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Journal of Microbiology

, Volume 56, Issue 8, pp 542–548 | Cite as

Flavobacterium parvum sp. nov., isolated from soil polluted by sewer water

  • Hyun Seo Lee
  • Woon Mo Hwang
  • Keunsoo Kang
  • Tae-Young AhnEmail author
Article

Abstract

A novel Gram-stain-negative, motile by means of gliding, and short rod-shaped bacterium, designated HS916T, was isolated from soil polluted by sewer water in Cheonan-si, South Korea. Growth occurred at 10–35°C (optimum 30°C), pH 6.0–8.0 (optimum pH 7.0), and 0–1% sodium chloride (NaCl, w/v). Based on similarities of 16S rRNA gene sequences, strain HS916T was closely related to members of the genus Flavobacterium, exhibiting the highest sequence similarities with Flavobacterium glycines Gm-149T (96.4%), followed by F. granuli Kw05T (96.3%), F. fluminis 3R17T (96.3%), F. aquicola TMd3a3T (96.2%), and F. nitratireducens N1T (96.2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HS916T was placed in a monophyletic cluster with F. nitratireducens N1T and F. fluminis 3R17T. The predominant fatty acids (> 5% of the total) of strain HS916T were iso-C15:0, anteiso-C15:0, iso-C15:0 3-OH, C17:1ω6с, C16:0 3-OH, iso-C17:0 3-OH, and summed feature 3 (C16:1ω7с and/or C16:1ω6с). The major polar lipids of the strain comprised phosphatidylethanolamine, unidentified aminolipids, and five unidentified lipids. The predominant respiratory quinone and the major polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content of strain HS916T was 34.9 mol%. Based on polyphasic analyses, strain HS916T represents a novel species belonging to the genus Flavobacterium, for which the name Flavobacterium parvum sp. nov. is proposed. The type strain is HS916T (= KACC 19448T = JCM 32368T).

Keywords

Flavobacterium parvum Flavobacterium HS916 soil sewer water 

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References

  1. Ahn, J.H., Kim, T.W., Kim, T.S., Joung, Y., and Kim, S.B. 2017. Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater. Int. J. Syst. Evol. Microbiol.67, 3117–3121.PubMedGoogle Scholar
  2. 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
  3. Anacker, R.L. and Ordal, E.J. 1955. Study of a bacteriophage infecting the Myxobacterium Chrondrococcus columnaris. J. Bacteriol.70, 738–741.PubMedPubMedCentralGoogle Scholar
  4. Aslam, Z., Im, W.T., Kim, M.K., and Lee, S.T. 2005. Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant. Int. J. Syst. Evol. Microbiol.55, 747–751.PubMedGoogle Scholar
  5. Barrow, G.I. and Feltham, R.K. 1993. Cowan and steel’s manual for the identification of medical bacteria, 3rd ed. Cambridge university press, London, UK.Google Scholar
  6. 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 Bergey’s manual of determinative bacteriology, Williams & wilkins, Baltimore, MD, USA.Google Scholar
  7. Bernardet, J.F. and Bowman, J.P. 2011. Genus I. Flavobacterium, pp. 112–154. In Krieg, N.R., Staley, J.T., Brown, D.R., Hedlund, B.P., Paster, B.J., Ward, N.L., Ludwig, W., and Whitman, W.B. (eds.), Bergey’s manual of systematic bacteriology, 2nd edn, vol. 4, Springer, New York, USA.Google Scholar
  8. Bernardet, J.F. and Kerouault, B. 1989. Phenotypic and genomic studies of “Cytophaga psychrophila” isolated from diseased rainbow trout (Oncorhynchus mykiss) in france. Appl. Environ. Microbiol.55, 1796–1800.PubMedPubMedCentralGoogle Scholar
  9. 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
  10. Bu, J.H. and Cha, C.J. 2018. Flavobacterium foetidum sp. nov., isolated from ginseng soil. Int. J. Syst. Evol. Microbiol.68, 616–622.PubMedGoogle Scholar
  11. Busse, H.J. and Auling, G. 1988. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst. Appl. Microbiol.11, 1–8.Google Scholar
  12. Chaudhary, D.K. and Kim, J. 2017. Flavobacterium olei sp. nov., a novel psychrotolerant bacterium isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol.67, 2211–2218.PubMedGoogle Scholar
  13. 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
  14. Chen, W.M., Su, C.L., and Sheu, S.Y. 2017a. Flavobacterium dispersum sp. nov., isolated from a freshwater spring. Int. J. Syst. Evol. Microbiol.67, 4416–4423.PubMedGoogle Scholar
  15. Chen, W.M., Su, C.L., and Sheu, S.Y. 2017b. Flavobacterium lacunae sp. nov., isolated from a freshwater pond. Int. J. Syst. Evol. Microbiol.67, 875–882.PubMedGoogle Scholar
  16. Collins, M.D. 1994. Isoprenoid quinones, pp. 265–309. In Goodfellow, M. and O’donnell, A.G. (eds.), Chemical methods in prokaryotic systematics, John Wiley & Sons Ltd, Chichester, UK.Google Scholar
  17. Collins, M.D., Pirouz, T., Goodfellow, M., and Minnikin, D.E. 1977. Distribution of menaquinones in actinomycetes and corynebacteria. J. Gen. Microbiol.100, 221–230.PubMedGoogle Scholar
  18. Dahal, R.H., Chaudhary, D.K., and Kim, J. 2017. Flavobacterium flaviflagrans sp. nov., a bacterium of the family Flavobacteriaceae isolated from forest soil. Int. J. Syst. Evol. Microbiol.67, 2653–2659.PubMedGoogle Scholar
  19. Dong, K., Xu, B., Zhu, F., and Wang, G. 2013. Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli. Int. J. Syst. Evol. Microbiol.63, 3237–3242.PubMedGoogle Scholar
  20. Ekwe, A.P., Ahn, J.H., and Kim, S.B. 2017. Flavobacterium keumense sp. nov., isolated from freshwater. Int. J. Syst. Evol. Microbiol.67, 2166–2170.PubMedGoogle Scholar
  21. Ekwe, A.P. and Kim, S.B. 2018. Flavobacterium commune sp. nov., isolated from freshwater and emended description of Flavobacterium seoulense. Int. J. Syst. Evol. Microbiol.68, 93–98.PubMedGoogle Scholar
  22. Fautz, E. and Reichenbach, H. 1980. A simple test for flexirubintype pigments. FEMS Microbiol. Lett.8, 87–91.Google Scholar
  23. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution39, 783–791.PubMedGoogle Scholar
  24. Fujii, D., Nagai, F., Watanabe, Y., and 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.PubMedGoogle Scholar
  25. Hatayama, K., Ushida, A., and Kuno, T. 2016. Flavobacterium aquicola sp. nov., isolated from river water. Int. J. Syst. Evol. Microbiol.66, 2789–2796.PubMedGoogle Scholar
  26. 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
  27. 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
  28. Komagata, K. and Suzuki, K. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol.19, 161–206.Google Scholar
  29. Koski, P., Hirvela-Koski, V., and Bernardet, J.F. 1993. Flexibacter columnaris infection in arctic char (Salvelinus alpinus l.); first isolation in finland. Bull. Eur. Assoc. Fish. Pathol.13, 66–69.Google Scholar
  30. Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115–175. In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, USA.Google Scholar
  31. 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
  32. 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
  33. Liu, Y., Jin, J.H., Zhou, Y.G., Liu, H.C., and Liu, Z.P. 2010. Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int. J. Syst. Evol. Microbiol.60, 417–421.PubMedGoogle Scholar
  34. Madhaiyan, M., Poonguzhali, S., Lee, J.S., Lee, K.C., and Sundaram, S. 2010. Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean. Int. J. Syst. Evol. Microbiol.60, 2187–2192.PubMedGoogle Scholar
  35. McCammon, S.A., Innes, B.H., Bowman, J.P., Franzmann, P.D., Dobson, S.J., Holloway, P.E., Skerratt, J.H., Nichols, P.D., and Rankin, L.M. 1998. Flavobacterium hibernum sp. nov., a lactose- utilizing bacterium from a freshwater antarctic lake. Int. J. Syst. Bacteriol.48, 1405–1412.PubMedGoogle Scholar
  36. Mesbah, M., Premachandran, U., and 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.Google Scholar
  37. Moya, G., Yan, Z.F., Won, K.H., Yang, J.E., Kook, M.C., and Yi, T.H. 2017. Flavobacterium limi sp. nov., isolated from forest mud. Int. J. Syst. Evol. Microbiol.67, 4667–4673.PubMedGoogle Scholar
  38. Nam, G.G., Joung, Y., Park, M., Kim, S., Jeon, H.T., and Cho, J.C. 2017. Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake. Int. J. Syst. Evol. Microbiol.67, 2440–2445.PubMedGoogle Scholar
  39. Nupur, Bhumika, V., Srinivas, T.N., and Kumar, P.A. 2013. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater. Int. J. Syst. Evol. Microbiol.63, 2490–2496.Google Scholar
  40. Park, S., Choi, J., Choi, S.J., and Yoon, J.H. 2018. Flavobacterium sediminilitoris sp. nov., isolated from a tidal flat. Int. J. Syst. Evol. Microbiol.68, 630–635.PubMedGoogle Scholar
  41. Park, M., Nam, G.G., Kim, S., Jeon, H.T., Joung, Y., and Cho, J.C. 2017. Flavobacterium chuncheonense sp. nov. and Flavobacterium luteum sp. nov., isolated from a freshwater lake. Int. J. Syst. Evol. Microbiol.67, 4409–4415.PubMedGoogle Scholar
  42. Peterson, W.J., Bell, T.A., Etchells, J.L., and Smart, W.W.Jr. 1954. A procedure for demonstrating the presence of carotenoid pigments in yeasts. J. Bacteriol.67, 708–713.PubMedPubMedCentralGoogle Scholar
  43. Pruesse, E., Peplies, J., and Glockner, F.O. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics28, 1823–1829.PubMedPubMedCentralGoogle Scholar
  44. 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.Google Scholar
  45. Ryu, S.H., Park, J.H., Moon, J.C., Sung, Y., Lee, S.S., and Jeon, C.O. 2008. Flavobacterium resistens sp. nov., isolated from stream sediment. Int. J. Syst. Evol. Microbiol.58, 2266–2270.PubMedGoogle Scholar
  46. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Midi inc., Newark, DE, USA.Google Scholar
  47. 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
  48. Smith, N.R., Gordon, R.E., and Clark, F.E. 1952. Aerobic sporeforming bacteria, USDA Agriculture Monograph no. 16. Government printing office, Washington DC, USA.Google Scholar
  49. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol.30, 2725–2729.PubMedPubMedCentralGoogle Scholar
  50. Tindall, B.J. 2005. Respiratory lipoquinones as biomarkers. In Akkermans, A., De bruijn, F., and Van elsas, D. (eds.), Molecular microbial ecology manual, section 4.1.5, supplement1, 2nd edn. Kluwer publishers, Dordrecht, Netherlands.Google Scholar
  51. Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017. 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
  52. Zhang, B., Liu, Z.Q., and Zheng, Y.G. 2017. Flavobacterium quisquiliarum sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol.67, 3965–3970.PubMedGoogle Scholar
  53. Zhou, M.Y., Zhang, X.Y., Yang, X.D., Zhang, Y.J., He, H.L., and Ning, D. 2017. Flavobacterium ardleyense sp. nov., isolated from antarctic soil. Int. J. Syst. Evol. Microbiol.67, 3996–4001.PubMedGoogle Scholar
  54. Zhou, M.Y., Zhang, Y.J., Zhang, X.Y., Yang, X.D., He, H.L., Ning, D., and Du, Z. 2018. Flavobacterium phocarum sp. nov., isolated from soils of a seal habitat in Antarctica. Int. J. Syst. Evol. Microbiol.68, 536–541.PubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer Nature B.V. 2018

Authors and Affiliations

  • Hyun Seo Lee
    • 1
  • Woon Mo Hwang
    • 1
  • Keunsoo Kang
    • 1
  • Tae-Young Ahn
    • 1
    Email author
  1. 1.Department of Microbiology, College of Natural SciencesDankook UniversityCheonanRepublic of Korea

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