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<p><UnorderedList Mark="Bullet"> <ItemContent> <p>Keystone bacteria’s effect on soil health was found by genome-resolved metagenomics.</p> </ItemContent> <ItemContent> <p>Soil pH and C/N content were important for affecting keystone communities.</p> </ItemContent> <ItemContent> <p>Available phosphorus lacked a significant effect on keystone bacteria.</p> </ItemContent> <ItemContent> <p>Lysogenic virus-host dynamics help keystone bacteria adaption by P-acquisition AMGs.</p> </ItemContent> </UnorderedList></p><p>Soil microbes are crucial for agricultural sustainability, yet the genomic evidence of their interactions with soil abiotic and biotic factors remains unclear. Herein, we evaluated the contribution of soil bacteria to soil functions and soybean yields by analyzing 4 281 bacterial metagenomic assembled genomes (MAGs) recovered from 113 natural fields across China, integrated 12 enzymic activities and 58 quantified nutrient-cycling genes. Genome-resolved metagenomics revealed the diverse genic traits of keystone bacteria, and their roles in nutrient accumulation, fungal pathogen suppression, and herbicide biodegradation, thereby promoting soybean yields. Soil pH and C/N content were important abiotic factors that determined the dominant life history strategy of keystone communities, thus affecting nutrient-cycling genes abundance. We proposed agricultural management suggestions based on diversified planting aligned with the soil environmental preferences of keystone bacteria, verified in two long-term cropping fields. By recovering 7 803 vMAGs, we found the lysogenic virus-host dynamics could promote keystone bacteria adaptation by providing P-acquisition auxiliary metabolic genes (AMGs), leading to ecological advantages. We reported a novel P-acquisition strategy involving <i>phnA</i>-associated phosphonate hydrolysis employed by viruses, significantly influencing keystone-host phosphorus cycling. Overall, our study significantly advances the understanding of keystone bacteria in supporting crop production, with implications for precision microbiome management in agroecosystems.</p>

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Genome-resolved metagenomics reveal soil and viral drivers of keystone bacterial traits shaping nutrient cycling and soybean yield across agroecosystems

  • 期刊论文

  • 发表日期：

    2025年10月9日

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  • Xiaowei Huang,
  • Xueling Yang,
  • Yuxuan Chen,
  • Jie Cheng,
  • Zhongyi Cheng,
  • Jiachun Shi,
  • Yan He,
  • Jianming Xu

摘要

Keystone bacteria’s effect on soil health was found by genome-resolved metagenomics.

Soil pH and C/N content were important for affecting keystone communities.

Available phosphorus lacked a significant effect on keystone bacteria.

Lysogenic virus-host dynamics help keystone bacteria adaption by P-acquisition AMGs.

Soil microbes are crucial for agricultural sustainability, yet the genomic evidence of their interactions with soil abiotic and biotic factors remains unclear. Herein, we evaluated the contribution of soil bacteria to soil functions and soybean yields by analyzing 4 281 bacterial metagenomic assembled genomes (MAGs) recovered from 113 natural fields across China, integrated 12 enzymic activities and 58 quantified nutrient-cycling genes. Genome-resolved metagenomics revealed the diverse genic traits of keystone bacteria, and their roles in nutrient accumulation, fungal pathogen suppression, and herbicide biodegradation, thereby promoting soybean yields. Soil pH and C/N content were important abiotic factors that determined the dominant life history strategy of keystone communities, thus affecting nutrient-cycling genes abundance. We proposed agricultural management suggestions based on diversified planting aligned with the soil environmental preferences of keystone bacteria, verified in two long-term cropping fields. By recovering 7 803 vMAGs, we found the lysogenic virus-host dynamics could promote keystone bacteria adaptation by providing P-acquisition auxiliary metabolic genes (AMGs), leading to ecological advantages. We reported a novel P-acquisition strategy involving phnA-associated phosphonate hydrolysis employed by viruses, significantly influencing keystone-host phosphorus cycling. Overall, our study significantly advances the understanding of keystone bacteria in supporting crop production, with implications for precision microbiome management in agroecosystems.