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Abstract

Two novel halophilic archaeal strains (XZGYJ-43 and ZJ1) were isolated from Mangkang ancient solar saltern (Tibet, PR China) and Zhujiang river inlet (Guangdong, PR China), respectively. The comparison of the 16S rRNA gene sequences revealed that strain XZGYJ-43 is related to the current species of the family (89.2–91.7% similarity) and strain ZJ1 showed 94.7–98.3% similarity to the current species of the genus . Phylogenetic analyses based on 16S rRNA genes, ′ genes and genomes indicated that strain XZGYJ-43 is separate from the related genera, , and of the family , and strain ZJ1 tightly clusters with the current species of the genus . The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between strain XZGYJ-43 and the current species of the family were 71–75, 20–25 and 59–68 %, and these values between strain ZJ1 and the current species of the genus were 77–81, 27–32 and 76–82 %, respectively, clearly below the thresholds for prokaryotic species demarcation. These two strains could be distinguished from their relatives according to differential phenotypic characteristics. The major polar lipids of strain XZGYJ-43 were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), mannosyl glucosyl diether (DGD-1; DGD-PA) and sulphated mannosyl glucosyl diether (S-DGD-1; S-DGD-PA), and those of strain ZJ1 were PA, PG, PGP-Me, DGD-PA, S-DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. Based on phenotypic, phylogenetic and genomic data, strain XZGYJ-43 (=CGMCC 1.13890=JCM 33735) represents a novel species of a new genus within the family , and strain ZJ1 (=CGMCC 1.18785=JCM 34917) represents a novel species of the genus , for which the names gen. nov., sp. nov. and sp. nov. are proposed, respectively.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070003)
    • Principle Award Recipient: Heng-LinCui
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2024-01-09
2024-12-04
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References

  1. Cui C, Han D, Hou J, Cui H-L. Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov. Int J Syst Evol Microbiol 2023; 73:005984 [View Article]
    [Google Scholar]
  2. Gibbons NE. Family V. Halobacteriaceae fam. nov. In Bergey’s Manual of Determinative Bacteriology, 8th. edn Baltimore: Williams & Wilkins; 1974 pp 269–273
    [Google Scholar]
  3. Savage KN, Krumholz LR, Oren A, Elshahed MS. Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 2007; 57:19–24 [View Article] [PubMed]
    [Google Scholar]
  4. Roh SW, Lee M-L, Bae J-W. Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus. Int J Syst Evol Microbiol 2010; 60:1187–1190 [View Article] [PubMed]
    [Google Scholar]
  5. Cui H-L, Sun F-F, Gao X, Dong Y, Xu X-W et al. Haladaptatus litoreus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haladaptatus. Int J Syst Evol Microbiol 2010; 60:1085–1089 [View Article]
    [Google Scholar]
  6. Liu B-B, Zhao W-Y, Chu X, Hozzein WN, Prabhu DM et al. Haladaptatus pallidirubidus sp. nov., a halophilic archaeon isolated from saline soil samples in Yunnan and Xinjiang, China. Antonie van Leeuwenhoek 2014; 106:901–910 [View Article] [PubMed]
    [Google Scholar]
  7. Xin Y-J, Bao C-X, Tan S, Hou J, Cui H-L. Haladaptatus halobius sp. nov. and Haladaptatus salinisoli sp. nov., two extremely halophilic archaea isolated from Gobi saline soil. Int J Syst Evol Microbiol 2022; 72:005543 [View Article] [PubMed]
    [Google Scholar]
  8. 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; 26:32 [View Article] [PubMed]
    [Google Scholar]
  9. Hu Y, Ma X, Li X-X, Tan S, Cheng M et al. Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine. Extremophiles 2023; 27:9 [View Article] [PubMed]
    [Google Scholar]
  10. Wang B-B, Bao C-X, Sun Y-P, Hou J, Cui H-L. 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 2023; 73:005922 [View Article] [PubMed]
    [Google Scholar]
  11. Sun Y-P, Wang B-B, Wu Z-P, Zheng X-W, Hou J et al. Halorarius litoreus gen. nov., sp. nov., Halorarius halobius sp. nov., Haloglomus halophilum sp. nov., Haloglomus salinum sp. nov., and Natronomonas marina sp. nov., extremely halophilic archaea isolated from tidal flat and marine solar salt. Front Mar Sci 2023; 10:1105929 [View Article]
    [Google Scholar]
  12. 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]
  13. 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] [PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. Han D, Cui H-L. Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria. Int J Syst Evol Microbiol 2020; 70:2879–2887 [View Article] [PubMed]
    [Google Scholar]
  16. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  17. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34:D354–D357 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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] [PubMed]
    [Google Scholar]
  20. 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] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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; 14:1–14 [View Article] [PubMed]
    [Google Scholar]
  23. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485 [View Article] [PubMed]
    [Google Scholar]
  27. Li X-X, Tan S, Cheng M, Hu Y, Ma X et al. Salinilacihabitans rarus gen. nov., sp. nov., Natrononativus amylolyticus gen. nov., sp. nov., Natronobeatus ordinarius gen. nov., sp. nov., and Halovivax gelatinilyticus sp. nov., halophilic archaea, isolated from a salt lake and soda lakes. Extremophiles 2023; 27:15 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Lobasso S, Pérez-Davó A, Vitale R, Sánchez MM, Corcelli A. Deciphering archaeal glycolipids of an extremely halophilic archaeon of the genus Halobellus by MALDI-TOF/MS. Chem Phys Lipids 2015; 186:1–8 [View Article] [PubMed]
    [Google Scholar]
  30. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [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] [PubMed]
    [Google Scholar]
  32. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475–19
    [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] [PubMed]
    [Google Scholar]
  34. 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] [PubMed]
    [Google Scholar]
  35. Minegishi H, Echigo A, Kuwahara A, Shimane Y, Kamekura M et al. Halocalculus aciditolerans gen. nov., sp. nov., an acid-tolerant haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2015; 65:1640–1645 [View Article] [PubMed]
    [Google Scholar]
  36. Sorokin DY, Messina E, Smedile F, Roman P, Damsté JSS et al. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME J 2017; 11:1245–1260 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
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