Environmentally dependent interactions shape patterns in gene content across natural microbiomes

Sequencing surveys of microbial communities in hosts, oceans, and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here, we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a roadmap for dissecting how associations between environmental variables and gene abundances arise from environmentally-modulated community interactions.