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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 65, Issue Pt_2

sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Free

Abstract

A taxonomic study was carried out on strain YN3, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3 was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were Cω7 and/or iso-C 2-OH, C and Cω7. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3 should be assigned to the genus . ‘’ KCTC 23325 and QM42 had the closest phylogenetic relationship to strain YN3, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YN3 ( = KCTC 32438 = JCM 19198). An emended description of the genus is also presented.

  • Published Online:
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award project no. 31170001)
  • Zhejiang Provincial Natural Science Foundation of China (Award contract no. LQ13D060002)
  • Scientific Research Fund of the Second Institute of Oceanography, SOA (Award contract no. JT1305)
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2015-02-01
2023-06-08
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References

  1. Aoki T., Araki T., Kitamikado M. ( 1990 ). Purification and characterization of a novel β-agarase from Vibrio sp. AP-2. . Eur J Biochem 187, 461–465. [View Article] [PubMed]
    [Google Scholar]
  2. Chung A. P., Rainey F., Nobre M. F., Burghardt J., da Costa M. S. ( 1997 ). Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. . Int J Syst Bacteriol 47, 1225–1230. [View Article] [PubMed]
    [Google Scholar]
  3. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133–142. [View Article] [PubMed]
    [Google Scholar]
  4. Dong X.-Z., Cai M.-Y. (editors) ( 2001 ). Determinative Manual for Routine Bacteriology.. Beijing:: Scientific Press (English translation);.
     [Google Scholar]
  5. Du Z.-J., Zhang D.-C., Liu S.-N., Chen J.-X., Tian X.-L., Zhang Z.-N., Liu H.-C., Chen G.-J. ( 2009 ). Gilvimarinus chinensis gen. nov., sp. nov., an agar-digesting marine bacterium within the class Gammaproteobacteria isolated from coastal seawater in Qingdao, China. . Int J Syst Evol Microbiol 59, 2987–2990. [View Article] [PubMed]
    [Google Scholar]
  6. Du Z.-J., Lv G.-Q., Rooney A. P., Miao T.-T., Xu Q.-Q., Chen G.-J. ( 2011 ). Agarivorans gilvus sp. nov. isolated from seaweed. . Int J Syst Evol Microbiol 61, 493–496. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368–376. [View Article] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783–791. [View Article]
    [Google Scholar]
  9. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Biol 20, 406–416. [View Article]
    [Google Scholar]
  10. 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. [View Article] [PubMed]
    [Google Scholar]
  11. Holt J. G., Krieg N. R., Sneath P. H. A., Williams S. T. (editors) ( 1994 ). Bergey’s Manual of Determinative Bacteriology, , 9th edn.. Baltimore, MD:: Lippincott Williams & Wilkins;.
     [Google Scholar]
  12. Jean W. D., Shieh W. Y., Liu T. Y. ( 2006 ). Thalassomonas agarivorans sp. nov., a marine agarolytic bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the genus Thalassomonas . . Int J Syst Evol Microbiol 56, 1245–1250. [View Article] [PubMed]
    [Google Scholar]
  13. Jeong S. H., Yang S.-H., Jin H. M., Kim J. M., Kwon K. K., Jeon C. O. ( 2013 ). Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments. . Int J Syst Evol Microbiol 63, 1335–1341. [View Article] [PubMed]
    [Google Scholar]
  14. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by Munro H. N. . New York:: Academic Press;. [View Article]
    [Google Scholar]
  15. Kim H. T., Lee S., Lee D., Kim H.-S., Bang W.-G., Kim K. H., Choi I.-G. ( 2010 ). Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type β-agarase producing neoagarobiose. . Appl Microbiol Biotechnol 86, 227–234. [View Article] [PubMed]
    [Google Scholar]
  16. Kim B.-C., Kim M. N., Lee K. H., Kim H. S., Min S. R., Shin K.-S. ( 2011 ). Gilvimarinus agarilyticus sp. nov., a new agar-degrading bacterium isolated from the seashore of Jeju Island. . Antonie van Leeuwenhoek 100, 67–73. [View Article] [PubMed]
    [Google Scholar]
  17. Kim B.-C., Poo H., Lee K. H., Kim M. N., Park D.-S., Oh H. W., Lee J. M., Shin K.-S. ( 2012a ). Simiduia areninigrae sp. nov., an agarolytic bacterium isolated from sea sand. . Int J Syst Evol Microbiol 62, 906–911. [View Article] [PubMed]
    [Google Scholar]
  18. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012b ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716–721. [View Article] [PubMed]
    [Google Scholar]
  19. Kirimura K., Masuda N., Iwasaki Y., Nakagawa H., Kobayashi R., Usami S. ( 1999 ). Purification and characterization of a novel β-agarase from an alkalophilic bacterium, Alteromonas sp. E-1. . J Biosci Bioeng 87, 436–441. [View Article] [PubMed]
    [Google Scholar]
  20. Leifson E. ( 1963 ). Determination of carbohydrate metabolism of marine bacteria. . J Bacteriol 85, 1183–1184.[PubMed]
    [Google Scholar]
  21. Leon O., Quintana L., Peruzzo G., Slebe J. C. ( 1992 ). Purification and properties of an extracellular agarase from Alteromonas sp. strain C-1. . Appl Environ Microbiol 58, 4060–4063.[PubMed]
    [Google Scholar]
  22. Lim J.-M., Jeon C. O., Lee J.-C., Song S.-M., Kim K.-Y., Kim C.-J. ( 2006 ). Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea. . Int J Syst Evol Microbiol 56, 653–657. [View Article] [PubMed]
    [Google Scholar]
  23. Long M., Yu Z., Xu X. ( 2010 ). A novel β-agarase with high pH stability from marine Agarivorans sp. LQ48. . Mar Biotechnol (NY) 12, 62–69. [View Article] [PubMed]
    [Google Scholar]
  24. Mac Faddin J. F. ( 1976 ). Biochemical Tests for Identification of Medical Bacteria. Baltimore, MD:: Williams & Wilkins;.
     [Google Scholar]
  25. Macián M. C., Ludwig W., Schleifer K. H., Pujalte M. J., Garay E. ( 2001 ). Vibrio agarivorans sp. nov., a novel agarolytic marine bacterium. . Int J Syst Evol Microbiol 51, 2031–2036. [View Article] [PubMed]
    [Google Scholar]
  26. Marmur J., Doty P. ( 1961 ). Thermal renaturation of deoxyribonucleic acids. . J Mol Biol 3, 585–594. [View Article] [PubMed]
    [Google Scholar]
  27. 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. [View Article]
    [Google Scholar]
  28. 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. [View Article]
    [Google Scholar]
  29. 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. [View Article] [PubMed]
    [Google Scholar]
  30. Park S., Choi W.-C., Oh T.-K., Yoon J.-H. ( 2011 ). Thalassomonas agariperforans sp. nov., an agarolytic bacterium isolated from marine sand. . Int J Syst Evol Microbiol 61, 2573–2576. [View Article] [PubMed]
    [Google Scholar]
  31. Pruesse E., Peplies J., Glöckner F. O. ( 2012 ). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. . Bioinformatics 28, 1823–1829. [View Article] [PubMed]
    [Google Scholar]
  32. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406–425.[PubMed]
    [Google Scholar]
  33. 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. [View Article] [PubMed]
    [Google Scholar]
  34. Schroeder D. C., Jaffer M. A., Coyne V. E. ( 2003 ). Investigation of the role of a β(1-4) agarase produced by Pseudoalteromonas gracilis B9 in eliciting disease symptoms in the red alga Gracilaria gracilis . . Microbiology 149, 2919–2929. [View Article] [PubMed]
    [Google Scholar]
  35. 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. [View Article] [PubMed]
    [Google Scholar]
  36. Shieh W. Y., Liu T. Y., Lin S. Y., Jean W. D., Chen J.-S. ( 2008 ). Simiduia agarivorans gen. nov., sp. nov., a marine, agarolytic bacterium isolated from shallow coastal water from Keelung, Taiwan. . Int J Syst Evol Microbiol 58, 895–900. [View Article] [PubMed]
    [Google Scholar]
  37. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013 ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30, 2725–2729. [View Article] [PubMed]
    [Google Scholar]
  38. Tindall B. J. ( 1990 ). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. . Syst Appl Microbiol 13, 128–130. [View Article]
    [Google Scholar]
  39. Wang C.-S., Wang Y., Xu X.-W., Zhang D.-S., Wu Y.-H., Wu M. ( 2009 ). Microbulbifer donghaiensis sp. nov., isolated from marine sediment of the East China Sea. . Int J Syst Evol Microbiol 59, 545–549. [View Article] [PubMed]
    [Google Scholar]
  40. 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. [View Article]
    [Google Scholar]
  41. Winker S., Woese C. R. ( 1991 ). A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. . Syst Appl Microbiol 14, 305–310. [View Article] [PubMed]
    [Google Scholar]
  42. Xin H., Itoh T., Zhou P., Suzuki K., Kamekura M., Nakase T. ( 2000 ). Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. . Int J Syst Evol Microbiol 50, 1297–1303. [View Article] [PubMed]
    [Google Scholar]
  43. Xu X.-W., Wu Y.-H., Wang C.-S., Oren A., Zhou P.-J., Wu M. ( 2007 ). Haloferax larsenii sp. nov., an extremely halophilic archaeon from a solar saltern. . Int J Syst Evol Microbiol 57, 717–720. [View Article] [PubMed]
    [Google Scholar]
  44. Yoon J., Ishikawa S., Kasai H., Yokota A. ( 2007 ). Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family ‘Flexibacteraceae’, isolated from seawater in Japan. . Int J Syst Evol Microbiol 57, 1014–1017. [View Article] [PubMed]
    [Google Scholar]
  45. Zhang D.-S., Huo Y.-Y., Xu X.-W., Wu Y.-H., Wang C.-S., Xu X.-F., Wu M. ( 2012 ). Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov., isolated from marine sediment. . Int J Syst Evol Microbiol 62, 505–510. [View Article] [PubMed]
    [Google Scholar]
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Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus
Int J Syst Evol Microbiol 65, 562 (2015); https://doi.org/10.1099/ijs.0.065078-0
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