Department of Environmental Life Sciences
Division of Genetic Ecology

Microbial Genetics and Genomics 分野

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.


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: 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 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:


Professor Masataka Tsuda
  1. Analysis of structural and functional dynamics and evolution of microbial genes for degradation of xenobiotics
  2. Genomics and metagenomics of environmental microbes
  3. Ecological genomics of environmental microbial communities
Associate Professor Yoshiyuki Otsubo
  • 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.

Awards Granted to Graduate Students

Name Award
Hirofumi Nagayama Excellent Poster Award in Annual Meeting of Japan Society for Environmental Biotechnology 2012
Ryo Endo Tohoku University Chancellor’s Award
Masahiro Soda Graduate School of Life Science Award
Ryo Miyazaki Graduate School of Life Science Award
Satoshi Yuhara Graduate School of Life Science Award

Thesis Titles

Master Degree

(2013) Conjugative transfer of naphthalene-catabolic plasmid: analysis of conjugation-specific DNA replication and host range of conjugation system Molecular mechanisms for Fur-mediated iron homeostasis system in Burkholderia multivorans Replacement of bacterial genetic information at intra- and inter-genome levels

Ph.D. Degree

(2013) Conjugative transfer of bacterial plasmid: recipient factors that control plasmid transfer

A Student’s View


Kohei Kishida 


Undergraduate University and Department

Faculty of Science, Ibaraki University, Japan

Research Subject

Conjugative transfer of plasmids that govern degradation of pollutants

Based on a consistent purpose to comprehensively understand the microbial degradation of chemical pollutants, the members in this laboratory employ various methods of traditional microbial genetics and molecular biology, protein engineering, genomics, and molecular ecology. There are also various entertainment programs by which all the laboratory members enjoy themselves very well.