1887

Abstract

Four extremely halophilic archaeal strains, LYG-108, LYG-24, DT1 and YSSS71, were isolated from salted produced in Lianyungang and saline soil from the coastal beach at Jiangsu, PR China. The four strains were found to be related to the current species of (showing 88.1–98.5% and 89.3–93.6% similarities, respectively) as revealed by phylogenetic analysis based on 16S rRNA and genes. These phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes (average nucleotide identity, DNA–DNA hybridization and average amino acid identity) among these four strains and the species were 77–84 %, 23–30 % and 71–83 %, respectively, clearly below the threshold values for species demarcation. Additionally, the phylogenomic and comparative genomic analyses revealed that YGH18 is related to the current species of rather than those of , Namwong . 2011 is a later heterotypic synonym of Ihara . 1997, and Oren . 1999 is a later heterotypic synonym of Oren . 1990. The major polar lipids of strains LYG-108, LYG-24, DT1 and YSSS71 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate, sulphated mannosyl glucosyl diether and additional glycosyl-cardiolipins. All these results showed that strains LYG-108 (=CGMCC 1.13607=JCM 32950) and LYG-24 (=CGMCC 1.13605=JCM 32949) represent a new species of the genus , for which the name sp. nov. is proposed; strains DT1 (=CGMCC 1.18928=JCM 35414) and YSSS71 (=CGMCC 1.18783=JCM 34915) also represent a new species of the genus , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32070003)
    • Principle Award Recipient: XueMa
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005889
2023-05-19
2024-05-01
Loading full text...

Full text loading...

References

  1. Cho E-S, Cha I-T, Roh SW, Seo M-J. Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment. Antonie van Leeuwenhoek 2021; 114:2065–2082 [View Article] [PubMed]
    [Google Scholar]
  2. Wang B-B, Sun Y-P, Wu Z-P, Zheng X-W, Hou J et al. Halorientalis salina sp. nov., Halorientalis marina sp. nov., Halorientalis litorea sp. nov.: three extremely halophilic archaea isolated from a salt lake and coarse sea salt. Extremophiles 2022; 26:26 [View Article] [PubMed]
    [Google Scholar]
  3. 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: [View Article]
    [Google Scholar]
  4. 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]
    [Google Scholar]
  5. 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]
  6. Echigo A, Minegishi H, Shimane Y, Kamekura M, Itoh T et al. Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2013; 63:3556–3562 [View Article] [PubMed]
    [Google Scholar]
  7. Zhang W-J, Cui H-L. Halomicroarcula limicola sp. nov., isolated from a marine solar saltern, and emended description of the genus Halomicroarcula. Int J Syst Evol Microbiol 2014; 64:1747–1751 [View Article] [PubMed]
    [Google Scholar]
  8. Zhang W-J, Cui H-L. Halomicroarcula salina sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2015; 65:1628–1633 [View Article] [PubMed]
    [Google Scholar]
  9. Chen F, Xu Y, Sun S, Shi X, Liu A et al. Halomicroarcula amylolytica sp. nov., a novel halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol 2020; 70:4978–4985 [View Article] [PubMed]
    [Google Scholar]
  10. Durán-Viseras A, Sánchez-Porro C, Ventosa A. Genomic insights into new species of the genus Halomicroarcula reveals potential for new osmoadaptative strategies in Halophilic Archaea. Front Microbiol 2021; 12:751746 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  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. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [View Article] [PubMed]
    [Google Scholar]
  21. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. 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:D354–7 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. Wu Z-P, Zheng X-W, Sun Y-P, Wang B-B, Hou J et al. Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from aiding salt lake. Int J Syst Evol Microbiol 2022; 72:005637
    [Google Scholar]
  31. 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]
  32. 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] [PubMed]
    [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 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  35. Namwong S, Tanasupawat S, Kudo T, Itoh T. Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce. Int J Syst Evol Microbiol 2011; 61:231–236 [View Article] [PubMed]
    [Google Scholar]
  36. Ihara K, Watanabe S, Tamura T. Haloarcula argentinensis sp. nov. and Haloarcula mukohataei sp. nov., two new extremely halophilic archaea collected in Argentina. Int J Syst Bacteriol 1997; 47:73–77 [View Article] [PubMed]
    [Google Scholar]
  37. Oren A, Ventosa A, Gutiérrez MC, Kamekura M. Haloarcula quadrata sp. nov., a square, motile archaeon isolated from a brine pool in Sinai (Egypt). Int J Syst Bacteriol 1999; 49 Pt 3:1149–1155 [View Article] [PubMed]
    [Google Scholar]
  38. Oren A, Ginzburg M, Ginzburg BZ, Hochstein LI, Volcani BE. Haloarcula marismortui (Volcani) sp. nov., nom. rev., an extremely halophilic bacterium from the Dead Sea. Int J Syst Bacteriol 1990; 40:209–210 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005889
Loading
/content/journal/ijsem/10.1099/ijsem.0.005889
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error