Multi-Generation Selection of Rhizosphere Ecosystem Associated with Plant Genotype and Biomass in Arabidopsis thaliana

The role of the microbiome in shaping the host phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizosphere microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet remains challenging. Here we ran an artificial ecosystem selection experiment, over eight generations, in Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with higher or lower biomass of the host. This resulted in divergent microbial communities, shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment have modest but significant impacts. Over time, the plant genotype and biomass treatments gain more influence, explaining [~]40% of the variation in the microbial community composition. Furthermore, a genotype-specific association of a plant growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, is observed under selection for high biomass.