Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis

Int J Syst Evol Microbiol. 2016 Oct;66(10):4191-4196. doi: 10.1099/ijsem.0.001334. Epub 2016 Jul 27.

Abstract

An endophytic actinobacterial strain, designated py1292T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, China, and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the family Dermacoccaceae and clustered with Yimella lutea (showing the highest similarity of 99.1 %). DNA-DNA relatedness between strain py1292T and Y. lutea YIM 45900T was 45.6±3.2 % (reciprocal 47.8±3.6 %). The novel isolate was found to be a Gram-staining-positive rod, catalase- and oxidase-positive. It grew at pH 6.0-8.0, with 0-9 % NaCl and at 20-45 ºC, optimally at pH 7.0, with 0-3 % NaCl and at 28 ºC. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phospholipids and two unknown polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole-cell hydrolysates contained mannose, ribose, rhamnose, glucose and galactose. The peptidoglycan contained alanine, glycine, serine, aspartic acid, glutamic acid and lysine. The genomic DNA G+C content was determined to be 65.6 mol%. Phylogenetic, phenotypic and chemotaxonomic data (especially the same peptidoglycan type) showed that strain py1292T should be classified as a representative of a novel species of the genus Yimella, for which the name Yimella radicis sp. nov. is proposed. The type strain is py1292T (=KCTC 39612T=LMG 29070T).

MeSH terms

  • Actinomycetales / classification*
  • Actinomycetales / genetics
  • Actinomycetales / isolation & purification
  • Bacterial Typing Techniques
  • Base Composition
  • Cell Wall / chemistry
  • China
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / genetics
  • Fatty Acids / chemistry
  • Melanthiaceae / microbiology*
  • Nucleic Acid Hybridization
  • Peptidoglycan / chemistry
  • Phospholipids / chemistry
  • Phylogeny*
  • Plant Roots / microbiology*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Vitamin K 2 / analogs & derivatives
  • Vitamin K 2 / chemistry

Substances

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