Summary Studies of microbial communities in natural ecosystems have been generally focused on mapping patterns of species and gene distributions. Although highly instrumental in expanding our understanding of microbial diversity and distribution patterns, such census studies often lack a meaningful and explicit definition of scale. Here, we discuss the importance of scale in environmental microbiology assessments and consider how patterning ecology can be redirected towards advancing concept and theory formation in ecosystem microbiome research. This article is protected by copyright. All rights reserved.