Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Microbacterium elymi sp. nov., Isolated from the Rhizospheric Soil of Elymus tsukushiensis, a Plant Native to the Dokdo Islands, Republic of Korea

  • Ye-Ji Hwang (Microbiology Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Soo-Yeong Lee (Microbiology Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Jin-Soo Son (Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB) ;
  • Jin-suk Youn (School of Life Sciences, Research Institute for Dok-do & Ulleung-do Island, Kyungpook National University) ;
  • Woong Lee (School of Life Sciences, Research Institute for Dok-do & Ulleung-do Island, Kyungpook National University) ;
  • Jae-Ho Shin (School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University) ;
  • Mi-Hwa Lee (Microbiology Research Department, Nakdonggang National Institute of Biological Resources) ;
  • Sa-Youl Ghim (School of Life Sciences, Research Institute for Dok-do & Ulleung-do Island, Kyungpook National University)
  • Received : 2022.11.13
  • Accepted : 2022.12.29
  • Published : 2023.02.28
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Abstract

Microbacterium elymi KUDC0405T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 ㎛. Based on 16S rRNA gene sequences, KUDC0405T was most closely related to Microbacterium bovistercoris NEAU-LLET (97.8%) and Microbacterium pseudoresistens CC-5209T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405T and M. bovistercoris NEAU-LLET and M. pseudoresistens CC-5209T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405T, M. bovistercoris NEAU-LLET, and M. pseudoresistens CC-5209T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C17:0 and iso-C16:0. Strain KUDC0405T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405T (=KCTC 49411T, =CGMCC1.18472T).

Keywords

Acknowledgement

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2016R1A6A1A05011910), and by a grant from the Nakdong-gang National Institute of Biological Resources (NNIBR) funded by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR202202108). We are grateful to Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (918010-4), for helping us with the genome sequencing.

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