His research interests include environmental microbiology and genomics; computational approaches for studying the ecology and evolution of microorganisms; development of genomic and proteomic techniques to investigate and quantify in-situ important microbial-mediated processes; population and single-cell genomics; assessing the extent and value of biodiversity within natural assemblages of Bacteria and Archaea; biotechnological applications of microbial functional diversity; and environmental relevance of microbial diseases.