Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation

Antonie Van Leeuwenhoek. 2015 Feb;107(2):565-73. doi: 10.1007/s10482-014-0352-8. Epub 2014 Dec 18.

Abstract

An ivory white, rod-shaped, non-motile, non-spore forming, Gram-staining-negative, and aerobic bacterium designated THG-G118T, was isolated from a soil sample collected in a bamboo plantation in Seoul, Republic of Korea. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain THG-G118T with the genus Pedobacter. Strain THG-G118T was found to show the closest phylogenetic relationship with Pedobacter metabolipauper WB2.3-71T with 16S rRNA gene sequence similarity of 97.3 %. The major cellular fatty acids of strain THG-G118T were identified as C16:0, C18:0, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and the predominant menaquinone as menaquinone MK-7. The major polar lipids were found to be phosphatidylethanolamine (PE), unidentified phospholipid and unidentified aminophospholipids. Strain THG-G118T was found to contain ceramide phosphorylethanolamine 2 (CerPE-2) and dihydrosphingosine as the major ceramide. The G+C content of the genomic DNA was found to be 41.7 mol%. DNA-DNA hybridization experiments revealed a low level of DNA-DNA relatedness (<42.5 %) between strain THG-G118T and its closest relatives. The phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-G118T could be clearly distinguished from the members of the genus Pedobacter. Based on the results of a polyphasic study, a new species, Pedobacter bambusae sp. nov., is proposed. The type strain is THG-G118T (=KACC 17544T = JCM 19364T).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aerobiosis
  • Bacterial Typing Techniques
  • Base Composition
  • Cluster Analysis
  • Cytosol / chemistry
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Fatty Acids / analysis
  • Korea
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Pedobacter / classification*
  • Pedobacter / genetics
  • Pedobacter / isolation & purification*
  • Pedobacter / physiology
  • Phospholipids / analysis
  • Phylogeny
  • Poaceae / growth & development
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Vitamin K 2 / analysis

Substances

  • DNA, Bacterial
  • DNA, Ribosomal
  • Fatty Acids
  • Phospholipids
  • RNA, Ribosomal, 16S
  • Vitamin K 2

Associated data

  • GENBANK/KF150694