Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System

Abstract

A novel light-yellow-coloured, Gram-stain-positive, nearly-coccoid, aerobic bacterium, designated strain ID2601ST was isolated from a car evaporator core collected from South Korea. Strain ID2601ST was catalase positive and oxidase negative, able to grow at pH 6.0–8.0, temperature 20–45 °C, and 0–6.0% (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain ID2601ST belonged to the genus Flexivirga, with the nearest phylogenetic neighbour being Flexivirga endophytica YIM 7505T (97.9% sequence similarity). The strain comprised diphosphatidylglycerol as the main polar lipid; MK-8(H4) as a predominant respiratory quinone; serine, alanine, glycine, glutamic acid, and lysine as main components of peptidoglycan and iso-C16:0, summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl), anteiso-C17:0, and C17:0 10-methyl as the major fatty acids. The average nucleotide identity (ANI) values between strain ID2601ST and the closest species (Flexivirga endophytica YIM 7505T and Flexivirga caeni BO-16T) were < 78%. The in silico DNA–DNA hybridization (dDDH) values of strain ID2601ST with the closest species were < 22%. These observations were below the threshold values of 95% (for ANI) and 70% (for dDDH) used for species delineation. The DNA G+C content was 69.8 mol%. Based on the polyphasic taxonomic data, the novel species Flexivirga aerilata sp. nov. is proposed with the type strain ID2601ST (=KCTC 49353T =NBRC 114622T).

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. 1.

    Anzai K, Sugiyama T, Sukisaki M et al (2011) Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae. J Antibiot 64:613–616

    CAS  Article  Google Scholar 

  2. 2.

    Keum DH, Lee YJ, Lee SY, Im WT (2020) Flexivirga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 70:1266–1272

    CAS  Article  Google Scholar 

  3. 3.

    Gao R, Liu BB, Yang W et al (2016) Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil. Int J Syst Evol Microbiol 66:3388–3392

    CAS  Article  Google Scholar 

  4. 4.

    Kang W, Hyun DW, Kim PS et al (2016) Flexivirga lutea sp. nov., isolated from the faeces of a crested ibis, Nipponia nippon, and emended description of the genus Flexivirga. Int J Syst Evol Microbiol 66:3594–3599

    CAS  Article  Google Scholar 

  5. 5.

    Hyeon JW, Kim HR, Lee HJ et al (2017) Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012. Int J Syst Evol Microbiol 67:479–484

    CAS  Article  Google Scholar 

  6. 6.

    Frank JA, Reich CI, Sharma S et al (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

    CAS  Article  Google Scholar 

  7. 7.

    Chaudhary DK, Kim J (2018) Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 68:305–309

    CAS  Article  Google Scholar 

  8. 8.

    Yoon SH, Ha SM, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    CAS  Article  Google Scholar 

  9. 9.

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

    CAS  Article  Google Scholar 

  10. 10.

    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    CAS  Article  Google Scholar 

  11. 11.

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

    CAS  PubMed  Google Scholar 

  12. 12.

    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406

    Article  Google Scholar 

  13. 13.

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

    CAS  Article  Google Scholar 

  14. 14.

    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

    CAS  Article  Google Scholar 

  15. 15.

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

    Google Scholar 

  16. 16.

    Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589

    CAS  Article  Google Scholar 

  17. 17.

    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214

    CAS  Article  Google Scholar 

  18. 18.

    Lee I, Chalita M, Ha S-M et al (2017) ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 67:2053–2057

    CAS  Article  Google Scholar 

  19. 19.

    Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624

    CAS  Article  Google Scholar 

  20. 20.

    Aziz RK, Bartels D, Best AA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  Google Scholar 

  21. 21.

    Blin K, Shaw S, Steinke K et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87

    CAS  Article  Google Scholar 

  22. 22.

    Yoon S-H, Ha S, Lim J et al (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

    CAS  Article  Google Scholar 

  23. 23.

    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  24. 24.

    Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN et al (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington DC, pp 21–33

    Google Scholar 

  25. 25.

    Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Reddy CA, Beveridge TJ, Breznak JA et al (eds) Methods for general and molecular bacteriology, 3rd edn. American Society of Microbiology, Washinton, DC, pp 309–329

    Google Scholar 

  26. 26.

    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 607–654

    Google Scholar 

  27. 27.

    Minnikin DE, O’Donnell AG, Goodfellow M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  28. 28.

    Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354

    CAS  Article  Google Scholar 

  29. 29.

    Komagata K, Suzuki KI (1988) 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  Google Scholar 

  30. 30.

    Bousfield GR, Sugino H, Ward DN (1985) Demonstration of a COOH-terminal extension on equine lutropin by means of a common acid-labile bond in equine lutropin and equine chorionic gonadotropin. J Biol Chem 260:9531–9533

    CAS  Article  Google Scholar 

  31. 31.

    Sasser M (1990) Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). MIDI Tech Note 101 Newwark, MIDI Inc

  32. 32.

    Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    CAS  Article  Google Scholar 

  33. 33.

    Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    CAS  Article  Google Scholar 

  34. 34.

    Wayne LG, Brenner DJ, Colwell RR et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464

    Article  Google Scholar 

  35. 35.

    Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This research was supported by Sangji University Research Fund, 2020 and grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202002108).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Dong-Uk Kim.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest regarding the publication of this manuscript.

Ethical Approval

This study does not describe any experimental work related to human.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Electronic supplementary material 1 (DOCX 1788 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chaudhary, D.K., Lee, H., Dahal, R.H. et al. Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System. Curr Microbiol 78, 796–802 (2021). https://doi.org/10.1007/s00284-020-02300-z

Download citation