1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 1

sp. nov., isolated from a natural salt meadow Free

Abstract

A Gram-stain-negative bacterium, designated I-24, was isolated from soil of a natural salt meadow. Strain I-24 was aerobic, non-motile, rod-shaped, catalase-positive, oxidase-positive and grew optimally at pH 7 and 25 °C. Comparative 16S rRNA gene analysis indicated that strain I-24 has closest similarities to KCTC 52727 (95.9 %) and KCTC 52035 (95.5 %). Strain I-24 contained summed feature 3 (C 7/C 6) and C 5 as the major fatty acids, the predominant respiratory quinone was menaquinone MK-7, and the major polar lipids were phosphatidylethanolamine as well as an unidentified phosphoaminolipid. The draft genome of strain I-24 consists of 10 326 072 base pairs with 9153 predicted coding sequences and a G+C content of 47.7 mol%. Clear distinctions between strain I-24 and KCTC 52727 or KCTC 52035 were shown in the pairwise average nucleotide identity results with values of 76.71 and 74.01 %, respectively. Moreover, the digital DNA–DNA relatedness values to these strains were 20.8 and 19.0 %. Based on its phenotypic, genotypic and chemotaxonomic characteristics, strain I-24 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is I-24 (DSM 111055=KCTC 72613).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , methanol , salt meadow and Spirosoma
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004601
2020-12-10
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/1/ijsem004601.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004601&mimeType=html&fmt=ahah

References

  1. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. The Prokaryotes, 4th ed. Springer Berlin Heidelberg; 2014
     [Google Scholar]
  2. Migula W. Über ein neues system Der Bakterien, Arbeiten AUS de, Bakteriologischen Institut Der Technischen Hochschule zu Karlsruhe; 1894
  3. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
     [Google Scholar]
  4. Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2009; 59:839–844 [View Article][PubMed]
     [Google Scholar]
  5. Ahn JH, Weon HY, Kim SJ, Hong SB, Seok SJ et al. Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2014; 64:3230–3234 [View Article][PubMed]
     [Google Scholar]
  6. Euzéby J. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2018; 59:923–925
     [Google Scholar]
  7. Kang H, Cha I, Kim H, Joh K. Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively. Int J Syst Evol Microbiol 2020; 70:5355–5362 [View Article][PubMed]
     [Google Scholar]
  8. Li W, Lee S-Y, Kang I-K, Ten LN, Jung H-Y. Spirosoma agri sp. nov., isolated from apple orchard soil. Curr Microbiol 2018; 75:694–700 [View Article][PubMed]
     [Google Scholar]
  9. Ten LN, Okiria J, Lee J-J, Lee S-Y, Park S et al. Spirosoma terrae sp. nov., isolated from soil from Jeju Island, Korea. Curr Microbiol 2018; 75:492–498 [View Article][PubMed]
     [Google Scholar]
  10. Li W, Ten LN, Lee SY, Lee DH, Jung HY. Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 2018; 200:431–438 [View Article][PubMed]
     [Google Scholar]
  11. Manirajan BA, Suarez C, Ratering S, Rusch V, Geissler-plaum R et al. Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.). Int J Syst Evol Microbiol 20181–7
     [Google Scholar]
  12. Weilan L, Lee JJ, Lee SY, Park S, Ten LN et al. Spirosoma humi sp. nov., isolated from soil in South Korea. Curr Microbiol 2018; 75:328–335 [View Article][PubMed]
     [Google Scholar]
  13. Li W, Ten LN, Lee S-Y, Kang I-K, Jung H-Y. Spirosoma horti sp. nov., isolated from apple orchard soil. Int J Syst Evol Microbiol 2018; 68:930–935 [View Article][PubMed]
     [Google Scholar]
  14. Ten LN, Elderiny N, Lee JJ, Lee SY, Park S et al. Spirosoma harenae sp. nov., a Bacterium Isolated from a Sandy Beach. Curr Microbiol 2018; 75:179–185 [View Article][PubMed]
     [Google Scholar]
  15. Li W, Lee S-Y, Kang I-K, Ten LN, Jung H-Y. Spirosoma pomorum sp. nov., isolated from apple orchard soil. J Microbiol 2018; 56:90–96 [View Article][PubMed]
     [Google Scholar]
  16. Widdel F, Bak F. Gram-Negative Mesophilic Sulfate-Reducing Bacteria. In: The Prokaryotes. New York, NY: Springer New York. pp. 3352–3378.
  17. Pitcher DG, Saunders NA, Owen RJ. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 1989; 8:151–156 [View Article]
     [Google Scholar]
  18. Kampmann K, Ratering S, Kramer I, Schmidt M, Zerr W et al. Unexpected stability of Bacteroidetes and Firmicutes communities in laboratory biogas reactors fed with different defined substrates. Appl Environ Microbiol 2012; 78:2106–2119 [View Article][PubMed]
     [Google Scholar]
  19. Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 2012; 78:717–725 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ et al. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  22. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
     [Google Scholar]
  23. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article][PubMed]
     [Google Scholar]
  24. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T et al. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003; 31:2187–2195 [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. 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. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F-J et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154 [View Article][PubMed]
     [Google Scholar]
  30. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–W346 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. Gerhardt P, Wood W, Murray RGE, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  33. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
     [Google Scholar]
  34. Kuykendall LD, Roy MA, O'NEILL JJ, Devine TE, Acids F. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  35. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  36. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  37. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
     [Google Scholar]
  38. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics. Methods for General and Molecular Microbiology, 3rd ed. American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  39. Zhang L, Zhou X-Y, Su X-J, Hu Q, Jiang J-D. Spirosoma sordidisoli sp. nov., a propanil-degrading bacterium isolated from a herbicide-contaminated soil. Antonie van Leeuwenhoek 2019; 112:1523–1532 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004601
Loading
Spirosoma endbachense sp. nov., isolated from a natural salt meadow
Int J Syst Evol Microbiol 71, 004601 (2020); https://doi.org/10.1099/ijsem.0.004601
/content/journal/ijsem/10.1099/ijsem.0.004601
/content/journal/ijsem/10.1099/ijsem.0.004601
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