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Microvirga pudoricolor sp. nov., and Microvirga alba sp. nov., isolated from soil in South Korea

Abstract

Two novel Gram-stain-negative, aerobic, rod-shaped, circular, convex, light-pink and white-colored bacterial strains BT291T and BT350T were isolated from soil collected in Uijeongbu city (37° 44′ 55″ N, 127° 2′ 20″ E) and Jeju island (33° 22′ 48″ N, 126° 31′ 48″ E), respectively, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each of the strains BT291T and BT350T belong to a distinct lineages within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alpha Proteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rRNA gene sequence similarity between the two strains BT291T and BT350T was 97.4%. The two strains were found to have the same quinone system, with Q-10 as the major respiratory quinone. The major polar lipids of strains BT291T and BT350T were phosphatidylethanolamine (PE), diphosphatydilglycerol (DPG), phosphatidylcholine (PC) and phosphatidylglycerol (PG). The major cellular fatty acids of strain BT291T were C18:1 ω7c (58.2%) and cyclo-C19:0 ω8c (25.7%). The major cellular fatty acids of strain BT350T were C18:1 ω7c (38.5%) and cyclo-C19:0 ω8c (27.7%). Based on the polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT291T and BT350T can be suggested as two novel bacterial species within the genus Microvirga and the proposed names are Microvirga pudoricolor and Microvirga alba, respectively. The type strain of Microvirga pudoricolor is BT291T (= KCTC 72368T = NBRC 114845T) and the type strain of Microvirga alba is BT350T (= KCTC 72385T = NBRC 114848T).

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References

  1. Cappuccino JG, Sherman N (2002) Microbiology—a laboratory manual, 6th edn. Pearson Education, Inc., Benjamin Cummings

    Google Scholar 

  2. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516

    CAS  Article  PubMed  Google Scholar 

  3. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x

    Article  PubMed  PubMed Central  Google Scholar 

  5. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.2307/2412116

    Article  Google Scholar 

  6. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469. https://doi.org/10.2323/jgam.42.457

    CAS  Article  Google Scholar 

  7. Jimenez-Gomez A, Saati-Santamaria Z, Igual JM, Rivas R, Mateos PF, Garcia-Fraile P (2019) Genome insights into the novel species Microvirga brassicacearum, a rapeseed endophyte with biotechnological potential. Microorganisms. https://doi.org/10.3390/microorganisms7090354

    Article  PubMed  PubMed Central  Google Scholar 

  8. Kanso S, Patel BK (2003) Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 53:401–406. https://doi.org/10.1099/ijs.0.02348-0

    CAS  Article  PubMed  Google Scholar 

  9. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  10. Komagata K, Suzuki K (1987) 4 Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 19:161–207. https://doi.org/10.1016/S0580-9517(08)70410-0

    CAS  Article  Google Scholar 

  11. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA x: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549

    CAS  Article  Google Scholar 

  12. Li J, Gao R, Chen Y, Xue D, Han J, Wang J, Dai Q, Lin M, Ke X, Zhang W (2020) Isolation and identification of Microvirga thermotolerans HR1, a novel thermo-tolerant bacterium, and comparative genomics among Microvirga Species. Microorganisms. https://doi.org/10.3390/microorganisms8010101

    Article  PubMed  PubMed Central  Google Scholar 

  13. Liu ZT, Xian WD, Li MM, Liu L, Ming YZ, Jiao JY, Fang BZ, Xiao M, Li WJ (2020) Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments. Antonie Van Leeuwenhoek 113:1147–1153. https://doi.org/10.1007/s10482-020-01421-6

    CAS  Article  PubMed  Google Scholar 

  14. 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 

  15. 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 Meth 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6

    CAS  Article  Google Scholar 

  16. Msaddak A, Rejili M, Duran D, Mars M, Palacios JM, Ruiz-Argueso T, Rey L, Imperial J (2019) Microvirga tunisiensis sp. nov., a root nodule symbiotic bacterium isolated from Lupinus micranthus and L. luteus grown in Northern Tunisia. Syst Appl Microbiol 42:126015. https://doi.org/10.1016/j.syapm.2019.126015

    Article  PubMed  Google Scholar 

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

    CAS  Article  Google Scholar 

  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    CAS  Article  Google Scholar 

  19. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids

  20. Tapase SR, Mawlankar RB, Sundharam SS, Krishnamurthi S, Dastager SG, Kodam KM (2017) Microvirga indica sp. nov., an arsenite-oxidizing Alphaproteobacterium, isolated from metal industry waste soil. Int J Syst Evol Microbiol 67:3525–3531. https://doi.org/10.1099/ijsem.0.002157

    CAS  Article  PubMed  Google Scholar 

  21. Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Wang F, Yang L, Deng J, Liu X, Lu Y, Chen W, Wu J (2019) Microvirga calopogonii sp. nov., a novel alphaproteobacterium isolated from a root nodule of Calopogonium mucunoides in Southwest China. Antonie Van Leeuwenhoek 112:1593–1602. https://doi.org/10.1007/s10482-019-01285-5

    CAS  Article  PubMed  Google Scholar 

  23. Weisburg WG, Barns SM, Pellerier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. Weon HY, Kwon SW, Son JA, Joee EH, Kim SJ, Kim YS, Kim BY, Kae JO (2010) Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga. Int J Syst Evol Microbiol 60:2596–2600. https://doi.org/10.1099/ijs.0.018770-0

    CAS  Article  PubMed  Google Scholar 

  25. Yoon S, Ha S, Kwon S, Lim J, Kim Y et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–16. https://doi.org/10.1007/s10482-017-0844-4

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Zhang XJ, Zhang J, Yao Q, Feng GD, Zhu HH (2019) Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga. Int J Syst Evol Microbiol 69:667–671. https://doi.org/10.1099/ijsem.0.003189

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

This work was supported by a research grant from Seoul Women’s University (2021) and by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202002203). In addition, we are grateful to Dr. Aharon Oren (The Hebrew University of Jerusalem, Israel) for helping with the etymology.

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Correspondence to Sathiyaraj Srinivasan.

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The 16S rRNA gene sequences of the strains BT291T and BT350T were deposited in GenBank/EMBL/DDBJ under the accession numbers are MT795755 and MT795757, respectively. The draft genome sequences of the strains BT291T and BT350T are available at the following accessions JAFEMB000000000 and JADQDO010000000, respectively.

Communicated by Erko Stackebrandt.

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Oh, H., Kim, M.K. & Srinivasan, S. Microvirga pudoricolor sp. nov., and Microvirga alba sp. nov., isolated from soil in South Korea. Arch Microbiol (2021). https://doi.org/10.1007/s00203-021-02569-z

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Keywords

  • Methylobacteriaceae
  • Microvirga
  • Taxonomy