1887

Abstract

Strain CJN36-1N, a Gram-stain-positive, non-flagellated, strictly aerobic and short rod-shaped bacterium, was isolated from flowerpot soil sampled in the Jeonju region of the Republic of Korea. Based on 16S rRNA gene sequences and the resulting phylogenetic tree, the strain belonged to the genus . Strain CJN36-1N contained a chromosome of 3.6 Mbp with a G+C content of 68.5 mol%. The strain grew at 10–37 °C (optimally at 28 °C), at pH 5.0–8.0 (optimally at pH 8.0), and in the presence of 0–7 % NaCl (w/v; optimally with 0 % NaCl). Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain CJN36-1N and its closest related species, DFW100M-13, were 82.0, 81.2, and 23.2 %, respectively. We propose naming this novel species sp. nov., with CJN36-1N (=KACC 23027=NBRC 116065) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006384
2024-05-14
2024-05-20
Loading full text...

Full text loading...

References

  1. Orla-Jensen S. The Lactic Acid Bacteria Høst; 1919
    [Google Scholar]
  2. Takeuchi M, Hatano K. Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J syst Evol Microbiol 1998; 48:739–747 [View Article] [PubMed]
    [Google Scholar]
  3. Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang SK et al. Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2012; 62:2187–2193 [View Article] [PubMed]
    [Google Scholar]
  4. Alves A, Correia A, Igual JM. Microbacterium endophyticum sp. nov. Microbiol 2014;37:474–479. 5. 6. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium. Syst Appl Microbiol 2014; 37:474–479
    [Google Scholar]
  5. Fidalgo C, Riesco R, Henriques I, Trujillo ME, Alves A. Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2016; 66:4492–4500 [View Article] [PubMed]
    [Google Scholar]
  6. Parte AC, Carbasse JS, 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]
  7. Goodfellow M, Peter K, Busse H-J, Trujillo ME, Ludwig W et al. Bergey’s Manual of Systematic Bacteriology New York: Springer; 2012
    [Google Scholar]
  8. Cho S-J, Lee S-S. Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea. Antonie van Leeuwenhoek 2017; 110:11–18 [View Article] [PubMed]
    [Google Scholar]
  9. Yang Z-W, Salam N, Mohany M, Chinnathambi A, Alharbi SA et al. Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil. Int J Syst Evol Microbiol 2018; 68:217–222 [View Article] [PubMed]
    [Google Scholar]
  10. Heo J, Cho H, Kim MA, Hamada M, Tamura T et al. Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 2020; 70:2226–2232 [View Article]
    [Google Scholar]
  11. Al-Sadi A, Al-Zakwani H, Nasehi A, Al-Mazroui S, Al-Mahmooli I. Analysis of bacterial communities associated with potting media. Springerplus 2016; 5:1–5 [View Article] [PubMed]
    [Google Scholar]
  12. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Tamura K, Stecher G, Kumar S. MEGA 11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 2:406–416 [View Article]
    [Google Scholar]
  19. 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]
  20. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
    [Google Scholar]
  21. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article] [PubMed]
    [Google Scholar]
  24. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:182–185 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Lee I, Kim YO, Park S-C, 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]
  27. 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; 50:801–807 [View Article] [PubMed]
    [Google Scholar]
  28. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI; 1990
    [Google Scholar]
  30. Minnikin D, O’Donnell A, 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]
  31. Schumann P. Peptidoglycan structure. In Methods in Microbiology vol 38 Academic press; 2011 pp 101–129
    [Google Scholar]
  32. Scalise M, Indiveri C. Amino acids transport and metabolism 2.0. Int J Mol Sci 2020; 21:1212 [View Article] [PubMed]
    [Google Scholar]
  33. Tan P, Du X, Shang Y, Zhu K, Joshi S et al. Ion transporters and their exploration for conferring abiotic stress tolerance in plants. Plant Growth Regul 2022; 96:1–23 [View Article]
    [Google Scholar]
  34. Đorđievski S, Vukašinović EL, Čelić TV, Pihler I, Kebert M et al. Spermidine dietary supplementation and polyamines level in reference to survival and lifespan of honey bees. Sci Rep 2023; 13:4329 [View Article] [PubMed]
    [Google Scholar]
  35. 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]
  36. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  37. Evtushenko LI, Takeuchi M. The family microbacteriaceae. In The Prokaryotes vol 3 2006 pp 1020–1098 [View Article]
    [Google Scholar]
  38. Vaz-Moreira I, Lopes AR, Falsen E, Schumann P, Nunes OC et al. Microbacterium luticocti sp. nov., isolated from sewage sludge compost. Int J Syst Evol Microbiol 2008; 58:1700–1704 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006384
Loading
/content/journal/ijsem/10.1099/ijsem.0.006384
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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