16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains

Bacteria living on and in leaves and roots influence many aspects of their hosts’ health, so the extent of plant genetic control over their microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies may overestimate the influence of certain plant genes on the microbiome and fail to detect others, because they do a poor job simulating true environmental heterogeneity. We conducted a large-scale field experiment to disentangle the effects of genotype, environment, age, and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta, a wild perennial mustard. Genetic control of the microbiome varied substantially among sites, and bacterial community composition shifted as plants aged. Furthermore, a large proportion of leaf bacteria were shared with roots, suggesting inoculation from soil. Our results highlight the complexity of microbiome formation in natural environments.