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Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field

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Abstract

A Gram-stain negative, strictly aerobic, motile by gliding, rod-shaped and yellow pigmented strain THG-G12T was isolated from soil of a bamboo field in Seoul, Republic of Korea. Strain THG-G12T was observed to grow well at 20–28 °C and pH 7.0–7.5 in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG-G12T was found to be most closely related to Pedobacter ginsengisoli Gsoil 104T (97.5 % sequence similarity), Pedobacter steynii WB2.3-45T (97.4 %), Pedobacter metabolipauper WB2.3-71T (97.2 %), Pedobacter nyackensis NWG-II14T (97.2 %), Pedobacter caeni LMG 22862T (97.1 %) and Pedobacter duraquae WB2.1-25T (97.0 %), but DNA relatedness between strain THG-G12T and its phylogenetically closest neighbours was below 9.5 %. The G+C content of the genomic DNA was determined to be 39.9 mol%. The only isoprenoid quinone detected in strain THG-G12T was menaquinone-7 (MK-7). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were found to be phosphatidylethanolamine, unidentified phosphoglycolipids, unidentified aminophosphoglycolipids, unidentified aminolipids and unidentified lipids. Strain THG-G12T showed the presence of two ceramide phosphorylethanolamines (CerPE-2′ and CerPE-2″), dihydrosphingosines and an unidentified ceramide as the major ceramide. The major fatty acids were identified as summed feature 3 (as defined by the MIDI system; C16:1 ω7c and/or C16:1 ω6c) and iso-C15:0. These data support the affiliation of strain THG-G12T to the genus Pedobacter. The results of physiological and biochemical tests enabled strain THG-G12T to be differentiated genotypically and phenotypically from the recognized species of the genus Pedobacter. Therefore, the novel isolate represents a novel species, for which the name Pedobacter seoulensis sp. nov. is proposed, with THG-G12T as the type strain (=KACC 17529T =JCM 19363T).

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Acknowledgments

This research was a part of the project titled ‘The development of functional foods to enhance immune from Hiziki extracts (HIMMS-1)(PJT200434)’, funded by the Ministry of Oceans and Fisheries, Korea.

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  1. Department of Oriental Medicinal Material & Processing, College of Life Science, Kyung Hee University, Yongin, Gyeonggi, 446-701, Republic of Korea

    Hien T. T. Ngo, Heung-Min Son, Sang-Yong Park & Tae-Hoo Yi

  2. Department of Genetic Engineering, College of Life Science, Kyung Hee University, Yongin, Gyeonggi, 446-701, Republic of Korea

    Ki-Young Kim

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  1. Hien T. T. Ngo
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Correspondence to Tae-Hoo Yi.

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Hien T. T. Ngo and Heung-Min Son have equally contributed to this work.

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Supplementary Fig. S5

Transmission electron micrograph of cells of strain THG–G12T after negative staining with uranyl acetate. Bar 200 nm (TIFF 1722 kb)

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Ngo, H.T.T., Son, HM., Park, SY. et al. Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field. Antonie van Leeuwenhoek 105, 961–970 (2014). https://doi.org/10.1007/s10482-014-0154-z

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