1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 10

sp. nov., sp. nov. and sp. nov., isolated from saltern soil No Access

Abstract

Three bacterial strains, designated SSBR10-3, SSTM10-2 and SSHM10-5, were isolated from saltern soil sampled in Jeollanam-do, Republic of Korea. Cells were aerobic, Gram-stain-positive, flagellated and rod-shaped. The strains grew optimally at 28°C and at pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains SSBR10-3, SSTM10-2 and SSHM10-5 were placed within the genus , showing the highest similarity to FP5 (98.6 %), ‘’ Marseille-Q1234 (98.5 %) and MSS-155 (98.6 %), respectively. The genomic similarity values between strains SSBR10-3, SSTM10-2 and SSHM10-5 and their related species were 17.6–22.6 % for digital DNA–DNA hybridization (dDDH) and 69.6–78.5 % for orthologous average nucleotide identity (OrthoANI), which were lower than the thresholds recommended for species delineation. The dDDH and OrthoANI values among the three strains were below 38.3 and 89.4 %, respectively. Besides the differences in genomic features, strains SSBR10-3, SSTM10-2 and SSHM10-5 were distinct from each other and from members of the genus in terms of phenotypic traits related to substrate assimilation. The cell-wall peptidoglycan contained -diaminopimelic acid, the major fatty acids were anteiso-C, iso-C and anteiso-C, and the predominant menaquinone was MK-7 for all three strains. Diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid were present in their polar lipid profiles. Based on a polyphasic approach incorporating genomic data, strains SSBR10-3, SSTM10-2 and SSHM10-5 represent novel species, for which the names sp. nov. (SSBR10-3=DSM 114353=KACC 21935=NBRC 115504), sp. nov. (SSTM10-2=DSM 114354=KACC 21936=NBRC 115505) and sp. nov. (SSHM10-5=DSM 114355= KACC 21937=NBRC 115506) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Halobacillus salinarum sp. nov. , Halobacillus shinanisalinarum sp. nov. , saltern and soil
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006098
2023-10-26
2024-05-08
Loading full text...

Full text loading...

References

  1. Spring S, Ludwig W, Marquez MC, Ventosa A, Schleifer K-H. Halobacillus gen. nov., with descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. Int J Syst Bacteriol 1996; 46:492–496 [View Article]
     [Google Scholar]
  2. Booncharoen A, Visessanguan W, Kuncharoen N, Yiamsombut S, Santiyanont P et al. Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  3. Kim SJ, Lee JC, Han SI, Whang KS. Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. Antonie Van Leeuwenhoek 2016; 109:713–720 [View Article] [PubMed]
     [Google Scholar]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  5. Yoon JH, Kang SJ, Lee CH, Oh HW, Oh TK. Halobacillus yeomjeoni sp. nov., isolated from a marine solar saltern in Korea. Int J Syst Evol Microbiol 2005; 55:2413–2417 [View Article] [PubMed]
     [Google Scholar]
  6. Yoon J-H, Kang KH, Park Y-H. Halobacillus salinus sp. nov., isolated from a salt lake on the coast of the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:687–693 [View Article] [PubMed]
     [Google Scholar]
  7. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  8. Yoon JH, Kang KH, Oh TK, Park YH. Halobacillus locisalis sp. nov., a halophilic bacterium isolated from a marine solar saltern of the Yellow Sea in Korea. Extremophiles 2004; 8:23–28 [View Article] [PubMed]
     [Google Scholar]
  9. Yoon JH, Kang SJ, Jung YT, Oh TK. Halobacillus campisalis sp. nov., containing meso-diaminopimelic acid in the cell-wall peptidoglycan, and emended description of the genus Halobacillus. Int J Syst Evol Microbiol 2007; 57:2021–2025 [View Article]
     [Google Scholar]
  10. Yoon JH, Kang SJ, Oh TK. Halobacillus seohaensis sp. nov., isolated from a marine solar saltern in Korea. Int J Syst Evol Microbiol 2008; 58:622–627 [View Article] [PubMed]
     [Google Scholar]
  11. Kim SJ, Lee JC, Han SI, Whang KS. Halobacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. Int J Syst Evol Microbiol 2015; 65:4434–4440 [View Article] [PubMed]
     [Google Scholar]
  12. Liu WY, Zeng J, Wang L, Dou YT, Yang SS. Halobacillus dabanensis sp. nov. and Halobacillus aidingensis sp. nov., isolated from salt lakes in Xinjiang, China. Int J Syst Evol Microbiol 2005; 55:1991–1996 [View Article] [PubMed]
     [Google Scholar]
  13. Romano I, Finore I, Nicolaus G, Huertas FJ, Lama L et al. Halobacillus alkaliphilus sp. nov., a halophilic bacterium isolated from a salt lake in Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 2008; 58:886–890 [View Article] [PubMed]
     [Google Scholar]
  14. Amoozegar MA, Malekzadeh F, Malik KA, Schumann P, Spröer C. Halobacillus karajensis sp. nov., a novel moderate halophile. Int J Syst Evol Microbiol 2003; 53:1059–1063 [View Article] [PubMed]
     [Google Scholar]
  15. Wang K, Zhang L, Yang Y, Pan Y, Meng L et al. Halobacillus andaensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soil. Int J Syst Evol Microbiol 2015; 65:1908–1914 [View Article] [PubMed]
     [Google Scholar]
  16. Oren A. Industrial and environmental applications of halophilic microorganisms. Environ Technol 2010; 31:825–834 [View Article] [PubMed]
     [Google Scholar]
  17. Oren A. Halophilic microbial communities and their environments. Curr Opin Biotechnol 2015; 33:119–124 [View Article] [PubMed]
     [Google Scholar]
  18. Lane D. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics Wiley; 1991 pp 115–175
     [Google Scholar]
  19. 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]
  20. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  26. Ripka K. Identification of Microorganisms on Stone and Muralpaintings Using Molecular Methods University of Wien; 2005
     [Google Scholar]
  27. Hufnagel DE, Hufford MB, Seetharam AS. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics 2020; 21:429 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  30. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  31. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  34. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  35. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  36. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article] [PubMed]
     [Google Scholar]
  37. Zhao S, Zhang Q, Hao G, Liu X, Zhao J et al. The protective role of glycine betaine in Lactobacillus plantarum ST-III against salt stress. Food Control 2014; 44:208–213 [View Article]
     [Google Scholar]
  38. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  39. Galinski EA, Pfeiffer HP, Trüper HG. 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid. A novel cyclic amino acid from halophilic phototrophic bacteria of the genus Ectothiorhodospira. Eur J Biochem 1985; 149:135–139 [View Article] [PubMed]
     [Google Scholar]
  40. Saum SH, Müller V. Growth phase-dependent switch in osmolyte strategy in a moderate halophile: ectoine is a minor osmolyte but major stationary phase solute in Halobacillus halophilus. Environ Microbiol 2008; 10:716–726 [View Article] [PubMed]
     [Google Scholar]
  41. Han J, Gao Q-X, Zhang Y-G, Li L, Mohamad OAA et al. Transcriptomic and ectoine analysis of halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress. Front Microbiol 2018; 9:618 [View Article]
     [Google Scholar]
  42. Gilchrist CLM, Chooi Y-H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 2021; 37:2473–2475 [View Article] [PubMed]
     [Google Scholar]
  43. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  44. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006098
Loading
Halobacillus salinarum sp. nov., Halobacillus shinanisalinarum sp. nov. and Halobacillus amylolyticus sp. nov., isolated from saltern soil
Int J Syst Evol Microbiol 73, 006098 (2023); https://doi.org/10.1099/ijsem.0.006098
/content/journal/ijsem/10.1099/ijsem.0.006098
/content/journal/ijsem/10.1099/ijsem.0.006098
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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