Using Synthetic Microbial Communities to Disentangle Biotic and Abiotic Interactions in the Rhizosphere

Microorganisms are known to aid plants through processes like nutrient acquisition or protection from pathogens, but the complexity of microbial has limited our ability to define general rules guiding the assembly and maintenance of a functionally robust microbiome.

In order to probe these assembly rules, we applied a synthetic ecology approach. We are using a 200-member synthetic community (SynCom) of genome-sequenced bacterial isolates, obtained from A. thaliana roots. Plants were inoculated with this SynCom under varying salinity, pH, temperature, and phosphate conditions, and the root colonization patterns under these gradients were measured using 16S amplicon sequencing. In parallel, plants were imaged to analyze the combined effect of the microbiome and the ambient conditions on root and shoot morphology.

A substantial core of plant-enriched stains, mainly Actinobacteria and Alphaproteobacteria, remain largely robust to across the different environmental conditions, indicating a strong selective pressure imposed by the plant. Other strains exhibited more complex, context-dependent patterns of colonization. We classified the SynCom into four modules of co-occurring strains and measured plant phenotypes when inoculated with each of these modules separately and in combination. Plant phenotypes induced by some modules were attenuated when co-inoculating with other modules. This demonstrates ecological epistasis occurring between functional guilds in the microbiome with profound influence on plant phenotypes.