Harnessing chemical communication in plant-microbiome and intra-microbiome interactions.

Hongfu LI; Yaxin HU; Siqi CHEN; Yusufjon GAFFOROV; Mengcen WANG; Xiaoyu LIU

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Harnessing chemical communication in plant-microbiome and intra-microbiome interactions.

Author: Hongfu LI ¹ ; Yaxin HU ¹ ; Siqi CHEN ¹ ; Yusufjon GAFFOROV ² ; Mengcen WANG ³ ; Xiaoyu LIU ⁴
Author Information

1. College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
2. Central Asian Center for Development Studies, New Uzbekistan University, Tashkent 100007, Uzbekistan.
3. College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China. wmctz@zju.edu.cn.
4. Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA 6430, Australia. wmctz@zju.edu.cn, Xiaoyu.liu@research.uwa.edu.au.
Publication Type:Review
Keywords: Artificial intelligence (AI); Chemical communication; Click chemistry; Genome editing; Intra-microbiome interaction; Plant–microbiome interaction
MeSH: Microbiota/physiology*; Plants/microbiology*; Artificial Intelligence; Ecosystem
From: Journal of Zhejiang University. Science. B 2025;26(10):923-934
CountryChina
Language:English
Abstract: Chemical communication in plant-microbiome and intra-microbiome interactions weaves a complex network, critically shaping ecosystem stability and agricultural productivity. This non-contact interaction is driven by small-molecule signals that orchestrate crosstalk dynamics and beneficial association. Plants leverage these signals to distinguish between pathogens and beneficial microbes, dynamically modulate immune responses, and secrete exudates to recruit a beneficial microbiome, while microbes in turn influence plant nutrient acquisition and stress resilience. Such bidirectional chemical dialogues underpin nutrient cycling, co-evolution, microbiome assembly, and plant resistance. However, knowledge gaps persist regarding validating the key molecules involved in plant-microbe interactions. Interpreting chemical communication requires multi-omics integration to predict key information, genome editing and click chemistry to verify the function of biomolecules, and artificial intelligence (AI) models to improve resolution and accuracy. This review helps advance the understanding of chemical communication and provides theoretical support for agriculture to cope with food insecurity and climate challenges.