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

Highlights

● 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.

Abstract

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.

Graphical abstract

Keywords

plant–soil continuums / beneficial bacteria / agricultural activities / multifunctionality / endosphere

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Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

We thank Prof. Yong-Guan Zhu for valuable comments and suggestions to improve the quality of this manuscript. This work was financially supported by the State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products (No.2021DG700024-KF202307).

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-023-0223-1 and is accessible for authorized users.

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