In the United States, nearly 35 million tons of food waste are delivered to landfills and wastewater treatment plants for disposal each year. This places a burden on landfills and the environment through the introduction of foreign chemicals. Utilizing hyperthermophilic heterotrophs for waste treatment in a consolidated bioprocess could potentially remediate these organics, increase reaction rates, kill pathogens, produce a bioenergy product (H2), and lower costs relative to mesophilic waste treatment options. However, it is unknown how various agricultural waste streams will affect hyperthermophilic growth and metabolite production. We investigated Thermococcales species for this purpose. Specifically, we chose Pyrococcus furiosus and Thermococcus paralvinellae because of their use as a model organism and their potential H2 production, respectively. In this set of studies, we determined 1) the genomic sequence of T. paralvinellae, 2) how representative these two microorganisms are of Thermococcales species, and 3) the physiology of both organisms when grown in different defined and waste-mediated environmental conditions. We found that T. paralvinellae is genomically most similar to T. barophilus and that P. furiosus and T. paralvinellae are good representatives of different potential metabolisms of the Thermococcales. Both P. furiosus and T. paralvinellae are amenable to the catabolism of carbohydrates and peptides with H2 production over a range of pH and acetate concentrations with little impact on growth and H2 production rates. The mechanisms that P. furiosus and T. paralvinellae are using for redox balance may not be the same, as seen by the differential expression of a number of enzymatic activities. T. paralvinellae consistently produced more H2 on both raw milk and spent grain wastes. Mesophilic bacteria were eliminated from the wastes in the process of hyperthermophilic growth, indicating that it is feasible to use hyperthermophilic heterotrophs in a single process step to reduce the organic load of food and agricultural wastes, generate H2 as an energy byproduct, and remove pathogens
