1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 1

sp. nov., a bacterium isolated from soil Free

Abstract

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10–33 °C, pH 6.0–7.5 and with 0–4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12 was in the same clade as Vu-144 and Gsoil809 with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12 and Vu-144 showed that average nucleotide identity value was 69.4 % and the digital DNA–DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C, iso-C G and iso-C 3-OH, which supported the affiliation of strain KIS59-12 with the genus . The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is KIS59-12 (=KACC 17340=NBRC 113161).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Arachidicoccus , novel species , polyphasic taxonomy and strain KIS59-12T
Funding
This study was supported by the:
  • Rural Development Administration (Award PJ01351901)
    • Principle Award Recipient: Hang-Yeon Weon
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004566
2020-11-18
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/1/ijsem004566.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004566&mimeType=html&fmt=ahah

References

  1. Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:578–586 [View Article][PubMed]
     [Google Scholar]
  2. Siddiqi MZ, Aslam Z, Im WT. Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2017; 67:1005–1010 [View Article][PubMed]
     [Google Scholar]
  3. Siddiqi MZ, Shafi SM, Im W-T, W-T I. Complete genome sequencing of Arachidicoccus ginsenosidimutans sp. nov., and its application for production of minor ginsenosides by finding a novel ginsenoside-transforming β-glucosidase. RSC Adv 2017; 7:46745–46759 [View Article]
     [Google Scholar]
  4. 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]
  5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  6. Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
     [Google Scholar]
  7. 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]
  8. 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]
  9. Yoon SH, Ha SM, 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]
  10. Na SI, Kim YO, Yoon SH, Ha SM, 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]
  11. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. Alori ET, Glick BR, Babalola OO. Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Front Microbiol 2017; 8:971 [View Article][PubMed]
     [Google Scholar]
  14. Moreno-Vivián C, Cabello P, Martínez-Luque M, Blasco R, Castillo F. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 1999; 181:6573–6584 [View Article][PubMed]
     [Google Scholar]
  15. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids; 1990
  16. 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]
  17. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 1995; 668:189–197 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004566
Loading
Arachidicoccus soli sp. nov., a bacterium isolated from soil
Int J Syst Evol Microbiol 71, 004566 (2020); https://doi.org/10.1099/ijsem.0.004566
/content/journal/ijsem/10.1099/ijsem.0.004566
/content/journal/ijsem/10.1099/ijsem.0.004566
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