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

  • Siqi Sun
  • Feilong Chen
  • Yao Xu
  • Jingwen Liu
  • Shaoxing ChenEmail author
Original Paper
  • 23 Downloads

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).

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) 

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

Notes

Acknowledgements

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

Author contributions

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.

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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

Supplementary material

10482_2019_1313_MOESM1_ESM.docx (2.5 mb)
Supplementary file1 (DOCX 2595 kb)

References

  1. Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134CrossRefGoogle Scholar
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefGoogle Scholar
  3. Boucher Y, Douady CJ, Sharma AK, Kamekura M, Doolittle WF (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186:3980–3990CrossRefGoogle Scholar
  4. Chen S, He J, Zhang J, Xu Y, Huang J, Ke LX (2017a) Halorubrum salsamenti sp. nov., a novel halophilic archaeon isolated from a brine of salt mine. Curr Microbiol 74:1358–1364CrossRefGoogle Scholar
  5. Chen S, Xu Y, Ke LX (2017b) Halorubrum trueperi sp. nov., a halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol 67:1564–1570CrossRefGoogle Scholar
  6. Chen S, Xu Y, Sun S, Chen F, Liu J (2019) Halalkalicoccus subterraneus sp. nov., an extremely halophilic archaeon isolated from a subterranean halite deposit. Antonie Van Leeuwenhoekvan Leeuwenhoek.  https://doi.org/10.1007/s10482-019-01241-3 Google Scholar
  7. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466CrossRefGoogle Scholar
  8. Cui HL, Tohty D, Zhou PJ, Liu SJ (2006) Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China. Int J Syst Evol Microbiol 56:1631–1634CrossRefGoogle Scholar
  9. Cui HL, Lin ZY, Dong Y, Zhou PJ, Liu SJ (2007) Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 57:2204–2206CrossRefGoogle Scholar
  10. Cui HL, Gao X, Yang X, Xu XW (2010) Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 14:493–499CrossRefGoogle Scholar
  11. de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT (2018) Genotypic and lipid analyses of strains from the archaeal genus Halorubrum reveal insights into their taxonomy, divergence, and population structure. Front Microbiol 9:512CrossRefGoogle Scholar
  12. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefGoogle Scholar
  13. Dussault HP (1955) An improved technique for staining red halophilic bacteria. J Bacteriol 70:484–485Google Scholar
  14. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
  15. Feng J, Zhou PJ, Liu SJ (2004) Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China. Int J Syst Evol Microbiol 54:1789–1791CrossRefGoogle Scholar
  16. Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Goqarten JP, Papke RT (2014) Population and genomic analysis of the Halorubrum. Front Microbiol 5:140CrossRefGoogle Scholar
  17. Gerhardt P, Murray RGE, Wood WA, Krieg NR (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, D.C.Google Scholar
  18. Gupta RS, Naushad S, Fabros R, Adeolu M (2016) A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov. Antonie Van Leeuwenhoek 109:1521–1523CrossRefGoogle Scholar
  19. Gutiérrez C, González C (1972) Method for simultaneous detection of proteinase and esterase activities in extremely halophilic bacteria. Appl Microbiol 24:516–517Google Scholar
  20. Gutiérrez MC, Castillo AM, Pagaling E, Heaphy S, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A (2008) Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake. Int J Syst Evol Microbiol 58:2031–2035CrossRefGoogle Scholar
  21. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  22. Kharroub K, Quesada T, Ferrer R, Fuentes S, Aguilera M, Boulahrouf A, Ramos-Cormenzana A, Monteoliva-Sánchez M (2006) Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria. Int J Syst Evol Microbiol 56:1583–1588CrossRefGoogle Scholar
  23. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNAgenes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefGoogle Scholar
  24. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18CrossRefGoogle Scholar
  25. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  26. McGenity TJ, Grant WD (1995) Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34041 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov. Syst Appl Microbiol 18:237–243CrossRefGoogle Scholar
  27. McGenity TJ, Grant WD (2015) Halorubrum. In: Whitman WB (ed) Bergey’s manual of systematics of Archaea and bacteria. Association with Bergey’s Manual Trust, Wiley, pp 1–11Google Scholar
  28. McGenity TJ, Oren A (2012) Life in saline environments. In: Bell E (ed) Life at extremes: environments, organisms, and strategies for survival. CABI International, Wallingford, pp 402–437Google Scholar
  29. Medlar AJ, Toronen P, Holm L (2018) AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 46:W479–W485CrossRefGoogle Scholar
  30. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418CrossRefGoogle Scholar
  31. Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, Hashimoto T (2010) Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B’ (rpoB’) gene. Int J Syst Evol Microbiol 60:2398–2408CrossRefGoogle Scholar
  32. Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935CrossRefGoogle Scholar
  33. Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Flodden EW, Gardner PP, Jones TA, Tate J, Finn RD (2014) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43:D130–137CrossRefGoogle Scholar
  34. Ochsenreiter T, Pfeifer F, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles 6:267–274CrossRefGoogle Scholar
  35. Oren A, Ventosa A, Grant WD (1997) Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 47:233–238CrossRefGoogle Scholar
  36. Oren A, Arahal DR, Ventosa A (2009) Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 59:637–642CrossRefGoogle Scholar
  37. Parte AC (2019) List of prokaryotic names with standing in nomenclature. https://www.bacterio.net
  38. Ram Mohan N, Fullmer MS, Makky AM, Wheeler R, Ventosa A, Naor A, Goqarten JP, Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front Microbiol 5:143CrossRefGoogle Scholar
  39. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  40. Schbert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes 9:88CrossRefGoogle Scholar
  41. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar
  42. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  43. Yim KJ, Cha IT, Lee HW, Song HS, Kim KN, Lee SJ, Nam YD, Hyun DW, Bae JW, Rhee SK, Seo MJ, Choi JS, Choi HJ, Roh SW, Kim D (2014) Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood. Antonie Van Leeuwenhoek 105:603–612CrossRefGoogle Scholar
  44. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.College of Life SciencesAnhui Normal UniversityWuhuPeople’s Republic of China
  2. 2.College of Life SciencesHonghe UniversityMengziPeople’s Republic of China

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