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Metabacillus elymi sp. nov., isolated from the Rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea

Abstract

Dokdo islands in Republic of Korea, is not suited to survive plant because strong wind, low organic content and high salinity. Nevertheless, 64 taxa of plants have a symbiotic relationship with microbe. The Metabacillus elymi KUDC1714T was isolated from the rhizosphere of Elymus tsukushiensis collected from Dokdo Islands. This bacterial strain was Gram-stain positive, non-motile, non-spore forming, aerobic and rod-shape bacteria with 0.4–0.5 × 2.5–3.0 μm in size. Colonies were smooth, yellowish-white circular and 2.0–3.0 mm in diameter. KUDC1714T was capable of growing at 10–45 °C (optimum, 30 °C), pH 7–11 (optimum, pH 8) and 0–8.0% (w/v) NaCl (optimum, 1.0–2.0%). Flagella were not observed by transmission electron microscopy. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that KUDC1714T belonged to the genus Metabacillus formed a phyletic lineage within the genus Metabacillus of the family Bacillaceae. The strain KUDC1714T was most closely related to Metabacillus sediminilitoris DSL-17 T (98.2%), Metabacillus litoralis SW-211 T (98.2%) and Metabacillus halosaccharovorans E33T (97.7%) based on 16S rRNA gene sequence. In silico DNA-DNA hybridization using genome-to-genome distance calculator were analysed at 25.8% and 23.5% in strain KUDC1714T and Metabacillus sediminilitoris DSL-17 T, and strain KUDC1714T and Metabacillus litoralis SW-211 T, respectively. Strain KUDC1714T and its closet type strain were all below cut-off point of the average nucleotide identity and average amino acid identity values. The genome contains 5197 CDSs, 3 rRNAs, 118 tRNAs, 5 ncRNAs. The genomic DNA G + C content was 34.8 mol%. Its polar lipids were diphosphatidylglycerol, phosphatidylglycerol and its major fatty acids were anteiso-C15:0 and iso-C15:0. The strain KUDC1714T contained menaquinone-7 as major isoprenoid quinone. Based on its genetic data, physiological and biochemical characteristics, strain KUDC1714T should be considered a novel species of the genus Metabacillus, for which we propose the name Metabacillus elymi sp. nov. the type strain is KUDC1714T (= KCTC 33222 T, = DSM 27608 T).

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Data availability

Category: New Taxa (Firmicutes and Related Organisms). The GenBank/EMBL/DDBJ accession number for the partial 16S rRNA gene sequence of KUDC1714T is KC414705 and CP055263.

Abbreviations

PG:

Phosphatidylglycerol

DPG:

Diphosphatidylglycerol

TSA:

Tryptic soy agar

TSB:

Tryptic soy broth

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Acknowledgements

We would like to thank the Strategic Initiative for Microbiomes in Agriculture and Food, which is funded by the Ministry of Agriculture, Food and Rural Affairs (918010-4), and the Basic Science Research Program of the National Research Foundation of Korea (NRF), which is funded by the Ministry of Education (No. 2016R1A05011910), for technical support.

Funding

This research was supported by the Basic Science Research Program of the National Research Foundation of Korea (NRF), funded by the Ministry of Education (No. 2016R1A05011910).

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S-Y, Lee and J-S, Son performed experiments and data collection. S-Y, Lee and J-S, Son wrote most of the paper. Y-J, Hwang offered data analysis and interpretation. J-H, shin carried out experiment of whole-genome sequences. S-Y, Ghim provided revisions to scientific content of manuscript. All authors participated this work and approved the final manuscript.

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Correspondence to Sa-Youl Ghim.

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Lee, SY., Son, JS., Hwang, YJ. et al. Metabacillus elymi sp. nov., isolated from the Rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea. Antonie van Leeuwenhoek 114, 1709–1719 (2021). https://doi.org/10.1007/s10482-021-01634-3

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Keywords

  • Metabacillus
  • Dokdo Islands
  • Plant rhizosphere
  • Novel species