Abstract
The novel Gram-stain-negative, rod-shaped, aerobic bacterial strain DCR-13T was isolated from a native plant belonging to the genus Campanula on Dokdo, an island in the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence indicated that this strain is closely related to Paraburkholderia peleae PP52-1T (98.43% 16S rRNA gene sequence similarity), Paraburkholderia oxyphila NBRC 105797T (98.42%), Paraburkholderia sacchari IPT 101T (98.28%), Paraburkholderia mimosarum NBRC 106338T (97.80%), Paraburkholderia denitrificans KIS30-44T (97.46%), and Paraburkholderia paradise WAT (97.45%). This analysis of the 16S rRNA gene sequence also suggested that DCR-13T and the six closely related strains formed a clade within the genus Paraburkholderia, but that DCR-13T was clearly separated from the established species. DCR-13T had ubiquinone 8 as its predominant respiratory quinone, and its genomic DNA G + C content was 63.9 mol%. The isolated strain grew at a pH of 6.0–8.0 (with an optimal pH of 6.5), 0–4% w/v NaCl (with an optimal level of 0%), and a temperature of 18–42°C (with an optimal temperature of 30°C). The predominant fatty acids were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1ω6c/C16:1ω7c) and summed feature 2 (C12:0 aldehyde), and the major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. On the basis of polyphasic evidence, it is proposed that strain DCR-13T (= KCTC 62811T = LMG 30889T) represents the type strain of a novel species, Paraburkholderia dokdonella sp. nov.
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Brämer, C.O., Vandamme, P., da Silva, L.F., Gomez, J.G., and Steinbuchel, A. 2001. Polyhydroxyalkanoate-accumulating bacterium isolated from soil of a sugar-cane plantation in Brazil. Int. J. Syst. Evol. Microbiol. 51, 1709–1713.
Chen, W.M., de Faria, S.M., James, E.K., Elliott, G.N., Lin, K.Y., Chou, J.H., Sheu, S.Y., Cnockaert, M., Sprent, J.I., and Vandamme, P. 2007. Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella. Int. J. Syst. Evol. Microbiol. 57, 1055–1059.
Choi, G.M. and Im, W.T. 2018. Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil. Int. J. Syst. Evol. Microbiol. 68, 310–316.
Dobritsa, A.P. and Samadpour, M. 2016. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int. J. Syst. Evol. Microbiol. 66, 2836–2846.
Ezaki, T., Hashimoto, Y., and 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.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.
Gao, Z.H., Zhong, S.F., Lu, Z.E., Xiao, S.Y., and Qiu, L.H. 2018. Paraburkholderia caseinilytica sp. nov., isolated from the pine and broad-leaf mixed forest soil. Int. J. Syst. Evol. Microbiol. 68, 1963–1968.
Hu, H.Y., Fujie, K., and Urano, K. 1999. Development of a novel solid phase extraction method for the analysis of bacterial quinones in activated sludge with a higher reliability. J. Biosci. Bioeng. 87, 378–382.
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.
Koh, H.W., Rani, S., Kim, S.J., Moon, E., Nam, S.W., Rhee, S.K., and Park, S.J. 2017. Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 67, 4298–4303.
Koh, H.W., Song, H.S., Song, U., Yim, K.J., Roh, S.W., and Park, S.J. 2015. Halolamina sediminis sp. nov., an extremely halophilic archaeon isolated from solar salt. Int. J. Syst. Evol. Microbiol. 65, 2479–2484.
Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.
Lee, Y. and Jeon, C.O. 2018. Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil. Int. J. Syst. Evol. Microbiol. 68, 1251–1257.
Lee, C.M., Weon, H.Y., Yoon, S.H., Kim, S.J., Koo, B.S., and Kwon, S.W. 2012. Burkholderia denitrificans sp. nov., isolated from the soil of Dokdo Island, Korea. J. Microbiol. 50, 855–859.
Nei, M., Kumar, S., and Takahashi, K. 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Natl. Acad. Sci. USA 95, 12390–12397.
Otsuka, Y., Muramatsu, Y., Nakagawa, Y., Matsuda, M., Nakamura, M., and Murata, H. 2011. Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives. Int. J. Syst. Evol. Microbiol. 61, 249–254.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glockner, F.O. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196.
Richter, M. and Rossello-Mora, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106, 19126–19131.
Rodriguez-R, L.M. and Konstantinidis, K.T. 2014. Bypassing cultivation to identify bacterial species. Microbe 9, 111–118.
Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.
Sawana, A., Adeolu, M., and Gupta, R.S. 2014. Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front. Genet. 5, 429.
Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Evol. Microbiol. 37, 463–464.
Weber, C.F. and King, G.M. 2017. Volcanic soils as sources of novel CO-oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a member of the Burkholderia cepacia complex. Front. Microbiol. 8, 207.
Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.
Yabuuchi, E., Kosako, Y., Oyaizu, H., Yano, I., Hotta, H., Hashimoto, Y., Ezaki, T., and Arakawa, M. 1992. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol. Immunol. 36, 1251–1275.
Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and 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.
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Jung, MY., Kang, MS., Lee, KE. et al. Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula. J Microbiol. 57, 107–112 (2019). https://doi.org/10.1007/s12275-019-8500-5
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DOI: https://doi.org/10.1007/s12275-019-8500-5