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Agronomy
Volume 15
Issue 11
10.3390/agronomy15112517
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Article

Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community

by
Xingxing Ping
1,
Chunyang Pan
2,
Yao Wang
1,
Meichun Xiang
3,
Jian Ling
2,
Jianlong Zhao
2,
Yan Li
2,
Zhenchuan Mao
2,
Bingyan Xie
2,4,* and
Xingzhong Liu
1,*
1
State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, Frontiers Science Center for Cell Responses, College of Life Science, Nankai University, Tianjin 300071, China
2
State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
4
Center for Biosafety, Chinese Academy of Inspection and Quarantine, Sanya 572024, China
*
Authors to whom correspondence should be addressed.
Agronomy 2025, 15(11), 2517; https://doi.org/10.3390/agronomy15112517
Submission received: 17 September 2025 / Revised: 27 October 2025 / Accepted: 28 October 2025 / Published: 29 October 2025
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—3rd Edition)
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Abstract

Although the effects of soil type, plant genotype, and pathogen invasion on plant rhizosphere microbiomes have been preliminarily explored, their relative contributions and interactive influences on rhizobacterial community assembly remain unclear. In this study, we used tomato as a model to evaluate the individual and combined impacts of these three factors on rhizosphere bacterial community structure and function within a unified experimental framework. Microbiome-based analyses revealed that soil type was the predominant driver, explaining 53.1% of structural and 49.6% of functional variation, followed by tomato genotype (15.6% and 36.1%, respectively) and Fusarium oxysporum f. sp. lycopersici (Fol) inoculation (2.1% and 0.9%). Notably, the interaction between soil type and tomato genotype exerted a stronger influence than any other factor combination. Total nitrogen emerged as the key abiotic factor shaping the taxonomic composition of rhizobacterial communities, whereas soil pH played a dominant role in determining their functional profiles. Distinct tomato genotypes harbored rhizobacterial communities with divergent taxonomic and functional compositions. Although pathogen inoculation triggered the recruitment of beneficial microbes by the host plants, its impact on rhizobacterial community assembly was considerably weaker compared with the effects of soil type and tomato genotype. These findings provide a framework for understanding how soil, host, and pathogen collectively shape rhizobacterial communities and offer insights for optimizing microbiome management in crop production.
Keywords: Fusarium oxysporum f. sp. lycopersici; rhizosphere bacterial communities; function prediction; co-occurrence network Fusarium oxysporum f. sp. lycopersici; rhizosphere bacterial communities; function prediction; co-occurrence network

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MDPI and ACS Style

Ping, X.; Pan, C.; Wang, Y.; Xiang, M.; Ling, J.; Zhao, J.; Li, Y.; Mao, Z.; Xie, B.; Liu, X. Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community. Agronomy 2025, 15, 2517. https://doi.org/10.3390/agronomy15112517

AMA Style

Ping X, Pan C, Wang Y, Xiang M, Ling J, Zhao J, Li Y, Mao Z, Xie B, Liu X. Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community. Agronomy. 2025; 15(11):2517. https://doi.org/10.3390/agronomy15112517

Chicago/Turabian Style

Ping, Xingxing, Chunyang Pan, Yao Wang, Meichun Xiang, Jian Ling, Jianlong Zhao, Yan Li, Zhenchuan Mao, Bingyan Xie, and Xingzhong Liu. 2025. "Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community" Agronomy 15, no. 11: 2517. https://doi.org/10.3390/agronomy15112517

APA Style

Ping, X., Pan, C., Wang, Y., Xiang, M., Ling, J., Zhao, J., Li, Y., Mao, Z., Xie, B., & Liu, X. (2025). Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community. Agronomy, 15(11), 2517. https://doi.org/10.3390/agronomy15112517

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