Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil

Int J Syst Evol Microbiol. 2016 Dec;66(12):5320-5327. doi: 10.1099/ijsem.0.001515. Epub 2016 Sep 23.


Ginseng-cultivated soil is an excellent habitat for soil-borne bacteria to proliferate. A novel strain, DCY87T, was isolated from ginseng-cultivated soil in Gochang County, Republic of Korea, and subsequently characterized by polyphasic approach. Cells were rod shaped, non-motile, aerobic, Gram-reaction-positive, oxidase-negative and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY87T shared the highest similarity to 'Phycicoccus ochangensis' L1b-b9 (98.7 %). Closely phylogenetic relatives of strain DCY87T were identified: Phycicoccus ginsenosidimutans BXN5-13T (97.9 %), Phycicoccus soli THG-a14T (97.8 %), Phycicoccus bigeumensis MSL-03T (97.3 %), Phycicoccus cremeus V2M29T (97.3 %), Phycicoccus aerophilus 5516T-20T (97.3 %), Phycicoccus dokdonensis DS-8T (97.3 %) and Phycicoccus jejuensis KSW2-15T (97.1 %). The major polar lipids were classified as phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were composed of iso-C15 : 0, anteiso-C15:0, C17 : 0 and C17 : 1ω8c. The menaquinone was resolved as MK-8(H4). Strain DCY87T contained meso-diaminopimelic acid as diamino acid in the cell-wall peptidoglycan and glucose, xylose and rhamnose in the whole-cell sugar. The genomic DNA G+C content was calculated to be 72.7 mol%. DNA-DNA hybridization value between strain DCY87T and 'P. ochangensis' L1b-b9 was estimated to be 50 %. However, DNA-DNA hybridization value obtained between strain DCY87T and P. ginsenosidimutans BXN5-13T, P. soli THG-a14T and P. bigeumensis MSL-03T was well below 17 %. In general, polyphasic taxonomy demonstrated that DCY87T strain represented a novel species within the genus Phycicoccus. Accordingly, we propose the name Phycicoccus ginsengisoli sp. nov. The type strain is DCY87T (=KCTC 39635T=JCM 31016T).

MeSH terms

  • Actinomycetales / classification*
  • Actinomycetales / genetics
  • Actinomycetales / isolation & purification
  • Bacterial Typing Techniques
  • Base Composition
  • DNA, Bacterial / genetics
  • Diaminopimelic Acid / chemistry
  • Fatty Acids / chemistry
  • Nucleic Acid Hybridization
  • Panax / microbiology*
  • Peptidoglycan / chemistry
  • Phospholipids / chemistry
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Republic of Korea
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Vitamin K 2 / analogs & derivatives
  • Vitamin K 2 / chemistry


  • DNA, Bacterial
  • Fatty Acids
  • Peptidoglycan
  • Phospholipids
  • RNA, Ribosomal, 16S
  • Vitamin K 2
  • vitamin MK 8
  • Diaminopimelic Acid