LAUSR

Significance Because microbiome research generally focuses on a single host or habitat, we know comparatively little about the diversity and distribution of microbiomes at a landscape scale. Our study demonstrates that most of the microbial diversity present within a watershed is maintained within environmental substrates like soil or stream water, and microbiomes of organisms are generally subsets of those that are lower on the food chain. This result challenges the notion that sources of microbial inoculum are likeliest derived from close relatives. By identifying sources of shared microbial diversity within the landscape, we can better understand the origins and assembly processes of symbiotic microbes and how this might abet global conservation, restoration, or bio-engineering goals, such as preserving biodiversity and ecosystem services.