Advertisement

Journal of Microbiology

, Volume 57, Issue 12, pp 1065–1072 | Cite as

Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea

  • Sanjit Chandra Debnath
  • Ahmed Mohammed Abdo Miyah
  • Can Chen
  • Huan Sheng
  • Xue-Wei Xu
  • Yue-Hong Wu
  • Dao-Qiong Zheng
  • Jin-Zhong Xu
  • Ya-Nan Di
  • Pin-Mei Wang
  • Li ShenEmail author
Microbial Systematics and Evolutionary Microbiology
  • 47 Downloads

Abstract

A yellow pigmented, Gram-stain-negative, aerobic bacterium designated A5.7T was studied to evaluate the taxonomic position following the modern polyphasic approach. The strain was isolated from sediments near Zhairuo Island, which is situated in the East China Sea. Cells were non-spore forming rods without flagella but showed motility by gliding. Growth was observed at 15–35°C (optimum 28°C), pH 6.0–9.0 (optimum pH 6.5) and 0–2% (w/v) NaCl (optimum 0–0.5%) in LB broth. The major respiratory quinone of A5.7T was menaquinone 6. The major polar lipid of A5.7T was phosphatidylethanolamine and the predominant fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, C15:1ω6c, iso-C15:0 3-OH, iso-C15:1 G, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 9 (iso-C17:1ω9c and/or C16:010-methyl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium and shares the highest sequence similarities with Flavobacterium sharifuzzamanii A7.6T (98.5%), Flavobacterium tistrianum GB 56.1T (98.3%), Flavobacterium nitrogenifigens NXU-44T (97.8%), Flavobacterium anhuiense D3T (97.6%), Flavobacterium ginsenosidimutans THG 01T (97.6%), and Flavobacterium foetidum CJ42T (97.6%). Digital DNA-DNA hybridization and average nucleotide identity values between the strain and its closest phylogenetic neighbors showed the ranges from 19.6 to 34.1% and 73.7 to 87.9%, respectively. Therefore, based on polyphasic characteristics, strain A5.7T represents a novel species of the genus Flavobacterium for which the name Flavobacterium zhairuonensis sp. nov. is proposed. The type strain is A5.7T (= KCTC 62406T = MCCC 1K03494T).

Keywords

Flavobacterium zhairuonensis polyphasic analysis genome sequence sediment East China Sea 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgements

This work was supported by the Natural Science Foundation of Zhejiang Province (LY18D060003 and LY18C060002). We would like to thank Prof. Min Wu (Zhejiang University) for technical support.

Supplementary material

12275_2019_9194_MOESM1_ESM.pdf (323 kb)
Supplementary material, approximately 228 KB.

References

  1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol.215, 403–410.PubMedGoogle Scholar
  2. Asker, D., Beppu, T., and Ueda, K. 2007. Mesoflavibacter zeaxanthinifaciens gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae. Syst. Appl. Microbiol.30, 291–296.PubMedGoogle Scholar
  3. Barrow, G.I. and Feltham, R.K.A. 1993. Cowan and Steel’s manual for the identification of medical bacteria, 3rd ed. Cambridge University Press, Cambridge, New York.Google Scholar
  4. Bergey, D.H., Harrison, F.C., Breed, R.S., Hammer, B.W., and Huntoon, F.M. 1923. Genus II. Flavobacterium gen. nov., pp. 97–117. In Whitman, W. (ed.), Bergey’s Manual of Determinative Bacteriology, Williams & Wilkins, Baltimore, USA.Google Scholar
  5. Bernardet, J.F., Nakagawa, Y., and 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.PubMedGoogle Scholar
  6. Bernardet, J.F., Segers, P., Vancanneyt, M., Berthe, F., Kersters, K., and 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.Google Scholar
  7. Cai, H., Zeng, Y., Wang, Y., Cui, H., and Jiang, H. 2018. Flavobacterium cyanobacteriorum sp. nov., isolated from cyanobacterial aggregates in a eutrophic lake. Int. J. Syst. Evol. Microbiol.68, 1279–1284.PubMedGoogle Scholar
  8. Chaudhary, D.K. and Kim, J. 2018. Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol.68, 305–309.PubMedGoogle Scholar
  9. Chen, C., Su, Y., Tao, T.Y., Fu, G.Y., Zhang, C.Y., Sun, C., Zhang, X.Q., and Wu, M. 2017. Maripseudobacter aurantiacus gen. nov., sp nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation basin. Int. J. Syst. Evol. Microbiol.67, 778–783.PubMedGoogle Scholar
  10. Choi, J.Y., Kim, J.H., and Lee, P.C. 2018. Flavobacterium kingsejongi sp. nov., a carotenoid-producing species isolated from Antarctic penguin faeces. Int. J. Syst. Evol. Microbiol.68, 911–916.PubMedGoogle Scholar
  11. Choi, S., Shin, S.K., Kim, E., and Yi, H. 2017. Flavobacterium crassostreae sp. nov., isolated from Pacific oyster. Int. J. Syst. Evol. Microbiol.67, 988–992.PubMedGoogle Scholar
  12. Debnath, S.C., Chen, C., Liu, S.X., Di, Y.N., Zheng, D.Q., Li, X.Y., Xu, X.W., Xu, J.Z., and Wang, P.M. 2019. Flavobacterium sharifuzzamanii sp. nov., isolated from the sediments of the East China Sea. Curr. Microbiol.76, 297–303.PubMedGoogle Scholar
  13. Dong, K., Chen, F., Du, Y., and 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.PubMedGoogle Scholar
  14. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol.17, 368–376.PubMedGoogle Scholar
  15. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution39, 783–791.PubMedGoogle Scholar
  16. Fitch, W.M. 1971. Toward defining course of evolution — minimum change for a specific tree topology. Syst. Zool.20, 406–416.Google Scholar
  17. Frankland, G.C. and Frankland, P.F. 1889. Über einige typische Mikroorganismen im Wasser und im Boden. Zeitschrift für Hygiene6, 373–400.Google Scholar
  18. Fu, Y., Tang, X., Lai, Q., Zhang, C., Zhong, H., Li, W., Liu, Y., Chen, L., Sun, F., and Shao, Z. 2011. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol.61, 205–209.PubMedGoogle Scholar
  19. Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Van-damme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol.57, 81–91.PubMedGoogle Scholar
  20. Hameed, A., Shahina, M., Lin, S.Y., Cho, J.C., Lai, W.A., and Young, C.C. 2013. Kordia aquimaris sp. nov., a zeaxanthin-producing member of the family Flavobacteriaceae isolated from surface seawater, and emended description of the genus Kordia. Int. J. Syst. Evol. Microbiol.63, 4790–4796.PubMedGoogle Scholar
  21. Hameed, A., Shahina, M., Lin, S.Y., Lai, W.A., Hsu, Y.H., Liu, Y.C., and Young, C.C. 2014. Aquibacter zeaxanthinifaciens gen. nov., sp nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int. J. Syst. Evol. Microbiol.64, 138–145.PubMedGoogle Scholar
  22. Kämpfer, P., Lodders, N., Martin, K., and Avendano-Herrera, R. 2012. Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. Int. J. Syst. Evol. Microbiol.62, 1402–1408.PubMedGoogle Scholar
  23. Kang, J.Y., Chun, J., and Jahng, K.Y. 2013. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int. J. Syst. Evol. Microbiol.63, 1633–1638.PubMedGoogle Scholar
  24. Kim, J.H., Choi, B.H., Jo, M., Kim, S.C., and Lee, P.C. 2014. Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins. Int. J. Syst. Evol. Microbiol.64, 2884–2890.PubMedGoogle Scholar
  25. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. J. Mol. Evol.16, 111–120.Google Scholar
  26. Komagata, K. and Suzuki, K. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol.19, 161–207.Google Scholar
  27. Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol.33, 1870–1874.Google Scholar
  28. Kuo, I., Saw, J., Kapan, D.D., Christensen, S., Kaneshiro, K.Y., and Donachie, S.P. 2013. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai’i, and emended description of the genus Flavobacterium. Int. J. Syst. Evol. Microbiol.63, 3280–3286.PubMedGoogle Scholar
  29. Lane, D. 1991. 16S/23S rRNA sequencing. In Stackebrandt, E. and Goodfellow, M. (eds.), pp. 115–175. Nucleic acid techniques in bacterial systematics, John Wiley and Sons, New York, USA.Google Scholar
  30. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. 2007. Clustal W and Clustal X version 2.0. Bio-informatics23, 2947–2948.Google Scholar
  31. Lee, Y. and Jeon, C.O. 2018. Flavobacterium alvei sp. nov., isolated from a freshwater river. Int. J. Syst. Evol. Microbiol.68, 1919–1924.PubMedGoogle Scholar
  32. Li, D.D., Liu, C., Zhang, Y.Q., Wang, X.J., Wang, N., Peng, M., Song, X.Y., Su, H.N., Zhang, X.Y., Zhang, Y.Z., et al. 2017. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int. J. Syst. Evol. Microbiol.67, 1070–1074.PubMedGoogle Scholar
  33. Liu, H., Liu, R., Yang, S.Y., Gao, W.K., Zhang, C.X., Zhang, K.Y., and Lai, R. 2008. Flavobacterium anhuiense sp. nov., isolated from field soil. Int. J. Syst. Evol. Microbiol.58, 756–760.PubMedGoogle Scholar
  34. Liu, H., Lu, P., Jin, L., and Zhu, G. 2017. Flavobacterium luticocti sp. nov., isolated from wastewater. Int. J. Syst. Evol. Microbiol.67, 369–373.PubMedGoogle Scholar
  35. Liu, Q., Siddiqi, M.Z., Liu, Q., Huq, M.A., Lee, S.Y., Choi, K.D., and Im, W.T. 2018. Flavobacterium hankyongi sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol.68, 1732–1736.PubMedGoogle Scholar
  36. Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics14, 60.PubMedPubMedCentralGoogle Scholar
  37. Miyashita, M., Fujimura, S., Nakagawa, Y., Nishizawa, M., Tomizuka, N., Nakagawa, T., and Nakagawa, J. 2010. Flavobacterium algicola sp. nov., isolated from marine algae. Int. J. Syst. Evol. Microbiol.60, 344–348.PubMedGoogle Scholar
  38. Nurk, S., Bankevich, A., Antipov, D., Gurevich, A., Korobeynikov, A., Lapidus, A., Prjibelsky, A., Pyshkin, A., Sirotkin, A., Sirotkin, Y., et al. 2013. Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads, Springer Berlin Heidelberg, Berlin, Heidelberg.Google Scholar
  39. Qi, Y.B., Wang, C.Y., Lv, C.Y., Lun, Z.M., and Zheng, C.G. 2017. Removal capacities of polycyclic aromatic hydrocarbons (PAHs) by a newly isolated strain from oilfield produced water. Int. J. Environ. Res. Public Health14, E215.PubMedGoogle Scholar
  40. Ren, Q., Yu, M., Li, Y., Zhang, Y., Shi, X., Wu, Y., Su, Y., Wang, Y., Wang, X., and Zhang, X.H. 2018. Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach. Int. J. Syst. Evol. Microbiol.68, 795–800.PubMedGoogle Scholar
  41. Richter, M. and Rosselló-Móra, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA106, 19126–19131.PubMedGoogle Scholar
  42. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425.PubMedGoogle Scholar
  43. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc., Newark, DE, USA.Google Scholar
  44. Sheu, S.Y., Su, C.L., Kwon, S.W., and Chen, W.M. 2017. Flavobacterium amniphilum sp. nov., isolated from a stream. Int. J. Syst. Evol. Microbiol.67, 5179–5186.PubMedGoogle Scholar
  45. Song, L., Liu, H., Huang, Y., Dai, X., and Zhou, Y. 2013. Flavobacterium marinum sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol.63, 3551–3555.PubMedGoogle Scholar
  46. Suwannachart, C., Rueangyotchanthana, K., Srichuay, S., Pheng, S., Fungsin, B., Phoonsiri, C., and Kim, S.G. 2016. Flavobacterium tistrianum sp. nov., a gliding bacterium isolated from soil. Int. J. Syst. Evol. Microbiol.66, 2241–2246.PubMedGoogle Scholar
  47. Tamaki, H., Hanada, S., Kamagata, Y., Nakamura, K., Nomura, N., Nakano, K., and Matsumura, M. 2003. Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int. J. Syst. Evol. Microbiol.53, 519–526.PubMedGoogle Scholar
  48. Tindall, B.J. 1990. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol. Lett.66, 199–202.Google Scholar
  49. Vela, A.I., Fernandez, A., Sánchez-Porro, C., Sierra, E., Mendez, M., Arbelo, M., Ventosa, A., Domínguez, L., and Fernández-Garayzábal, J.F. 2007. Flavobacterium ceti sp. nov., isolated from beaked whales (Ziphius cavirostris). Int. J. Syst. Evol. Microbiol.57, 2604–2608.PubMedGoogle Scholar
  50. Wu, Y.H., Yu, P.S., Zhou, Y.D., Xu, L., Wang, C.S., Wu, M., Oren, A., and Xu, X.W. 2013. Muricauda antarctica sp. nov., a marine member of the Flavobacteriaceae isolated from Antarctic seawater. Int. J. Syst. Evol. Microbiol.63, 3451–3456.PubMedGoogle Scholar
  51. Yang, J.E., Kim, S.Y., Im, W.T., and Yi, T.H. 2011. Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol.61, 1408–1412.PubMedGoogle Scholar
  52. Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017a. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol.67, 1613–1617.PubMedPubMedCentralGoogle Scholar
  53. Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., and Chun, J. 2017b. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek110, 1281–1286.PubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea 2019

Authors and Affiliations

  • Sanjit Chandra Debnath
    • 1
  • Ahmed Mohammed Abdo Miyah
    • 1
  • Can Chen
    • 1
  • Huan Sheng
    • 1
  • Xue-Wei Xu
    • 1
    • 2
    • 3
  • Yue-Hong Wu
    • 2
    • 3
  • Dao-Qiong Zheng
    • 1
  • Jin-Zhong Xu
    • 1
  • Ya-Nan Di
    • 1
  • Pin-Mei Wang
    • 1
  • Li Shen
    • 1
    Email author
  1. 1.Ocean CollegeZhejiang UniversityZhoushanP. R. China
  2. 2.Key Laboratory of Marine Ecosystem and BiogeochemistryState Oceanic AdministrationHangzhouP. R. China
  3. 3.Second Institute of OceanographyMinistry of Natural ResourcesHangzhouP. R. China

Personalised recommendations