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Yujun Zhong,

Yujun Zhong

CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences

,

Shenyang

,

China

University of Chinese Academy of Sciences

,

Beijing

,

China

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Yingyue Zhang,

Yingyue Zhang

CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences

,

Shenyang

,

China

Institute of Carbon Neutrality Technology and Policy, Shenyang University

,

Shenyang

,

China

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José Luis López Arcondo,

José Luis López Arcondo

Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena

,

Jena

,

Germany

Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales

,

Bariloche, Rio Negro

,

Argentina

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Ruoyi Xu,

Ruoyi Xu

CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences

,

Shenyang

,

China

University of Chinese Academy of Sciences

,

Beijing

,

China

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Mark Radosevich,

Mark Radosevich

Department of Biosystems Engineering and Soil Science, The University of Tennessee

,

Knoxville, TN

,

U.S.A

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Jeffery L Dangl,

Jeffery L Dangl

Department of Biology, University of North Carolina at Chapel Hill

,

Chapel Hill, NC, U.S.A

Howard Hughes Medical Institute, University of North Carolina at Chapel Hill

,

Chapel Hill, NC, U.S.A

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Bas E Dutilh,

Bas E Dutilh

Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena

,

Jena

,

Germany

Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University

,

Utrecht

,

The Netherlands

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Xiaolong Liang

Xiaolong Liang

CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences

,

Shenyang

,

China

University of Chinese Academy of Sciences

,

Beijing

,

China

Corresponding author. Mailing address: Institute of Applied Ecology, Chinese Academy of Sciences, No. 72 Wenhua Road, Shenyang, Liaoning Province 110016, China. E-mail: [email protected]

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Co-first authors

Current affiliation: Howard Hughes Medical Institute, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

Author Notes

Received:

30 December 2024

Revision received:

13 June 2025

Accepted:

04 November 2025

Published:

06 November 2025

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Yujun Zhong, Yingyue Zhang, José Luis López Arcondo, Ruoyi Xu, Mark Radosevich, Jeffery L Dangl, Bas E Dutilh, Xiaolong Liang, Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development, ISME Communications, 2025;, ycaf203, https://doi.org/10.1093/ismeco/ycaf203

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Abstract

Bacteriophages, lytic or lysogenic, play critical roles in structuring different soil bacteriomes and driving their functionality. Lysogeny is favored in the plant rhizosphere and may play a major role in plant-rhizobacteria assembly and function. However, the ecological footprint and consequence of prophage activity in the rhizosphere are poorly understood. Here, we conducted a 35-day pot experiment to examine how prophage induction influences soybean rhizosphere viromes and bacterial communities, along with associated changes in nutrient cycling and plant development. The results showed that mitomycin C-induced prophage induction triggered immense viral production, altering virome structure (with more observed species richness in the rhizosphere). We observed a greater impact on the rhizosphere virome than on the bulk soil virome. The resulting lysis decreased the soil organic matter content but significantly increased dissolved organic carbon and nitrate contents in soil, which improved soil nutrient conditions and stimulated soybean root development. Prophage induction markedly influenced rhizobacterial community structure, resulting in reduced community diversity. The enrichment of fast-growing bacterial populations was stimulated, suggesting that viral lysis increased microbial activities and accelerated nutrient turnover. The bacterial interaction network was drastically shifted, with complexity being decreased in bulk soil and increased in the rhizosphere, potentially stimulating the differentiation of the bacterial communities. Together, our results demonstrated that induction of prophages can cause extensive nutrient turnover and variations in plant-rhizobacteria interactions driving the rhizobacterial community assembly process. This study provides novel insights into the mechanisms of phages controlling microbial function in primary production and soil carbon storage by modulating microbial traits (e.g., carbon use efficiency, growth rate, death, and community assembly) and via processes like the viral shunt.

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Co-first authors

Current affiliation: Howard Hughes Medical Institute, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

© The Author(s) 2025. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.