This thesis examined the development of an oleaginous yeast or microalgae based biorefinery process. First, improvements were made to the Nile Red assay, a high-throughput method for monitoring lipid accumulation in oleaginous organisms resulting in a significantly more reproducible and accurate assay. This assay was then used to optimize lipid production during heterotrophic cultivation of microalgae on glucose using response surface methodology resulting in microalgae with high lipid content (37.6% wt.). In order to improve the renewability of heterotrophic lipid production, both oleaginous yeast and microalgae were cultivated using pyrolytic sugars, produced via fast pyrolysis of pinewood waste. The effects of inhibitors on glucose consumption and lipid accumulation as well as the quality of the produced fatty acid methyl esters (FAME) were examined.

Upon the establishment of cultivation processes for these two organisms, the overall objective of this work shifted towards the development of a fractionation process for producing and recovering multiple end products. Over 20 ionic liquids were screened for the ability to disruption microalgal cell structure. This was the first report of non-imidazolium ionic liquids assessed for algal bioprocessing applications and the first examining room temperature ionic liquids. The leading candidate ionic liquid was further studied for its ability to disrupt fresh microalgal cultures which were dewatered containing up to 82% water content. This was the first in depth report of the effect of process parameters on the use of ionic liquds for algae disruption. The resulting lipid extraction process was minimized to a simple 1.5 h process conducted at ambient temperature with wet algae.

This was further extended to include a catalyst in order to directly convert intracellular lipid to biodiesel from whole yeast biomass. The effects of the reagent ratios, reaction temperatures, and reaction time were studied in depth using response surface methodology. Recovery of the ionic liquid and catalyst for reuse was quantified. Finally, the carbohydrates and protein fractions were recovered after the ionic liquid lipid extraction process using microalgae and it was demonstrated that the resulting sugars primarily in the form of starch could be directly fermented to biobutanol, bioethanol, and acetone using a traditional ABE fermentation process.