Abstract
Two novel Gram-stain-negative, aerobic, rod shaped bacterial strains BT290T and BT689T were isolated from soil collected in South Korea. Colony morphologies of both strains were circular and convex while the colors of BT290T and BT689T were light-pink and white, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that BT290T and BT689T belong to a distinct lineage within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alphaproteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rR NA gene sequence similarity between two strains was 97.9%. Both strains had the similar quinone system, with ubiquinone 10 (Q-10) as the major respiratory quinone. The major polar lipids of strains BT290T and BT689T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), and phosphatidylglycerol (PG). The major cellular fatty acids of strain BT290T were C18:1 ω7c (58.2%) and C16:0 (17.7%), while those of strain BT689T were C18:1 ω7c (61.8%) and C16:0 (10.8%). On the bases of polyphasic analysis (phylogenetic, chemotaxonomic, and biochemical), strains BT290T and BT689T can be suggested as novel bacterial species within the genus Microvirga and the proposed names are Microvirga terrestris and Microvirga arvi, respectively. The type strain of Microvirga terrestris is BT290T (= KCTC 72367T = NBRC 114844T) and the type strain of Microvirga arvi is BT689T (= KACC 22016T = NBRC 114858T), respectively.
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References
Cappuccino JG, Sherman N (2002) Microbiology-A laboratory manual, 6th edn. Pearson Education, Inc., Benjamin Cummings, California
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
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
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.1093/sysbio/20.4.406
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
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
Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge
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
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. https://doi.org/10.1093/molbev/msy096
Meier-Kolthof JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confdence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Minnikin DE, O’Donnell AG, Goodfellow M et al (1984a) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984b) 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
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
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
Sasser M (1990) Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 MIDI Inc, Newark, DE
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
Veyisoglu A, Tatar D, Saygin H, Inan K, Cetin D, Guven K, Tuncer M, Sahin N (2016) Microvirga makkahensis sp. nov., and Microvirga arabica sp. nov., isolated from sandy arid soil. Anton Leeuw J Microbiol 109:287–296. https://doi.org/10.1007/s10482-020-01421-6
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
Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, JO Ka (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
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 67:1613–1616. https://doi.org/10.1099/ijsem.0.001755
Zhang J, Song F, Xin YH, Zhang J, Fang C (2009) Microvirga guangxiensis sp. nov., a novel alphaproteobacterium from soil, and emended description of the genus Microvirga. Int J Syst Evol Microbiol 59:1997–2001. https://doi.org/10.1099/ijs.0.007997-0
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
Acknowledgements
This work was supported by a research grant from Seoul Women’s University (2020-0268) 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), and by R&D Program for Forest Science Technology (Project No. 2021375C10-2123-BD02) provided by Korea Forest Service (Korea Forestry Promotion Institute).
We are grateful to Dr. Aharon Oren (The Hebrew University of Jerusalem, Israel) for helping with the etymology.
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Ministry of Environment, NIBR202002203
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The 16S rRNA gene sequences of strains BT290T and BT689T were deposited in GenBank/EMBL/DDBJ under the accession numbers MT795754 and MT795749 Respectively. The draft genome sequences of strains BT290T and BT689T are available under the following accession numbers NZ_JADQDN000000000 and NZ_JAFEMD000000000, respectively.
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Damdintogtokh, T., Park, Y., Maeng, S. et al. Microvirga terrestris sp. nov., and Microvirga arvi sp. nov., isolated from soil in South Korea. Arch Microbiol 204, 525 (2022). https://doi.org/10.1007/s00203-022-03109-z
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DOI: https://doi.org/10.1007/s00203-022-03109-z