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Nitrogen cycles

One of major research interests explores the microbial diversity contributing in the global nitrogen cycles including nitrogen fixation, nitrification and denitrification. It becomes increasingly clear that alteration of the global nitrogen cycles represents a major emerging challenge that has receive too little attention. We are using the multidisciplinary approach to identify and characterize the active microbial community related to the nitrogen cycles. Especially, we are currently focusing on two research topics. i) identification of the stress tolerant nitrogen fixing bacteria tightly associated plant growth promotion under environmental stress from climate changes, ii) Development of soil ecological risk model based on changes of nitrogen flux and active microbial community in the contaminated or bioremediated soil.

Single cell dynamics

The spectral technologies directly prompt the blossom of microbial ecology and produce a lots of useful and applicable scientific achievements. Particularly, Raman microspectroscopy allows to characterize the biomolecule changes at single cell level and identify the active population labeled with stable isotopes. In conjunction with optical tweezers or microfludic chips, it is also possible to sort bacterial strains of interest from environmental samples for further single cell genomics and cultivation of uncultured bacteria. These approaches will undoubtedly become an increasingly important approach for microbial ecology and microbiome studies.

Synthetic ecosystem

Environmental microbial communities act as both engines and engineers in ecosystems. Although microbial communities play an important role in contributing to maintaining the ecosystem in spite of changes in the external environment, much research on functional redundancy, which is a very important mechanism for controlling ecosystem stability, is scarcely understood due to the lack of information on the relationship between microorganisms. We have developed a unique synthetic ecosystem to identify microbial interactions among isolates from nature microbial communities. Spectroscopy (e.g. Raman microspectroscopy and flow cytometry), multi-omics (e.g. metagenomics, transcriptomics), stochastic modeling and Mass spectrometry-based assays examine the phenotypic changes and chemical interactions underlay a diversity of relationships from commensalism to antagonisms. These synthetic ecosystem model will facilitate a better understanding of microbial diversity, adaptation and evolutions related to the microbiome stability and functionality in the nature. We have applied our approached on the soil microbiome and skin microbiome to reveal microbial interactions that affect nitrogen cycles and skin disease, respectively.