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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 11

sp. nov. and sp. nov., two novel halophilic archaea Free

Abstract

Two halophilic archaeal strains, C90 and YPL13, were isolated from a salt lake and a salt mine in PR China. The two strains were found to form two clusters (97.5 and 89.5 % similarity between them, respectively) separating them from the three current members of the genus (95.4–97.0 % and 86.6–89.3 % similarity, respectively) on the basis of the 16S rRNA and gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains C90 and YPL13 from current members. The polar lipids of strain C90 were phosphatidic acid, phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate, two unidentified glycolipids, a major glycolipid and a minor glycolipid, while those of strain YPL13 were PG, PGP-Me, two unidentified phospholipids and a glycolipid. The average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values between the two strains were 79.8 and 27.1 %, respectively, which were much lower than the threshold values proposed as a species boundaries (ANI 95–96 % and DDH 70 %), which revealed that the two strains represent two novel species; these values (ANI 76.6–80.0 % and DDH 21.6–27.0 %) of the strains examined in this study and the current members of are much lower than the recommended threshold values, suggesting that strains C90 and YPL13 represent two genomically different species of . These results showed that strains C90 (=CGMCC 1.13738=JCM 32961) and YPL13 (=CGMCC 1.13884=JCM 31111) represent two novel species of , for which the names sp. nov. and sp. nov. are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): halophilic archaea , Natronomonas halophila sp. nov. , Natronomonas salina sp. nov. , salt lake and salt mine
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-Lin Cui
© 2020 The Authors
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2020-09-16
2024-05-20
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References

  1. Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT. Microbial diversity of hypersaline environments: a metagenomic approach. Curr Opin Microbiol 2015; 25:80–87 [View Article][PubMed]
     [Google Scholar]
  2. Xiao W, Wang Z-G, Wang Y-X, Schneegurt MA, Li Z-Y et al. Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in Southwest China. J Basic Microbiol 2013; 53:942–952 [View Article][PubMed]
     [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][PubMed]
     [Google Scholar]
  4. Kamekura M, Dyall-Smith ML, Upasani V, Ventosa A, Kates M. Diversity of alkaliphilic halobacteria: proposals for transfer of Natronobacterium vacuolatum, Natronobacterium magadii, and Natronobacterium pharaonis to Halorubrum, Natrialba, and Natronomonas gen. nov., respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., respectively. Int J Syst Bacteriol 1997; 47:853–857 [View Article][PubMed]
     [Google Scholar]
  5. Burns DG, Janssen PH, Itoh T, Minegishi H, Usami R et al. Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas. Int J Syst Evol Microbiol 2010; 60:1173–1176 [View Article][PubMed]
     [Google Scholar]
  6. Kim T-Y, Kim S-J, Park S-J, Kim J-G, Cha I-T et al. Natronomonas gomsonensis sp. nov., isolated from a solar saltern. Antonie van Leeuwenhoek 2013; 104:627–635 [View Article][PubMed]
     [Google Scholar]
  7. Durán-Viseras A, Sánchez-Porro C, Ventosa A. Natronomonas salsuginis sp. nov., a new inhabitant of a marine solar saltern. Microorganisms 2020; 8:605 [View Article][PubMed]
     [Google Scholar]
  8. Soliman GSH, Trüper HG. Halobacterium pharaonis sp. nov., a new, extremely haloalkaliphilic archaebacterium with low magnesium requirement. Zentralbl Bakteriol Hyg Abt I Orig 1982; 3:318–329 [View Article]
     [Google Scholar]
  9. Mwatha WE, Grant WD. Natronobacterium vacuolatum sp. nov., a haloalkaliphilic archaeon isolated from lake Magadi, Kenya. Int J Syst Bacteriol 1993; 43:401–404 [View Article]
     [Google Scholar]
  10. Han D, Cui H-L. Halostella pelagica sp. nov. and Halostella litorea sp. nov., isolated from salted brown alga Laminaria. Int J Syst Evol Microbiol 2020; 70:1969–1976 [View Article][PubMed]
     [Google Scholar]
  11. 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][PubMed]
     [Google Scholar]
  12. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  17. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  18. Yoon S-H, Ha S-M, 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][PubMed]
     [Google Scholar]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  20. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article][PubMed]
     [Google Scholar]
  21. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:277D–280 [View Article][PubMed]
     [Google Scholar]
  22. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article][PubMed]
     [Google Scholar]
  23. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  24. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
     [Google Scholar]
  25. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
     [Google Scholar]
  26. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  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]
  31. Wainø M, Tindall BJ, Ingvorsen K. Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the archaea from great salt lake, Utah. Int J Syst Evol Microbiol 2000; 50:183–190 [View Article][PubMed]
     [Google Scholar]
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Natronomonas halophila sp. nov. and Natronomonas salina sp. nov., two novel halophilic archaea
Int J Syst Evol Microbiol 70, 5686 (2020); https://doi.org/10.1099/ijsem.0.004463
/content/journal/ijsem/10.1099/ijsem.0.004463
/content/journal/ijsem/10.1099/ijsem.0.004463
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