Microbacterium elymi sp. nov., Isolated from the Rhizospheric Soil of Elymus tsukushiensis, a Plant Native to the Dokdo Islands, Republic of Korea

Abstract

The genus Microbacterium was classified by Orla-Jensen S [1] based on the d-lactic acid-producing bacteria in milk. At that time, the genus Microbacterium comprised 157 species, including Microbacterium aerolatum V-73 T [2], M. agarici CC-SBCK-209 T Microbacterium can be isolated from various sources, such as seawater, desert soil, maize rhizosphere, cow dung, and microfiltered milk. Members of this genus are Gramstain-positive, rod-shaped, and have an optimum growth temperature of 20-30°C. Here, we report a taxonomic analysis of the novel bacterial strain, KUDC0405 T , isolated from the rhizospheric soil of Elymus tsukushiensis, a plant native to the Dokdo Islands (37°14′24.2′′ N, 131°52′12.2′′ E). During microbial diversity monitoring in April 2014, rhizospheric soil samples were collected from native plants of the Ulleungdo and Dokdo Islands (Ulleunggun, Gyeongsangbuk-do). E. tsukushiensis var. trasiens (Hack.) Osada is native to the Dokdo Islands and is the dominant plant species on these islands, and its distribution is expanding [9]. The Dokdo Islands are a group of volcanic islands located in the middle of the East Sea, east of the Republic of Korea (37°14′24.2′′N, 131°52′12.2′′E; Uljin-gun, Gyeongsangbuk-do). The island group consists of two large islands (Dong-do and Seo-do) and 89 small islets, and high concentrations of Ba, K, and Rb have been detected in soil [10]. Despite the difficult survival Microbacterium elymi KUDC0405 T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405 T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405 T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 μm. Based on 16S rRNA gene sequences, KUDC0405 T was most closely related to Microbacterium bovistercoris NEAU-LLE T (97.8%) and Microbacterium pseudoresistens CC-5209 T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405 T and M. bovistercoris NEAU-LLE T and M. pseudoresistens CC-5209 T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405 T , M. bovistercoris NEAU-LLE T , and M. pseudoresistens CC-5209 T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405 T 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-C 17:0 and iso-C 16:0 . Strain KUDC0405 T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405 T 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 KUDC0405 T (=KCTC 49411 T , =CGMCC1.18472 T ).