1887

Abstract

Phylogenetic and taxonomic characterization was performed for 14 strains of bacteria that produce anticancer antibiotics (pelagiomicins) (represented by strain Ni-2088) and one strain that produces UV-absorbing substances (strain F-104), isolated from marine algae and seagrass collected from coastal areas of tropical Pacific islands and a subtropical island of Japan. All 15 isolates were Gram-negative, strictly aerobic, non-motile and non-spore-forming. Sequence analysis of the 16S rRNA gene showed that the isolates occupied positions in the phylogenetic radiation of the genus , with similarities of 93.6–97.6 %. The cells possessed a clearly discernible rod–coccus cell cycle in association with the growth phase; cells were rods during the growth phase and all converted to coccoid–ovoid cells when proliferation ceased. The coccoid–ovoid cells were optically denser than the rod cells and were viable for extended periods. They were considered to constitute a resting form. The type strains of described species of were also found to possess identical rod–coccus cell cycles. The G+C content of the DNA was 48.1–49.7 mol%. The major respiratory quinone system was ubiquinone-8. The major fatty acids were C 7 and C, and the hydroxy acids comprised C 3-OH, C 3-OH and iso-C 3-OH. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The group of 14 pelagiomicin-producing strains and strain F-104 each constituted a single genomic species. Based on phylogenetic affiliation, phenotypic characteristics and genomic distinctness, the isolates represent two novel species in the genus , for which the names sp. nov. (type strain Ni-2088 =MBIC01082 =ATCC 700307) and sp. nov. (type strain F-104 =MBIC03330 =DSM 18651) are proposed.

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2009-07-01
2024-03-28
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References

  1. Altschul, S. F., Madden, T. F., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef] [Google Scholar]
  2. Baker, D. A. & Park, R. W. A.(1975). Changes in morphology and cell wall structure that occur during growth of Vibrio sp. NCTC4716 in batch culture. J Gen Microbiol 86, 12–28.[CrossRef] [Google Scholar]
  3. Barrow, G. I. & Feltham, R. K. A.(1993).Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
  4. Baumann, P. & Baumann, L.(1981). The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In The Prokaryotes, pp. 1302–1331. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. G. Schlegel. Berlin: Springer.
  5. Berleman, J. E. & Bauer, C. E.(2004). Characterization of cyst cell formation in the purple photosynthetic bacterium Rhodospirillum centenum. Microbiology 150, 383–390.[CrossRef] [Google Scholar]
  6. Clark-Walker, G. D.(1969). Association of microcyst formation in Spirillum itersonii with the spontaneous induction of a defective bacteriophage. J Bacteriol 97, 885–892. [Google Scholar]
  7. Dworkin, M.(1996). Recent advances in the social and developmental biology of the myxobacteria. Microbiol Rev 60, 70–102. [Google Scholar]
  8. Ezaki, T., Hashimoto, Y. & Yabuuchi, E.(1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[CrossRef] [Google Scholar]
  9. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  10. Felter, R. A., Colwell, R. R. & Chapman, G. B.(1969). Morphology and round body formation in Vibrio marinus. J Bacteriol 99, 326–335. [Google Scholar]
  11. González, J. M., Mayer, F., Moran, M. A., Hodson, R. E. & Whitman, W. B.(1997).Microbulbifer hydrolyticus gen. nov., sp. nov. and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 47, 369–376.[CrossRef] [Google Scholar]
  12. Hall, T. A.(1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98. [Google Scholar]
  13. Hanzawa, N., Kanai, S., Kastuta, A., Nakagawa, Y. & Yamasato, K.(1995). 16S rDNA-based phylogenetic analysis of marine flavobacteria. J Mar Biotechnol 3, 111–114. [Google Scholar]
  14. Heulin, T., Barakat, M., Christen, R., Lesourd, M., Sutra, L., De Luca, G. & Achouak, W.(2003).Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 53, 589–594.[CrossRef] [Google Scholar]
  15. Hoeniger, J. F. M., Ladwig, R. & Moor, H.(1972). The fine structure of “resting bodies” of Bdellovibrio sp. strain W developed in Rhodospirillum rubrum. Can J Microbiol 18, 87–92.[CrossRef] [Google Scholar]
  16. Humm, H. J.(1946). Marine-agar digesting bacteria of the South Atlantic coast. Duke Univ Mar Stn Bull 3, 45–75. [Google Scholar]
  17. Imamura, N., Nishijima, M., Takadera, T., Adachi, K., Sakai, M. & Sano, H.(1997). New anticancer antibiotics pelagiomicins, produced by a new marine bacterium Pelagiobacter variabilis. J Antibiot (Tokyo) 50, 8–12.[CrossRef] [Google Scholar]
  18. Katayama-Fujimura, Y., Komatsu, Y., Kuraishi, H. & Kaneko, T.(1984). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. Agric Biol Chem 48, 3169–3172.[CrossRef] [Google Scholar]
  19. Kawasaki, H., Hoshino, Y., Kuraishi, H. & Yamasato, K.(1992).Rhodocista centenaria gen. nov., sp. nov., a cyst-forming anoxygenic photosynthetic bacterium and its phylogenetic position in the Proteobacteria alpha group. J Gen Appl Microbiol 38, 541–551.[CrossRef] [Google Scholar]
  20. Komagata, K. & Suzuki, K.(1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207. [Google Scholar]
  21. Krieg, N. R.(1976). Biology of the chemoheterotrophic spirilla. Bacteriol Rev 40, 55–115. [Google Scholar]
  22. Krieg, N. R.(1984). Aerobic/microaerophic, motile, helical/vibrioid Gram-negative bacteria. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 71–124. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  23. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  24. Levin, R. E. & Vaughn, R. H.(1968). Spontaneous spheroplast formation by Desulfovibrio aestuarii. Can J Microbiol 14, 1271–1276.[CrossRef] [Google Scholar]
  25. Marmur, J.(1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef] [Google Scholar]
  26. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H.(1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef] [Google Scholar]
  27. Miyazaki, M., Nogi, Y., Ohta, Y., Hatada, Y., Fujiwara, Y., Ito, S. & Horikoshi, K.(2008).Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment. Int J Syst Evol Microbiol 58, 1128–1133.[CrossRef] [Google Scholar]
  28. Nagao, T., Adachi, K., Nishida, F., Nishijima, M. & Mochida, K.(2000).Butyl and octyl 3-acetamido-4-hydroxybenzoate as fat-soluble UV absorbers, and their manufacture with Pelagiobacter species. Japanese patent no. 2000016976.
  29. Nishijima, M., Araki-Sakai, M. & Sano, H.(1997). Identification of isoprenoid quinones by frit-FAB liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 28, 113–122.[CrossRef] [Google Scholar]
  30. Palleroni, N. J.(1984). Genus Pseudomonas Migula 1894. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  31. Rahalkar, M., Bussman, I. & Schink, B.(2007).Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance. Int J Syst Evol Microbiol 57, 1073–1080.[CrossRef] [Google Scholar]
  32. Reichenbach, H.(1992). The order Cytophagales. In The Prokaryotes, 2nd edn, vol. 4, pp. 3631–3675. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  33. Reichenbach, H. & Dworkin, M.(1992). The myxobacteria. In The Prokaryotes, 2nd edn, vol. 4, pp. 3416–3487. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  34. Romanenko, L. A., Schumann, P., Zhukova, N. V., Rohde, M., Mikhailov, V. V. & Stackebrandt, E.(2003).Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments. Int J Syst Evol Microbiol 53, 1885–1888.[CrossRef] [Google Scholar]
  35. Sadasivan, L. & Neyra, C. A.(1985). Flocculation in Azospirillum brasilense and Azospirillum lipoferum: exopolysaccharides and cyst formation. J Bacteriol 163, 716–723. [Google Scholar]
  36. Sadasivan, L. & Neyra, C. A.(1987). Cyst production and brown pigment formation in aging cultures of Azospirillum brasilense ATCC 29145. J Bacteriol 169, 1670–1677. [Google Scholar]
  37. Sadoff, H. L.(1975). Encystment and germination in Azotobacter vinelandii. Bacteriol Rev 39, 516–539. [Google Scholar]
  38. Saito, H. & Miura, K.(1963). Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72, 619–629.[CrossRef] [Google Scholar]
  39. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  40. Socolofsky, M. D. & Wyss, O.(1962). Resistance of the Azotobacter cyst. J Bacteriol 84, 119–124. [Google Scholar]
  41. Stackebrandt, E.(2006). Defining taxonomic ranks. In The Prokaryotes. A Handbook on the Biology of Bacteria, 3rd edn, vol. 1, pp. 29–57. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
  42. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  43. Sudo, S. Z. & Dworkin, W.(1969). Resistance of vegetative cells and microcysts of Myxococcus xanthus. J Bacteriol 98, 883–887. [Google Scholar]
  44. Terasaki, Y.(1970). Some observations on the life history of Spirillum serpens. Bull Suzugamine Women's Coll Nat Sci 15, 9–17. [Google Scholar]
  45. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  46. Trüper, H. G. & Schleifer, K. H.(2006). Prokaryote characterization and identification. In The Prokaryotes. A Handbook on the Biology of Bacteria, 3rd edn, vol. 1, pp. 58–79. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
  47. Tudor, J. J. & Conti, S. F.(1977). Characterization of bdellocysts of Bdellovibrio sp. J Bacteriol 131, 314–322. [Google Scholar]
  48. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J.(1996). Polyphasic taxonomy: a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438. [Google Scholar]
  49. Whittenbury, R., Davis, S. L. & Davey, J. F.(1970). Exospores and cysts formed by methane-utilizing bacteria. J Gen Microbiol 61, 219–226.[CrossRef] [Google Scholar]
  50. Williams, M. A. & Rittenberg, S. C.(1956). Microcyst formation and germination in Spirillum lunatum. J Gen Microbiol 15, 205–209.[CrossRef] [Google Scholar]
  51. Yamamoto, S. & Harayama, S.(1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104–1109. [Google Scholar]
  52. Yoon, J.-H., Kim, I.-G., Shin, D.-Y., Kang, K. H. & Park, Y.-H.(2003a).Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. Int J Syst Evol Microbiol 53, 53–57.[CrossRef] [Google Scholar]
  53. Yoon, J.-H., Kim, H., Kang, K. H., Oh, T.-K. & Park, Y.-H.(2003b). Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov. Int J Syst Evol Microbiol 53, 1357–1361.[CrossRef] [Google Scholar]
  54. Yoon, J.-H., Kim, I.-G., Oh, T.-K. & Park, Y.-H.(2004).Microbulbifer maritimus sp. nov., isolated from an intertidal sediment from the Yellow Sea, Korea. Int J Syst Evol Microbiol 54, 1111–1116.[CrossRef] [Google Scholar]
  55. Yoon, J.-H., Jung, S.-Y., Kang, S.-J. & Oh, T.-K.(2007).Microbulbifer celer sp. nov., isolated from a marine solar saltern of the Yellow Sea in Korea. Int J Syst Evol Microbiol 57, 2365–2369.[CrossRef] [Google Scholar]
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[PDF file of Supplementary Tables S1-S3](89 KB)

PDF

Phylogenetic affiliation of sp. nov. Ni-2088 and sp. nov. F-104 based on concatenated and gene sequences. [PDF of Supplementary Fig. S1](26 KB)

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Phase-contrast micrographs of two sheets of coccoid cells of sp. nov. Ni-2088 with different depths of focus. Each sheet of coccoid cells was released from a microcolony on 1/10 MA and floated in 75 % ASW, which was added for microscopic observation. The peripheries of the sheets were at right angles to each other. Bar, 2 µm. Micrographs are focused on the upper sheet (left) and the lower sheet (right).

IMAGE

Phase-contrast micrographs of two sheets of coccoid cells of sp. nov. Ni-2088 with different depths of focus. Each sheet of coccoid cells was released from a microcolony on 1/10 MA and floated in 75 % ASW, which was added for microscopic observation. The peripheries of the sheets were at right angles to each other. Bar, 2 µm. Micrographs are focused on the upper sheet (left) and the lower sheet (right).

IMAGE

Phase-contrast micrographs of cells of the type strains of four species of . [PDF of Supplementary Fig. S3](6059 KB)

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Phase-contrast micrograph of optically dense and faint coccoid cells of sp. nov. Ni-2088 taken from a culture on 1/10 MA plates maintained at room temperature (23–27 °C) for 14 months.

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Transmission electron micrograph of a spherical body of sp. nov. Ni-2088 formed on the tip of a rod cell. The culture was grown on MA at 30 °C for 4 days and negatively stained with uranyl acetate. Bar, 1 µm.

IMAGE

[PDF file of Supplementary Figs S6 and S7](66 KB)

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