Intercrops Maintain Orchard Soil Nutrients Accumulation with Variation in Soil Microbiome Composition and Function

The intercropping system is used for weed control in orchards, but the intercrops need to be well-designed to fit into the row spaces of fruit trees. In this study, the citrus (Citrus reticulata cv. Chachiensis) row spaces were intercropped with either soybean (Glycine max (L.) Merr.) or sweet potato (Ipomoea batatas (L.) Lam.), and their effects on weed control, soil physiochemical properties, and soil microbiome were compared to the natural weeds. Both plant species were effective in reducing the orchard weeds, and their different varieties commonly improved soil organic matter, available P and K, and beneficial metal elements compared to the weeds. Even though the soil fungal and bacterial richness and diversity of the intercrops were not significantly altered, their composition, structure, and function were distinctive to those of the weeds. The soils of the intercrops generally enriched with the fungal genera of Talaromyces and Penicillium and the bacterial genera Sphingomonas, Knoellia, and Nocardioides. Accordingly, the altered microbial communities, in taxonomy, correlated to the enriched cellular functional pathways of glycolysis and gluconeogenesis, homologous recombination, nitrogen metabolism, lipoic acid metabolism, mismatch repair, DNA replication, nicotinate and nicotinamide metabolism. Taken together, these results imply that intercrops and weeds exert distinct effects on soil nutrient accumulation, and these effects are associated with their differential impacts on soil microbiomes—which are likely driven by the rhizosphere activities of the intercrops.