The role of soil microbes in local adaptation and the evolution of plant functional traits

Background/Question/Methods
Soil-dwelling microorganisms are an active and variable part of a plant’s natural habitat. Like other sources of environmental variation, soil microbial communities potentially impact plant evolution in two ways: by causing phenotypic plasticity of functional traits, and by causing differential natural selection. Although the general importance of microbes to plant health is uncontroversial, it is less clear how microbial neighbors affect plant evolution in the context of complex natural habitats. To address this question we conducted large-scale field and greenhouse experiments using Boechera stricta, a wild perennial mustard native to western North America. In the field, a diverse panel of B. stricta genotypes was planted in common gardens in three distinct natural habitats in central Idaho. We measured associations of plant growth, herbivore damage, and reproductive fitness with bacterial and fungal communities in soil, roots, and leaves. In the greenhouse, we directly tested the effects of naturally-occurring soil microbes by inoculating potting soil with biotic communities isolated from several B. stricta habitats.

Results/Conclusions
Data from 16S rDNA sequencing confirmed that Boechera stricta habitats, separated by ~100 km and >800 m in elevation, harbor highly distinct belowground bacterial communities in addition to strong differences in soil chemical profiles. Root bacterial microbiomes also showed strong spatial patterns both among gardens (P=10^-6) and at the meter scale within gardens (P=0.007). The effect of plant genetic variation on microbiome alpha diversity and community composition was stronger in leaves than in roots; however, multiple root-associated taxa showed differential abundance among host genotypes. Furthermore, several components of the root microbiome changed with plant age (P=10^-7), while controlling for the effect of year of observation (P=10^-4). This spatial, temporal, genetic, and ontogenetic variation in root-dwelling bacterial communities highlights the complexity of plant-microbe associations in the wild. Manipulation of microbial communities in greenhouse experiments confirmed that soil microbes can alter evolutionary trajectories of plant functional traits through both phenotypic plasticity and differential selection. Distinct soil communities extracted from natural habitats altered flowering time by >2 days (P=0.0005) and reversed the direction of selection on both flowering time (P=0.016) and on glucosinolate defensive chemistry (P=0.034). Finally, over 80% of leaf-associated bacterial taxa were also present in roots within the same plant, suggesting that soil is a reservoir for phyllosphere as well as root community members. Our results indicate that differences in plant trait expression and reproductive fitness among complex habitats are partially attributable to natural variation in soil-dwelling bacteria and fungi.