Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan

Abstract

An aerobic, gram-negative, yellow-pigmented, and non-motile bacterium designated KMM 9535T was isolated from a marine sediment sample obtained from the Sea of Japan seashore and subjected to a phylogenetic and phenotypic study. On the basis of 16S rRNA gene sequence analysis, strain KMM 9535T was placed to the genus Flavobacterium sharing the highest sequence similarities to Flavobacterium ahnfeltiae KCTC 32467T (99.3 %), Flavobacterium jumunjinense KCTC 23618T (96.5 %), Flavobacterium ponti KCTC 22802T (96.3 %), Flavobacterium urocaniciphilum JCM 19142T (96.1 %), and Flavobacterium gelidilacus LMG 21477T (95.8 %). The DNA–DNA hybridization value between strain KMM 9535T and the closest related F. ahnfeltiae KCTC 32467T was 33 %. Strain KMM 9535T grew at 5–36 °C and in the presence of 0–3 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone, and the major fatty acids were iso-C15:0, iso-C17:1, iso-C15:1, and iso-C17:0 3-OH. The DNA G+C content was 28.8 mol%. On the basis of the results obtained, it is proposed strain KMM 9535T to be classified as a novel species of the genus Flavobacterium, Flavobacterium maris sp. nov., with the type strain of the species KMM 9535T (=NRIC 0920T = KCTC 42093T).

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References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM (1923) Genus II. Flavobacterium gen. nov. In: Bergey’s manual of determinative bacteriology. Williams & Wilkins, Baltimore, pp 97–117

  2. Bernardet JF, Bowman JP (2011) Genus I. Flavobacterium Bergey et al. 1923. In: Whitman W (ed) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Williams & Wilkins, Baltimore, pp 112–154

    Google Scholar 

  3. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148

    Article  Google Scholar 

  4. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    CAS  Article  PubMed  Google Scholar 

  5. Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surface of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868

    CAS  PubMed  Google Scholar 

  6. Bruns A, Rohde M, Berthe-Corti L (2001) Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North sea intertidal sediment. Int J Syst Evol Microbiol 51:1997–2006

    CAS  Article  PubMed  Google Scholar 

  7. Collins MD, Shah HN (1984) Fatty acid, menaquinone and polar lipid composition of Rothia dentosacariosa. Arch Microbiol 137:247–249

    CAS  Article  Google Scholar 

  8. Dong K, Chen F, Du Y, Wang G (2013) Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 63:886–892

    CAS  Article  PubMed  Google Scholar 

  9. 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 39:224–229

    Article  Google Scholar 

  10. Fautz E, Reichenbach H (1980) A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8:87–91

    CAS  Article  Google Scholar 

  11. Fujii D, Nagai F, Watanabe Y, Shirasawa Y (2014) Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena. Int J Syst Evol Microbiol 64:1488–1494

    CAS  Article  PubMed  Google Scholar 

  12. Joung Y, Kim H, Joh K (2013) Flavobacterium jumunjinense sp. nov., isolated from a lagoon, and emended descriptions of Flavobacterium cheniae, Flavobacterium dongtanense and Flavobacterium gelidilacus. Int J Syst Evol Microbiol 63:3937–3943

    CAS  Article  PubMed  Google Scholar 

  13. Kang JY, Chun J, Jahng KY (2013) Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 63:1633–1638

    CAS  Article  PubMed  Google Scholar 

  14. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  Article  PubMed  Google Scholar 

  15. Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118

    CAS  Article  PubMed  Google Scholar 

  16. Nedashkovskaya OI, Balabanova LA, Zhukova NV, Kim SJ, Bakunina IY, Rhee SK (2014) Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a pacific red alga. Arch Microbiol 196:745–752

    CAS  Article  PubMed  Google Scholar 

  17. Owen J, Hill LR, Lapage SP (1969) Determination of DNA base composition from melting profiles in dilute buffers. Biopolymers 7:503–516

    CAS  Article  PubMed  Google Scholar 

  18. Pruesse E, Peplies J, Glöckner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  19. Romanenko LA, Schumann P, Rohde M, Mikhailov VV, Stackebrandt E (2004) Reinekea marinisedimentorum gen. nov., sp. nov., a novel gammaproteobacterium from marine coastal sediments. Int J Syst Evol Microbiol 54:669–673

    CAS  Article  PubMed  Google Scholar 

  20. Romanenko LA, Uchino M, Frolova GM, Mikhailov VV (2007) Marixanthomonas ophiurae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star. Int J Syst Evol Microbiol 57:457–462

    CAS  Article  PubMed  Google Scholar 

  21. Romanenko LA, Tanaka N, Svetashev VI (2013) Devosia submarina sp. nov., isolated from deep sea surface sediments. Int J Syst Evol Microbiol 63:3079–3085

    CAS  Article  PubMed  Google Scholar 

  22. Sasser M (1990) Microbial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). Technical note 101. MIDI, Newark

    Google Scholar 

  23. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47:289–298

    CAS  Article  PubMed  Google Scholar 

  24. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–655

    Google Scholar 

  25. Stackebrandt E, Goebel BM (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

    CAS  Article  Google Scholar 

  26. 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

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  27. Van Trappen S, Mergaert J, Swings J (2003) Flavobacterium gelidilacus sp. nov., isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 53:1241–1245

    Article  PubMed  Google Scholar 

  28. Yoon JH, Park S, Kang SJ, Oh SJ, Myung SC, Kim W (2011) Flavobacterium ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 61:81–85

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

We would like to thank Dr. Claudine Vereecke, BCCM™/LMG Bacteria Collection, Ghent University, Belgium, and Dr. Jung-Sook Lee, the Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea, and Dr. Moriya Ohkuma, JCM, Japan Collection of Microorganisms, Japan, for providing Flavobacterium type strains for comparative analyses. This study was supported by a grant from the RSF “Biodiversity and biotechnological potential of marine bacteria and fungi” no. 14-14-00030.

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Correspondence to Lyudmila A. Romanenko.

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The DDBJ/GenBank/EMBL accession number of the 16S rRNA gene sequence of strain KMM 9535T is AB973429.

Communicated by Erko Stackebrandt.

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Romanenko, L.A., Tanaka, N., Svetashev, V.I. et al. Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan. Arch Microbiol 197, 941–947 (2015). https://doi.org/10.1007/s00203-015-1128-x

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Keywords

  • Flavobacterium maris sp. nov.
  • Marine sediments
  • Biodiversity
  • The Sea of Japan