Nibribacter flagellatus sp. nov., isolated from rhizosphere of Hibiscus syriacus and emended description of the genus Nibribacter

Abstract

A Gram-stain negative, aerobic, motile by flagella, rod-shaped strain (THG-T16T) was isolated from rhizosphere of Hibiscus syriacus. Growth occurred at 10–40 °C (optimum 28–30 °C), at pH 6.0–8.0 (optimum 7.0) and at 0–1.0% NaCl (optimum 0%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-T16T were identified as Nibribacter koreensis KACC 16450T (98.6%), Rufibacter roseus KCTC 42217T (94.7%), Rufibacter immobilis CCTCC AB 2013351T (94.5%) and Rufibacter tibetensis CCTCC AB 208084T (94.4%). The DNA G+C content of strain THG-T16T was determined to be 46.7 mol%. DNA–DNA hybridization values between strain THG-T16T and N. koreensis KACC 16450T, R. roseus KCTC 42217T, R. immobilis CCTCC AB 2013351T, R.tibetensis CCTCC AB 208084T were 33.5 ± 0.5% (31.7 ± 0.7% reciprocal analysis), 28.1 ± 0.2% (25.2 ± 0.2%), 17.1 ± 0.9% (10.2 ± 0.6%) and 8.1 ± 0.3% (5.2 ± 0.1%). The polar lipids were identified as phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and three unidentified lipids. The quinone was identified as MK-7 and the polyamine as sym-homospermidine. The major fatty acids were identified as C16:1 ω5c, C17:1 ω6c, iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics, and DNA–DNA hybridization data, strain THG-T16T represents a novel species of the genus Nibribacter, for which the name Nibribacter flagellatus sp. nov. is proposed. The type strain is THG-T16T(= KACC 19188T = CCTCC AB 2016246T).

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References

  1. Abaydulla G, Luo X, Shi J, Peng F, Liu M, Wang YQ, Dai J, Fang CX (2012) Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 101:725–731

    CAS  Article  Google Scholar 

  2. Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K (2017) Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiol Ecol. https://doi.org/10.1093/femsec/fix050

    Article  PubMed  Google Scholar 

  3. Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    CAS  Article  Google Scholar 

  5. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  Article  Google Scholar 

  6. Deng LJ et al (2015) Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil. Appl Microbiol Biotechnol 99:8259–8269

    CAS  Article  Google Scholar 

  7. 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 Bacteriol 39:224–229

    Article  Google Scholar 

  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  Article  Google Scholar 

  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791

    Article  Google Scholar 

  10. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series Vol. 41, No. 41, pp. 95–98

  11. Hu HY, Lim BR, Goto N, Fujie K (2001) Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 47:17–24

    CAS  Article  Google Scholar 

  12. Kang JY, Chun J, Jahng KY (2013) Nibribacter koreensis gen. nov., sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 63:4663–4668

    CAS  Article  Google Scholar 

  13. Kimura M (1984) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Google Scholar 

  14. Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Biol 18:1–32

    Article  Google Scholar 

  15. Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    CAS  Article  Google Scholar 

  16. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    CAS  Article  Google Scholar 

  17. Larkin MA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  Article  Google Scholar 

  18. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  19. Minnikin DE, O’donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  20. Polkade AV, Ramana VV, Joshi A, Pardesi L, Shouche YS (2015) Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake. Int J Syst Evol Microbiol 65:1592–1597

    CAS  Article  Google Scholar 

  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  22. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark, DE

  23. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams & Wilkins, Baltimore

    Google Scholar 

  24. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A, Boero F, Alifano P (2008) Epibiotic Vibrio luminous bacteria isolated from some Hydrozoa and Bryozoa species. Microb Ecol 56:625–636

    CAS  Article  Google Scholar 

  25. Taibi G, Schiavo M, Gueli M, Rindina PC, Muratore R, Nicotra C (2000) Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B 745:431–437

    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

    CAS  Article  Google Scholar 

  27. Wayne LG et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  28. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    CAS  Article  Google Scholar 

  29. Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook MC, Yi TH (2015) Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the nationalflower of South Korea. Int J Syst Evol Microbiol 66:4754–4759

    Google Scholar 

  30. Yan ZF, Lin P, Chu X, Kook MC, Li CT, Yi TH (2016) Aeromicrobium halotolerans sp. nov., isolated from desert soil sample. Arch Microbiol 198:423–427

    CAS  Article  Google Scholar 

  31. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, 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

    Article  Google Scholar 

  32. Zhang ZD, Gu MY, Zhu J, Li SH, Zhang LJ, Xie YQ, Shi YH, Wang W, Li WJ (2015) Rufibacter roseus sp. nov., isolated from radiation-polluted soil. Int J Syst Evol Microbiol 65:1572–1577

    CAS  Article  Google Scholar 

Download references

Funding

This work was conducted under the industrial infrastructure program for fundamental technologies which is funded by the Ministry of Trade, Industry & Energy (MOTIE), Korea (No. N0000888).

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Correspondence to Tae-Hoo Yi.

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It is the original work of the authors. The work described has not been submitted elsewhere for publication, in whole or in part, and all authors listed carry out the data analysis and manuscript writing and “This article does not contain any studies with human participants or animals performed by any of the authors”. Moreover, all authors read and approved the final manuscript. The authors declare that they have no direct or indirect conflict of interest.

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Lin, P., Yan, ZF., Li, CT. et al. Nibribacter flagellatus sp. nov., isolated from rhizosphere of Hibiscus syriacus and emended description of the genus Nibribacter. Antonie van Leeuwenhoek 111, 1777–1784 (2018). https://doi.org/10.1007/s10482-018-1065-1

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Keywords

  • Nibribacter flagellatus sp. nov
  • Polyphasic analysis
  • 16S rRNA gene
  • Phenotypic characteristics