1887

Abstract

Two marine bacteria, designated strains MBE#61 and MBE#74, were isolated from a piece of sunken bamboo in the marine environment in Japan. Both of these strains were Gram-stain-negative, but had different cell shapes: MBE#61 was spiral, whereas MBE#74 was rod-shaped. The temperature, pH and salt concentration ranges for growth of strain MBE#61 were 4–38 °C (optimal at 32 °C), pH 4.5–11.0 (optimal at pH 7.0–8.0) and 1–11 % (optimal at 2 %) NaCl, whereas those of strain MBE#74 were 4–36 °C (optimal at 30 °C), pH 4.0–10.5 (optimal at pH 7.0–8.0) and 1–12 % (optimal at 4 %) NaCl. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that both strains belong to the genus within the class . Similarity between the 16S rRNA gene sequence of strain MBE#61 and those of the type strains of species of the genus was 97.5–99.0 %, and that of strain MBE#74 was 96.9–98.6 %; these two isolates were most closely related to QMT2. However, the DNA–DNA hybridization values between QMT2 and strain MBE#61 or MBE#74 were only 16.0 % and 7.1 %, respectively. The DNA G+C content of strain MBE#61 was 54.4 mol%, and that of strain MBE#74 was 55.9 mol%. The predominant isoprenoid quinone of the two strains was Q-10 (MBE#61, 97.3 %; MBE#74, 93.5 %). The major cellular fatty acids of strain MBE#61 were Cω7 (31.1 %), summed feature 3 comprising Cω7/iso-C 2-OH (26.1 %) and C (20.9 %); those of strain MBE#74 were C (26.2 %), C cyclo (19.9 %) and Cω7 (12.1 %). On the basis of these results, strain MBE#61 and strain MBE#74 are considered to represent novel species of the genus , for which names sp. nov. and sp. nov. are proposed. The type strains are MBE#61 ( = JCM 18968 = CECT 8273) and MBE#74 ( = JCM 18969 = CECT 8274), respectively. An emended description of the genus is also proposed.

Funding
This study was supported by the:
  • , Japan Society for the Promotion of Science (JSPS) , (Award GS031)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.056028-0
2014-01-01
2020-12-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/1/107.html?itemId=/content/journal/ijsem/10.1099/ijs.0.056028-0&mimeType=html&fmt=ahah

References

  1. Balch W. E., Fox G. E., Magrum L. J., Woese C. R., Wolfe R. S. ( 1979 ). Methanogens: reevaluation of a unique biological group. . Microbiol Rev 43, 260296.
    [Google Scholar]
  2. Crawford D. L., Pometto A. L., Crawford R. L. ( 1983 ). Lignin degradation by Streptomyces viridosporus: isolation and characterization of a new polymeric lignin degradation intermediate. . Appl Environ Microbiol 45, 898904.[PubMed]
    [Google Scholar]
  3. Deacon J. W. . ( 2009 ). Fungal Biology. Hoboken, NJ:: Wiley;. [CrossRef]
    [Google Scholar]
  4. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in micro-dilution 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, 224229. [CrossRef]
    [Google Scholar]
  5. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [CrossRef]
    [Google Scholar]
  7. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [CrossRef]
    [Google Scholar]
  8. Gold M. H., Alic M. ( 1993 ). Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium . . Microbiol Rev 57, 605622.[PubMed]
    [Google Scholar]
  9. Ivanova E. P., Zhukova N. V., Lysenko A. M., Gorshkova N. M., Sergeev A. F., Mikhailov V. V., Bowman J. P. ( 2005 ). Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. . Int J Syst Evol Microbiol 55, 22032207. [CrossRef] [PubMed]
    [Google Scholar]
  10. Kodama Y., Stiknowati L. I., Ueki A., Ueki K., Watanabe K. ( 2008 ). Thalassospira tepidiphila sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from seawater. . Int J Syst Evol Microbiol 58, 711715. [CrossRef] [PubMed]
    [Google Scholar]
  11. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics, pp. 173199. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [Google Scholar]
  12. Kumar Y., Westram R., Behrens S., Fuchs B., Glöckner F. O., Amann R., Meier H., Ludwig W. ( 2005 ). Graphical representation of ribosomal RNA probe accessibility data using arb software package. . BMC Bioinformatics 6, 61. [CrossRef] [PubMed]
    [Google Scholar]
  13. Kumar Y., Westram R., Kipfer P., Meier H., Ludwig W. ( 2006 ). Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using arb software package. . BMC Bioinformatics 7, 240. [CrossRef] [PubMed]
    [Google Scholar]
  14. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
    [Google Scholar]
  15. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al. ( 2007 ). Clustal W and Clustal X version 2.0. . Bioinformatics 23, 29472948. [CrossRef] [PubMed]
    [Google Scholar]
  16. Liu C., Wu Y., Li L., Ma Y., Shao Z. ( 2007 ). Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.. Int J Syst Evol Microbiol 57, 316320. [CrossRef] [PubMed]
    [Google Scholar]
  17. López-López A., Pujalte M. J., Benlloch S., Mata-Roig M., Rosselló-Mora R., Garay E., Rodríguez-Valera F. ( 2002 ). Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the α-Proteobacteria . . Int J Syst Evol Microbiol 52, 12771283. [CrossRef] [PubMed]
    [Google Scholar]
  18. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [CrossRef] [PubMed]
    [Google Scholar]
  19. Masai E., Katayama Y., Nishikawa S., Fukuda M. ( 1999 ). Characterization of Sphingomonas paucimobilis SYK-6 genes involved in degradation of lignin-related compounds. . J Ind Microbiol Biotechnol 23, 364373. [CrossRef] [PubMed]
    [Google Scholar]
  20. 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, 159167. [CrossRef]
    [Google Scholar]
  21. Minnikin D. E., Patel P. V., Alshamaony L., Goodfellow M. ( 1977 ). Polar lipid composition in the classification of Nocardia and related bacteria. . Int J Syst Bacteriol 27, 104117. [CrossRef]
    [Google Scholar]
  22. 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, 233241. [CrossRef]
    [Google Scholar]
  23. 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, 113122. [CrossRef]
    [Google Scholar]
  24. Ohta Y., Nishi S., Haga T., Tsubouchi T., Hasegawa R., Konishi M., Nagano Y., Tsuruwaka Y., Shimane Y. et al. ( 2012 ). Screening and phylogenetic analysis of deep-sea bacteria capable of metabolizing lignin-derived aromatic compounds. . Open J Marine Sci 2, 177187. [CrossRef]
    [Google Scholar]
  25. Plotnikova E. G., Anan’ina L. N., Krausova V. I., Ariskina E. V., Prisyazhnaya N. V., Lebedev A. T., Demakov V. A., Evtushenko L. I. ( 2011 ). Thalassospira permensis sp. nov., a new terrestrial halotolerant bacterium isolated from a naphthalene-utilizing microbial consortium. . Mikrobiologiia 80, 691699.[PubMed]
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  27. Sjöström E. ( 1993 ). Wood Chemistry: Fundamentals and Applications, , 2nd edn.. San Diego, CA:: Academic Press;.
    [Google Scholar]
  28. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characteristics. . In Manual of Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  29. Tavaré S. ( 1986 ). Some probabilistic and statistical problems in the analysis of DNA sequences. . Lect Math Life Sci 17, 5786.
    [Google Scholar]
  30. Trojanowski J., Haider K., Sundman V. ( 1977 ). Decomposition of 14C-labelled lignin and phenols by a Nocardia sp.. Arch Microbiol 114, 149153. [CrossRef] [PubMed]
    [Google Scholar]
  31. Tsubouchi T., Shimane Y., Usui K., Shimamura S., Mori K., Hiraki T., Tame A., Uematsu K., Maruyama T., Hatada Y. ( 2013 ). Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment. . Int J Syst Evol Microbiol 63, 19871994. [CrossRef] [PubMed]
    [Google Scholar]
  32. 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. et al. ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [CrossRef]
    [Google Scholar]
  33. Wilson K. ( 1987 ). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology, pp. 2.4.12.4.5. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Wiley;.
    [Google Scholar]
  34. Zhao B., Wang H., Mao X., Li R. ( 2009 ). Biodegradation of phenanthrene by a halophilic bacterial consortium under aerobic conditions. . Curr Microbiol 58, 205210. [CrossRef] [PubMed]
    [Google Scholar]
  35. Zhao B., Wang H., Li R., Mao X. ( 2010 ). Thalassospira xianhensis sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium. . Int J Syst Evol Microbiol 60, 11251129. [CrossRef] [PubMed]
    [Google Scholar]
  36. Zwickl D., Holder M. ( 2004 ). Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. . Syst Biol 53, 877888. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.056028-0
Loading
/content/journal/ijsem/10.1099/ijs.0.056028-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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