Dr. Mukhopadhyay’s work is focused on understanding membrane transport, signaling, stress response and tolerance phenotypes in microbial systems. She studies both engineered and environmental microbes. She utilizes a wide variety of microbiological, biochemical and systems biology tools to examine environmentally important organisms such as sulfate and metal reducing bacteria as well as cyanobacteria. She has specific interest in signaling mechanisms in novel non-model organisms like Pseudomonas stuzeri, Desulfovibrio vulgaris and Microcoleus vaginatus and has conducted detailed studies in model organisms such as Agrobacterium tumefaciens. She develops tools, and uses host engineering and protein engineering strategies, to improve the production of fuel and chemicals production, and conduct bioremediation, using model microbes such as Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae.