Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

TLDR

Bacteria on leaves and roots influence plant health, and understanding how plant genetics shape these microbiota is important, yet laboratory studies may miss host gene effects due to limited environmental realism. The study conducts a large‑scale field experiment to separate genotype, environment, age, and harvest‑year effects on leaf and root bacterial communities in Boechera stricta. The experiment sampled leaves and roots across multiple sites, ages, and harvest years to assess bacterial community composition. Leaf microbiomes show strong host genetic control that varies by site, while root microbiomes do not; bacterial communities change with plant age, many leaf taxa are also found in roots indicating soil inoculation, and genotype‑by‑environment interactions add complexity to natural microbiome assembly.

Abstract

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report 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 (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.