Prokaryotes are characterised by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Some are able to use light or organic matter to harvest energy and fix carbon, while others utilise chemo- or lithotrophic modes which use theredox potential of molecules found in their particular environment to harness energy for their survival. Molecular evolution studies, coupled to data from the geologic record, indicate that the variety of bioenergetic pathways seen in extant prokaryotes originated within the firstbillion years of life on Earth. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. How did this metabolic diversity evolve? Did each pathway evolve independently or did they all evolve from acommon ancestral metabolic mode? As in organismal evolution, it is likely that parts of pre-existing pathways were co-opted to evolve into new pathways. The aim is to test this hypothesis through comparative genomics and phylogenetic analysis of the core protein complexesinvolved in energy metabolism. Apart from fermentation, most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobileelectron carriers, and an ATP synthase. Therefore, the different protein complexes that participate in distinct electron transport chains will be compared to each other, to establish their homology and evolutionary relationships. This analysis will yield insights into the origin of keyinnovations and the evolutionary flexibility of electron carriers, with potential applications in microbial fuel cell technology. A database to facilitate the comparison of bioenergetic pathways will also be constructed, and metagenomic data will be examined for the identification ofnovel bioenergetic enzymes.