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Elevated CO₂ reinforces PT11-dependent symbiotic phosphate uptake to reprogram root nutrient acquisition in rice

ABSTRACT: Plants acquire phosphate either directly through their roots or through symbiosis with arbuscular mycorrhizal (AM) fungi. When this symbiosis is established, the direct uptake pathway is downregulated. As atmospheric CO₂ concentrations rise, it is critical to understand how increased carbon availability alters plant nutrient acquisition strategies, with implications for crop productivity and carbon sequestration. Here, we investigated how phosphate availability, AM symbiosis, and elevated CO₂ interact in rice, a major C₃ crop. We also used the rice pt11 mutant, which is defective in symbiotic phosphate transport, to distinguish the effects of functional nutrient exchange from early symbiotic signalling. Elevated CO₂ enhanced mycorrhizal colonization, total phosphate acquisition, and root biomass in rice. Using split-root systems, dual radioisotope tracing, and transcriptomic profiling in wild-type and pt11 plants, we demonstrate that suppression of the direct phosphate uptake pathway occurs locally in colonized roots and requires functional symbiotic phosphate transport. In contrast, changes in root architecture — including reduced fine lateral root development — are governed by both systemic and local signals, with local regulation dependent on processes downstream of PT11. Transcriptomic analyses identify symbiotic phosphate transport as a regulatory checkpoint that stabilizes the mycorrhizal transcriptional program and coordinates the selection of nutrient acquisition pathways under elevated CO₂. Together, these findings reveal that rising CO₂ reinforces symbiotic phosphate uptake through carbon-driven regulation, reshaping root nutrient acquisition. This work provides a mechanistic framework for integrating plant–microbe interactions into strategies aimed at sustaining crop productivity and managing carbon in a high-CO₂ world.

ORGANISM(S): Oryza sativa

PROVIDER: GSE333245 | GEO | 2026/09/08

REPOSITORIES: GEO

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Project description:Arbuscular mycorrhizal (AM) symbiosis develops through successive colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, tree-like intracellular structures that are transient yet essential sites of nutrient exchange. To dissect the cellular and structural complexity of AM establishment in rice roots colonized by Rhizophagus irregularis, we applied dual-species spatial transcriptomics to simultaneously monitor plant and fungal gene expression at single-cell resolution. This approach revealed surprising differences in transcriptional activity between fungal structures and showed that morphologically similar arbuscules can be transcriptionally distinct. These findings suggest hidden functional diversity among arbuscules, indicating that nutrient exchange is not uniform but finely modulated across individual structures. Because arbuscules form and degenerate within only a few days, we further sought to capture translational regulation across their life span. We pioneered AM-inducible TRAP-seq (Translating Ribosome Affinity Purification followed by RNA-seq) using stage-specific promoters, enabling cell-type- and stage-resolved profiling for the first time in AM symbiosis. This revealed extensive spatiotemporal reprogramming of nutrient transport and signaling, with distinct sets of phosphate, nitrogen, and carbon transporters and regulators upregulated or repressed at different stages of arbuscule development, suggesting that nutrient exchange is dynamically regulated across the arbuscule life cycle. More broadly, cell wall biosynthesis genes and key defence markers were suppressed during arbuscule formation, whereas upon collapse, defence markers were strongly upregulated, suggesting a host-driven shift towards symbiosis termination. Together, these findings highlight the nuanced and dynamic regulation of AM symbiosis at cellular resolution, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time, and providing a framework for further functional exploration.

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Elevated CO₂ reinforces PT11-dependent symbiotic phosphate uptake to reprogram root nutrient acquisition in rice

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