Application of Molecular Tools to Determine Effects of Key Growth Factors on Cultivated Algal Biofilm Communities

Cultivating microalgae as a biofilm may overcome some of the challenges of conventional suspended cultivation for the production sustainable biofuels and bioproducts. However, strategies to enhance the growth of product-producing species within biofilms should be investigated to optimize the profitability of algal bioprocesses. The objective of this thesis was to investigate how biofilm attachment material, wastewater, and inoculation strategy influence the accumulation of algal biofilm biomass and the composition of the community. To achieve specific and accurate quantification of target algal species, quantitative polymerase chain reaction (qPCR) assays were designed to estimate the cell abundance of Chlorella vulgaris and Scenedesmus obliquus. Additionally, a workflow was developed to simultaneously estimate absolute abundance of bacterial and algal taxa by targeting 16S rRNA genes. These tools were used to determine how manipulating the growth factors influence the biomass and composition of biofilms cultivated in a parallel-plate air-lift reactor. Pretreating reactors with wastewater and growing biofilms on cotton increased biofilm biomass by up to a factor of 5.6, and inoculating S. obliquus into cotton attachment materials increased its abundance in biofilms by up to a factor of 13.5. Depending on inoculation strategy or presence of wastewater, biofilm community compositions were distinct from that in their corresponding suspensions and that in the inoculum. In conclusion, the interactions between wastewater, attachment material, and inoculation strategy can have significant, species-specific influences on algal biofilm growth, thus may be exploited to simultaneously increase biomass and the growth of target species in cultivated biofilms. The experimental work described in this thesis contributes to the suite of molecular tools available for the analysis of species in algal biofilms and demonstrates the utility of qPCR and amplicon sequencing for evaluating the performance of algal biofilm cultivation systems, specifically determining the abundance of desired species in biofilms. The developed tools and findings in this thesis can be used to inform, not only the optimization of biofilm cultivation systems for the commercialization of algal products, but also the study of mixed algal communities in the environment.Ph.D