The Principles and Applications of Plasmid Transfer in Microbial Communities

Abstract

Conjugative plasmids can mediate the spread and maintenance of diverse traits and functions in microbial communities. This role depends on the plasmid’s ability to persist in a population. However, for a community consisting of multiple populations transferring multiple plasmids, the conditions underlying plasmid persistence are poorly understood. Here, I described a plasmid-centric framework that makes it computationally feasible to analyze gene flow in complex communities. Using this framework, I derived the ‘persistence potential’: a general, heuristic metric that predicts the persistence and abundance of any plasmids. I validated the metric with engineered microbial consortia transferring mobilizable plasmids and with quantitative data available in the literature. I used the learned principles governing plasmid persistence to propose a new strategy to control community functional stability. The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, I proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. I combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the decoupling and functional stability of microbial communities. I and my collaborator further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the re-analysis of data from the literature. Next, I applied the general principles underlying plasmid persistence to understand how population bottlenecks affect plasmid fates. Natural microbiomes often experience population bottlenecks, which create heterogenous local communities, each with reduced population size and biodiversity. Based on the concept of ‘persistence potential’, I and my collaborators demonstrated that bottlenecks can paradoxically promote the persistence of a plasmid that would otherwise not persist in a well-mixed global community. In particular, among the local communities created by a bottleneck, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance. They serve as a local haven that protects the plasmid from being eliminated. Our results provide new insights into the microbiome functional stability and suggest a generalizable approach to modulate plasmid maintenance in complex communities. These works will facilitate a quantitative understanding of natural microbial communities and the engineering of microbial consortia.