Strategies for tailoring functional microbial synthetic communities

Abstract

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While synthetic communities have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional synthetic communities to reveal common principles and discuss multi-dimensional approaches for community design. We propose a strategy for tailoring the design of functional synthetic communities based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.