1887

Abstract

A novel Gram-positive, rod-shaped, non-motile, non-spore-forming bacterium, strain DSE10, was isolated from a deep-sea sediment sample collected at a depth of 5904 m from the Chagos–Laccadive ridge system in the Indian Ocean. Cells of strain DSE10 were positive for catalase, oxidase, urease and lipase activities and contained iso-C, iso-C, iso-C and anteiso-C as the major fatty acids. The major respiratory quinones were MK-6 and MK-8 and the major lipids were phosphatidylglycerol and diphosphatidylglycerol. The cell-wall peptidoglycan contained diaminopimelic acid as the diagnostic diamino acid. A sequence similarity search based on 16S rRNA gene sequences indicated that the genera , , and were the nearest phylogenetic neighbours to the novel isolate with gene sequence similarities ranging from 94.9 to 95.2 %. Phylogenetic analyses using neighbour-joining, minimum-evolution and maximum-parsimony methods indicated that strain DSE10 formed a deeply rooted lineage distinct from the clades represented by the genera , , and . Further, strain DSE10 could be distinguished from the above-mentioned genera based on the presence of signature nucleotides G, A, C, T, C, A, G, C and T at positions 182, 444, 480, 492, 563, 931, 1253, 1300 and 1391, respectively, in the 16S rRNA gene sequence. Based on the phenotypic and phylogenetic characteristics determined in this study, strain DSE10 was assigned as the type species of a new genus, gen. nov., as sp. nov. The type strain of gen. nov., sp. nov. is DSE10 (=LMG 24411=JCM 14375). The genomic DNA G+C content of strain DSE10 is 59.5±2.5 mol%.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.002691-0
2009-10-01
2019-10-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/59/10/2618.html?itemId=/content/journal/ijsem/10.1099/ijs.0.002691-0&mimeType=html&fmt=ahah

References

  1. Arakawa, S., Nogi, Y., Sato, T., Yoshida, Y., Usami, R. & Kato, C. ( 2006; ). Diversity of piezophilic microorganisms in the closed ocean Japan Sea. Biosci Biotechnol Biochem 70, 749–752.[CrossRef]
    [Google Scholar]
  2. Arfman, N., Dijkhuizen, L., Kirchhof, G., Ludwig, W., Schleifer, K. H., Bulygina, E. S., Chumakov, K. M., Govorukhina, N. I., Trotsenko, Y. A. & other authors ( 1992; ). Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Int J Syst Bacteriol 42, 439–445.[CrossRef]
    [Google Scholar]
  3. Claus, D. & Berkeley, R. C. W. ( 1986; ). Genus Bacillus Cohn 1872. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1105–1139. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  4. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef]
    [Google Scholar]
  5. Delaporte, B. & Sasson, A. ( 1967; ). Study of bacteria from arid soils of Morocco: Brevibacterium haloterans n. sp. and Brevibacterium frigoritolerans n. sp. C R Acad Sci Hebd Seances Acad Sci D 264, 2257–2260.
    [Google Scholar]
  6. Farrow, J. A., Ash, C., Wallbanks, S. & Collins, M. D. ( 1992; ). Phylogenetic analysis of the genera Planococcus, Marinococcus and Sporosarcina and their relationships to members of the genus Bacillus. FEMS Microbiol Lett 72, 167–172.
    [Google Scholar]
  7. Hao, M. V. & Komagata, K. ( 1985; ). A new species of Planococcus, P. kocurii isolated from fish, frozen foods, and fish curing brine. J Gen Appl Microbiol 31, 441–455.[CrossRef]
    [Google Scholar]
  8. Heijs, S. K., Aloisi, G., Bouloubassi, I., Pancost, R. D., Pierre, C., Sinninghe Damsté, J. S., Gottschal, J. C., van Elsas, J. D. & Forney, L. J. ( 2006; ). Microbial community structure in three deep-sea carbonate crusts. Microb Ecol 52, 451–462.[CrossRef]
    [Google Scholar]
  9. Heyrman, J., Vanparys, B., Logan, N. A., Balcaen, A., Rodriguez-diaz, M., Felske, A. & de Vos, P. ( 2004; ). Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst Evol Microbiol 54, 47–57.[CrossRef]
    [Google Scholar]
  10. Kaneko, R., Hayashi, T., Tanahashi, M. & Naganuma, T. ( 2007; ). Phylogenetic diversity and distribution of dissimilatory sulfite reductase genes from deep-sea sediment cores. Mar Biotechnol (NY) 9, 429–436.[CrossRef]
    [Google Scholar]
  11. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  12. Kimura, H., Ishibashi, J., Masuda, H., Kato, K. & Hanada, S. ( 2007; ). Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere. Appl Environ Microbiol 73, 2110–2117.[CrossRef]
    [Google Scholar]
  13. Komagata, K. & Suzuki, K. ( 1987; ). Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
    [Google Scholar]
  14. 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]
  15. Lanyi, B. ( 1987; ). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67.
    [Google Scholar]
  16. Lauro, F. M. & Bartlett, D. H. ( 2008; ). Prokaryotic lifestyles in deep-sea habitats. Extremophiles 12, 15–25.[CrossRef]
    [Google Scholar]
  17. Logan, N. A., Lebbe, L., Hoste, B., Goris, J., Forsyth, G., Heyndrickx, M., Murray, B. L., Syme, N., Wynn-Williams, D. D. & de Vos, P. ( 2000; ). Aerobic endospore-forming bacteria from geothermal environments in northern Victoria Land, Antarctica, and Candlemas Island, South Sandwich archipelago, with the proposal of Bacillus fumarioli sp. nov. Int J Syst Evol Microbiol 50, 1741–1753.
    [Google Scholar]
  18. Ludwig, W., Strunk, O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M. & Schleifer, K. H. ( 1998; ). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19, 554–568.[CrossRef]
    [Google Scholar]
  19. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  20. Marmur, J. & Doty, P. ( 1962; ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[CrossRef]
    [Google Scholar]
  21. Miroshnichenko, M. L. & Bonch-Osmolovskaya, E. A. ( 2006; ). Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents. Extremophiles 10, 85–96.[CrossRef]
    [Google Scholar]
  22. Naganuma, T., Miyoshi, T. & Kimura, H. ( 2007; ). Phylotype diversity of deep-sea hydrothermal vent prokaryotes trapped by 0.2- and 0.1 μm-pore-size filters. Extremophiles 11, 637–646.[CrossRef]
    [Google Scholar]
  23. Nagel, M. & Andreesen, J. R. ( 1991; ). Bacillus niacini sp. nov., a nicotinate-metabolizing mesophile isolated from soil. Int J Syst Bacteriol 41, 134–139.[CrossRef]
    [Google Scholar]
  24. Nakagawa, T., Nakagawa, S., Inagaki, F., Takai, K. & Horikoshi, K. ( 2004; ). Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures. FEMS Microbiol Lett 232, 145–152.[CrossRef]
    [Google Scholar]
  25. Nazina, T. N., Tourova, T. P., Poltaraus, A. B., Novikova, E. V., Grigoryan, A. A., Ivanova, A. E., Lysenko, A. M., Petrunyaka, V. V., Osipov, G. A. & other authors ( 2001; ). Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int J Syst Evol Microbiol 51, 433–446.
    [Google Scholar]
  26. Prokofeva, M. I., Kublanov, I. V., Nercessian, O., Tourova, T. P., Kolganova, T. V., Lebedinsky, A. V., Bonch-Osmolovskaya, E. A., Spring, S. & Jeanthon, C. ( 2005; ). Cultivated anaerobic acidophilic/acidotolerant thermophiles from terrestrial and deep-sea hydrothermal habitats. Extremophiles 9, 437–448.[CrossRef]
    [Google Scholar]
  27. Raghukumar, C., Raghukumar, S., Sheelu, G., Gupta, S. M., Nath, B. N. & Rao, B. R. ( 2004; ). Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench, Indian Ocean. Deep-Sea Res 51, 1759–1768.[CrossRef]
    [Google Scholar]
  28. Reddy, G. S. N., Aggarwal, R. K., Matsumoto, G. I. & Shivaji, S. ( 2000; ). Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. Int J Syst Evol Microbiol 50, 1553–1561.[CrossRef]
    [Google Scholar]
  29. Reddy, G. S. N., Nagy, M. & Garcia-Pichel, F. ( 2006; ). Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. Int J Syst Evol Microbiol 56, 51–58.[CrossRef]
    [Google Scholar]
  30. Reysenbach, A. L., Liu, Y., Banta, A. B., Beveridge, T. J., Kirshtein, J. D., Schouten, S., Tivey, M. K., Von Damm, K. L. & Voytek, M. A. ( 2006; ). A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442, 444–447.[CrossRef]
    [Google Scholar]
  31. Romano, I., Giordano, A., Lama, L., Nicolaus, B. & Gambacorta, A. ( 2003; ). Planococcus rifietensis sp. nov., isolated from algal mat collected from a sulfurous spring in Campania (Italy). Syst Appl Microbiol 26, 357–366.[CrossRef]
    [Google Scholar]
  32. Scheldeman, P., Rodríguez-díaz, M., Goris, J., Pil, A., de Clerck, E., Herman, I., de Vos, P., Logan, N. A. & Heyndrickx, M. ( 2004; ). Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms. Int J Syst Evol Microbiol 54, 1355–1364.[CrossRef]
    [Google Scholar]
  33. Shivaji, S., Bhadra, B., Rao, R. S., Chaturvedi, P. & Raghukumar, C. ( 2007; ). Microbacterium indicum sp. nov. isolated from a deep sea sediment sample from Chagos trench in the Indian Ocean. Int J Syst Evol Microbiol 57, 1819–1822.[CrossRef]
    [Google Scholar]
  34. Smibert, R. M. & Krieg, N. R. ( 1994; ). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  35. Tamaoka, J., Katayama-Fujimura, Y. & Kuraishi, H. ( 1983; ). Analysis of bacterial menaquinone mixture by high performance liquid chromatography. J Appl Bacteriol 54, 31–36.[CrossRef]
    [Google Scholar]
  36. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: 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]
  37. Tiago, I., Pires, C., Mendes, V., Morais, P. V., da Costa, M. S. & Veríssimo, A. ( 2006; ). Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater. Int J Syst Evol Microbiol 56, 2571–2574.[CrossRef]
    [Google Scholar]
  38. Yoon, J. H., Kang, S. S., Lee, K. C., Lee, E. S., Kho, Y. H., Kang, K. H. & Park, Y. H. ( 2001; ). Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol 51, 1511–1520.
    [Google Scholar]
  39. Yoon, J. H., Weiss, N., Kang, K. H., Oh, T. K. & Park, Y. H. ( 2003; ). Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. Int J Syst Evol Microbiol 53, 2013–2017.[CrossRef]
    [Google Scholar]
  40. ZoBell, C. E. ( 1941; ). Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 4, 42–75.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.002691-0
Loading
/content/journal/ijsem/10.1099/ijs.0.002691-0
Loading

Data & Media loading...

Supplements

Minimum-evolution and maximum-parsimony (DNAPARS) trees based on 16S rRNA gene sequences showing the phylogenetic relationship between gen. nov., sp. nov. DSE10  and other related reference micro-organisms. [ PDF] 175 KB

PDF

16S rRNA gene signature nucleotides that differentiate the genus gen. nov. from the genera , , and . [ PDF] 30 KB

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error