Long-term cropping rotation with soybean enhances soil health as evidenced by improved nutrient cycles through keystone phylotypes interaction

Highlights

● We estimated the effect of three crop strategies on soil health based on 63 functional genes in long-term fields.

● The keystone microbial phylotypes support the agroecosystem sustainability.

● Rotation management thrives keystone phylotypes and soil functions.

● Rotation with soybean is beneficial for the subsequent crops.

Abstract

Given the often-independent study of microbial diversity and function, the comprehensive impact of various cropping patterns on both aspects, as well as the interconnections between them, remains unclear. This gap constrainsus from evaluating the impact of soil microbiome shifts on soil health across varying agricultural management regimes. Here, we examined the associations between microbial diversity and soil multifunctionality in three long-term cropping patterns: continuous soybean cropping, soybean-corn rotation, and continuous corn cropping. We targeted 63 functional genes associated with carbon, nitrogen, phosphorus and sulfur cycling to assess soil multifunctionality. Our study demonstrated that the biodiversity and interactions of keystone phylotypes had significant positive associations with multiple soil functional genes, such as organic carbon degradation and fixation, nitrogen fixation and phosphorus solubilization. The analysis of retrieved complete genome revealed that the keystone bacteria identified in our study harbored these functional genes. Moreover, these keystone phylotypes showed associations with the dissipation of herbicide residues. Above all, we revealed that rotation of soybean with corn cropping enhanced a greater diversity of keystone phylotypes and thus fueled soil functions. Collectively, our results highlighted the importance of rotation with soybean in maintaining soil health, which could give a mechanism-based guidance for a sustainable agroecosystem.

Graphical abstract

Keywords

soil nutrient cycles / keystone phylotypes / rotation / soybean / sustainable agroecosystem

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Acknowledgements

This research was financially supported by Zhejiang Provincial Key Research and Development Program of China (Grant No. 2023C02004), the National Natural Science Foundation of China (Grant Nos. 42225705 and 42177006), and China Agriculture Research System of MOF and MARA (Grant No. CARS-04).

Competing interests

The authors declare no competing interests.

Data availability

The raw data were deposited in the NCBI Sequence Read Archive (SRA) database with accession ID of PRJNA895965 and PRJNA895966 for the bacteria and the fungus, respectively.

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-024-0251-5 and is accessible for authorized users.

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