This is where we deposited scripts and data from Lopez et al. 2022 paper "Copiotrophs dominate rhizosphere microbiomes and growth rate potential is a major factor explaining the rhizosphere effect".
Microbiota 🦠 living in close association with plants roots are diverse and can be neutral, pathogenic or beneficial to their host. The rhizosphere microbiome assembly, which involves a change in microbiome composition between soil bacteria and rhizosphere bacteria and has been named the "rhizosphere effect", is a complex and still unknown process which depends of many known factors such as root exudate composition, plant species, soil moisture, and others unknown factors which should account for the extense variability still observed between studies. Here, we show that the most relevant factor determining the rhizosphere effect is growth rate potential using different metagenomic approaches. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA metabarcoding datasets from 18 different plants and soil types, performed differential abundance analyses and estimated growth rates for each bacterial genus. This analysis revealed that bacteria with a high growth rate potential consistently dominated the rhizosphere. Next, we analyzed the genome sequences of 3270 bacterial isolates and 6707 MAGs from 1121 plant- and soil-associated metagenomes, confirming this trend in different bacterial phyla. We next investigated which functional traits were enriched in the rhizosphere, expanding the catalog of rhizosphere-associated traits with hundreds of new functions. When we compared the importance of different functional categories to the predicted growth rate potential using a machine learning model, we found that growth rate potential was the main feature for differentiating rhizosphere and soil bacteria, revealing the broad importance of this factor for explaining the rhizosphere effect. Together, we contribute new understanding of the bacterial traits needed for rhizosphere competence. As this trait may be inferred from (meta-) genome data, our work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.