Enhancement of beneficial microbiomes in plant-soil continuums through organic fertilization: Insights into the composition and multifunctionality

Organic fertilization increased the richness and abundance of beneficial communities.The increase in the beneficial communities resulted from soil property optimization.Organic fertilization enhanced the functionality of bacterial communities.Plants exhibited a preference for internalizing beneficial bacteria.Soil microbiomes play a crucial role in maintaining ecological functions and are of great importance for soil health. Some of them could bring benefits to plants for growth promotion. Despite numerous studies have focused on specific beneficial bacteria and their interactions with soils and plants, we still lack a comprehensive understanding of beneficial communities in plant-soil continuums and their responses to agricultural activities. To address this gap, we carried out a microcosm experiment using 16S rRNA amplicon sequencing to explore the effects of organic fertilization on beneficial communities in plant-soil continuums and assess their potential multifunctionality. Our findings reveal that organic fertilization had a positive impact on the beneficial functionality of bacterial communities in plant-soil continuums. This improvement was primarily attributed to the optimized soil physicochemical conditions resulting from organic fertilization. Additionally, organic fertilization increased the complexity of bacterial co-occurrence networks in both soils and the endosphere. Keystone taxa in the endosphere undergone a shift of functions toward pathogen suppression as the result of organic fertilization. Furthermore, this study revealed that plants exhibited a preference for internalizing beneficial bacteria over other type of bacteria. We also provided new insights for evaluating the multifunctionality of microbiomes, and found that the functionality of beneficial communities in plant-soil continuums is enhanced by organic fertilization. All these findings suggested that organic fertilization can be an effective strategy for maintaining plant and soil health.