The Role of Plant Mic robiomes in Sustainable Production of Horticultural Crops with a Focus on the Synthesis of Primary and Secondary Metabolites: A Review

Document Type : Review Paper

Authors

Department of Horticultural Sciences, Faculty of Agriculture & Natural Resources, Arak University, Arak, Iran

Abstract

Plant microbiomes are recognized as key factors in improving the quantity and quality of horticultural crops. This systematic review, examining studies published in 2018 to date, analyzed the role of microbial communities residing in the rhizosphere, endosphere, and phyllosphere in regulating primary and secondary metabolites of horticultural crops. The findings indicate that beneficial microorganisms affect plant metabolism through multiple direct and indirect mechanisms. Direct mechanisms include improving the uptake of less mobile nutrients such as phosphorus and zinc, producing growth-promoting phytohormones, and fixing nitrogen. In contrast, indirect mechanisms include inducing systemic resistance in plants and suppressing pathogens through the production of antimicrobial metabolites and activation of defense signaling pathways such as jasmonic acid and salicylic acid. These effects not only lead to increased plant growth and yield but also significantly enhance the accumulation of valuable secondary metabolites related to quality, aroma, flavor, medicinal properties, and resistance to biotic and abiotic stresses. The practical application of this knowledge in the form of biofertilizers and designed microbial consortia has shown great potential to move towards sustainable horticultural production systems with reduced dependence on chemical inputs. However, there are several challenges, including the inherent complexity of host-microbiome interactions, variability of performance under different environmental and field conditions, and technical and regulatory barriers to commercialization of this technology. Overcoming these challenges requires the use of integrated approaches such as holomics, novel imaging technologies, and artificial intelligence-assisted modeling to gain a deeper understanding of this complex biological system. Finally, the application of microbiome-based strategies as a new and promising paradigm seems essential for ensuring food security and realizing sustainable agriculture in the current century.

Keywords

Main Subjects

References

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Journal of Medicinal plants and By-products
Volume 15, Issue 5
September and October 2026
Pages 543-557

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