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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

sp. nov. and sp. nov., isolated from salt lake and saline soil Free

Abstract

Two halophilic archaeal strains, Gai3-2 and NJ-3-1, were isolated from salt lake and saline soil samples, respectively, collected in PR China. The 16S rRNA gene sequences of the two strains were 97.5% similar to each other. Strains Gai3-2 and NJ-3-1 had the highest sequence similarities to ‘’ G22 (96.7 and 97.8%, respectively), and displayed similarities of 91.5–93.5% and 92.3–94.7%, respectively, to members. Phylogenetic analysis revealed that the two strains formed different branches and clustered tightly with ‘’ G22 and members. The average nucleotide identity (ANI), in silico DNA–DNA hybridization (DDH) and amino acid identity (AAI) values between the two strains were 83.1, 26.9 and 77.9%, respectively, much lower than the threshold values proposed as a species boundary. These values between the two strains and ‘’ G22 (ANI 77.9–78.2%, DDH 22.5–22.6% and AAI 68.8–69.3%) and members (ANI 77.53–77.63%, DDH 21.8–22.3% and AAI 68.4–69.4%) were almost identical, and much lower than the recommended threshold values for species delimitation. These results suggested that strains Gai3-2 and NJ-3-1 represent two novel species of . Based on phenotypic, chemotaxonomic and phylogenetic properties, strains Gai3-2 (=CGMCC 1.16080=JCM 33550) and NJ-3-1 (=CGMCC 1.16040=JCM 33552) represent two novel species of the genus , for which the name sp. nov. and sp. nov. are proposed.

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  • Accepted:
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Keyword(s): Halobaculum halophilum sp. nov. , Halobaculum salinum sp. nov. , halophilic archaea , saline soil and salt lake
Funding
This study was supported by the:
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2019FY100700)
    • Principle Award Recipient: Heng-LinCui
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2017FY100302)
    • Principle Award Recipient: Heng-LinCui
  • National Natural Science Foundation of China (Award 32070003)
    • Principle Award Recipient: Heng-LinCui
  • National Natural Science Foundation of China (Award 31770005)
    • Principle Award Recipient: Heng-LinCui
© 2021 The Authors
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2021-07-20
2024-12-03
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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. 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]
  3. 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
     [Google Scholar]
  4. 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 [J]. Int J Syst Evol Microbiol 2020; 70:4261–4268 [View Article] [PubMed]
     [Google Scholar]
  5. Oren A. Candidatus Halobonum. In Bergey’s Manual of Systematics of Archaea and Bacteria West Sussex, UK: John Wiley & Sons, Inc; 2020
     [Google Scholar]
  6. Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE. Draft genome sequence of “Candidatus Halobonum tyrrellensis” strain G22, isolated from the hypersaline waters of Lake Tyrrell, Australia. Genome Announc 2013; 1:e01001-13 [View Article] [PubMed]
     [Google Scholar]
  7. Oren A, Garrity M, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956–4042 [View Article] [PubMed]
     [Google Scholar]
  8. Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB et al. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 2013; 8:e61692 [View Article] [PubMed]
     [Google Scholar]
  9. Han D, Cui HL. 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]
  10. Cui HL, Yang X, Mou YZ. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625–631 [View Article] [PubMed]
     [Google Scholar]
  11. Cui HL, Zhou PJ, Oren A, Liu SJ. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 2009; 13:31–37 [View Article] [PubMed]
     [Google Scholar]
  12. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  16. Yoon SH, 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
     [Google Scholar]
  17. 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]
     [Google Scholar]
  18. Yoon SH, Ha SM, 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]
     [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. 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]
  21. 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]
  22. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–D280 [View Article]
     [Google Scholar]
  23. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
     [Google Scholar]
  24. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  25. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  26. Nguyen LT, 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. Cui HL, 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
     [Google Scholar]
  32. Vaskovsky VE, Kostetsky EY. Modified spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1968; 9:396 [View Article] [PubMed]
     [Google Scholar]
  33. 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 [View Article]
     [Google Scholar]
  34. 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]
     [Google Scholar]
  35. Elling FJ, Becker KW, Köneke M, Schröer 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
     [Google Scholar]
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Halobaculum halophilum sp. nov. and Halobaculum salinum sp. nov., isolated from salt lake and saline soil
Int J Syst Evol Microbiol 71, 004900 (2021); https://doi.org/10.1099/ijsem.0.004900
/content/journal/ijsem/10.1099/ijsem.0.004900
/content/journal/ijsem/10.1099/ijsem.0.004900
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