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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Tago, Kanako, Itoh, Hideomi, Kikuchi, Yoshitomo, Hori, Tomoyuki, Sato, Yuya, Nagayama, Atsushi, Okubo, Takashi, Navarro, Ronald, Aoyagi, Tomo, Hayashi, Kentaro, Hayatsu, Masahito
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Japanese Society of Microbial Ecology (JSME)/The Japanese Society of Soil Microbiology (JSSM) 2014
Materias:
Short Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262370/
https://www.ncbi.nlm.nih.gov/pubmed/25410730
http://dx.doi.org/10.1264/jsme2.ME14122
_version_ 1782348419367436288
author Tago, Kanako
Itoh, Hideomi
Kikuchi, Yoshitomo
Hori, Tomoyuki
Sato, Yuya
Nagayama, Atsushi
Okubo, Takashi
Navarro, Ronald
Aoyagi, Tomo
Hayashi, Kentaro
Hayatsu, Masahito
author_facet Tago, Kanako
Itoh, Hideomi
Kikuchi, Yoshitomo
Hori, Tomoyuki
Sato, Yuya
Nagayama, Atsushi
Okubo, Takashi
Navarro, Ronald
Aoyagi, Tomo
Hayashi, Kentaro
Hayatsu, Masahito
author_sort Tago, Kanako
collection PubMed
description 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 (10(7) 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.
format Online
Article
Text
id pubmed-4262370
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher The Japanese Society of Microbial Ecology (JSME)/The Japanese Society of Soil Microbiology (JSSM)
record_format MEDLINE/PubMed
spelling pubmed-42623702014-12-16 A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil Tago, Kanako Itoh, Hideomi Kikuchi, Yoshitomo Hori, Tomoyuki Sato, Yuya Nagayama, Atsushi Okubo, Takashi Navarro, Ronald Aoyagi, Tomo Hayashi, Kentaro Hayatsu, Masahito Microbes Environ Short Communication 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 (10(7) 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. The Japanese Society of Microbial Ecology (JSME)/The Japanese Society of Soil Microbiology (JSSM) 2014-12 2014-11-20 /pmc/articles/PMC4262370/ /pubmed/25410730 http://dx.doi.org/10.1264/jsme2.ME14122 Text en Copyright 2014 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Communication
Tago, Kanako
Itoh, Hideomi
Kikuchi, Yoshitomo
Hori, Tomoyuki
Sato, Yuya
Nagayama, Atsushi
Okubo, Takashi
Navarro, Ronald
Aoyagi, Tomo
Hayashi, Kentaro
Hayatsu, Masahito
A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title_full A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title_fullStr A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title_full_unstemmed A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title_short A Fine-Scale Phylogenetic Analysis of Free-Living Burkholderia Species in Sugarcane Field Soil
title_sort fine-scale phylogenetic analysis of free-living burkholderia species in sugarcane field soil
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262370/
https://www.ncbi.nlm.nih.gov/pubmed/25410730
http://dx.doi.org/10.1264/jsme2.ME14122
work_keys_str_mv AT tagokanako afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT itohhideomi afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT kikuchiyoshitomo afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT horitomoyuki afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT satoyuya afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT nagayamaatsushi afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT okubotakashi afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT navarroronald afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT aoyagitomo afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT hayashikentaro afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT hayatsumasahito afinescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT tagokanako finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT itohhideomi finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT kikuchiyoshitomo finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT horitomoyuki finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT satoyuya finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT nagayamaatsushi finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT okubotakashi finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT navarroronald finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT aoyagitomo finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT hayashikentaro finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil
AT hayatsumasahito finescalephylogeneticanalysisoffreelivingburkholderiaspeciesinsugarcanefieldsoil

Ejemplares similares