1887

Abstract

Indigenous bacteria found in the sediment of the Emerald Basin (depth of 215 m, Atlantic Ocean) located offshore of Halifax Harbour (Nova Scotia, Canada) were previously found to be able to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, a novel obligately respiratory, denitrifying and RDX-mineralizing bacterium, designated strain HAW-EB4, was isolated from the marine sediment. This bacterium utilized peptone, yeast extract, Casamino acids, esters (Tweens 20, 40 and 80), sugars (-acetyl--glucosamine, ribose), several C and C acids (acetate, pyruvate, lactate, propionate) and amino acids (serine, proline) as sole carbon and energy sources. Aerobically grown cells (in marine broth 2216 at 10 °C) contained C (6 %), iso-C (12 %), C (20 %), C 7 (37 %), C 7 (7 %) and C 3 (7 %) as major membrane fatty acids, and Q7 (28·1 %) and MK-7 (60·9 %) as dominant respiratory quinones, consistent with deep-sea species of . The novel bacterium had a DNA G+C content of 45 mol% and showed similarity to species in terms of 16S rRNA and gene sequences (93–99 and 67·3–88·4 % similarity, respectively), with being the most closely related species. Genomic DNA–DNA hybridization between strain HAW-EB4 and revealed a level of relatedness of 17·9 %, lower than the 70 % species cut-off value, indicating that strain HAW-EB4 (=NCIMB 14093=DSM 17350) is the type strain of a novel species of , for which the name sp. nov. is proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63829-0
2006-01-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/56/1/205.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63829-0&mimeType=html&fmt=ahah

References

  1. Akagawa-Matsushita, M., Itoh, T., Katayama, Y., Kuraishi, H. & Yamasato, K.(1992). Isoprenoid quinone composition of some marine Alteromonas, Marinomonas, Deleya, Pseudomonas and Shewanella species. J Gen Microbiol 138, 2275–2281.[CrossRef] [Google Scholar]
  2. Beveridge, T., Popkin, T. J. & Cole, R. M.(1994). Electron microscopy. In Methods for General and Molecular Bacteriology, pp. 42–71. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  3. Bowman, J. P.(2001). Methods for psychrophilic bacteria. Methods Microbiol 30, 591–615. [Google Scholar]
  4. Bowman, J. P., McCammon, S. A., Nichols, D. S., Skerratt, J. H., Rea, S. M., Nichols, P. D. & McMeekin, T. A.(1997).Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20 : 5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 1040–1047.[CrossRef] [Google Scholar]
  5. Bowman, J. P., McCammon, S. A., Lewis, T., Skerratt, J. H., Nichols, D. S. & McMeekin, T. A.(1998).Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology 144, 1601–1609.[CrossRef] [Google Scholar]
  6. Bozal, N., Montes, M. J., Tudela, E., Jimenez, F. & Guinea, J.(2002).Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52, 195–205. [Google Scholar]
  7. Brettar, R. C. & Hofle, M. G.(2002).Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic–anoxic interface of the Gotland Deep in the central Baltic Sea. Int J Syst Evol Microbiol 52, 2211–2217.[CrossRef] [Google Scholar]
  8. Collins, M. D.(1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 325–366. [Google Scholar]
  9. 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.
  10. Deming, J. W., Hada, H., Colwell, R. R., Luehrsen, K. R. & Fox, G. E.(1984). The ribonucleotide sequence of 5S rRNA from two strains of deep-sea barophilic bacteria. J Gen Microbiol 130, 1911–1920. [Google Scholar]
  11. Fay, L. & Richli, U.(1991). Location of double bonds in polyunsaturated fatty acids by gas chromatography–mass spectrometry after 4,4-dimethyloxazoline derivatization. J Chromatogr 541, 89–98.[CrossRef] [Google Scholar]
  12. Gillis, M., Vandamme, P., De Vos, P., Swings, J. & Kersters, K.(2001). Polyphasic taxonomy. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 43–48. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
  13. Ivanova, E. P., Sawabe, T., Gorshkova, N. M., Svetashev, V. I., Mikhailov, V. V., Nicolau, D. V. & Christen, R.(2001).Shewanella japonica sp. nov. Int J Syst Evol Microbiol 51, 1027–1033.[CrossRef] [Google Scholar]
  14. Ivanova, E. P., Nedashkovskaya, O. I., Zhukova, N. V., Nicolau, D. V., Christen, R. & Mikhailov, V. V.(2003a).Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum). Int J Syst Evol Microbiol 53, 1471–1477.[CrossRef] [Google Scholar]
  15. Ivanova, P. E., Sawabe, T., Hayashi, K., Gorshkova, N. M., Zhukova, N. V., Nedashkovskaya, N. V., Mikhailov, O. I., Nicolau, V. V. & Christen, R.(2003b).Shewanella fidelis sp. nov., isolated from sediments and sea water. Int J Syst Evol Microbiol 53, 577–582.[CrossRef] [Google Scholar]
  16. Ivanova, E. P., Nedashkovskaya, O. I., Sawabe, T., Zhukova, N. V., Frolova, G. M., Nicolau, D. V., Mikhailov, V. V. & Bowman, J. P.(2004a).Shewanella affinis sp. nov., isolated from marine invertebrates. Int J Syst Evol Microbiol 54, 1089–1093.[CrossRef] [Google Scholar]
  17. Ivanova, E. P., Gorshkova, N. M., Bowman, J. P., Lysenko, A. M., Zhukova, N. V., Sergeev, A. F., Mikhailov, V. V. & Nicolau, D. V.(2004b).Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. Int J Syst Evol Microbiol 54, 1083–1087.[CrossRef] [Google Scholar]
  18. Ivanova, E. P., Flavier, S. & Christen, R.(2004c). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 54, 1773–1788.[CrossRef] [Google Scholar]
  19. Jensen, M. J., Tebo, B. M., Baumann, P., Mandel, M. & Nealson, K. H.(1980). Characterization of Alteromonas hanedai (sp. nov.), a non-fermentative luminous species of marine origin. Curr Microbiol 3, 311–315.[CrossRef] [Google Scholar]
  20. Johnson, J. L.(1985a). Determination of DNA base composition. Methods Microbiol 18, 23–24. [Google Scholar]
  21. Johnson, J. L.(1985b). DNA reassociation and RNA hybridisation of bacterial nucleic acids. Methods Microbiol 18, 33–74. [Google Scholar]
  22. Johnson, J. L.(1994). Similarity analysis of DNAs. In Methods for General and Molecular Bacteriology, pp. 655–682. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  23. Kato, C. & Nogi, Y.(2001). Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiol Ecol 35, 223–230.[CrossRef] [Google Scholar]
  24. Kato, C., Li, L., Nogi, Y., Nakamura, Y., Tamaoka, J. & Horikoshi, K.(1998). Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 meters. Appl Environ Microbiol 64, 1510–1513. [Google Scholar]
  25. Kumar, S., Tamura, K., Jakobsen, I.-B. & Nei, M.(2001).mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef] [Google Scholar]
  26. Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt, E. & Nealson, K. H.(1999).Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49, 1341–1351.[CrossRef] [Google Scholar]
  27. Long, H. F. & Hammer, B. W.(1941). Classification of organisms important in dairy products. III. Pseudomonas putrefaciens. Iowa Agric Exp Stn Bull 285, 176–195. [Google Scholar]
  28. MacDonell, M. T. & Colwell, R. R.(1985). Phylogeny of the Vibrionaceae, and recommendation for two new genera, Listonella and Shewanella. Syst Appl Microbiol 6, 171–182.[CrossRef] [Google Scholar]
  29. Makemson, J. C., Fulayfil, N. R., Landry, W., Van Ert, L. M., Wimpee, C. F., Widder, E. A. & Case, J. F.(1997).Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea. Int J Syst Bacteriol 47, 1034–1039.[CrossRef] [Google Scholar]
  30. Myers, C. R. & Nealson, K. H.(1988). Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319–1321.[CrossRef] [Google Scholar]
  31. 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]
  32. Nogi, Y., Kato, C. & Horikoshi, K.(1998). Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol 170, 331–338.[CrossRef] [Google Scholar]
  33. Nozue, H., Hayashi, T., Hashimoto, Y., Ezaki, T., Hamasaki, K., Ohwada, K. & Terawaki, Y.(1992). Isolation and characterization of Shewanella alga from human clinical specimens and emendation of the description of S. alga Simidu et al., 1990 , 335. Int J Syst Bacteriol 42, 628–634.[CrossRef] [Google Scholar]
  34. Petrovskis, E. A., Vogel, T. M. & Adriaens, P.(1994). Effects of electron acceptors and donors on transformation of tetrachloromethane by Shewanella putrefaciens MR-1. FEMS Microbiol Lett 121, 357–364.[CrossRef] [Google Scholar]
  35. Prevost, M. C., Lesourd, M., Arpin, M., Vernel, F., Mounier, J., Hellio, R. & Sansonetti, P. J.(1992). Unipolar reorganization of F-actin layer at bacterial division and bundling of actin filaments by plastin correlate with movement of Shigella flexneri within HeLa cells. Infect Immun 60, 4088–4099. [Google Scholar]
  36. Russell, N. J. & Nichols, D. S.(1999). Polyunsaturated fatty acids in marine bacteria – a dogma rewritten. Microbiology 145, 767–779.[CrossRef] [Google Scholar]
  37. Sambrook, J. & Russell, D. W.(2001).Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  38. Satomi, M., Oikawa, H. & Yano, Y.(2003).Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov., novel eicosapentaenoic-acid-producing marine bacteria isolated from sea-animal intestines. Int J Syst Evol Microbiol 53, 491–499.[CrossRef] [Google Scholar]
  39. Semple, K. M. & Westlake, D. W. S.(1987). Characterization of iron reducing Alteromonas putrefaciens strains from oil field fluids. Can J Microbiol 35, 925–931. [Google Scholar]
  40. Simidu, U., Kita-Tsukamoto, K., Yasumoto, T. & Yotsu, M.(1990). Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int J Syst Bacteriol 40, 331–336.[CrossRef] [Google Scholar]
  41. Skerratt, J. H., Bowman, J. P. & Nichols, P. D.(2002).Shewanella olleyana sp. nov., a marine species isolated from a temperate estuary which produces high levels of polyunsaturated fatty acids. Int J Syst Evol Microbiol 52, 2101–2106.[CrossRef] [Google Scholar]
  42. 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.
  43. 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]
  44. Toffin, L., Bidault, A., Pignet, P., Tindall, B. J., Slobodkin, A., Kato, C. & Prieur, D.(2004).Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. Int J Syst Evol Microbiol 54, 1943–1949.[CrossRef] [Google Scholar]
  45. Venkateswaran, K., Dohmoto, N. & Harayama, S.(1998a). Cloning and nucleotide sequence of the gyrB gene of Vibrio parahaemolyticus and its application in detection of this pathogen in shrimp. Appl Environ Microbiol 64, 681–687. [Google Scholar]
  46. Venkateswaran, K., Dollhopf, M. E., Aller, R., Stackebrandt, E. & Nealson, K. H.(1998b).Shewanella amazonensis sp. nov., a novel metal-reducing facultative anaerobe from Amazonian shelf muds. Int J Syst Bacteriol 48, 965–972.[CrossRef] [Google Scholar]
  47. Venkateswaran, K., Moser, D. P., Dollhopf, M. E. & 10 other authors(1999). Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49, 705–724.[CrossRef] [Google Scholar]
  48. 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.[CrossRef] [Google Scholar]
  49. Xu, M., Guo, J., Cen, Y., Zhong, X., Cao, W. & Sun, G.(2005).Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant. Int J Syst Evol Microbiol 55, 363–368.[CrossRef] [Google Scholar]
  50. 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]
  51. Yoon, J.-H., Kang, K.-H., Oh, T.-K. & Park, Y.-H.(2004a).Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea. Int J Syst Evol Microbiol 54, 487–491.[CrossRef] [Google Scholar]
  52. Yoon, J. H., Yeo, S. H., Kim, I. G. & Oh, T. K.(2004b).Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 54, 2347–2352.[CrossRef] [Google Scholar]
  53. Zhao, J.-S., Greer, C. W., Thiboutot, S., Ampleman, G. & Hawari, J.(2004a). Biodegradation of nitramine explosives hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in cold marine sediment under anaerobic and oligotrophic conditions. Can J Microbiol 50, 91–96.[CrossRef] [Google Scholar]
  54. Zhao, J.-S., Spain, J., Thiboutot, S., Ampleman, G., Greer, C. & Hawari, J.(2004b). Phylogeny of cyclic nitramine-degrading psychrophilic bacteria in marine sediment and their potential role in the natural attenuation of explosives. FEMS Microbiol Ecol 49, 349–357.[CrossRef] [Google Scholar]
  55. Zhao, J.-S., Manno, D., Beaulieu, C., Paquet, L. & Hawari, J.(2005).Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. Int J Syst Evol Microbiol 55, 1511–1520.[CrossRef] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63829-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63829-0
Loading

Data & Media loading...

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