Nutrient balance regulates soil microbial health under long-term fertilization

Da Lin; Qing Xu Ma; Yu Qiu Ye; Wolfgang Wanek; Andrew S. Gregory; Davey L. Jones; David W. Graham; Dong Zhu; Josep Penuelas; Yong Guan Zhu

doi:10.1016/j.celrep.2026.117274

Nutrient balance regulates soil microbial health under long-term fertilization

Da Lin
, Qing Xu Ma
, Yu Qiu Ye
, Wolfgang Wanek
, Andrew S. Gregory
, Davey L. Jones
, David W. Graham
, Dong Zhu (Corresponding author)
, Josep Penuelas
, Yong Guan Zhu

Department of Microbiology and Ecosystem Science

Publications: Contribution to journal › Article › Peer Reviewed

Abstract

Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.

Original language	English
Article number	117274
Number of pages	22
Journal	Cell Reports
Volume	45
Issue number	4
DOIs	https://doi.org/10.1016/j.celrep.2026.117274
Publication status	Published - 28 Apr 2026

Funding

We acknowledge funding from the National Natural Science Foundation of China (U25A20803 and 42222701), the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB0750400), Fujian Provin cial Natural Science Foundation of China (2023J02031), the Youth Innovation Promotion Association of the Chinese Academy of Sciences (2023321), and the Ningbo Yongjiang Talent Project (2022A-163-G). The Broadbalk Winter Wheat Classical Experiment is part of the Rothamsted Long-Term Experi ments-National Bioscience Research Infrastructure (RLTE-NBRI), funded by the UK Research and Innovation-Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) under award BBS/E/RH/23NB0007 (2023– 2028). The RLTE-NBRI is also supported by the Lawes Agricultural Trust.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 2 Zero Hunger
SDG 13 Climate Action

Austrian Fields of Science 2012

106022 Microbiology
106026 Ecosystem research

Keywords

virus-host interaction
antibiotic resistomes
microbial health
nutrient management
180-year-old fertilization

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10.1016/j.celrep.2026.117274Licence: CC BY-ND 4.0

Cite this

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title = "Nutrient balance regulates soil microbial health under long-term fertilization",

abstract = "Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through {"}piggyback the winner{"} strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.",

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AU - Lin, Da

AU - Ma, Qing Xu

AU - Ye, Yu Qiu

AU - Wanek, Wolfgang

AU - Gregory, Andrew S.

AU - Jones, Davey L.

AU - Graham, David W.

AU - Zhu, Dong

AU - Penuelas, Josep

AU - Zhu, Yong Guan

PY - 2026/4/28

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N2 - Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.

AB - Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.

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Nutrient balance regulates soil microbial health under long-term fertilization

Abstract

Funding

UN SDGs

Austrian Fields of Science 2012

Keywords

Access to Document

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