Microalgae are photosynthetic organisms considered to be one of the most promising high-value chemicals and biofuel-producing organisms. However, there are several challenges for the widespread implementation of industrial processes using microalgae. The work presented in this dissertation proposes solutions to the different challenges involving the use of microalgae as microbial cell factories. To investigate the application of anaerobic digestion as a way to generate nutrients for microbial growth, salmon offal was used as substrate for anaerobic digestion, and soil from a flooded run-off pond on the Virginia Tech campus in Blacksburg, VA. A fast reduction in volatile solids and the short-chain fatty acid production profile is favorable for the growth of microalgae. A novel algae strain Scenedesmus sp. A6 was isolated from a decorative waterfountain in a hotel in Madison, IN. Mixotrophic growth trials were conducted using wastewater from the salmon offal digestion, that demostrated the A6 isolate grows six times faster in the wastewater then autotrophically. Bioassays of ethanolic cell extracts of A6 cultures demonstrated antimicrobial activity against E. coli cells at concentrations above 50 µg/ml. Genome sequencing and assembly revealed multiple copies of genes involved with acetate and ammonia metabolism, and several genes involved with secondary metabolite synthesis. An alternative to the high capital investment of photobioreactors for the cultivation of microalgae is the use of open-source and open-hardware bioreactor controller. Here, the concept of an open-hardwate bioreactor control called ``BioBrain'' is introduced. The BioBrain device is based on the Arduino Mega micro-controller board, and is capable of monitoring and controlling culture conditions during simple strain characterization studies, with an estimated construction cost of less than $800 USD. Finally, a new primer design tool for the ligation-independant cloning technique 𝜆-PCR was developed called lambdaPrimeR. The contributions of this work are the discovery and development of different tools that can overcome the challenges of the use of microalgae as microbial cell factories in industrial processes. / Ph. D. / Microalgae are single-celled organisms capable of photosynthesis and have the potential to revolutionize fuel and high-value chemical production. However, the high process costs involving the cultivation and biomass harvesting of these organisms limits the number of industrial applications of microalgae. Therefore, reduction of the overall costs of any process involving microalgae is vital for the widespread use of these organisms in industry. On this dissertation, I explore different approaches to tackle the challenges of using microalgae as a high-value chemicals cell factories. First, the use of anaerobic digestion of salmon offal to generate low-cost nutrients for algae growth is successfully demonstrated, with the discovery of a novel algae isolate Scenedesmus sp. A6, capable of very robust growth on the anaerobic digestion wastewater. Further characterization of this novel isolate showed that it has antimicrobial activity against E. coli cells. Therefore, the Scenedesmus sp. A6 isolate has the potential to be used as a high-value chemical cell factory. Reduction in equipment and instrumentation costs was also achieved by the design and construction of an open-hardware and open-source bioreactor controller device called the “BioBrain”, and a low-cost modular bubble column photobioreactor called “The Big Large Tube”. Together, these two devices represent a significant reduction in equipment costs for the cultivation of microalgae. Finally, an open-source Bioinformatics tool called “lambdaPrimeR” was developed to facilitate the use of a novel Genetic Engineering technique called λ-PCR, that has the potential to make genetic engineering of microalgae much easier.