A central project aim is adaptation of a new single cell transcriptome (SCT) sequencing approach called SeqWell for analysis of natural microbial communities. The method addresses two overarching obstacles to microbial symbiosis investigations: 1) the requirement that symbionts be brought into culture for ‘omics analyses, and 2) time resolution limits on bulk approaches because populations are asynchronous. With enough SCTs, pseudotime methods can establish the time course of host and symbiont interactions. SeqWell is a straightforward settling-chamber based system that can capture >10,000 SCTs in a single experiment. Compared to competing methods, it is also low-cost and readily adaptable for a broad range of protist shapes and sizes. We aim to address three major challenges inherent to scRNAseq of protist communities in the environment: 1) the morphological diversity (size/shapes) of protists across taxonomic groups; 2) cost; and 3) a need for bioinformatic pipelines that can analyze SCTs from natural microbial communities.

Funding for this project provided by the Moore Foundation