Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome

Microdiversity, the organization of microorganisms into groups with closely related but ecologically different sub-types, is widespread and represents an important linchpin between microbial ecology and evolution. However, the drivers of microdiversification remain largely unknown. Here we show that selection promotes microdiversity in the microbiome associated with sediments in glacier-fed streams (GFS). Applying a novel phylogenetic framework, we identify several clades that are under homogeneous selection and that contain genera with higher levels of microdiversity than the rest of the genera. Overall these clades constituted ∼44% and ∼64% of community α-diversity and abundance, and both percentages increased further in GFS that were largely devoid of primary producers. Our findings show that strong homogeneous selection drives the microdiversification of specialized microbial groups putatively underlying their success in the extreme environment of GFS. This microdiversity could be threatened as glaciers shrink, with unknown consequences for microbial diversity and functionality in these ecosystems.