Strategies to reveal genomic function in natural soil systems

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

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


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 languageEnglish
Title of host publicationBiodegradative Bacteria
Subtitle of host publicationHow Bacteria Degrade, Survive, Adapt, and Evolve
PublisherSpringer Japan
Number of pages13
ISBN (Electronic)9784431545200
ISBN (Print)4431545190, 9784431545194
Publication statusPublished - 2014 Jan 1


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