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Volume 73, Issue 5

sp. nov. and sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern No Access

Abstract

Two novel halophilic archaeal strains, Gai3-17 and XZYJT26, were isolated from the sediment of Gaize salt lake and the saline soil of Mangkang ancient solar saltern in Tibet, PR China, respectively. Strains Gai3-17 and XZYJT26 were related to each other (96.5 and 89.7% similarity, respectively) and showed 97.5–95.4 and 91.5–87.7% similarities to the current members of based on 16S rRNA and genes. The phylogenomic analysis indicated that strains Gai3-17 and XZYJT26 formed two distinct clades and clustered with the species. The two strains can be differentiated from the type strains of the six species with validly published names based on several phenotypic characteristics. The phospholipids of the two strains were phosphatidic acid, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. One major glycolipid, sulphated galactosyl mannosyl glucosyl diether, was detected in strain Gai3-17, while four glycolipids, mannosyl glucosyl diether, sulphated mannosyl glucosyl diether, disulphated mannosyl glucosyl diether and sulphated galactosyl mannosyl glucosyl diether were observed in strain XZYJT26. The average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values among the two strains and the members of were no more than 81, 25 and 77 %, respectively. These overall genome-related indices were below the threshold values for species boundary, indicating that strains Gai3-17 and XZYJT26 represent two novel species of . Thus, two novel species, sp. nov. and sp. nov., are proposed to accommodate strains Gai3-17 (=CGMCC 1.16101=JCM 33551) and XZYJT26 (=CGMCC 1.16682=JCM 33556), respectively.

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  • Accepted:
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Keyword(s): Halobacterium wangiae sp. nov. , Halobacterium zhouii sp. nov. , halophilic archaea , salt lake and solar saltern
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070003)
    • Principle Award Recipient: Heng-LinCui
© 2023 The Authors
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2023-05-30
2024-05-01
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References

  1. Cui H-L, Dyall-Smith ML. Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Mar Life Sci Technol 2021; 3:243–251 [View Article] [PubMed]
     [Google Scholar]
  2. Fan H, Xue Y, Ma Y, Ventosa A, Grant WD. Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China. Int J Syst Evol Microbiol 2004; 54:1213–1216 [View Article] [PubMed]
     [Google Scholar]
  3. Xue Y, Fan H, Ventosa A, Grant WD, Jones BE et al. Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea. Int J Syst Evol Microbiol 2005; 55:2501–2505 [View Article] [PubMed]
     [Google Scholar]
  4. Tao C-Q, Ding Y, Zhao Y-J, Cui H-L. Natronorubrum halophilum sp. nov. isolated from two inland salt lakes. J Microbiol 2020; 58:105–112 [View Article] [PubMed]
     [Google Scholar]
  5. Cui H-L, Shi X-W, Yin X-M, Yang X-Y, Hou J et al. Halobaculum halophilum sp. nov. and Halobaculum salinum sp. nov., isolated from salt lake and saline soil. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  6. Zheng X-W, Wu Z-P, Sun Y-P, Wang B-B, Hou J et al. Halorussus vallis sp. nov., Halorussus aquaticus sp. nov., Halorussus gelatinilyticus sp. nov., Halorussus limi sp. nov., Halorussus salilacus sp. nov., Halorussus salinisoli sp. nov.: six extremely halophilic archaea isolated from solar saltern, salt lake and saline soil. Extremophiles 2022; 26: [View Article] [PubMed]
     [Google Scholar]
  7. Elazari-Volcani B. Genus XII. Halobacterium Elazari-Volcani 1940. In Breed RS, Murray EGD, Smith NR. eds Bergey’s Manual of Determinative Bacteriology, 7th ed. Baltimore: Williams & Wilkins; 1957 pp 207–212
     [Google Scholar]
  8. Oren A, Ventosa A. 2017 Halobacterium. Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc; Hoboken, NJ:
     [Google Scholar]
  9. Ventosa A, Oren A. Halobacterium salinarum nom. corrig., a name to replace Halobacterium salinarium (Elazari-Volcani) and to include Halobacterium halobium and Halobacterium cutirubrum. Int J Syst Bacteriol 1996; 46:347 [View Article]
     [Google Scholar]
  10. Gruber C, Legat A, Pfaffenhuemer M, Radax C, Weidler G et al. Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. Extremophiles 2004; 8:
     [Google Scholar]
  11. Yang Y, Cui H-L, Zhou P-J, Liu S-J. Halobacterium jilantaiense sp. nov., a halophilic archaeon isolated from a saline lake in Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:2353–2355 [View Article] [PubMed]
     [Google Scholar]
  12. Han D, Cui H-L. Halobacterium rubrum sp. nov., isolated from a marine solar saltern. Arch Microbiol 2014; 196:847–851 [View Article] [PubMed]
     [Google Scholar]
  13. Han D, Cui H-L. Halobacterium rubrum sp. nov., isolated from a marine solar saltern. Arch Microbiol 2014; 196:847–851 [View Article] [PubMed]
     [Google Scholar]
  14. Myers MR, King GM. Halobacterium bonnevillei sp. nov., Halobaculum saliterrae sp. nov. and Halovenus carboxidivorans sp. nov., three novel carbon monoxide-oxidizing Halobacteria from saline crusts and soils. Int J Syst Evol Microbiol 2020; 70:4261–4268 [View Article]
     [Google Scholar]
  15. Oren A, Arahal DR, Ventosa A. Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 2009; 59:637–642 [View Article] [PubMed]
     [Google Scholar]
  16. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. 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]
  19. Vaskovsky VE, Kostetsky EY. Modified spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1968; 9:396 [PubMed]
     [Google Scholar]
  20. Xin Y-J, Bao C-X, Li S-Y, Hu X-Y, Zhu L et al. Genome-based taxonomy of genera Halomicrobium and Halosiccatus, and description of Halomicrobium salinisoli sp. nov. Syst Appl Microbiol 2022; 45:126308 [View Article] [PubMed]
     [Google Scholar]
  21. Cui H-L, Yang X, Mou Y-Z. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625–631 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  27. 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]
     [Google Scholar]
  28. Li S-Y, Xin Y-J, Bao C-X, Hou J, Cui H-L. Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil. Extremophiles 2021; 26:6 [View Article] [PubMed]
     [Google Scholar]
  29. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
     [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  31. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
     [Google Scholar]
  33. Sun Y-P, Wang B-B, Zheng X-W, Wu Z-P, Hou J et al. Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  34. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article]
     [Google Scholar]
  35. Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2017; 2:1533–1542 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Kim M, Oh HS, Park SC, 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]
     [Google Scholar]
  38. 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]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  40. Serrano S, Mendo S, Caetano T. Haloarchaea have a high genomic diversity for the biosynthesis of carotenoids of biotechnological interest. Res Microbiol 2022; 173:103919 [View Article] [PubMed]
     [Google Scholar]
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Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern
Int J Syst Evol Microbiol 73, 005922 (2023); https://doi.org/10.1099/ijsem.0.005922
/content/journal/ijsem/10.1099/ijsem.0.005922
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