1887

Abstract

A Gram-stain-negative, aerobic, non-motile and rod- or coccoid-shaped novel bacterial strain, designated MAH-25, was isolated from soil sampled in a pine garden. The colonies were observed to be light pink-coloured, smooth, spherical and 1–2 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-25 was found to be able to grow at 15–35 °C, at pH 5.0–8.0 and at 0–2.0 % NaCl. Cell growth occurred on Reasoner's 2A agar and nutrient agar. The strain was found to be positive in both oxidase and catalase tests. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus and closely related to 5-10 (98.0 % similarity), TMB834 (97.7 %), TTB310 (97.6 %) and YS3.2.7 (97.3 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-25 and the four closely related type strains were in the range of 78.8–81.3 % and 22.3–24.1 %, respectively. The novel strain MAH-25 has a draft genome size of 5 505 957 bp (11 contigs), annotated with 5210 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content was determined to be 70.3 mol%. The predominant isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were identified as C, summed feature 3 (C 7 and/or C 6) and summed feature 8 (C 7 and/or C 6). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of DNA–DNA hybridization, genotypic analysis, chemotaxonomic and physiological data, strain MAH-25 represents a novel species within the genus , for which the name sp. nov. is proposed, with MAH-25 (=KACC 19839=CGMCC1.13660) as the type strain.

Funding
This study was supported by the:
  • National Research Foundation of Korea (Award Project no. NRF-2018R1C1B5041386)
    • Principle Award Recipient: Md. Amdadul Huq
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004486
2020-09-23
2021-10-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5841.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004486&mimeType=html&fmt=ahah

References

  1. Heulin T, Barakat M, Christen R, Lesourd M, Sutra L et al. Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 2003; 53:589–594 [View Article][PubMed]
    [Google Scholar]
  2. Lee HJ, Lee SH, Lee S-S, Lee JS, Kim Y et al. Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter. Int J Syst Evol Microbiol 2014; 64:1317–1322 [View Article][PubMed]
    [Google Scholar]
  3. Chaudhary DK, Kim J. Ramlibacter monticola sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:4468–4474 [View Article][PubMed]
    [Google Scholar]
  4. Yan Z-F, Trinh H, Moya G, Lin P, Li C-T et al. Ramlibacter rhizophilus sp. nov., isolated from rhizosphere soil of national flower Mugunghwa from South Korea. Int J Syst Evol Microbiol 2017; 67:3773–3777 [View Article][PubMed]
    [Google Scholar]
  5. Wang L, An D-S, Kim S-G, Jin F-X, Kim S-C et al. Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity. J Microbiol Biotechnol 2012; 22:311–315 [View Article][PubMed]
    [Google Scholar]
  6. Lee DH, Cha CJ. Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng. Int J Syst Evol Microbiol 2017; 67:4619–4623 [View Article][PubMed]
    [Google Scholar]
  7. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematic New York: Wiley; 1991 pp 115–175
    [Google Scholar]
  8. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  9. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  10. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  11. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  12. 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]
  13. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  15. Yoon SH, 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]
  16. 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]
  17. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  18. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A et al. Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 2008; 56:625–636 [View Article][PubMed]
    [Google Scholar]
  19. Gillis M, De Ley J, De Cleene M. The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 1970; 12:143–153 [View Article][PubMed]
    [Google Scholar]
  20. McConaughy BL, Laird CD, McCarthy BJ. Nucleic acid reassociation in formamide. Biochemistry 1969; 8:3289–3295 [View Article][PubMed]
    [Google Scholar]
  21. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  22. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  23. Huq MA. Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden. Arch Microbiol 2018; 200:581-587 [View Article][PubMed]
    [Google Scholar]
  24. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  25. Huq MA. Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden. Arch Microbiol 2018; 200:343–348 [View Article][PubMed]
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  27. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  28. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article][PubMed]
    [Google Scholar]
  29. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004486
Loading
/content/journal/ijsem/10.1099/ijsem.0.004486
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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