Advertisement

Nevskia lacus sp. nov., a gammaproteobacterium isolated from a eutrophic lake

  • Yingshun Cui
  • Seong-Jun Chun
  • A-Ra Cho
  • Shu Kuan Wong
  • Hyung-Gwan Lee
  • Hee-Mock Oh
  • Chi-Yong Ahn
Original Paper

Abstract

A novel Gram-stain negative, rod-shaped and motile bacterial strain, designated strain Seoho-38T, was isolated from a eutrophic lake in South Korea. Polyphasic taxonomic studies were performed to investigate the taxonomic position of the new isolate. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain Seoho-38T formed a distinct cluster with Nevskia ramosa Soe1T, Nevskia persephonica G6M-30T, Nevskia soli GR15-1T, Nevskia terrae KIS13-15T and Nevskia aquatilis F2-63T with bootstrap resampling value of 100%. Of those Nevskia strains, the new isolate shows high sequence similarity with N. ramosa Soe1T (98.7%) and N. persephonica G6M-30T (97.2%), and values lower than 96.5% with the other type strains. The new isolate was observed to grow aerobically in 0–1.5% (w/v) NaCl (optimum 0%), at pH 7.0–9.0 (optimum pH 7.0) and temperature 15–36 °C (optimum 20–30 °C) on R2A medium. DNA–DNA relatedness values between strain Seoho-38T and the type strains of reference species in the genus Nevskia were < 24%. The genomic DNA G + C content was determined to be 67.4 mol%. Ubiquinone-8 (Q-8) (95%) and ubiquinone-7 (Q-7) (5%) were identified as the respiratory quinones. The cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phosphoaminolipid, two glycolipids, an aminolipid and four unidentified lipids. The major fatty acid components were found to include summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:0 ω7c and/or C18:0 ω6c), C16:0 and C14:0. Based on the above polyphasic evidence, strain Seoho-38T (= KCTC 52221T = JCM 31888T) represents a new species of the genus Nevskia, for which the name Nevskia lacus sp. nov. is proposed.

Keywords

Nevskia lacus sp. nov. Nevskia Polyphasic taxonomy Harmful cyanobacterial blooms 

Notes

Acknowledgements

This research was supported by the Basic Core Technology Development Program for the Oceans and the Polar Regions of the National Research Foundation (NRF) and Korea Research Fellowship program, funded by the Ministry of Science and ICT (2016M1A5A1027453 and 2015H1D3A1060001).

Authors contribution

Y.C. analysed data, interpreted results and wrote the manuscript; S.J.C. and C.Y.A took samples; Y.C. and S.J.C. performed genetic, morphological, physiological and chemotaxonomical analysis. A.R.C helped to interpret data analysis. S.K.W, H.G.L, H.M.O. and C.Y.A. revised the manuscript. All authors reviewed and approved the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10482_2018_1206_MOESM1_ESM.docx (484 kb)
Supplementary material 1 (DOCX 483 kb)

References

  1. Cui Y, Baek SH, Wang L, Lee HG, Cui C, Lee ST, Im WT (2012) Streptomyces panacagri sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 62:780–785CrossRefGoogle Scholar
  2. Dastager SG, Mawlankar R, Mual P, Verma A, Krishnamurthi S, Joseph N, Shouche YS (2015) Bacillus encimensis sp. nov. isolated from marine sediment. Int J Syst Evol Microbiol 65:1421–1425CrossRefGoogle Scholar
  3. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229Google Scholar
  4. Famintzin A (1892) Eine neue Bakterienform: Nevskia ramosa. Bull Acad Imp Sci St Petersb New Ser 2:481–486Google Scholar
  5. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  7. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  8. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by highperformance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469CrossRefGoogle Scholar
  9. Jin L, Lee HG, La HJ, Ko SR, Ahn CY, Oh HM (2014) Ferruginibacter profundus sp. nov., a novel member of the family Chitinophagaceae, isolated from freshwater sediment of a reservoir. Antonie Van Leeuwenhoek 106:319–323CrossRefGoogle Scholar
  10. Jin L, Ko SR, Cui Y, Lee CS, Oh HM, Ahn CY, Lee HG (2017) Pusillimonas caeni sp. nov., isolated from a sludge sample of a biofilm reactor. Antonie Van Leeuwenhoek 110:125–132CrossRefGoogle Scholar
  11. Kim SJ, Weon HY, Kim YS, Park IC, Son JA, Kwon SW (2011) Nevskia terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:1226–1229CrossRefGoogle Scholar
  12. 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 62:716–721CrossRefGoogle Scholar
  13. Kimura M (1984) The neutral theory of molecular evolution. Cambridge University Press, CambridgeGoogle Scholar
  14. Lane D (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterialsystematics. Wiley, ChichesterGoogle Scholar
  15. Leandro T, Franca L, Nobre MF, Schumann P, Rossello-Mora R, da Costa MS (2012) Nevskia aquatilis sp. nov. and Nevskia persephonica sp. nov., isolated from a mineral water aquifer and the emended description of the genus Nevskia. Syst Appl Microbiol 35:297–301CrossRefGoogle Scholar
  16. Minnikin D, Patel P, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Evol Microbiol 27:104–117Google Scholar
  17. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie Van Leeuwenhoek 110:455–456CrossRefGoogle Scholar
  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  19. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI Inc, NewarkGoogle Scholar
  20. Sturmeyer H, Overmann J, Babenzien HD, Cypionka H (1998) Ecophysiological and phylogenetic studies of Nevskia ramosa in pure culture. Appl Environ Microbiol 64:1890–1894PubMedPubMedCentralGoogle Scholar
  21. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128CrossRefGoogle Scholar
  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefGoogle Scholar
  23. Tarrand JJ, Groschel DH (1982) Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 16:772–774PubMedPubMedCentralGoogle Scholar
  24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar
  25. Weon HY, Kim BY, Son JA, Song MH, Kwon SW, Go SJ, Stackebrandt E (2008) Nevskia soli sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 58:578–580CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Cell Factory Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonRepublic of Korea
  2. 2.University of Science and Technology (UST)DaejeonRepublic of Korea
  3. 3.Marine Microbiology, Department of Marine Ecosystem Dynamics, Atmosphere and Ocean Research InstituteUniversity of TokyoKashiwaJapan

Personalised recommendations