My research focuses on the ecology, diversity, and evolution of microbes and viruses in the environment. My research subjects includes genes, genomes, cells, ecosystems, and material cycling, and our research methods includes field sampling, experimental work (wet), and bioinformatics analysis (dry). The wide range of research scales is what makes microbial ecology attractive. It is also a rapidly growing research field making remarkable progress with the introduction of new methods and technologies such as meta-omics and long-read sequencing.
My main research field is freshwater lakes. By leveraging the unique characteristics of lake ecosystems, I will not limit my focus to aquatic microbial ecology but will try to expand the range of my research to challenge broader research topics of microbiology, ecology, and life sciences in general. In particular, I am interested in an approach that considers each lake as a "replicate" or "control" of an ecosystem. By comparing their microbial diversity at high resolution, we may be able to uncover the driver of genome diversification and their evolutionary trajectories.
My previous works
My current research projects
Construction of an ecogenomic database of lake microbial communities
I am collecting total DNA and RNA samples of eukaryotes, prokaryotes, and viruses from deep freshwater lakes all over Japan, and accumulating metagenome and metatranscriptome data covering the diversity of microorganisms and their genes in the lakes. Particularly in Lake Biwa, the samples were taken spatiotemporally from two water layers over 12 months, and in addition to conventional DNA/RNA sequencing using short-reads, long-read metagenomic analysis and single-cell sequencing were performed to generte high-quality genomic information. The data obtained will be used as a basis for research into the diversity and ecophysiology of environmental microbes. In particular, I am interested in the intra-lineage genomic microdiversity of bacteria and their viruses within populations, across time series, and between habitats, to elucidate the generation and maintenance processes of microbial genomic diversity.
Challenging for isolation of hypolimnion-specifc bacterioplankton lineages
Culture-independent approaches including FISH, 16S rRNA gene amplicon sequencing, and metagenomic analysis can deduce ecophysiological characteristics but needs further experimental verification using a cultivated isolate. The acquisition of an isolate is also the key to isolate viruses infecting them and to characterize their responses to various environmental stresses. High-throughput dilution-to-extinction cultivation is a promising approach that is successful in isolating numbers of bacterioplankton lineages inhabiting oligotrophic systems. Using the method, I am attempting to isolate bacterial lineages specific to oxygenated hypolimnion.
Other colloborative researches
By leveraging the data and samples I have collected from many lakes and my expertise and experience in working on them, I am collaborating with researchers in a variety of research fields. For instance, I am currently working on (meta)genomic analyses of algae, eukaryotic microbes, and viruses in Lake Biwa, and identifying bacterial lineages involved in the dynamics of semi-labile organic matter in the hypolimnion of deep lakes. If you are interested in lake samples and genomic data or have an interesting research idea, please feel free to contact me.