Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.

Long-term farming practices leave an imprint on soil microbiomes, but how these changes influence crop drought resilience remains poorly understood. Here, we examined avocado orchards managed organically or conventionally for two decades and recurrently exposed to drought, to assess how management history shapes the rhizosphere microbiota and its contribution to plant stress tolerance. Organic and conventional systems resulted in distinct soil physicochemical profiles that were associated with shifts in rhizosphere microbial community composition. Organic management was characterized by higher soil pH, phosphorus availability, water content, and C:N ratio, together with a consistent enrichment of spore-forming bacteria, especially members of the Bacillaceae family. We established a culture collection from the organic rhizosphere, dominated by Bacillaceae, and identified three top-performing strains: Bacillus halotolerans B19 and B21, and Bacillus subtilis B26. In greenhouse assays, B. halotolerans strains mitigated drought stress by preserving biomass and reducing leaf proline accumulation, while B. subtilis provided partial protection. Gene expression analysis revealed strain-specific responses that nonetheless converged on bdh (2,3-butanediol dehydrogenase) induction, highlighting a common mechanism for drought mitigation. Together, these findings establish a mechanistic link between long-term organic farming and microbial functions underpinning drought resilience in perennial agroecosystems, paving the way for climate-smart farming strategies.