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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 3

sp. nov., isolated from marine solar salterns Free

Abstract

Three halophilic archaeal strains, YJ-53, ZS-5 and DYF38, were isolated from marine solar salterns located in different provinces of China. The three strains formed a single cluster (99.7–99.8 and 97.9–99.2 % similarities, respectively) that was separate from the current two members of (96.7–98.0 and 89.8–92.9 % similarities, respectively) on the basis of 16S rRNA and gene sequence comparisons and phylogenetic analysis. Diverse phenotypic characteristics differentiated strains YJ-53, ZS-5 and DYF38 from GX10 and YJ-50-S2. The major polar lipids of isolated strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two major glycolipids chromatographically identical to mannosyl glucosyl diether and sulfated mannosyl glucosyl diether, detected in the current members of . The OrthoANI and DNA–DNA hybridization (DDH) values between the three strains were in the range of 97.7–98.4 % and 80.3–86.1 %, respectively, much higher than the threshold values proposed as species boundaries (average nucleotide identity 95–96 % and DDH 70 %), revealing that the three strains represent one species. Results of comparative OrthoANI and DDH analyses of the strains described in this study with validly described members of the genus supported that strains YJ-53 (=CGMCC 1.12860=JCM 30238), ZS-5 (=CGMCC 1.12867=JCM 30240) and DYF38 (=CGMCC 1.13779=JCM 33557) represent a novel species of the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): halophilic archaeon , marine solar saltern and Salinigranum halophilum sp. nov.
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-Lin Cui
  • National Natural Science Foundation of China (Award 31600069)
    • Principle Award Recipient: Lin Zhu
© 2020 The Authors
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2020-01-08
2024-04-26
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References

  1. Oren A, Meng F-W. 'Red - the magic color for solar salt production' - but since when?. FEMS Microbiol Lett 2019; 366:fnz050 [View Article]
     [Google Scholar]
  2. Viver T, Cifuentes A, Díaz S, Rodríguez-Valdecantos G, González B et al. Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: evidence that unexplored sites constitute sources of cultivable novelty. Syst Appl Microbiol 2015; 38:266–275 [View Article]
     [Google Scholar]
  3. Cui H-L, Gao X, Sun F-F, Dong Y, Xu X-W et al. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 2010; 60:1366–1371 [View Article]
     [Google Scholar]
  4. 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]
     [Google Scholar]
  5. Cui H-L, Li X-Y, Gao X, Xu X-W, Zhou Y-G et al. Halopelagius inordinatus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Int J Syst Evol Microbiol 2010; 60:2089–2093 [View Article]
     [Google Scholar]
  6. Cui H-L, Mou Y-Z, Yang X, Zhou Y-G, Liu H-C et al. Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern. Syst Appl Microbiol 2012; 35:30–34 [View Article]
     [Google Scholar]
  7. Cui H-L, Zhang W-J. Salinigranum rubrum gen. nov., sp. nov., a member of the family Halobacteriaceae isolated from a marine solar saltern. Int J Syst Evol Microbiol 2014; 64:2029–2033 [View Article]
     [Google Scholar]
  8. Hou J, Zhao Y-J, Zhu L, Cui H-L. Salinirubellus salinus gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2018; 68:1874–1878 [View Article]
     [Google Scholar]
  9. Cui H-L, Qiu X-X. Salinarubrum litoreum gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from Chinese marine solar salterns. Antonie van Leeuwenhoek 2014; 105:135–141 [View Article]
     [Google Scholar]
  10. Cui H-L, Lü Z-Z, Li Y, Zhou Y. Salinirussus salinus gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2017; 67:3622–3626 [View Article]
     [Google Scholar]
  11. Sutcliffe IC. Valediction: descriptions of novel prokaryotic taxa published in Antonie van Leeuwenhoek-change in editorial policy and a signpost to the future?. Antonie van Leeuwenhoek 2019; 112:1281–1282 [View Article]
     [Google Scholar]
  12. Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2015; 65:1050–1069 [View Article]
     [Google Scholar]
  13. Gupta RS, Naushad S, Fabros R, Adeolu M. A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov. Antonie van Leeuwenhoek 2016; 109:565–587 [View Article]
     [Google Scholar]
  14. Wang Z, Xu J-Q, Xu W-M, Li Y, Zhou Y et al. Salinigranum salinum sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2016; 66:3017–3021 [View Article]
     [Google Scholar]
  15. Cui H-L, Yang X, Gao X, Xu X-W. Halogranum gelatinilyticum sp. nov. and Halogranum amylolyticum sp. nov., isolated from a marine solar saltern, and emended description of the genus Halogranum . Int J Syst Evol Microbiol 2011; 61:911–915 [View Article]
     [Google Scholar]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
     [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  21. 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]
  22. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article]
     [Google Scholar]
  23. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article]
     [Google Scholar]
  24. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
     [Google Scholar]
  25. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article]
     [Google Scholar]
  26. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
     [Google Scholar]
  27. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article]
     [Google Scholar]
  28. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article]
     [Google Scholar]
  29. 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]
     [Google Scholar]
  30. 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]
     [Google Scholar]
  31. 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]
     [Google Scholar]
  32. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
     [Google Scholar]
  33. 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]
     [Google Scholar]
  34. 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]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
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Salinigranum halophilum sp. nov., isolated from marine solar salterns
Int J Syst Evol Microbiol 70, 1648 (2020); https://doi.org/10.1099/ijsem.0.003951
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