The main objective of this thesis was to evaluate aqueous ammonia soaking (AAS) as a pretreatment method for lignocellulosic biomass preparation for biofuel production, in a variety of settings. This thesis, partially fulfills the Master of Science degree requirement, is prepared in the journal paper format, and includes three papers that have been published in or are prepared for submission to a journal.

The objective of the first chapter was to design and fabricate a pilot-scale soaking and washing system to safely and effectively generate AAS-pretreated switchgrass. Based on economic, safety and convenience factors, a 75-L soaking vessel was constructed and demonstrated to be effective in pretreating 4 kg of dry switchgrass per run with 20-L of aqueous ammonia. This pilot-scale system increased cellulose content and decreased hemicellulose and Klason lignin content of the remaining solids in a similar manner as observed in bench-scale experiments. To our knowledge, this is the first description and report of design, operation, and handling of a pilot-scale AAS biomass pretreatment system.

The objective of the second research paper was to quantify acid soluble lignin and acid insoluble lignin content following four pretreatment methods of eight transgenic and one wild type poplar varieties. The transgenic varieties of poplar (Populus spp) had modifications in the lignin biosynthesis pathway to reduce lignin content or make varieties more susceptible to delignification. All pretreatment techniques were successful in removing a fraction of both acid soluble lignin (ASL) and acid insoluble lignin (AIL) from the transgenic varieties removing 12-70% ASL and 5-52% AIL.

The objective of the last paper was to evaluate the energy yields from the anaerobic digestion (AD) of AAS-pretreated switchgrass and AAS-pretreated switchgrass plus hydrolytic enzymes. The results show that anaerobic digestion of AAS-pretreated switchgrass significantly increases biogas energy production over the AD of untreated switchgrass, and that the addition of sufficient commercially available hydrolytic enzymes greatly increased biogas yields, methane concentration, and total methane yields. At the highest enzyme loading, gross energy production from AD was over twice the gross energy production from ethanol fermentation of the same material.