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Volume 72, Issue 12

sp. nov., a halotolerant bacteria isolated from a salt flat No Access

Abstract

A novel Gram-stain-negative, rod-shaped, cream-coloured, motile, halotolerant bacterium, designated as YJPS3-2, was isolated from saltern sediment of the Yellow sea in Yongyu-do, Republic of Korea. Strain YJPS3-2 grew at pH 5.0–10.0 (optimum, pH 7.0), 4–40 °C (optimum, 30 °C) and with 1–15% (w/v) NaCl (optimum 3 %). The 16S rRNA gene sequence analysis indicated that strain YJPS3-2 was closely related to those of F5-7 (98.75 %), F8-11 (98.74 %), AAD6 (98.66 %), G-16.1 (98.34 %), SS20 (97.98 %) and NTU-107 (96.93 %). The average nucleotide identity and digital DNA–DNA hybridization values between YJPS3-2 and related type strains were 86.9–91.6 % and 32.0–44.8 %. Strain YJPS3-2 was characterized as having Q-9 as the predominant respiratory quinone and the principal fatty acids (>10 %) were C (31.4 %), C 8 cyclo (16.3 %), C cyclo (11.9 %) and C 3-OH (10.4 %). The polar lipids consisted of phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of strain YJPS3-2 is 68.1mol %. Based on the polyphasic taxonomic evidence presented in this study, YJPS3-2 should be classified as representing a novel species within the genus , for which name is proposed, with the type strain YJPS3-2 (= KCTC 92124=KACC 22561=JCM 35085).

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  • Accepted:
  • Published Online:
Keyword(s): Getbol , Halomonas , halophile , halotolerant bacteria and marine bacteria
Funding
This study was supported by the:
  • Development of living shoreline technology based on blue carbon science toward climate change adaptation (Award KIMST-20220526)
    • Principle Award Recipient: YeonjaeYoo
© 2022 The Authors
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2022-12-16
2024-09-18
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References

  1. Valderrama MJ, Quesada E, Bejar V, Ventosa A, Gutierrez MC et al. Deleya salina sp. nov., a moderately halophilic Gram-negative bacterium. Int J Syst Bacteriol 1991; 41:377–384 [View Article]
     [Google Scholar]
  2. Ventosa A, de la Haba RR, Arahal DR, Sánchez‐Porro C. Halomonas. In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons; 2015 pp 1–111
     [Google Scholar]
  3. González-Domenech CM, Martínez-Checa F, Quesada E, Béjar V. Halomonas fontilapidosi sp. nov., a moderately halophilic, denitrifying bacterium. Int J Syst Evol Microbiol 2009; 59:1290–1296 [View Article]
     [Google Scholar]
  4. Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan D. Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 2013; 63:10–18 [View Article] [PubMed]
     [Google Scholar]
  5. Bouchotroch S, Quesada E, del Moral A, Llamas I, Béjar V. Halomonas maura sp. nov., a novel moderately halophilic, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 2001; 51:1625–1632 [View Article] [PubMed]
     [Google Scholar]
  6. Wang Y-N, Cai H, Chi C-Q, Lu A-H, Lin X-G et al. Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium. Int J Syst Evol Microbiol 2007; 57:1222–1226 [View Article] [PubMed]
     [Google Scholar]
  7. Franzmann PD, Burton HR, Mcmeekin TA. Halomonas subglaciescola, a new species of Halotolerant bacteria isolated from Antarctica. Int J Syst Bacteriol 1987; 37:27–34 [View Article]
     [Google Scholar]
  8. Corral P, Amoozegar MA, Ventosa A. Halophiles and their biomolecules: recent advances and future applications in biomedicine. Mar Drugs 2019; 18:E33 [View Article]
     [Google Scholar]
  9. Singh H, Kaur M, Jangra M, Mishra S, Nandanwar H et al. Antimicrobial properties of the novel bacterial isolate Paenibacilllus sp. SMB1 from a halo-alkaline lake in India. Sci Rep 2019; 9:1–12 [View Article] [PubMed]
     [Google Scholar]
  10. Arasu MV, Esmail GA, Al-Dhabi NA. Hypersaline actinomycetes and their biological applications. In Actinobacteria: Basics and Biotechnological Applications IntechOpen; 2016 p 229
     [Google Scholar]
  11. Thomas T, Sudesh K, Bazire A, Elain A, Tan HT et al. PHA production and PHA synthases of the halophilic bacterium Halomonas sp. SF2003. Bioengineering 2020; 7:29 [View Article]
     [Google Scholar]
  12. Lee H, Heo YM, Kwon SL, Yoo Y, Lee AH et al. Recovery of the benthic bacterial community in coastal abandoned saltern requires over 35 years: a comparative case study in the Yellow Sea. Environ Int 2020; 135:105412 [View Article]
     [Google Scholar]
  13. Takizawa M, Colwell RR, Hill RT. Isolation and diversity of actinomycetes in the Chesapeake Bay. Appl Environ Microbiol 1993; 59:997–1002 [View Article] [PubMed]
     [Google Scholar]
  14. Yoo Y, Lee DW, Lee H, Kwon B-O, Khim JS et al. Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1676–1681 [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. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  17. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
     [Google Scholar]
  18. 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]
  19. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article] [PubMed]
     [Google Scholar]
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:1–14 [View Article] [PubMed]
     [Google Scholar]
  24. 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] [PubMed]
     [Google Scholar]
  25. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. 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:D206–14 [View Article]
     [Google Scholar]
  28. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017; 45:W36–W41 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  31. Yoo Y, Lee H, Kwon B-O, Khim JS, Baek S et al. Marinobacter halodurans sp. nov., a halophilic bacterium isolated from sediment of a salt flat. Int J Syst Evol Microbiol 2020; 70:6294–6300 [View Article] [PubMed]
     [Google Scholar]
  32. Yoo Y, Kim D, Lee H, Khim JS, Kim B et al. Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  33. Quesada E, Ventosa A, Ruiz-berraquero F, Ramos-cormenzana A. Deleya halophila, a new species of moderately halophilic bacteria. Int J Syst Bacteriol 1984; 34:287–292 [View Article]
     [Google Scholar]
  34. García MT, Mellado E, Ostos JC, Ventosa A. Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int J Syst Evol Microbiol 2004; 54:1723–1728 [View Article] [PubMed]
     [Google Scholar]
  35. Lim J-M, Yoon J-H, Lee J-C, Jeon CO, Park D-J et al. Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. Int J Syst Evol Microbiol 2004; 54:2037–2042 [View Article] [PubMed]
     [Google Scholar]
  36. Wang C-Y, Wu S-J, Ng C-C, Tzeng W-S, Shyu Y-T. Halomonas beimenensis sp. nov., isolated from an abandoned saltern. Int J Syst Evol Microbiol 2012; 62:3013–3017 [View Article] [PubMed]
     [Google Scholar]
  37. Vreeland RH, Litchfield CD, Martin EL, Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int J Syst Bacteriol 1980; 30:485–495 [View Article]
     [Google Scholar]
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Halomonas getboli sp. nov., a halotolerant bacteria isolated from a salt flat
Int J Syst Evol Microbiol 72, 005634 (2023); https://doi.org/10.1099/ijsem.0.005634
/content/journal/ijsem/10.1099/ijsem.0.005634
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