The major focus of my research has been on ecology of bacterioplankton in deep freshwater lakes.
My previous works
I have revealed the oxygenated hypolimnia of deep freshwater lakes are inhabited by unique bacterioplankton lineages that are significantly different from those in the epilimnia.
I. Seasonal dominance of the CL500-11 lineage in the hypolimnion of Lake Biwa
Dominance of the CL500-11 lineage was discovered in the oxygenated hypolimnion of Lake Biwa. A spatiotemporal profiling of their abundance indicated their exclusive occurrence in the hypolimnion during the stratified period, concluding that CL500-11 is hypolimnion-specific bacterioplankton (Okazaki et al., 2013).
II. Vertical partitioning of bacterioplankton community in Lake Biwa
A spatiotemporal survey of bacterioplankton community composition in Lake Biwa revealed that the community was different by phylum-level between the epilimnion and hypolimnion during the stratified period. The result allowed to identify numbers of hypolimnion-specific lineages other than CL500-11 (Okazaki & Nakano 2016).
III. Comparative investigation of 10 Japanese deep-water freshwater lakes
Ubiquity and quantitative significance of the hypolimnion-specific lineages identified in Lake Biwa were confirmed by comprehensive sampling in 10 deep Japanese freshwater lakes with the oxygenated hypolimnia. The results established a first general overview of bacterioplankton lineages inhabiting the oxygenated hypolimnia of deep freshwater lakes (Okazaki et al., 2017).
Current research subjects
The previous studies revealed the presence of hypolimnion-specific bacterioplankton lineages and highlighted the need for further studies on their ecological roles. As priority subjects, my current focus is on the following topics.
Metagenomic analysis to reveal the ecophysiology of the hypolimnion-specific lineages
Unlike epilimnetic bacterioplankton that are constantly supplied with fresh organic matter derived from photosynthetic primary production, microbial community in the dark hypolimnion are considered to be consuming relatively refractory organic matter which eluded instant degradation in the surface layer. In deep freshwater lakes, the hypolimnion occupies a large proportion of the lake volume, and microbial material decomposition and conversion in the hypolimnion are essential processes in the lake's ecosystem. In this project, I am trying to reveal ecophysiologies of bacterioplankton in deep freshwater lakes by reconstructing metagenome-assembled genomes (MAGs) of individual lineages and find their key metabolic genes.
Viromics to uncover diversity and ecology of bacteriophage in deep freshwater lakes
While vast viral diversity in the ocean is being clarified by rapidly developing sequencing and bioinformatics technologies, such studies in freshwater systems are still scarce, and almost nothing is known for viral diversity in deep freshwater lakes. In this project, viral shotgun metagenomics (viromics) is carried out using the viral samples (<0.2 μm) secondarily obtained from the cellular metagenomic sampling. Under a hypothesis that "viral community is vertically stratified in deep freshwater lakes, reflecting the distribution of their host (bacterioplankton)", analyses of the assembled viral genomes and contigs will reveal unknown viral diversity and ecology in deep freshwater lakes.
Quantification of the metagenomic and viromic data by metatranscriptomics
The metagenomic and viromic analyses described above are powerful techniques that can exhaustively collect target's genomic information without cultivating them. However, the genomic information just indicates presence or absence of each gene, in other words, just "potential" of metabolism. To evaluate functioning of the genes in environment, transcription of the genes should be assessed. In this project, comprehensive sequencing of viral and bacterial mRNA in lake water (metatranscriptmics) is carried out to quantify expression of each gene and reveal its spatiotemporal pattern. By discovering genes of ecological importance that are highly expressed or showing clear seasonal trends, the results will allow to better understand roles and functions of microbial ecosystem in deep freshwater lakes.
Phylogeographic study of microbial community in deep freshwater lakes
In the previous studies, I have clarified that the hypolimnion-specific bacterioplankton lineages widely distribute in deep freshwater lakes across the continents. Why does the same lineage of bacterioplankton inhabit the hypolimnia of different lakes, which are physically isolated to each other? How phylogenetically isolated are they in different lakes, and what are the factors making the difference? These questions make me feel that deep freshwater lakes is a suitable system to study phylogeography of microbes. In this project, I am attempting a high-resolution phylogenetic comparison of shared bacterioplankton lineages among different lakes, using long-read amplicon sequencing and metagenomics. By analyzing their phylogenetic relatedness and shared/unique genes among lakes, the research will give clues to understand evolutional and dispersal backgrounds of ubiquitously distributed bacterioplankton.
Long term perspectives
Deep freshwater lakes are relatively accessible environment for sampling, yet the unique microbial community there has just been started to be uncovered. The microbial community there shows relatively predictable and stable seasonal dynamics, and the sample is feasible for size fractionation, microscopy, and DNA extraction, compared with more disturbance-prone, particle-rich environments such as soil, sediments, or eutrophic aquatic systems. Further, each habitat (= lake) is physically isolated, showing different physical, chemical, and historical characteristics, which makes comparison or replication of a study feasible. To make the best use of these technical advantages of the system, I will not limit my focus to aquatic microbial ecology but will try to expand the range of my interests and techniques interdisciplinary and make the microbial ecology in deep freshwater lakes answer questions from more general microbiology and ecology.