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Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample

Abstract

A novel strain, YIM 131921T, was isolated from a Physcia sp. lichen collected from the South Bank Forest of the Baltic Sea. The strain is Gram-negative, catalase positive and oxidase negative, strictly aerobic, asporogenous, non-motile and reddish brown in colour. The temperature and pH for growth were found to be 20–30 °C (optimum 28 °C) and pH 6.5–12.0 (optimum pH 7.0 ± 0.5). No growth was observed in the presence of NaCl. Based on 16S rRNA gene sequence similarity, strain YIM 131921T shares high similarities with Rubellimicrobium roseum YIM 48858T (98.3%), followed by Rubellimicrobium mesophilum MSL-20T (96.8%), Rubellimicrobium aerolatum 5715S-9T (96.1%) and Rubellimicrobium thermophilum DSM 16684T (96.0%). Phylogenetic trees showed YIM 131921T forms a cluster with type strains of the genus Rubellimicrobium. The predominant cellular fatty acids (> 20%) were identified as summed feature 8 (C18:1ω7c) and C16:0. Q-10 was found to be the predominant respiratory ubiquinone. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, glycolipid, phospholipids and an unidentified aminolipid. The DNA G + C content of the draft genome sequence is 66.6 mol%. Strain YIM 131921T showed an average nucleotide identity value of 80.3% and a digital DNA–DNA hybridizations value of 26.1% with the reference strain R. roseum YIM 48858T based on draft genome sequences. Based on comparative analyses of phenotypic, molecular, chemotaxonomic data and genomic comparisons, strain YIM 131921T is concluded to represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium rubrum sp. nov. is proposed. The type strain is YIM 131921T (= CGMCC 1.13958T = NBRC 114054T = KCTC 72461T).

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Acknowledgements

Funding was provided by National Natural Science Foundation of China (31460005).

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L-QJ: performed the experiments and wrote the manuscript; X-YW: collected the lichen samples; KZ and G-DL: analysed the data; S-BS and Q-YL: performed the study; D-FA and LL: analysed the data; L-SW: identified the lichen samples; YJ: guided the experiments and revised the manuscript; C-LJ: designed the study.

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Correspondence to Yi Jiang.

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Jiang, LQ., Zhang, K., Li, GD. et al. Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample. Antonie van Leeuwenhoek 112, 1739–1745 (2019). https://doi.org/10.1007/s10482-019-01304-5

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Keywords

  • Rubellimicrobium rubrum
  • New species
  • Physcia sp. lichen
  • 16S rRNA gene
  • Draft genome sequences