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.