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Deinococcus terrigena sp. nov., a novel member of the family Deinococcaceae

Abstract

A bacterial strain, S13-1-2-1T, was isolated from a soil sample collected in Gyeongsangnam-do province, South Korea. Cells were observed to be Gram-stain negative, short rod-shaped and colonies to be pale pink in colour. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus Deinococcus in the family Deinococcaceae, with high levels of sequence similarity with Deinococcus ficus CC-FR2-10T (97.9%) and Deinococcus enclensis NIO-1023T (95.4%). Growth of strain S13-1-2-1T was observed at 10–42 °C, pH 6–8, and in the presence of 0–1.0% NaCl. The isolate was found to exhibit resistance to gamma radiation (D10 10.1 KGy) and UV-light (D10 612 J/m2). The major peptidoglycan amino acids were identified as d-glutamic acid, glycine, alanine and l-ornithine. The predominant respiratory quinone of the strain was identified as menaquinone-8, the major fatty acids were found to be C16:1ω7c (31.4%), C16:0 (18.4%), and C17:1ω8c (17.4%) and the major polar lipids were observed to be an unidentified phosphoglycolipid and an unidentified glycolipid. The genomic DNA G + C content of the strain was determined to be 69.2 mol%. DNA–DNA hybridization with D. ficus showed a relatedness value of 31.5 ± 4.2%. The DNA–DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain S13-1-2-1T represents a novel species in the genus Deinococcus, for which the name Deinococcus terrigena sp. nov. is proposed. The type strain is S13-1-2-1T (= KCTC 33939T = JCM 32248T).

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Acknowledgements

This work was supported by Brain Pool Program (Grant No. 2018H1D3A2065415) through the National Research Foundation (NRF) Funded by the Ministry of Science and ICT, Republic of Korea.

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Leonid N. Ten analysed the data and wrote the manuscript. Huiyun Cho made the original isolation and performed the phenotypic characterisation and 16S rRNA phylogeny. Young-Je Cho performed the phylogenetic and taxonomic analysis. Hee-Young Jung designed, planned the study and wrote the manuscript. All authors approved the final version of the manuscript.

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Correspondence to Hee-Young Jung.

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Fig. S1

Neighbor-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the phylogenetic position of strain S13-1-2-1 T among related strains in the genus Deinococcus. Bootstrap values greater than 50% (percentage of 1000 replications) are shown at branching points. The tree was rooted using Meiothermus ruber ATCC 35948T (Z15059) as outgroup. Bar, 0.02 substitutions per nucleotide position (PPTX 50 kb)

Fig. S2

Transmission electron micrograph of strain S13-1-2-1T grown on R2A agar at 25 °C for 3 days. Bar, 1 µm (PPTX 258 kb)

Fig. S3

Two-dimensional thin layer chromatography of the polar lipids of strain S13-1-2-1T and related Deinococcus species. Strains: (a), S13-1-2-1T; (b), Deinococcus ficus DSM 19119T; (c), Deinococcus radiodurans DSM 20539T. Chloroform/methanol/water (65:25:4, v/v/v) was used in the first dimension, followed by chloroform/acetic acid/methanol/water (80:15:12:4, v/v/v/v) in the second dimension. The following spray reagents were used for detection: 10% ethanolic molybdophosphoric acid (for total lipids); ninhydrin (for aminolipids); molybdenum blue (for phospholipids); and α-naphthol-sulfuric acid reagent (for glycolipids). Abbreviations: APL1, an unidentified aminophospholipid. GL1–GL6, unidentified glycolipids; L1–L4, unidentified polar lipids; PGL1–PGL7, unidentified phosphoglycolipids; PL1–PL3, unidentified phospholipids (PPTX 1274 kb)

Fig. S4

The absorption spectrum of a methanolic pigment extract from strain S13-1-2-1T (PPTX 68 kb)

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Ten, L.N., Cho, H., Cho, YJ. et al. Deinococcus terrigena sp. nov., a novel member of the family Deinococcaceae. Antonie van Leeuwenhoek 112, 389–399 (2019). https://doi.org/10.1007/s10482-018-1167-9

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Keywords

  • Deinococcus
  • Deinococcaceae
  • Polyphasic taxonomy
  • Radiation-resistant
  • Soil bacteria