1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 9

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

Abstract

A halophilic archaeon named strain LR21 was isolated from a salt mine in Yunnan Province, PR China. Cells were spherical, Gram-stain-negative and motile. Strain LR21 grew at 20–50 °C (optimum, 42 °C), with 8–30 % (w/v) NaCl (optimum, 23 %) and at pH 5.5–9.5 (optimum, pH 7.5–8.5). Mg was not required for growth. The major polar lipid profile comprised phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Strain LR21 had two dissimilar 16S rRNA genes ( and ) and they were closely related to YGHS32, BNERC31 and YGHS18 with sequence similarities of 95.3–99.0, 93.0–96.2 and 93.2–95.9 %, respectively, and much lower values to other members. The ′ gene sequence similarities between strain LR21 and YGHS32, BNERC31 and YGHS18 were 95.2, 91.2 and 91.2 % respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain LR21 and YGHS32, were 89.0 and 90.1 %, respectively. DNA relatedness between strains LR21 and YGHS32 determined by DNA–DNA hybridization was 36.8 %. Values of ANI and AAI between strain LR21 and other members in the genus were far below 95 % and the DNA–DNA relatedness values between strain LR21 and its close relatives were much lower than 70 %, which is far below the boundary for delineation of a new species prokaryote. The DNA G+C content of strain LR21 was 62.0 mol% (genome). The results suggested that strain LR21 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LR21 (=CGMCC 1.13611=NBRC 113588).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Haloarchaea , Halomicroarcula , multilocus sequence analysis (MLSA) , phylogenomics , polyphasic taxonomy and salt mine
Funding
This study was supported by the:
  • Anhui Provincial Natural Science Research Project (Award KJ2019A0504)
    • Principle Award Recipient: Shaoxing Chen
  • Excellent Young Talents Fund Project for Universities in Anhui Province, China (Award gxyqZD2017011)
    • Principle Award Recipient: Shaoxing Chen
  • the Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources (Award 591601)
    • Principle Award Recipient: Shaoxing Chen
  • National Natural Science Foundation of China (Award 31460003)
    • Principle Award Recipient: Shaoxing Chen
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004368
2020-08-12
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/9/4978.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004368&mimeType=html&fmt=ahah

References

  1. Oren A. Halophilic microbial communities and their environments. Curr Opin Biotechnol 2015; 33:119–124 [View Article]
     [Google Scholar]
  2. Oren A. Industrial and environmental applications of halophilic microorganisms. Environ Technol 2010; 31:825–834 [View Article]
     [Google Scholar]
  3. Chen S, Xu Y, Helfant L. Geographical isolation, buried depth, and physicochemical traits drive the variation of species diversity and prokaryotic community in three typical hypersaline environments. Microorganisms 2020; 8:120 [View Article]
     [Google Scholar]
  4. Echigo A, Minegishi H, Shimane Y, Kamekura M, Itoh T et al. Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2013; 63:3556–3562 [View Article]
     [Google Scholar]
  5. Zhang W-J, Cui H-L. Halomicroarcula limicola sp. nov., isolated from a marine solar saltern, and emended description of the genus Halomicroarcula . Int J Syst Evol Microbiol 2014; 64:1747–1751 [View Article]
     [Google Scholar]
  6. Zhang WJ, Cui HL. Halomicroarcula salina sp. nov., isolated from a marine solar saltern, and emended description of the genus Halomicroarcula . Int J Syst Evol Microbiol 2015; 65:1628–1633
     [Google Scholar]
  7. Oren A, Ventosa A, Grant WD. Proposed minimal standards for description of new taxa in the order Halobacteriales . Int J Syst Bacteriol 1997; 47:233–238 [View Article]
     [Google Scholar]
  8. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485 [View Article]
     [Google Scholar]
  9. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for general and molecular microbiology. American Society for Microbiology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  10. Cui H-L, Lin Z-Y, Dong Y, Zhou P-J, Liu S-J. Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2007; 57:2204–2206 [View Article]
     [Google Scholar]
  11. Gutiérrez C, González C. Method for simultaneous detection of proteinase and esterase activities in extremely halophilic bacteria. Appl Microbiol 1972; 24:516–517 [View Article]
     [Google Scholar]
  12. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, D.C: American Society for Microbiology; 1994
     [Google Scholar]
  13. Kharroub K, Quesada T, Ferrer R, Fuentes S, Aguilera M et al. Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria. Int J Syst Evol Microbiol 2006; 56:1583–1588 [View Article]
     [Google Scholar]
  14. Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R et al. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B′ (rpoB′) gene. Int J Syst Evol Microbiol 2010; 60:2398–2408 [View Article]
     [Google Scholar]
  15. Chen S, Xu Y, Sun S, Chen F, Liu J. Halalkalicoccus subterraneus sp. nov., an extremely halophilic archaeon isolated from a subterranean halite deposit. Antonie van Leeuwenhoek 2019; 112:10671075 [View Article]
     [Google Scholar]
  16. Sun S, Chen F, Xu Y, Liu J, Chen S. Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine. Antonie van Leeuwenhoek 2019; 112:1849–1861 [View Article]
     [Google Scholar]
  17. Burland TG. DNASTAR's Lasergene sequence analysis software. Methods Mol Biol 2000; 132:71–91
     [Google Scholar]
  18. Yoon S-H, Ha S-min, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
     [Google Scholar]
  19. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article]
     [Google Scholar]
  21. Cui H-L, Zhou P-J, Oren A, Liu S-J. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium . Extremophiles 2009; 13:31–37 [View Article]
     [Google Scholar]
  22. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 2012; 19:455–477 [View Article]
     [Google Scholar]
  24. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article]
     [Google Scholar]
  25. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
     [Google Scholar]
  26. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article]
     [Google Scholar]
  27. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article]
     [Google Scholar]
  28. Papke RT, White E, Reddy P, Weigel G, Kamekura M et al. A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales . Int J Syst Evol Microbiol 2011; 61:2984–2995 [View Article]
     [Google Scholar]
  29. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [View Article]
     [Google Scholar]
  30. Cui H-L, Gao X, Yang X, Xu X-W. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010; 14:493–499 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004368
Loading
Halomicroarcula amylolytica sp. nov., a novel halophilic archaeon isolated from a salt mine
Int J Syst Evol Microbiol 70, 4978 (2020); https://doi.org/10.1099/ijsem.0.004368
/content/journal/ijsem/10.1099/ijsem.0.004368
/content/journal/ijsem/10.1099/ijsem.0.004368
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error