Synthetic biology reprograms plant–microbe partnerships for resilient agriculture
image: Plant roots secrete various flavonoids that are vital in establishing mutually beneficial relationships with rhizobial and mycorrhizal symbionts. Additionally, plants release other signaling molecules such as strigolactones (SL) and 2-hydroxy fatty acids, which play crucial roles in facilitating these symbiotic interactions. These signals control the expression of numerous microbial genes, including nod genes and stimulate fungal hyphal branching. They also stimulate the production of signaling molecules by the symbionts, such as rhizobial lipo-chitooligosaccharides (LCOs) (e.g. Nod factors) and mycorrhizal LCOs (e.g. Myc factors). These LCOs are detected by different receptor complexes. LCOs produced by rhizobia bacteria are perceived at the plasma membrane by receptor like kinases (RLKs) (e.g. NFR1 and NFR5). The perception of mycorrhizal LCOs also involve plant RLKs. LysM-RLKs are the most studied in symbioses with beneficial mycorrhizal fungi. Recently, a LysM-RLK receptor complex consisting of OsMYR1/OsLYK2 and OsCERK1 has been identified in rice mediating AMF perception [59]. These examples are highlighted because the key receptors for mycorrhizal LCOs have yet to be characterized in other plant species. In addition to LysM-RLKs, a G-type Lectin-RKs (LecRK) that mediates the symbiotic interaction between Populus and Laccaria bicolor has been reported. The downstream signaling cascades for lecRKs have not been extensively studied and remain largely unknown compared to LysM-RLKs. The signal emitted by LysM receptors activates the symbiosis receptor kinase (SymRK) that associates with essential proteins like SymRK interacting protein 1 and 2 (SIP1 and 2), SymRK-interacting E3 ligase (SIE3), and the 3-hydroxy-3-methylglutaryl coenzyme A reductase1 (HMGR1) involved in mevalonate biosynthesis, which triggers calcium oscillations in the nuclear region, also known as calcium spiking. Downstream of calcium spiking, a module involving calcium/CaM-dependent protein kinase (CCaMK) and Cyclops promotes mycorrhizal symbiosis by activating the expression of Reduced Arbuscular Mycorrhiza1 (RAM1) and promotes rhizobial symbiosis by forming a complex with Nodulation Signaling Pathways 1 and 2 (NSP1/NSP2) to regulate the expression of Nodule Inception (NIN). Created with BioRender.com.
Credit: The authors
By integrating engineering principles with plant biology, this 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.
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 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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References
DOI
Original Source URL
https://doi.org/10.1016/j.bidere.2025.100007
Funding information
The writing of this manuscript was supported by the U.S. Department of Energy (DOE) Genomic Science Program, as part of the Plant-Microbe Interfaces (PMI) Scientific Focus Area (under FWP ERKP730) and the Secure Ecosystem Engineering and Design (SEED) Scientific Focus Area (under FWP ERKPA17), and the Center for Bioenergy Innovation (CBI; under FWP ERKP886), a DOE Research Center supported by the Biological and Environmental Research (BER) program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. DOE under Contract Number DE-AC05-00OR22725. This work was also supported by the National Science Foundation Plant Genome Research Program (award no. IOS-2224203) to S.X., and a SPRINT award from the University of Tennessee, Institute of Agriculture to F.C. and J.T.
About BioDesign Research
BioDesign Research is dedicated to information exchange in the interdisciplinary field of biosystems design. Its unique mission is to pave the way towards the predictable de novo design and assessment of engineered or reengineered living organisms using rational or automated methods to address global challenges in health, agriculture, and the environment.