Metagenomic Analysis for Unveiling Agricultural Microbiome—3rd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Farming Sustainability".

Deadline for manuscript submissions: 15 February 2026 | Viewed by 158

Special Issue Editors


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Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: plant microbiome; metagenomics; bioinformatics
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Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
Interests: maize; abiotic stress; root development; microbiome; rhizosphere
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Special Issue Information

Dear Colleagues,

The agricultural microbiome plays a significant role in nutrient absorption, disease resistance, and stress resistance in plants and animals; it is an important concept in achieving sustainable agriculture. The purpose of this Special Issue is to promote the development of the field of agricultural microbiomes; submissions that focus on microbiome research related to agriculture, including crops, vegetables, fruits, agricultural products, animal husbandry, aquatic products, and one-health will be accepted. Research on amplicon sequencing is acceptable and works on metagenome, metatranscriptome, metaproteome, metametabolome, bacterial genome, population association analysis, and multi-omics analysis are also recommended in order to more comprehensively use meta-omics technology to analyze the role of the microbiome in agriculture. This research aims to improve our environment and realize the harmonious development of science, technology, and agriculture for one-health.

Prof. Dr. Yong-Xin Liu
Dr. Peng Yu
Guest Editors

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Keywords

  • plant microbiome
  • root microbiota
  • amplicon
  • metagenomics
  • metatranscriptome

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Published Papers (1 paper)

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Research

25 pages, 5731 KB  
Article
Soil Type, Tomato Genotype, and Pathogen Stress Shape the Tomato Rhizobacterial Community
by Xingxing Ping, Chunyang Pan, Yao Wang, Meichun Xiang, Jian Ling, Jianlong Zhao, Yan Li, Zhenchuan Mao, Bingyan Xie and Xingzhong Liu
Agronomy 2025, 15(11), 2517; https://doi.org/10.3390/agronomy15112517 - 29 Oct 2025
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 [...] Read more.
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. Full article
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