The Plant Nutrition Innovation Team at the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, discovered that nitrogen-induced copiotrophic non-decomposer Staphylococcus sciuri restricts the growth of weak decomposers through sugar depletion, thereby restructuring the community dominated by strong decomposers Bacillus that maintain robust degradation abilities. This breakthrough, detailed in Nature Communications, highlight important role of usually overlooked fast-growing non-decomposers in agricultural soil carbon cycling. 

Residue return is a critical measure for ensuring national food security, reducing fertilizer use, and promoting sustainable agricultural development. However, the high ratio of carbon:nitrogen inherent in lignocellulosic materials stimulates soil microbes to "mine" nitrogen, leading to competition for nitrogen between crops and microbes. Thus, the combined application of nitrogen fertilizers and crop residues represents a promising strategy to balance the C:N ratio to allow for both microbial decomposition and crop growth. Currently, the in situ residue decomposition process under nitrogen application and its microbial regulatory mechanisms remain unclear.

This study utilized wheat residue bag experiment under three nitrogen application gradients and microbial multi-omics technologies. It was found that nitrogen application shaped a microbial community dominated by Bacillus decomposers and non-decomposer Staphylococcus sciuri at the early stages of residue decomposition. Based on this, a synthetic microbial community (SynComs) composed of decomposers and non-decomposers was constructed. Transcriptomics and metabolomics confirmed that non-decomposer Staphylococcus sciuri restricts the growth of weak decomposers through sugar depletion, thereby restructuring the community dominated by strong decomposers Bacillus. This shift increases the residue decomposition rate by 16.77% under N fertilization. This study reveals the important role of usually overlooked fast-growing non-decomposers in agricultural soil carbon cycling, providing important theoretical and technical support for developing new strategies for residue decomposition and carbon sequestration in agricultural ecosystems.

Assistant researcher Zhang Meiling from the Institute of Agricultural Resources and Regional Planning is the first author of the paper, and researcher Ai Chao is the corresponding author, with guidance from Academician Zhou Wei. The study was supported by the State Key Laboratory of Efficient Utilization of Arable Land in China, the China Agriculture Research System, the National Key Research and Development Program, the Smart Fertilization Project, the National Natural Science Foundation of China, the Cultivated Land Science Center of the Chinese Academy of Agricultural Sciences, and the Innovation Project of the Chinese Academy of Agricultural Sciences.

Citation and Original Link:

Zhang, M., Zhang, L., Li, J. et al. Nitrogen-shaped microbiotas with nutrient competition accelerate early-stage residue decomposition in agricultural soils. Nat Commun 16, 5793 (2025). 

Original link: 

https://doi.org/10.1038/s41467-025-60948-2