castaneus sp. nov., and Catenuloplanes nepalensis sp. nov. Int J Syst Bacteriol 45, 858-860.
67. Tamura, T., Hayakawa, M. & Hatano, K. (1997). A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov. Int J Syst Bacteriol 47, 97-102.
68. Tamura, T., Hayakawa, M. & Hatano, K. (2001). A new genus of the order Actinomycetales, Virgosporangium gen. nov., with descriptions of Virgosporangium ochraceum sp. nov. and Virgosporangium aurantiacum sp. nov. Int J Syst Evol Microbiol 51, 1809-1816.
69. Uchida, K., Kudo, T., Suzuki, K. & Nakase, T. (1999). A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45, 49-56.
70. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
71. Williams, S. T., Goodfellow, M., Alderson, G., Wellington, E. M. H., Sneath, P. H. A. & Sackin, M. J. (1983). Numerical classification of Streptomyces and related genera. J Gen Microbiol 129, 1743-1813.
72. Yokota, A., Tamura, T., Hasegawa, T. & Huang, L. H. (1993). Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 43, 805-812.
73. Zhang, Z., Kudo, T., Nakajima, Y. & Wang, Y. (2001). Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S-23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 373-383.