Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities

Li Xie,Wenying Shou

doi:10.1038/s41467-021-26647-4

Abstract

Microbial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and “reproduce” the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a “community function landscape”, we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/.

Highlights

Microbial communities often perform important functions that depend on inter-species interactions
We start with a highly simplified case where the community function of interest varies due to variations in two determinants— one heritable and one nonheritable
Our work serves as a fundamental building block for conceptualizing community selection, akin to physicists studying the ideal gas, or population geneticists studying a single-locus two-allele trait

Summary

Introduction

Microbial communities often perform important functions that depend on inter-species interactions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. One could mutagenize individual community members, assemble them at various ratios, and screen the resultant communities for high community function This requires community members to be culturable, and the number of combinatorial possibilities increases rapidly with the number of species and genotypes. Artificial community selection could fail, unless one promotes both variation (e.g., choosing a sufficiently large number of Adult communities to reproduce) and heritability of community function (e.g., promoting species coexistence)[6,15,25,26,28]

Methods

Results

Conclusion