Plants are in constant interactions with a large diversity of microorganisms, that belong to various biological kingdoms including archaea, bacteria, fungi and protista. In nature, these inter-kingdom interactions can be both cooperative and detrimental to the host-plants. Our major research focus is to understand the dynamics of inter-kingdom microbiome-interactions and how it affects the crop production. We use cutting-edge culture-independent (metagenomics, metatranscriptomics and metabolomics) and culture-dependent (culturomics) methods combined with computational biology. We especially employ a systematics-based approach, so that we can identify individual organisms involved in these interactions, their biological functions, impacts on neighboring niches, and metabolic activity.