New Zealand glacier-fed stream sediments samples.

Microdiversity is an important linchpin between ecology and evolution. However, the generation of microdiversity in natural microbial communities remains poorly documented and understood to date. Here we show that strong environmental selection promotes microdiversity in the microbiome of glacier-fed streams (GFS). Using a novel method, we identified phylogenetic clades, mostly affiliated to Betaproteobacteria and Alphaproteobacteria, under selection and driving community assembly. Several genera within these clades, all belonging to the core microbiome, exhibited a higher level of microdiversity than genera that were not under selection. Genera under selection were diverse, abundant and present in all GFS, indicative of their success to thrive in an extreme environment. Our findings demonstrate that strong selective forces, typical for extreme environments, push microbial diversity towards microdiversity residing within specific phylogenetic clades. Thus microdiversity, and therefore overall microbial diversity, in GFS may be under threat as the selective forces relax with glacier shrinkage.