Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt

Abstract

A novel extremely halophilic strain, designated ZY19T, was isolated from a rock salt sample from Yunnan salt mine, PR China. Strain ZY19T is neutrophilic, non-motile and requires at least 10% (w/v) NaCl for growth. Optimal growth is observed at 20–25% (w/v) NaCl, pH 7.5–8.0 and 42 °C. Mg2+ is not required for growth. The cells do not lyse in distilled water. On the basis of 16S rRNA gene sequence analysis, strain ZY19T belongs to the genus Haloterrigena (Htg.) and is closely related to Haloterrigena salina XH-65T (98.5% sequence similarity) and Haloterrigena turkmenica DSM 5511T (97.9%). Phylogenetic and phylogenomic analysis showed that strain ZY19T clusters with the species Htg. salina and Htg. turkmenica forming an independent clade separated from other members of the genus. The value of genomic average nucleotide identity (ANI) between strains ZY19T and its close relative, Htg. salina XH-65T was 94.2%. DNA–DNA relatedness between strains ZY19T and Htg. salina XH-65T revealed by in silico DNA–DNA hybridization (DDH) was 56.3%. Both the ANI value and the degree of in silico DDH are below the accepted threshold for members of the same species. The major polar lipids were found to consist of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl-diether-1 and mannose-2, 6-disulfate (1 → 2)-glucose glycerol diether. The genomic DNA G+C content was determined to be 64.5 mol%. Based on the results of the phenotypic, chemotaxonomic, genetic similarity and inferred phylogeny, strain ZY19T is distinct from other validly named species and thus represents a novel species within the genus Haloterrigena, for which the name Haloterrigena salifodinae sp. nov. is proposed. The type strain is ZY19T (=CGMCC 1.16114T=NBRC 112981T).

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3

Abbreviations

BLAST:

Basic local alignment search tool

ANI:

Average nucleotide identity

CGMCC:

China General Microbiological Culture Collection Center

DSM, DSMZ:

Deutsche Sammlung von Mikroorganismen und Zellkulturen

DMSO:

Dimethyl sulphoxide HPLC, high performance liquid chromatography

References

  1. Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A (2017) Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology 163:623–645

    Article  CAS  PubMed  Google Scholar 

  2. 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 2:117–134

    Article  PubMed  PubMed Central  Google Scholar 

  3. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, 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 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. 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 68:461–466

    Article  PubMed  Google Scholar 

  5. Corcelli A, Lobasso S (2006) Characterization of lipids of halophilic archaea. In: Rainey FA, Oren A (eds) Methods in microbiology, extremophiles. Elsevier/Academic, Amsterdam, pp 585–613

    Google Scholar 

  6. Cui HL, Tohty D, Zhou PJ, Liu SJ (2006) Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake. Int J Syst Evol Microbiol 56:1837–1840

    Article  CAS  PubMed  Google Scholar 

  7. Ding JY, Chen SC, Lai MC, Liao TL (2017) Haloterrigena mahii sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 67:1333–1338

    Article  CAS  PubMed  Google Scholar 

  8. Dussault HP (1955) An improved technique for staining red halophilic bacteria. J Bacteriol 70:484–485

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  10. Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715

    Article  CAS  PubMed  Google Scholar 

  11. Gutiérrez MC, Castillo AM, Kamekura M, Ventosa A (2008) Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 58:2880–2884

    Article  CAS  PubMed  Google Scholar 

  12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  13. Kamekura M (1993) Lipids of extreme halophiles. In: Vreeland RH, Hochstein LI (eds) The biology of halophilic bacteria. CRC Press, Boca Raton, pp 135–161

    Google Scholar 

  14. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218

    Article  CAS  Google Scholar 

  16. 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–W485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418

    Article  CAS  PubMed  Google Scholar 

  18. 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 60:2398–2408

    Article  Google Scholar 

  19. Montalvo-Rodríguez R, López-Garriga J, Vreeland RH, Oren A, Ventosa A, Kamekura M (2000) Haloterrigena thermotolerans sp. nov., a halophilic archaeon from Puerto Rico. Int J Syst Evol Microbiol 3:1065–1071

    Article  Google Scholar 

  20. Oren A, Ventosa A, Grant WD (1997) Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 47:233–238

    Article  Google Scholar 

  21. Oren A, Arahal DR, Ventosa A (2009) Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 59:637–642

    Article  PubMed  Google Scholar 

  22. Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A (2011) A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales. Int J Syst Evol Microbiol 61:2984–2995

    Article  CAS  PubMed  Google Scholar 

  23. Roh SW, Nam YD, Chang HW, Kim KH, Sung Y, Kim MS, Oh HM, Bae JW (2009) Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food. Int J Syst Evol Microbiol 59:2359–2363

    Article  CAS  PubMed  Google Scholar 

  24. Romano I, Poli A, Finore I, Huertas FJ, Gambacorta A, Pelliccione S, Nicolaus G, Lama L, Nicolaus B (2007) Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 57:1499–1503

    Article  PubMed  Google Scholar 

  25. Segata N, Börnigen D, Morgan XC, Huttenhower C (2013) PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Selim S, Hagagy N (2015) Genome sequence of carboxylesterase, carboxylase and xylose isomerase producing alkaliphilic haloarchaeon Haloterrigena turkmenica WANU15. Genomics Data 7:70–72

    Article  PubMed  PubMed Central  Google Scholar 

  27. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  28. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Ventosa A, Gutiérrez MC, Kamekura M, Dyall-Smith ML (1999) Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. Int J Syst Bacteriol 1:131–136

    Article  Google Scholar 

  30. Wang S, Yang Q, Liu ZH, Sun L, Wei D, Zhang JZ, Song JZ, Yuan HF (2010) Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil. Int J Syst Evol Microbiol 60:2267–2271

    Article  CAS  PubMed  Google Scholar 

  31. Xu XW, Liu SJ, Tohty D, Oren A, Wu M, Zhou PJ (2005) Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China. Int J Syst Evol Microbiol 55:2539–2542

    Article  CAS  PubMed  Google Scholar 

  32. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zvyagintseva IS, Tarasov AL (1987) Extreme halophilic bacteria from alkaline soils. Mikrobiologiya 56:839–844 (in Russian)

    Google Scholar 

Download references

Acknowledgements

We thank Professor Zhu L. Yang and Dr. Bang Feng from the Kunming Institute of Botany, Chinese Academy of Sciences for their helps in sample collection and data analysis, and we also thank Dr. Hao Yan from the College of Life Sciences, Anhui Normal University, for his technical assistance.

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.

Author information

Affiliations

Authors

Contributions

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

Corresponding author

Correspondence to Shaoxing Chen.

Ethics declarations

Conflicts of interest

The authors declare that they have no conflict of interest.

Ethical statement

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

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The cell morphology, thin-layer chromatogram of polar lipids and Neighbor-Joining phylogenetic trees of 16S rRNA and rpoB′ are available with the online supplementary material.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 29959 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chen, S., Xu, Y., Sun, S. et al. Haloterrigena salifodinae sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Antonie van Leeuwenhoek 112, 1317–1329 (2019). https://doi.org/10.1007/s10482-019-01264-w

Download citation

Keywords

  • Halobacteria
  • Haloarchaea
  • Salt mine
  • Rock salt
  • Haloterrigena
  • Polyphasic taxonomy
  • Multilocus sequence analysis