The lipid-accumulating marine Chlorella strain C596-R1, previously studied for its promise as a feedstock for biodiesel production, grows in stable association with a diverse bacterial consortium. Alteration of this bacterial community, via streaking of C596-R1 on agar plates resulted in a new algal-bacterial consortium, C596-S1, that exhibits lower growth rates, maximum cell densities and lipid accumulation than C596-R1. Experiments to reintroduce bacteria or medium filtrate isolated from C596-R1 into the -S1 culture suggested an algal-bacterial symbiosis via a combination of cell-cell interactions and the production of growth promoting factors. 16S rRNA analysis indicated a correlation between the relative abundance of the genera Rhodobacter and Ruegeria and the growth rate and neutral lipid content in C596 cultures. In summary, our data reveal biochemical changes caused by different microbial backgrounds, enabling us to link previously hypothesized mechanisms of symbiotic algae-bacteria relationships to altered algal culture phenotypes.