<b>Temporal divergence and genome expansion in soil microbes sustain positive plant</b><b>–</b><b>soil feedbacks under crop rotation</b>

Sustainable food production relies on cropping systems that harness, rather than exhaust, the soil microbiome. Plant–soil feedbacks (PSFs) are shaped by interactions between microbial legacies from past crops and the microbial communities of current season. Still, their temporal dynamics and functional bases remain unclear. Using a multi-phase experiment with continuous wheat monoculture and wheat–soybean rotation, we show that monoculture progressively amplifies negative PSFs, while rotation sustains positive feedbacks enhancing plant growth. These outcomes were linked to a temporal partitioning of microbial influence: contemporary bacterial communities and persistent fungal legacies jointly determined feedback effects. Metagenomic analyses revealed that rotation consistently enriched microbes with larger genomes and broader functional capacity for nutrient cycling and pathogen defense. Inoculation experiments confirmed that large-genome bacteria promoted wheat growth, as supported by transcriptomic analyses showing upregulation of genes involved in nutrient mobilization, pathogen defense, and stress adaptation. Together, our results demonstrate that crop rotation drives eco-evolutionary shifts in soil microbiomes, favoring metabolically versatile, large-genome taxa, and highlight microbial genome size as a predictive trait for designing resilient and productive cropping systems.