Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine

Abstract

A pleomorphic and non-motile halophilic archaeon forming light-red pigmented colonies, strain ZC67T, was isolated from the Yuanyongjing Salt Mine, Yunnan, China. Based on similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain ZC67T belongs to the genus Halorubrum and is closely related to the species of Halorubrum (Hrr.) saccharovorum JCM 8865T, Hrr. persicum C49T, Hrr. halophilum B8T, Hrr. lipolyticum 9-3T, Hrr. salsamenti Y69T and Hrr. depositum Y78T with 16S rRNA gene sequence similarities of 99.0%, 98.7%, 98.5%, 98.4%, 98.1% and 97.7%, respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain ZC67T and its close relatives were less than 90.5% and 89.3%, respectively. In silico DNA-DNA hybridization (DDH) analysis showed that DNA-DNA relatedness between strain ZC67T and its relatives is less than 45%. Values of ANI, AAI and in silico DDH were clearly below the thresholds used for the delineation of a new species. The major polar lipids of strain ZC67T were similar to other neutrophilic members in the genus Halorubrum containing phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl-glucosyl-glycerol diether-1. The DNA G+C content was determined to be 66.3 mol% (based on the draft genome). Combined with other diagnostic characteristics, e.g. phenotypic and chemotaxonomic differences, strain ZC67T is concluded to represent a novel species in the genus Halorubrum, for which the name Halorubrum amylolyticum sp. nov. is proposed. The type strain is ZC67T (=CGMCC 1.15718T = JCM 31850T).

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Abbreviations

MES:

2-Morpholinoethanesulfonic acid

PIPES:

1, 4-Piperazine bis (ethanesulfonic acid)

HEPES:

4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid

CHES:

2-(Cyclohexylamino) ethanesulfonic acid

DMSO:

dimethylsulfoxide

CGMCC:

China General Microbiological Culture Collection Center

JCM:

Japan Collection of Microorganisms

IU:

International Unit of enzyme activity

MEGA:

Molecular Evolutionary Genetics Analysis

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Acknowledgements

We thank Professor Zhu L. Yang from the Kunming Institute of Botany, Chinese Academy of Sciences for the help in sample collection.

Funding

This work was supported by grants from the National Natural Science Foundation of China (31460003), the Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources (591601), the China Scholarship Council (201808340054) and the Department of Education Anhui Province, China.

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SC conceived the project. SS, FC, YX, JL and SC performed the experiments. SS and SC analysed the data, and drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to Shaoxing Chen.

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The authors declare that they have no conflict of interest.

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No specific ethical or institutional permits were required to conduct sampling and the experimental studies did not involve endangered or protected species.

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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and rpoB′ genes of strain ZC67T are KX376720 and KX595316, respectively. The accession numbers for the genome sequences of strains ZC67T, Hrr. salsamenti Y69T and Hrr. depositum Y78T are SDJP00000000, VCNL00000000 and VCNM00000000, respectively.

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Sun, S., Chen, F., Xu, Y. et al. Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine. Antonie van Leeuwenhoek 112, 1849–1861 (2019). https://doi.org/10.1007/s10482-019-01313-4

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Keywords

  • Haloarchaea
  • Salt mine
  • Halorubrum
  • Polyphasic taxonomy
  • In silico DNA-DNA hybridization
  • Average nucleotide identity (ANI)
  • Average amino-acid identity (AAI)
  • Multilocus sequence analysis (MLSA)