Dr. Holden's research focuses on the physiology and genomics of thermophilic and hyperthermophilic archaea and the geomicrobiology of the geothermal environments where these organisms are found. His lab is developing a reactive transport model for the growth of methanogens and production of CH4 in hydrothermal vents, determining microbe-mineral interactions and biogenic mineral transformations in hydrothermal ‘black smoker’ chimneys, and examining H2 production and syntrophy by heterotrophs. His genome analysis projects examine each of the organisms involved in these processes (Methanocaldococcus, Pyrodictium, Thermococcus). His field research occurs at deep-sea hydrothermal vents at Axial Seamount and the Endeavour Segment in the northeastern Pacific Ocean and uses the deep-sea submarine Alvin and remotely-operated submarines such as Jason II and ROPOS. His hyperthermophilic H2 production studies are being translated into new ways of remediating agricultural wastes in bioreactors to produce bioenergy, kill pathogens, and prevent eutrophication.