Growth rate potential is a main predictor of the rhizosphere effect

The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3,270 bacterial isolates and 6,707 metagenome-assembled genomes (MAGs) from 1,121 plant- and soil-associated metagenomes.

We then investigated which functional traits were enriched in rhizosphere MAGs and identified hundreds of new rhizosphere-associated functions. We compared the importance of these functions and predicted growth rate potential and found that the latter was the main feature for differentiating rhizosphere and soil bacteria, revealing the broad importance of this complex trait in explaining the rhizosphere effect. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.