Engineering Plant-Microbe Systems for Functional Food Production and Sustainable Agriculture: From Microbiome Assembly to Fermented Innovations

Plants engage with diverse microbial communities across the rhizosphere, phyllosphere, and endosphere, forming integrated holobiont systems that determine nutrient availability, stress resilience, and crop productivity. Beneficial microorganisms—plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi, and endophytes—enhance nutrient acquisition, prime immune defenses, and confer stress tolerance. Yet successful microbiome engineering first requires understanding how communities assemble: the recruitment, persistence, and conservation of core microbiomes, and how plant–microbe and microbiome–consortium interactions reshape the holobiome under stress. Beyond the field, plant-associated microbes are central to fermentation biotechnology: edible fungi and fermentation bacteria transform plant-derived substrates into functional foods with enhanced bioavailability and probiotic properties. Advances in multi-omics, synthetic biology, and microbiome engineering have revealed mechanisms of plant-microbe crosstalk—quorum sensing, effector proteins, epigenetic modifications—yet translation into engineered microbiomes and scalable fermentation innovations remains limited.This Research Topic brings together fundamental and applied research on plant-microbe systems to address interconnected challenges spanning mechanism and application. It seeks work that first elucidates the principles of microbial community assembly—recruitment, persistence, and conservation of core microbiomes under stress—and the plant–synthetic community (SynCom) and microbiome–SynCom interactions that drive dynamic changes in the plant holobiome, since these fundamentals underpin any rational engineering effort. Building on this foundation, it invites the design and validation of engineered microbiomes that enhance crop resilience under specific stressors—particularly heavy metal contamination, drought, and xenobiotics—while sustaining soil health. Distinctively, it then extends the same systems logic downstream, leveraging plant-microbe interactions to generate high-quality raw materials for fermentation and engineered functional foods with enhanced bioactive and probiotic profiles. By connecting agricultural microbiology with food fermentation biotechnology, we position plant-microbe engineering as a dual-benefit innovation—securing crop productivity under climate stress while enabling health-promoting fermented foods—attracting global contributions aligned with the UN Sustainable Development Goals.This Research Topic welcomes high-quality original research, reviews, and methods papers on engineered plant-microbe systems, including:· Mechanisms of microbial community assembly—recruitment, persistence, and conservation of core microbiomes under stress conditions· Plant–SynCom and microbiome–SynCom interactions driving dynamic changes in the plant holobiome under stress· Design, formulation, and field validation of engineered or assembled microbial consortia; inoculant development and large-scale production· Plant-microbe responses to specific stressors (e.g., heavy metals, glyphosate, microplastics); molecular mechanisms of microbial-mediated stress tolerance and detoxification· The agriculture-to-fermentation mechanistic bridge: how rhizosphere/phyllosphere microbes shape fermentation outcomes, raw-material quality, and functional-food bioactive composition· Translational research: field trials across agroecological conditions, inoculant formulation, bioeconomic analyses, and industrial-scale fermentation development· Multi-omics approaches revealing plant-microbe crosstalk, microbiome function, and consortium assembly principles; contributions from Global South, smallholder farming, and underrepresented crop systems are particularly welcome-------We welcome contributions from researchers across the field, and we are glad to support you as you prepare your submission. If you would like early feedback on whether your planned manuscript fits the scope of this Research Topic, please write to us at plantscience@frontiersin.org before submitting. A quick check at this stage helps confirm your work is a strong fit and can save you time later in the process.To take part, click “Participate in this topic” at the top right of this page, then confirm through the “Participate” link in the follow-up email. This lets us know to expect your contribution, keeps you informed of key deadlines, and gives you access to resources that guide you through submission. We look forward to your participation and to building a vibrant, cohesive Research Topic together. Topic editors: FEI XU, Gong Chen, Mrinal Samtiya, Denver Inladchang Walitang, Abdoulaye SOUMARE Source: https://www.frontiersin.org/research-topics/82752/engineering-plant-microbe-systems-for-functional-food-production-and-sustainable-agriculture-from-microbiome-assembly-to-fermented-innovations