Epistatic interactions inform rational design of synthetic microbial communities for bioremediation

The metabolism of microbial communities is essential for host and environmental health. The rational design of microbiomes with targeted functional properties is an important objective but remains challenging due to complex interactions and environmental heterogeneity. Community–function landscapes address this challenge by statistically inferring impacts of species presence or absence on function. Similar to fitness landscapes, community–function landscapes estimate both additive effects and interactions (epistasis) between species that influence function. We apply landscapes to design synthetic consortia to degrade the toxic contaminant bisphenol-A (BPA). Using synthetic communities of ten BPA-degrading bacteria, we map community–function landscapes across increasing BPA concentrations, where higher BPA means greater toxicity. Epistasis increases with toxicity, indicating that collective effects become more important for degradation. Designed communities are able to remediate BPA in contaminated soils. Our results demonstrate that toxicity can drive epistatic interactions in community–function landscapes and that these landscapes can guide microbial consortia design for bioremediation.