Strategies to reveal genomic function in natural soil systems

Yoshiyuki Ohtsubo; Eri Nishiyama; Yoko Ishibashi; Yuji Nagata; Masataka Tsuda

doi:10.1007/978-4-431-54520-0_14

Strategies to reveal genomic function in natural soil systems

Yoshiyuki Ohtsubo, Eri Nishiyama, Yoko Ishibashi, Yuji Nagata, Masataka Tsuda

LIF - Molecular and Chemical Life Science

Tohoku University

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Abstract

IVET IVET (in vivo expression technology) and STM STM (signature-tagged mutagenesis) are suitable methods for revealing genes that are induced in soil and are essential in soil, respectively. These methods are potentially advantageous over newer methods, such as microarray and RNA-seq, because they allow analyses of bacteria under non-sterile conditions. However, their application to non-sterile soil also presents challenges that must be overcome. In this work, we describe the difficulties we faced when using IVET to identify genes that are upregulated in Burkholderia multivorans ATCC 17616 ATCC 17616 in soil. We also describe the future perspectives of these and other analytical schemes, including the potential use of next-generation sequencing technologies that might allow comprehensive isolation of soil-relevant genes and also might improve the quality of research from a qualitative point of view.

Original language	English
Title of host publication	Biodegradative Bacteria
Subtitle of host publication	How Bacteria Degrade, Survive, Adapt, and Evolve
Publisher	Springer Japan
Pages	279-291
Number of pages	13
ISBN (Electronic)	9784431545200
ISBN (Print)	4431545190, 9784431545194
DOIs	https://doi.org/10.1007/978-4-431-54520-0_14
Publication status	Published - 2014 Jan 1

Keywords

Illumina illumina
IVET IVET
STM STM

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10.1007/978-4-431-54520-0_14

Cite this

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AU - Ohtsubo, Yoshiyuki

AU - Nishiyama, Eri

AU - Ishibashi, Yoko

AU - Nagata, Yuji

AU - Tsuda, Masataka

PY - 2014/1/1

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Strategies to reveal genomic function in natural soil systems

Abstract

Keywords

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