A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil

Kanako Tago; Hideomi Itoh; Yoshitomo Kikuchi; Tomoyuki Hori; Yuya Sato; Atsushi Nagayama; Takashi Okubo; Ronald Navarro; Tomo Aoyagi; Kentaro Hayashi; Masahito Hayatsu

doi:10.1264/jsme2.ME14122

Short Communications

A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil

Kanako Tago, Hideomi Itoh, Yoshitomo Kikuchi, Tomoyuki Hori, Yuya Sato, Atsushi Nagayama, Takashi Okubo, Ronald Navarro, Tomo Aoyagi, Kentaro Hayashi, Masahito Hayatsu

Author information

Kanako Tago
Environmental Biofunction Division, National Institute for Agro–Environmental Sciences
Hideomi Itoh
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
Yoshitomo Kikuchi
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
Tomoyuki Hori
Research Institute for Environmental Management Technology, AIST
Yuya Sato
Research Institute for Environmental Management Technology, AIST
Atsushi Nagayama
Okinawa Prefectural Agricultural Research Center
Takashi Okubo
Environmental Biofunction Division, National Institute for Agro–Environmental Sciences
Ronald Navarro
Research Institute for Environmental Management Technology, AIST
Tomo Aoyagi
Research Institute for Environmental Management Technology, AIST
Kentaro Hayashi
Environmental Biofunction Division, National Institute for Agro–Environmental Sciences
Masahito Hayatsu
Environmental Biofunction Division, National Institute for Agro–Environmental Sciences

Keywords: Burkholderia, Illumina sequencing, sugarcane field

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Supplementary material

2014 Volume 29 Issue 4 Pages 434-437

DOI https://doi.org/10.1264/jsme2.ME14122

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Abstract

The diversity and abundance of Burkholderia species in sugarcane field soils were investigated by a 16S rRNA gene-based approach using genus-specific primers. A total of 365,721 sequences generated by the Illumina MiSeq platform were assigned to the genus Burkholderia. Nearly 58% of these sequences were placed in a previously defined cluster, including stinkbug symbionts. Quantitative PCR analysis revealed a consistent number of 16S rRNA gene copies for Burkholderia species (10⁷ g⁻¹ soil) across the sampled fields. C/N, pH, and nitrate concentrations were important factors shaping the Burkholderia community structure; however, their impacts were not significant considering the overall genus size.

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