Uncovering microbial inter-domain interactions in complex communities

Abstract

Interactions between unicellular eukaryotes and bacteria are difficult to characterize in the environment owing to their large number and inherently microscopic scale. Although particular co-occurrences can be recovered through targeted approaches, e.g. single-cell sequencing or fluorescence in situ hybridization, the vast majority of the interactions remain unseen. Here, we discuss Emulsion, Paired Isolation and Concatenation polymerase chain reaction (epicPCR) as a tool to uncover these interactions in very high throughput. Originally developed for taxonomy-to-function linkage in bacterial communities, epicPCR has the potential to recover the complete interaction network in a given environment at single-cell resolution. This approach relies on the encapsulation of protistan single cells in emulsion droplets that can subsequently be gelified into beads. In this way, encapsulated cells can be exposed to lysis reagents and further phylogenetic paired marker amplification. A bacterium that physically co-occurs with the eukaryote will be jointly trapped, and the amplification will generate a concatenated PCR product containing physically coupled taxonomic markers from both partners, creating a link. Further amplification and sequencing enable the construction of an association pattern with statistically verified physical co-occurrences. Here, we discuss the potential, challenges and limitations of epicPCR. We argue that the microscopic scale at which epicPCR operates, the high throughput it delivers and its exploratory nature make it an unparalleled approach to unravel associations between microbes directly from environmental samples. This article is part of a discussion meeting issue ‘Single cell ecology’.