Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field

Abstract

A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107T was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107T was found to occur at 4–37 °C (optimum, 20–30 °C), at pH 5.5–10 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107T was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5T (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107T was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C15:0 (26.3 %), iso-C17:0 3OH (12.6 %) and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107T has β-glucosidase activity to convert ginsenosides Rb1 and Rd into Gyp17 and F2. DNA-DNA hybridization with F. denitrificans ED5T was 52 %. Strain THG-107T could be distinguished from F. denitrificans ED5T and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107T = KACC 16219T = LMG 26575T).

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Acknowledgments

This work was supported by the 2012 research program of a grant from the Kyung Hee University in 2012 (20120596), Republic of Korea.

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Correspondence to Tae-Hoo Yi.

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Heung-Min Son and Moochang Kook equally contributed to this work.

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Supplementary Fig S1

Maximum-likelihood tree based on 16S rRNA gene sequences showing the relationships between strain THG-107T and other related type species. Numbers at nodes represent percentages of bootstrap support based on a maximum-likelihood analysis of 1,000 resampled datasets. (TIFF 4708 kb)

Supplementary Fig. S2

RP-HPLC analyses of polyamines of strains THG-107T. (a) Strain THG-107T, (b) Homospermidine standard strain: Sphingomonas kyungheensis THG-B283T (Son et al. 2013), (c) Spermidine standard, (d) Spermine standard. Abbreviations: HSPD, Homospermidine; SPD, Spermidine; SPM, Spermine; DAO, 1ֽ8-Diaminooctane. (TIFF 4442 kb)

Supplementary Fig. S3

Two-dimensional thin-layer chromatography of polar lipids of strain THG-107T. (a) Total lipids detected by spraying with 5% molybdatophosphoric acid, (b) Phospholipids detected by spraying with molybdenum blue, (c) Aminolipids detected by spraying with 0.2% ninhydrin. Abbreviations: PE, phosphatidylethanolamine; AL1-4, unidentified aminolipids; L1-2, unidentified lipids. (TIFF 3320 kb)

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Son, HM., Kook, M., Park, SY. et al. Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field. Antonie van Leeuwenhoek 104, 1029–1037 (2013). https://doi.org/10.1007/s10482-013-0023-1

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Keywords

  • Flavobacterium kyungheensis sp. nov.
  • 16S rRNA gene
  • Polyphasic taxonomy