By integrating engineering principles with plant biology, a new review highlights how redesigned genetic pathways and plant-based biosensors can deepen understanding of plant responses to both harmful and beneficial microbes. The authors emphasize that these approaches could reshape sustainable agriculture, improving crop resilience to pathogens, drought, and other stresses while reducing reliance on chemical inputs.
Plants coexist with diverse microbial communities—ranging from fungi and bacteria to viruses—that can either benefit or harm their hosts. Mutualistic microbes, such as mycorrhizal fungi and nitrogen-fixing bacteria, boost nutrient uptake and stress tolerance, while pathogenic microbes cause severe yield losses.
Traditional molecular genetics has revealed functions of individual genes involved in these interactions but struggles to capture the complex networked responses plants mount under real-world conditions. Breeding for enhanced resistance or beneficial symbioses has often relied on single-gene manipulations, which are time-consuming and limited in scope. Advances in multi-omics, genome-wide association studies, and synthetic biology now allow simultaneous manipulation of multiple genes and pathways, offering a more holistic and rapid route to engineer plant–microbe systems.
A study (DOI:10.1016/j.bidere.2025.100007) published in BioDesign Research on 18 March 2025 by Xiaohan Yang’s & Jin-Gui Chen’s team, Biosciences Division, Oak Ridge National Laboratory, demonstrates that plant synthetic biology provides powerful new tools—such as pathway engineering, biosensors, and microbiome design—to dissect and reprogram plant–microbe interactions for agricultural and ecological resilience.
Molecular pathways
The review begins by mapping key molecular pathways that regulate how plants interact with microbes. On the defensive side, plants deploy layered immune responses: pattern-triggered immunity (PTI), which recognizes microbial signatures like chitin or flagellin through pattern recognition receptors, and effector-triggered immunity (ETI), which detects pathogen effectors via resistance proteins and often culminates in hypersensitive cell death. These mechanisms converge to provide systemic acquired resistance, bolstered further by beneficial microbes that induce systemic resistance.
Conversely, plants establish symbioses by emitting chemical signals such as flavonoids and strigolactones, which stimulate microbial partners like rhizobia or mycorrhizal fungi. Symbiotic signaling pathways, including the common symbiosis signaling pathway (CSSP), involve calcium oscillations and transcription factors that regulate nodulation and mycorrhization.
Interestingly, several immune and symbiotic pathways overlap, requiring plants to finely tune responses depending on whether microbes are friends or foes.
Synthetic biology
Synthetic biology offers solutions to unravel and manipulate these processes. Genetically encoded plant-based biosensors now allow in vivo monitoring of calcium, reactive oxygen species, or hormone signaling during microbial encounters. Pathway engineering can modify production of metabolites such as flavonoids or volatile organic compounds, clarifying their dual roles in attracting allies and deterring pathogens.
Researchers also envision engineering synthetic receptors or signaling molecules to create new symbioses, as well as designing plants with altered root exudates to shape the soil microbiome. These capabilities are complemented by in situ microbiome engineering, where plants are modified to recruit or support specific microbial consortia.
Together, these strategies present a toolkit for re-designing plants as dynamic partners in sustainable agriculture, moving beyond single-gene approaches to network-level manipulation.
This review provides a overview of how synthetic biology can transform research on plant–microbe interactions. By leveraging biosensors, pathway engineering, and microbiome manipulation, researchers are uncovering fundamental mechanisms and opening new possibilities for engineering crops that are more disease-resistant, stress-tolerant, and environmentally sustainable.
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