Shining new light on cyanobacteria genomes

The manipulation of gene activity in cyanobacteria offers the possibility of producing energy and materials directly from sunlight, water and carbon dioxide, contributing to food production, innovative bioproducts and reliable bioenergy solutions that reduce human carbon emissions. However, current applications of cyanobacteria for these purposes remain in early stages of development. A limited capacity to study and control genetic information in many strains is a barrier to both optimizing metabolic flux through central metabolic pathways and programming these pathways for production of user defined products at industrial scales. Additionally, even in strains that have successfully been engineered for production of various commodity compounds, such as Synechocystis and Synechococcus, limitations in scalability and knowledge of carbon processing pathways continue to stymie industrial applications. This thesis is focused on genome sequencing of an industrial cyanobacterial strain called AB48 a strain optimized to grow as a biofilm using modular photobioreactors developed by AlgaBloom International Ltd, a local biotechnology company. These biofilm-based photobioreactors employ proprietary substrate-based growth paradigms that permit minimal water and energy consumption, while maximizing bioreactor productivity. The AB48 genome was initially sequenced directly from photobioreactor biomass on the PacBio platform at the DOE Joint Genome Institute. In the process of assembling and annotating the genome, additional metagenome assembled genomes (MAGs) associated with co-occurring microorganisms and mobile genetic elements (MGEs) including plasmids and phage were identified. An AB48 strain was later isolated and sequenced on the Illumina HiSeq and Oxford Nanopore MinION platforms. After hybrid assembly a complete closed reference genome and plasmid sequence were resolved, enabling formal classification of AB48 as a new species within the genus Phormidium called Phormidium yuhuli AB48. Encouraged by these results, efforts were made to reassemble and analyze raw sequencing data from other cyanobacterial genome sequencing projects with an eye toward identifying co-occurring microorganisms and MGEs. Typically, sequence information associated with co-cultured bacteria is not reported in published cyanobacterial genome reports despite the potential for uncovering known or novel interactions. The resulting MAGs for cyanobacteria, co-occurring microorganisms and MGEs provide a lineage-resolved resource of biological parts and putative metabolic interactions for sustainable bioproduction and biotechnology innovation.Science, Faculty ofGraduat