1887

Abstract

A halophilic archaeal strain, designated C46, was isolated from an inland salt lake in Qinghai Province, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C46 belongs to the genus , and the closest phylogenetic relative is DSM 9297 with 97.7 % similarity. Despite this, strain C46 was more related to WSA2 than other members of the genus based on genome comparison and analysis, and the average nucleotide identity, DNA–DNA hybridization, amino acid identity and percentage of conserved protein values between the two strains were 89.1, 53.3, 89.2 and 75.6 %, respectively, which are lower than the cutoff values proposed for species delimitation. The physiological, biochemical, genetic and genomic characteristics of strain C46 were different from those of its closest phylogenetic neighbours, which indicated that this strain represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is C46 (=CGMCC 1.13737=JCM 32959).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-LinCui
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005242
2022-02-23
2022-05-22
Loading full text...

Full text loading...

References

  1. Oren A, Gurevich P, Gemmell RT, Teske A. Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Bacteriol 1995; 45:747–754 [View Article] [PubMed]
    [Google Scholar]
  2. Gupta RS, Naushad S, Fabros R, Adeolu M. Erratum to: 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; 109:1521–1523 [View Article]
    [Google Scholar]
  3. 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; 71:004900 [View Article]
    [Google Scholar]
  4. Shimoshige H, Yamada T, Minegishi H, Echigo A, Shimane Y et al. Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2013; 63:861–866 [View Article] [PubMed]
    [Google Scholar]
  5. Chen S, Xu Y, Liu H-C, Yang A-N, Ke L-X. Halobaculum roseum sp. nov., isolated from underground salt deposits. Int J Syst Evol Microbiol 2017; 67:818–823 [View Article]
    [Google Scholar]
  6. 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] [PubMed]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. 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]
  9. 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]
  10. 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] [PubMed]
    [Google Scholar]
  11. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Li S, Li R, Li H, Lu J, Li Y et al. SOAPindel: efficient identification of indels from short paired reads. Genome Res 2013; 23:195–200 [View Article] [PubMed]
    [Google Scholar]
  17. 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] [PubMed]
    [Google Scholar]
  18. 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 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
    [Google Scholar]
  22. 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 [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. 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]
  27. 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] [PubMed]
    [Google Scholar]
  28. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  29. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  30. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. 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; 50:183–190 [View Article] [PubMed]
    [Google Scholar]
  34. 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 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005242
Loading
/content/journal/ijsem/10.1099/ijsem.0.005242
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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