Linking inhibitory phenotypes of soil Streptomyces to resource inputs, resource-use tradeoffs, and soil microbiome composition and diversity

Abstract

Soil bacteria produce a diverse array of antibiotics which mediate interactions among microbes. Resource competition and tradeoffs between inhibitory ability and growth are thought to be important in shaping the evolution of inhibitory phenotypes, but tests of these ideas in naturally-occurring microbial populations remain scarce. In my dissertation, I used soil-borne Streptomyces isolates from a long-term agricultural experiment to examine the relationships between resource inputs (nitrogen fertilizer and crop residues), resource use traits, and inhibitory phenotypes, as well as relationships between Streptomyces inhibitory phenotypes and the diversity and composition of the soil microbiome. I found that long-term nitrogen addition resulted in lower frequencies of antibiotic inhibitory phenotypes among indigenous Streptomyces in nitrogen fertilized plots than in non-fertilized plots, while crop residue incorporation had only limited effects on inhibitor frequencies. Streptomyces isolates with greater ability to inhibit other Streptomyces had lower niche width and mean growth across carbon sources they utilized. This tradeoff between inhibitory ability and resource use was consistent across plots with different histories of nitrogen and crop residue inputs. The frequency of inhibitory phenotypes among Streptomyces was correlated with abundances of many individual OTUs from diverse phyla. Inhibitor frequency was also correlated with soil pH, but not with OTU richness or diversity. Taken together, my findings suggest that resource inputs can have substantial effects on the frequencies of antibiotic-producing microbes in soil microbial communities. However, these effects appear to mediated in complex ways by microbial densities, soil physicochemical characteristics, and/or changes in the composition of the soil microbiome. Further research is needed to better understand the mechanisms by which resource inputs affect the evolution of inhibitory capacities among naturally-occurring soil microbial populations.