Characterization of microbial metabolism at diverse complexity levels: Extending integrated metaproteomics from simple cell-free systems to complex environmental microbiomes

The growing energy demand coupled with the rising climate crisis warrant a need for greener and sustainable energy and chemical production routes, which although feasible, are currently not economical. As an alternate to fossil resources, the metabolic activities of microorganisms thriving under relatively extreme environments can be harnessed and improved to achieve desired technological advancements. Omics techniques such as proteomics are uniquely suited to systemically investigate the metabolism of these microbes at a molecular level and provide mechanistic clues to their response under industrially relevant conditions. To this end, my dissertation focuses on the use of integrated omics (especially proteomics) to explore metabolic activities of different microorganisms and microbe-derived toolkits important for bioenergy and bioproduct research. In particular, I am utilizing high-performance liquid chromatography mass spectrometry and bioinformatic methods to study the mechanisms employed for the deconstruction of complex substrates by pure cultures, co-cultures, and microbial communities; and then using these analytical technologies to identify essential players in metabolic engineering efforts for efficient production of bioproducts. In total, my research involves multiple projects ranging from studying microbial communities and single microbes derived from natural environments to cell-free lysates under varying conditions. As detailed in the individual chapters, by multifaceted application of bioanalytical mass spectrometry, I have contributed significantly to the inter-disciplinary bioenergy research area- from new method development to comprehensive implementation of existing methodologies and provided novel insights that fill gaps in our understanding and set the tone for future research.