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 proceedingChapter

    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 languageEnglish
    Title of host publicationBiodegradative Bacteria
    Subtitle of host publicationHow Bacteria Degrade, Survive, Adapt, and Evolve
    PublisherSpringer Japan
    Pages279-291
    Number of pages13
    ISBN (Electronic)9784431545200
    ISBN (Print)4431545190, 9784431545194
    DOIs
    Publication statusPublished - 2014 Jan 1

    Keywords

    • IVET IVET
    • Illumina illumina
    • STM STM

    ASJC Scopus subject areas

    • Immunology and Microbiology(all)
    • Agricultural and Biological Sciences(all)
    • Environmental Science(all)

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  • Cite this

    Ohtsubo, Y., Nishiyama, E., Ishibashi, Y., Nagata, Y., & Tsuda, M. (2014). Strategies to reveal genomic function in natural soil systems. In Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve (pp. 279-291). Springer Japan. https://doi.org/10.1007/978-4-431-54520-0_14