Symbiotic and commensal root microbes are key determinants of plant responses to rising CO₂

Rising atmospheric CO₂ stimulates plant growth, but this effect is often constrained by nutrient availability. While beneficial soil-derived microbial symbionts such as nitrogen-fixing rhizobia and mycorrhizal fungi are known to mitigate this limitation, the role of plant commensal microbiota remains unclear. Here, using a gnotobiotic growth system and the model legume Lotus japonicus, we show that the magnitude of plant responses to elevated CO₂ is largely explained by the composition of its root-associated microbial community. Axenic plants exhibited limited physiological responses to increasing CO₂ but inoculation with symbiotic and commensal microbes significantly amplified this effect. Commensal bacteria alone, while not increasing overall biomass, shifted plant carbon allocation belowground. Microbial abundances in roots increased with atmospheric CO₂, even when normalized to plant DNA. The strongest plant and microbial responses were observed when rhizobia, arbuscular mycorrhizal fungi, and the commensal bacterial community were all present. These findings indicate that multi-partner microbial associations will shape both plant growth and the allocation of carbon belowground as atmospheric CO₂ concentrations continue to rise.