Organic and conventional agricultural management trigger differential arbuscular mycorrhizal fungal responses to water limitation and elevated CO 2

Societal Impact Statement Agriculture faces significant challenges under climate change, including rising atmospheric CO 2 concentrations and increasingly frequent water limitation, which threaten food security and ecosystem health. Our study included collaborations with local farmers and highlights how arbuscular mycorrhizal (AM) fungi, key plant symbionts, respond differently to these stressors based on the agricultural system they originate from. AM fungal communities from the two inoculum sources showed different responses in richness, phylogenetic diversity and taxonomic composition. These insights are a first step towards developing climate‐smart farming strategies under future climate. Summary Arbuscular mycorrhizal (AM) fungi are important plant symbionts with the ability to enhance plant resilience against abiotic stressors, making them important to understand in agricultural systems in a changing climate. Agricultural management can affect AM fungal community composition, yet how these management‐moulded communities respond to climate change remains poorly understood. To address this knowledge gap, we tested representatives of AM fungal communities shaped by organic and conventional management and their response to water limitation, elevated CO 2 (eCO 2 ) and their interaction when grown with Sorghum bicolor . We observed that AM fungal communities responded differently to water limitation and eCO 2 depending on the agricultural system they were sourced from. AM fungal virtual taxon (VT) richness and Faith's phylogenetic diversity showed treatment‐dependent responses that differed between the two inoculum sources. This was reflected by a higher VT richness for AM fungi sourced from organic systems. Further, water limitation resulted in an increased relative abundance of Paraglomus in organic systems. Under eCO 2 without water limitation, the organic treatment had higher VT richness and Faith's phylogenetic diversity than the conventional treatment. In contrast, Archaeospora was primarily detected in the organic treatment, particularly under eCO 2 . Thus, promoting organic agricultural practices, such as reduced soil disturbance, organic instead of synthetic amendments and diversified cropping systems, may be able to support AM fungal diversity under changing climatic conditions; their effects on fungal functioning and plant performance require further testing.