1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 57, Issue 12

sp. nov., a novel marine member of the family within the phylum ‘’ isolated from seagrass Free

Abstract

An obligately aerobic, spherical, non-motile, pale-yellow pigmented bacterium was isolated from a piece of leaf of seagrass, (L.f.) Royle, grown in Okinawa, Japan and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the novel isolate N5FB36-5 shared approximately 96–98 % sequence similarity with the species of the genus of the family within the phylum ‘’. The DNA–DNA relatedness values of strain N5FB36-5 with 02PA-Ca-133 and YM14-201 were below 70 %, which is accepted as the phylogenetic definition of a novel species. -Lactam antibiotic susceptibility test and amino acid analysis of the cell wall hydrolysates indicated the absence of muramic acid and diaminopimelic acid in the cell walls, which suggested that this strain lacks an ordinary Gram-negative type of peptidoglycan in the cell wall. The DNA G+C content of strain N5FB36-5 was 51.6 mol%; MK-7 was the major menaquinone; and the presence of C, C 7 and anteiso-C as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus . On the basis of polyphasic taxonomic data, it was concluded that this strain should be classified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is N5FB36-5 (=MBIC08282=KCTC 12903).

  • Published Online:
SGM

Erratum

An erratum has been published for this content:
sp. nov., a novel marine member of the family within the phylum ‘’ isolated from seagrass
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65286-0
2007-12-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/12/2874.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65286-0&mimeType=html&fmt=ahah

References

  1. Alain K., Olagnon M., Desbruyères D., Pagé A., Barbier G., Juniper S. K., Quérellou J., Cambon-Bonavita M.-A. 2002; Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis . FEMS Microbiol Ecol 42:463–476 [CrossRef]
     [Google Scholar]
  2. Bowman J. P., Nowak B. 2004; Salmonid gill bacteria and their relationship to amoebic gill disease. J Fish Dis 27:483–492 [CrossRef]
     [Google Scholar]
  3. Chin K.-J., Liesack W., Janssen P. H. 2001; Opitutus terrae gen. nov., sp. nov., to accommodate novel strain of the division ‘ Verrucomicrobia ’ isolated from rice paddy soil. Int J Syst Evol Microbiol 51:1965–1968 [CrossRef]
     [Google Scholar]
  4. Choo Y.-J., Lee K., Song J., Cho J.-C. 2007; Puniceicoccus vermicola gen. nov., sp. nov., a new marine bacterium and description of Puniceicoccaceae fam.nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov., and Opitutae classis nov. in the phylum ‘ Verrucomicrobia ’. Int J Syst Evol Microbiol 57:532–537 [CrossRef]
     [Google Scholar]
  5. Dedysh S. N., Pankratov T. A., Belova S. E., Kulichevskaya I. S., Liesack W. 2006; Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog. Appl Environ Microbiol 72:2110–2117 [CrossRef]
     [Google Scholar]
  6. 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]
  7. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  8. Garrity G. M., Holt J. G. 2001; The road map to the Manual . In Bergey's Manual of Systematic Bacteriology . , 2nd edn. vol 1 pp 119–166 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
  9. Harper J. J., Davis G. H. G. 1979; Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 29:56–58 [CrossRef]
     [Google Scholar]
  10. Haukka K., Heikkinen E., Kairesalo T., Karjalainen H., Sivonen K. 2005; Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms. Environ Microbiol 7:620–630 [CrossRef]
     [Google Scholar]
  11. Haukka K., Kolmonen E., Hyder R., Hietala J., Vakkilainen K., Kairesalo T., Haario H., Sivonen K. 2006; Effect of nutrient loading on bacterioplankton community composition in lake mesocosms. Microb Ecol 51:137–146 [CrossRef]
     [Google Scholar]
  12. Hedlund B. P., Gosink J. J., Staley J. T. 1997; Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prothecobacter . Antonie Van Leeuwenhoek 72:29–38 [CrossRef]
     [Google Scholar]
  13. Hirsch A. M. 1999; Role of lectins (and rhizobial exopolysaccharides) in legume nodulation. Curr Opin Plant Biol 2:320–326 [CrossRef]
     [Google Scholar]
  14. Hugenholtz P., Goebel B. M., Pace N. R. 1998; Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774
     [Google Scholar]
  15. Joseph S. J., Hugenholtz P., Sangwan P., Osborne C. A., Janssen P. H. 2003; Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215 [CrossRef]
     [Google Scholar]
  16. Kanokratana P., Chanapan S., Pootanakit K., Eurwilaichitr L. 2004; Diversity and abundance of Bacteria and Archaea in the Bor Khlueng hot spring in Thailand. J Basic Microbiol 44:430–444 [CrossRef]
     [Google Scholar]
  17. Kasai H., Katsuta A., Sekiguchi H., Matsuda S., Adachi K., Kazutoshi S., Yoon J., Yokota A., Shizuri Y. 2007; Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum ‘ Verrucomicrobia ’. Int J Syst Evol Microbiol 57:1630–1634 [CrossRef]
     [Google Scholar]
  18. Katsuta A., Adachi K., Matsuda S., Shizuri Y., Kasai H. 2005; Ferrimonas marina sp. nov. Int J Syst Evol Microbiol 55:1851–1855 [CrossRef]
     [Google Scholar]
  19. Koike K., Jimbo M., Sakai R., Kaeriyama M., Muramoto K., Ogata T., Maruyama T., Kamiya H. 2004; Octocoral chemical signaling selects and controls dinoflagellate symbionts. Biol Bull 207:80–86 [CrossRef]
     [Google Scholar]
  20. 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]
  21. Lyman J., Fleming R. H. 1940; Composition of sea water. J Mar Res 3:134–146
     [Google Scholar]
  22. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218 [CrossRef]
     [Google Scholar]
  23. McCowen S. M., MacArthur L., Gates J. E. 1986; Azolla fern lectins that specifically recognize endosymbiotic cyanobacteria. Curr Microbiol 14:329–333 [CrossRef]
     [Google Scholar]
  24. 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 [CrossRef]
     [Google Scholar]
  25. Murray R. G. E., Doetsch R. N., Robinow C. F. 1994; Determinative and cytological light microscopy. In Methods for General and Molecular Bacteriology . pp 21–41 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
  26. O'Farrell K. A., Janssen P. H. 1999; Detection of Verrucomicrobia in a pasture soil by PCR-mediated amplification of 16S rRNA genes. Appl Environ Microbiol 65:4280–4284
     [Google Scholar]
  27. Petroni G., Spring S., Schleifer K.-H., Verni F., Rosati G. 2000; Defensive extrusive ectosymbionts of Euplotidium (Ciliophora) that contain microtubule-like structures are bacteria related to Verrucomicrobia . Proc Natl Acad Sci U S A 97:1813–1817 [CrossRef]
     [Google Scholar]
  28. Rappé M. S., Giovannoni S. J. 2003; The uncultured microbial majority. Annu Rev Microbiol 57:369–394 [CrossRef]
     [Google Scholar]
  29. Scheuermayer M., Gulder T. A., Bringmann G., Hentschel U. 2006; Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘ Verrucomicrobia ’, isolated from a sponge ( Porifera ). Int J Syst Evol Microbiol 56:2119–2124 [CrossRef]
     [Google Scholar]
  30. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477
     [Google Scholar]
  31. Shieh W. Y., Jean W. D. 1998; Alterococcus agarolyticus , gen. nov., sp. nov., a halophilic thermophilic bacterium capable of agar degradation. Can J Microbiol 44:637–645 [CrossRef]
     [Google Scholar]
  32. Sikes D. S., Lewis P. O. 2001 Beta software, version 1. PAUPRat: paup implementation of the parsimony ratchet Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs;
     [Google Scholar]
  33. Swofford D. L. 2002 paup*: Phylogenetic analysis using parsimony (*and other methods Sunderland, MA: Sinauer Associates;
     [Google Scholar]
  34. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
     [Google Scholar]
  35. Vandekerckhove T. T. M., Willems A., Gillis M., Coomans A. 2000; Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum -group species (Nematoda, Longidoridae. Int J Syst Evol Microbiol 50:2197–2205 [CrossRef]
     [Google Scholar]
  36. Venkataraman C., Haack B. J., Bondada S., Kwaik Y. A. 1997; Identification of a Gal/GalNAc lectin in the protozoan Hartmannella vermiformis as a potential receptor for attachment and invasion by the legionnaires’ disease bacterium. J Exp Med 186:537–547 [CrossRef]
     [Google Scholar]
  37. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. other authors 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
     [Google Scholar]
  38. Weidner S., Arnold W., Stackebrandt E., Pühler A. 2000; Phylogenetic analysis of bacterial communities associated with leaves of the seagrass Halophila stipulacea by a culture-independent small subunit rRNA gene approach. Microb Ecol 39:22–31 [CrossRef]
     [Google Scholar]
  39. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
     [Google Scholar]
  40. Yasumoto-Hirose M., Nishijima M., Ngirchechol M. K., Kanoh K., Shizuri Y., Miki W. 2006; Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam. Mar Biotechnol (NY 8:227–237 [CrossRef]
     [Google Scholar]
  41. Yokota A., Tamura T., Nishii T., Hasegawa T. 1993; Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, gram-positive, motile coccus with meso -diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43:52–57 [CrossRef]
     [Google Scholar]
  42. Yoon J., Yasumoto-Hirose M., Katsuta A., Sekiguchi H., Matsuda S., Kasai H., Yokota A. 2007a; Coraliomargarita akajimensis gen. nov., sp. nov, a novel member of the phylum ‘ Verrucomicrobia ’ isolated from seawater in Japan. Int J Syst Evol Microbiol 57:959–963 [CrossRef]
     [Google Scholar]
  43. Yoon J., Yasumoto-Hirose M., Matsuo Y., Nozawa M., Matsuda S., Kasai H., Yokota A. 2007b; Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov.,three novel members of subdivision 4 within the phylum ‘ Verrucomicrobia ’ isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 57:1377–1385 [CrossRef]
     [Google Scholar]
  44. Yoon J., Matsuo Y., Matsuda S., Adachi K., Kasai H., Yokota A. 2007c; Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum ‘ Verrucomicrobia ’ isolated from marine sand. Int J Syst Evol Microbiol 57:2067–2072 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65286-0
Loading
Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’ isolated from seagrass
Int J Syst Evol Microbiol 57, 2874 (2007); https://doi.org/10.1099/ijs.0.65286-0
/content/journal/ijsem/10.1099/ijs.0.65286-0
/content/journal/ijsem/10.1099/ijs.0.65286-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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