Molecular and Chemical Life Science :
Molecular and Network Genomics


Microbial Genetics and Genomics

Microbial Genetics and Genomics

The aim of this laboratory is to elucidate the molecular mechanisms of environmental adaptation and the evolution of microbial strains and their communities from standpoints of genetics, molecular biology, genomics, and molecular ecology. Particular emphasis is placed on the environmental microbes capable of degrading various chemical pollutants. The following are major topics of our research projects:
  1. Analysis of microbial biodegradation of various recalcitrant pollutants.
  2. Analysis of mobile genetic elements involved in the degradation of various pollutants.
  3. Structural and functional genomics of environmental microbes under laboratory conditions and in natural environments.
  4. Integrative genomic analysis of environmental microbial communities under natural environments.

Research Overview

Our targets are microbial strains able to degrade various recalcitrant pollutants, especially aromatic and aliphatic hydrocarbons and their halogenated compounds. The microbial genes and enzymes directly and indirectly involved in this degradation have been analyzed in detail. We have demonstrated that 1) the degradation genes and their clusters are often loaded on various mobile genetic elements (MGEs) such as transposons, plasmids, and integrative and conjugative elements and 2) their intra- and intercellular movement greatly contributes to i) wide dissemination of nearly identical genes and their clusters in various phylogenetically distant microbial strains, and ii) rapid evolution of the pollutant-degrading microbes. Comparative genomic analysis of our target microbes has also definitely supported the important roles of the MGEs in the establishment of the present structures of microbial genomes. For completion of whole genome sequencing and genome comparison, we have developed our own original software programs, which are available freely to academic scientists. The programs are deposited on our website: http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html. More than 99% of microbes in natural environments are still difficult to cultivate under laboratory conditions, meaning that we only understand a tiny fraction of the microbial world. To better understand microbial lifestyles and their potential to degrade recalcitrant compounds in the natural environment, we have clarified the environmental microbial genes that are specifically expressed and/or pivotal for survival/proliferation in the soil environment. We have also employed function- and sequence-driven metagenomic approaches to i) directly isolate and characterize genes for the degradation of pollutants, and ii) investigate the time-course response of the microbial community to pollutants in soil microcosms. For more details, please access http://www.ige.tohoku.ac.jp/joho/index.html. Some of our recent work is summarized in the Springer-Verlag book: Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve. (2014); Nojiri, H., M. Tsuda, M. Fukuda, and Y. Kamagata (eds). A comprehensive list of our recent papers and reviews can be found at the following URL: http://www.ige.tohoku.ac.jp/joho/labhome/publication.html.
URLs http://www.ige.tohoku.ac.jp/joho/index.html

Faculty Members

Professor NAGATA Yuji (C)
Associate Professor OTSUBO Yoshiyuki
  • Molecular and genetic research for elucidating catabolite control mechanisms in soil bacteria that are capable of degrading man-made chemicals of environmental concerns.
  • Creation of software programs for various analytical purposes, including comparative genomics and finishing of microbial draft genomes.