Top-Down and Bottom-up Approaches for Investigating the Microcystis Phycosphere

Understanding how cell-cell interactions compound into dynamics observed in natural communities is crucial for predicting and engineering microbial communities. Both metagenomic studies of natural communities and “synthetic ecology” with defined microbial communities have provided insight into composition, dynamics, and potential mechanisms. However, for microbial systems that lack well-characterized and tractable representatives for synthetic ecology, they are heavily limited to study by culture-independent techniques. Despite tremendous improvements in culture-independent techniques, the high-resolution needed to study these interactions in natural communities is confounded by their sheer complexity. This work presents two approaches, one top-down approach and one bottom-up approach, to provide insight into interactions between difficult-to-study, toxic bloom-forming Microcystis aeruginosa and the heterotrophic partners that inhabit the carbohydrate-rich matrix surrounding Microcystis cells - referred to as the phycosphere. The top-bottom approach involves using droplets to encapsulate single Microcystis-heterotroph colonies from blooms in Lake Erie to study membership and strain-level association at the local scale. The bottom-up approach utilizes microfluidic droplets, which are sub-nanoliter to microliter scale water-in-oil emulsions. These “microdroplets” serve as miniaturized, self-contained bioreactors for microbial cultivation, rendering ultra-high throughput investigation. In particular, the small size and stochastic nature of microdroplets enable the decomposition of a mixed culture composed of Microcystis aeruginosa and heterotrophic partners to interrogate critical pairwise interactions. We believe that both efforts can bridge the mechanistic understanding from synthetic ecology with the observed ecology from metagenomic studies to understand how the microbial partnerships contribute to the resiliency of Microcystis-dominated harmful cyanobacterial blooms.