A quantitative microbiome atlas reveals hidden diversity, eukaryotic keystones, and evolutionary trade-offs in plant rhizospheres

Abstract The evolutionary success of land plants is tied to their rhizosphere microbiomes. However, the principles governing how bacteria, fungi, and protists assemble and function across wild plants remain unresolved, limiting our ability to predict co-evolutionary patterns or harness microbiomes for sustainable agriculture. Most studies focus only on bacteria in model crops and rely on relative abundance data that distort interkingdom interactions. Here, we present the One Thousand Plant Microbiomes (1KPM) initiative, a quantitative, multi-kingdom atlas of 1,549 rhizospheres from 590 wild plant species. We performed spike-in–based quantitative microbiomes profiling and ultra-deep metagenomics, discovering conserved functional cores alongside microbial “dark matter” and unprecedented novelty. Despite bacterial dominance, protists and fungi emerge as keystone hubs of rhizosphere stability. We also uncover an evolutionary paradox in Fabales, where low taxonomic but high functional diversity reflects symbiotic optimization. This atlas redefines microbiome assembly rules and establishes rhizospheres as untapped frontiers for microbiome engineering.