Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field

Antonie Van Leeuwenhoek. 2014 May;105(5):961-70. doi: 10.1007/s10482-014-0154-z.

Abstract

A Gram-stain negative, strictly aerobic, motile by gliding, rod-shaped and yellow pigmented strain THG-G12T was isolated from soil of a bamboo field in Seoul, Republic of Korea. Strain THG-G12T was observed to grow well at 20–28 °C and pH 7.0–7.5 in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG-G12T was found to be most closely related to Pedobacter ginsengisoli Gsoil 104T (97.5 % sequence similarity), Pedobacter steynii WB2.3-45T (97.4 %), Pedobacter metabolipauper WB2.3-71T (97.2 %), Pedobacter nyackensis NWG-II14T (97.2 %), Pedobacter caeni LMG 22862T (97.1 %) and Pedobacter duraquae WB2.1-25T (97.0 %), but DNA relatedness between strain THG-G12T and its phylogenetically closest neighbours was below 9.5 %. The G+C content of the genomic DNA was determined to be 39.9 mol%. The only isoprenoid quinone detected in strain THG-G12T was menaquinone-7 (MK-7). The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were found to be phosphatidylethanolamine, unidentified phosphoglycolipids, unidentified aminophosphoglycolipids, unidentified aminolipids and unidentified lipids. Strain THG-G12T showed the presence of two ceramide phosphorylethanolamines (CerPE-2′ and CerPE-2″), dihydrosphingosines and an unidentified ceramide as the major ceramide. The major fatty acids were identified as summed feature 3 (as defined by the MIDI system; C16:1 ω7c and/or C16:1 ω6c) and iso-C15:0. These data support the affiliation of strain THG-G12T to the genus Pedobacter. The results of physiological and biochemical tests enabled strain THG-G12T to be differentiated genotypically and phenotypically from the recognized species of the genus Pedobacter. Therefore, the novel isolate represents a novel species, for which the name Pedobacter seoulensis sp. nov. is proposed, with THG-G12T as the type strain (=KACC 17529T =JCM 19363T).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • Cluster Analysis
  • 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
  • Polyamines / analysis
  • Quinones / analysis
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology*

Substances

  • DNA, Bacterial
  • DNA, Ribosomal
  • Fatty Acids
  • Phospholipids
  • Polyamines
  • Quinones
  • RNA, Ribosomal, 16S

Associated data

  • GENBANK/KF150693