Rare rather than abundant phoD-harboring bacteria shape soil phosphorus bioavailability in karst orchard–medicinal plant intercropping systems

Abstract

Cultivating medicinal plants in orchards has emerged as a promising strategy to improve soil nutrient profiles, utilize under-tree space effectively, and boost farmers’ incomes. However, the mechanisms influencing soil phosphorus (P) bioavailability in orchard–medicinal plant intercropping systems (OMIs) remain unclear, particularly in karst regions where P is severely deficient, and intercropping effects vary by medicinal plant species. This study assessed the short-term effects of medicinal plant intercropping on soil P bioavailability in four OMIs (Prunus. salicina + Hypericum monogynum [PH], P. salicina + Polygala fallax [PP], P. salicina + Rubus suavissmus, and P. salicina + Semiliquidambar cathayensis + Illicium difengpi) in the karst region of the Lijiang River Basin, Southwest China, with P. salicina monoculture (Pm) as a control. Compared with Pm, OMIs generally reduced soil bioavailable P fractions, except CaCl₂-P, while increasing microbial biomass P, potentially enhancing temporary organic P (P_o) reserves. These changes supported plant inorganic P (P_i) uptake from the rhizosphere soil, as shown by shifts in P activation, supply capacity, and acquisition strategies. Furthermore, OMIs significantly altered the composition and structure, though not the diversity, of phoD-harboring bacterial communities. While abundant taxa (e.g., Bradyrhizobium) and rare taxa (e.g., Pseudomonas) responded differently to nutrient changes, rare taxa exhibited greater responsiveness, particularly in the PH and PP systems. Soil bioavailable P fractions were primarily regulated by rare phoD-harboring bacteria, influenced by soil N:P ratio, pH, and moisture. Overall, OMIs, particularly PH and PP, shifted P utilization strategies from P_i acquisition to temporary P_o preservation, improving P-use efficiency through plant-specific impacts on rare phoD-harboring bacteria. These findings highlight the importance of selecting medicinal plants for optimizing P cycling and suggest that targeted P fertilization in OMIs could enhance karst soil productivity.