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Burkholderia ginsengiterrae sp. nov. and Burkholderia panaciterrae sp. nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil

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Abstract

Strain DCY85T and DCY85-1T, isolated from rhizosphere of ginseng, were rod-shaped, Gram-reaction-negative, strictly aerobic, catalase positive and oxidase negative. 16S rRNA gene sequence analysis revealed that strain DCY85T as well as DCY85-1T belonged to the genus Burkholderia and were closely related to Burkholderia fungorum KACC 12023T (98.1 and 98.0 % similarity, respectively). The major polar lipids of strain DCY85T and DCY85-1T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified phospholipids. The major fatty acids of both strains are C16:0, C18:1 ω7c and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant isoprenoid quinone of each strain DCY85T and DCY85-1T was ubiquinone (Q-8) and the G+C content of their genomic DNA was 66.0 and 59.4 mol%, respectively, which fulfill the characteristic range of the genus Burkholderia. The polyamine content of both DCY85T and DCY85-1T was putrescine. Although both DCY85T and DCY85-1T have highly similar 16S rRNA and identical RecA and gyrB sequences, they show differences in phenotypic and chemotaxonomic characteristics. DNA–DNA hybridization results proved the consideration of both strains as two different species. Based on the results from our polyphasic characterization, strain DCY85T and DCY85-1T are considered novel Burkholderia species for which the name Burkholderia ginsengiterrae sp. nov and Burkholderia panaciterrae sp. nov are, respectively, proposed. An emended description of those strains is also proposed. DCY85T and DCY85-1T showed antagonistic activity against the common root rot pathogen of ginseng, Cylindrocarpon destructans. The proposed type strains are DCY85T (KCTC 42054T = JCM 19888T) and DCY85-1T (KCTC 42055T = JCM 19889T).

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Acknowledgments

This research was supported by Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (KIPET NO: 313038-03-1-SB010) and Next-Generation BioGreen 21 Program (SSAC, Grant#: PJ009529032014), Republic of Korea.

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Authors and Affiliations

  1. Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, Yongin, Gyeonggi-do, 449-701, Republic of Korea

    Mohamed El-Agamy Farh, Yeon-Ju Kim, Hoang Van An, Johan Sukweenadhi, Priyanka Singh, Md. Amdadul Huq & Deok-Chun Yang

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  1. Mohamed El-Agamy Farh
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  2. Yeon-Ju Kim
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Correspondence to Yeon-Ju Kim or Deok-Chun Yang.

Additional information

Communicated by Erko Stackebrandt.

The GenBank/EMBL/DDBJ accession number for the 16S rRNA, gyrB and recA gene sequence of strain DCY85T and DCY85-1T are KF915802, KF999960, KM501455, KM501454, KM495734 and KM495735, respectively.

Electronic supplementary material

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203_2014_1075_MOESM1_ESM.tif

Supplementary Fig. S1. Neighbor-joining tree based on the recA gene sequences (approx. 566 bp) of DCY 85T and DCY 85-1T strains with other Burkholderia species. Bootstrap values after 1,000 replicates are expressed as percentages, values less than 50 % are not shown. Bar shows 0.1 substitutions per nucleotide position. (TIFF 619 kb)

203_2014_1075_MOESM2_ESM.tif

Supplementary Fig. S2. Neighbor-joining tree based on the gyrB gene sequences (approx. 690 bp) of DCY 85T and DCY 85-1T strains with reference species. Bootstrap values after 1,000 replicates are expressed as percentages, values less than 50 % are not shown. Bar shows 0.02 substitutions per nucleotide position. (TIFF 536 kb)

203_2014_1075_MOESM3_ESM.tif

Supplementary Fig. S3. Transmission electron microscope (TEM) pictures of both; a, DCY85T and b, DCY85-1T. (TIFF 1623 kb)

203_2014_1075_MOESM4_ESM.tif

Supplementary Fig. S4. Two-dimensional TLC of the total polar lipids of; a, B. ginsengiterrae DCY85T; b, B. panaciterrae DCY85-1T; c, B. fungorum KACC 12023T, stained with 5 % ethanolic molybdophosphoric acid. Abbreviations: PE, phosphatidylethanolamine; (AL), unidentified amino lipids; (PL), unidentified phospholipids and (L), unidentified polar lipids. (TIFF 1476 kb)

203_2014_1075_MOESM5_ESM.tif

Supplementary Fig. S5. Antagonistic activity of DCY85T and DCY85-1T along with B. fungorum KACC 12023T against; (a–d) F. solani; a, control; b, B. fungorum KACC 12023T; c, strain DCY 85T; d, strain DCY 85-1T. (e–h) F. oxysporum; e, control; f, B. fungorum KACC 12023T; g, DCY 85T; h, DCY 85-1T. (i–l) B. cinerea; i, control; j, B. fungorum KACC 12023T; k, DCY 85T; l, DCY 85-1T. (m–p) C. gloeosporioides; m, control; n, B. fungorum KACC 12023T; o, DCY 85T; p, DCY 85-1T. (q–t) C. destructans; q, control; r, B. fungorum KACC 12023T; s, DCY 85T and t, DCY 85-1T. The growth of the pathogens were recorded after 10 days except C. destructans, after 20 days. (TIFF 4892 kb)

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Farh, M.EA., Kim, YJ., Van An, H. et al. Burkholderia ginsengiterrae sp. nov. and Burkholderia panaciterrae sp. nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil. Arch Microbiol 197, 439–447 (2015). https://doi.org/10.1007/s00203-014-1075-y

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