Subinhibitory concentrations of antibiotics mediate primary metabolism and shape diverse species interactions among...

Antibiotics produced by soil microbes have provided critical advances in human health, yet their roles within natural soil ecosystems remain poorly understood. Though traditionally viewed as inhibitory weapons, antibiotics at subinhibitory concentrations (SICA) can alter transcription across a wide range of gene targets, with documented impacts on microbial metabolism and hypothesized consequences for community resource competition. However, work to date has focused primarily on SICA outside of the context of coevolved microbial populations. As interest in leveraging the power of microbiomes grows, a deeper understanding of the roles of SICA within natural, cooccurring communities is critical to our ability to both predict and harness microbial dynamics. In this work, we explored the impacts of SICA on the primary metabolism of sympatric populations of soil Streptomyces sourced from high- and low-nutrient soil habitats. Within each population, the effects of six antibiotic compounds at SICA were quantified on both nutrient-use phenotypes and pairwise resource competition. Overall, isolates from low-nutrient soil were found to be more resilient to changes in primary metabolism in the presence of SICA compared to isolates from high-nutrient soil. Across both populations, SICA significantly modified apparent resource competition among coevolved Streptomyces with individual isolates experiencing both increases and decreases in resource use overlap with sympatric partners. The diverse phenotypic shifts observed in this work emphasize that SICA can mediate a broad spectrum of competitive outcomes and highlight the importance of long-term nutrient history in shaping the functional role of antibiotics within microbial communities.