1887

Abstract

A polyphasic study was undertaken to determine the taxonomic position of two halophilic archaeal strains, TH32 and YPL4, isolated from saline soil and a salt mine in PR China, respectively. Strains TH32 and YPL4 both have two dissimilar 16S rRNA genes. The two strains exhibited sequence similarities of 91.5–95.5 % for 16S rRNA genes and 90.9 % for the gene. Sequence similarities of 16S rRNA genes and the gene between the two strains and the current four members of were 90.6–97.4 % and 91.4–93.5 %, respectively. Phylogenetic analysis revealed that the two strains formed different branches separating them from the current members. Several phenotypic characteristics differentiate strains TH32 and YPL4 from current members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and four glycolipids. Two of the glycolipids are chromatographically identical to disulfated mannosyl glucosyl diether and sulfated mannosyl glucosyl diether, respectively, and the remaining two glycolipids are unidentified. The average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values between the two strains and the current members of (ANI 80.4–89.2 % and DDH 24.0–41.8 %) were much lower than the threshold values proposed as a species boundary, suggesting that the two strains represent novel species of . The values between the two strains (ANI 81.3 % and DDH 24.9 %) were also much lower than the recommended threshold values, which revealed that the two strains represent two genomically different species of . These results showed that strains TH32 (=CGMCC 1.15190=JCM 30840) and YPL4 (=CGMCC 1.15329=JCM 31108) represent two novel species of , for which the names sp. nov. and sp. nov. are proposed.

Funding
This study was supported by the:
  • National Science & Technology Infrastructure Program of China (Award 2017FY100302)
    • Principle Award Recipient: Heng-LinCui
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-LinCui
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2021-04-21
2021-05-15
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References

  1. Nan L, Guo Q, Cao S. Archaeal community diversity in different types of saline-alkali soil in arid regions of Northwest China. J Biosci Bioeng 2020; 130:382–389 [CrossRef][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 [CrossRef][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:E120120 16 01 2020 [CrossRef][PubMed]
    [Google Scholar]
  4. Liu Q, Ren M, Zhang L-L. Natribaculum breve gen. nov., sp. nov. and Natribaculum longum sp. nov., halophilic archaea isolated from saline soil. Int J Syst Evol Microbiol 2015; 65:604–608 [CrossRef][PubMed]
    [Google Scholar]
  5. Yin X-Q, Liu B-B, Chu X, Salam N, Li X et al. Saliphagus infecundisoli gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline soil. Int J Syst Evol Microbiol 2017; 67:4154–4160 [CrossRef][PubMed]
    [Google Scholar]
  6. Han D, Hong L-G, Xu Q, Cui H-L. Halostella limicola sp. nov., isolated from saline soil sampled at the Tarim Basin. Int J Syst Evol Microbiol 2019; 69:3299–3304 [CrossRef][PubMed]
    [Google Scholar]
  7. Xu Q, Cui H-L, Meng F. Haloprofundus halophilus sp. nov., isolated from the saline soil of Tarim Basin. Antonie Van Leeuwenhoek 2019; 112:553–559 [CrossRef][PubMed]
    [Google Scholar]
  8. Chen S, Liu H-C, Zhou J, Xiang H. Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae . Int J Syst Evol Microbiol 2016; 66:2327–2334 [CrossRef][PubMed]
    [Google Scholar]
  9. Chen S, Xu Y, Sun S, Liu J, Chen F. Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit. Int J Syst Evol Microbiol 2020; 70:4425–4431 [CrossRef][PubMed]
    [Google Scholar]
  10. Vreeland RH, Straight S, Krammes J, Dougherty K, Rosenzweig WD et al. Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 2002; 6:445–452 [CrossRef][PubMed]
    [Google Scholar]
  11. Han D, Cui H-L. Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov., isolated from salted brown alga Laminaria, and emended description of the genus Halosimplex . Int J Syst Evol Microbiol 2014; 64:169–173 [CrossRef][PubMed]
    [Google Scholar]
  12. Yuan P-P, Xu J-Q, Xu W-M, Wang Z, Yin S et al. Halosimplex litoreum sp. nov., isolated from a marine solar saltern. Antonie Van Leeuwenhoek 2015; 108:483–489 [CrossRef][PubMed]
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. 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 [CrossRef][PubMed]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Zhao Y-J, Tao C-Q, Zeng C-L, Zhu L, Cui H-L. Salinigranum halophilum sp. nov., isolated from marine solar salterns. Int J Syst Evol Microbiol 2020; 70:1648–1655 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:277D–280 [CrossRef][PubMed]
    [Google Scholar]
  26. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [CrossRef][PubMed]
    [Google Scholar]
  27. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  28. 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 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. 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 [CrossRef][PubMed]
    [Google Scholar]
  31. 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 [CrossRef][PubMed]
    [Google Scholar]
  32. 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 [CrossRef][PubMed]
    [Google Scholar]
  33. 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 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef][PubMed]
    [Google Scholar]
  35. Vaskovsky VE, Kostetsky EY. Modified spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1968; 9:396 [CrossRef][PubMed]
    [Google Scholar]
  36. Siakotos AN, Rouser G. Analytical separation of nonlipid water soluble substances and gangliosides from other lipids by dextran gel column chromatography. J Am Oil Chem Soc 1965; 42:913–919 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 Pt 1:183–190 [CrossRef][PubMed]
    [Google Scholar]
  38. Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY et al. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2016; 18:692–707 [CrossRef][PubMed]
    [Google Scholar]
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