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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 8

sp. nov., isolated from a marine red alga, reclassification of and as comb. nov. and comb. nov., and emended description of the genus Joshi . 2022 No Access

Abstract

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16, was isolated from a marine red alga, , in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16 was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16 contained anteiso-C, iso-C, iso-C and iso-C, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16 was 40.8 mol%. Strain P16 was most closely related to P203, DSM 8722 and LMG 21005 with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16, , and formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is P16 (=KACC 19520=JCM 32931). In addition, and are reclassified as comb. nov. (type strain P203=DSM 19153=NCIMB 14288) and comb. nov. (type strain PN-109=ATCC 700164=DSM 8722=KCCM 41407), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alkalicoccobacillus gibsonii , Alkalicoccobacillus plakortidis , Alkalicoccobacillus porphyridii , new taxa , reclassification and red alga
Funding
This study was supported by the:
  • National Institute of Biological Resources (Award NIBR No. 2022-02-001)
    • Principle Award Recipient: CheOk Jeon
  • Ministry of Ocean and Fisheries (KR) (Award 20210469)
    • Principle Award Recipient: CheOk Jeon
© 2023 The Authors
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2023-08-23
2024-05-08
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References

  1. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
     [Google Scholar]
  2. Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: an antibiotic-producing bacterium isolated from Lonar lake and reclassification of the genus Alkalihalobacillus into seven novel genera. Front Microbiol 2021; 12:722369 [View Article] [PubMed]
     [Google Scholar]
  3. Borchert MS, Nielsen P, Graeber I, Kaesler I, Szewzyk U et al. Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6. Int J Syst Evol Microbiol 2007; 57:2888–2893 [View Article] [PubMed]
     [Google Scholar]
  4. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article] [PubMed]
     [Google Scholar]
  5. Jung HS, Jeong SE, Chun BH, Quan Z-X, Jeon CO. Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum. Int J Syst Evol Microbiol 2019; 69:1656–1661 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Yumoto I, Hirota K, Goto T, Nodasaka Y, Nakajima K. Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile. Int J Syst Evol Microbiol 2005; 55:907–911 [View Article] [PubMed]
     [Google Scholar]
  10. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  11. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 3rd edn Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001
     [Google Scholar]
  12. 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]
  13. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. 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]
  16. Kim J, Na SI, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  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. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:
     [Google Scholar]
  22. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Helliwell KE. The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects. New Phytol 2017; 216:62–68 [View Article] [PubMed]
     [Google Scholar]
  27. Kim KH, Jia B, Jeon CO. Identification of trans-4-hydroxy-L-proline as a compatible solute and its biosynthesis and molecular characterization in Halobacillus halophilus. Front Microbiol 2017; 8:2054 [View Article] [PubMed]
     [Google Scholar]
  28. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146
     [Google Scholar]
  29. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article] [PubMed]
     [Google Scholar]
  30. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  31. 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]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–208
     [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  34. 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]
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Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022
Int J Syst Evol Microbiol 73, 006019 (2023); https://doi.org/10.1099/ijsem.0.006019
/content/journal/ijsem/10.1099/ijsem.0.006019
/content/journal/ijsem/10.1099/ijsem.0.006019
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