Plant Microbiome as the Golden Key to Sustainable Agriculture: From Interaction Mechanisms to Technological Applications and Future Challenges

Plant Microbiome in Sustainable Agriculture

Abstract

Introduction: The plant microbiome, comprising dynamic and complex communities of microorganisms including bacteria, fungi, viruses, and archaea, plays a fundamental role in plant health, growth, productivity, and the sustainability of agroecosystems. 

Materials & Methods: This comprehensive review is based on a systematic search of peer-reviewed literature published between 2012 and 2026 using PubMed, Scopus, Web of Science, and Google Scholar databases. A total of 53 relevant articles were selected for inclusion. 

Results: Microbial communities inhabit various plant compartments including the rhizosphere, phyllosphere, endosphere, and spermosphere. They enhance plant growth through direct mechanisms such as nitrogen fixation, phosphate solubilization, siderophore and phytohormone production, as well as indirect mechanisms including induced systemic resistance (ISR) and biological control. Beyond direct effects, microbiomes are the primary drivers of biogeochemical cycles of nitrogen, phosphorus, carbon, and sulfur in soil, improving soil fertility and carbon sequestration. From an ecological and evolutionary perspective, the plant microbiome acts as a "hologenome," providing phenotypic plasticity and rapid adaptation to environmental changes. Synthetic microbial communities (SynComs) designed based on ecological principles represent one of the most promising approaches for disease management, nutrient acquisition, and stress tolerance enhancement. 

Conclusion: Despite significant challenges in commercialization and field application, the transition from chemistry-based to biology-based agriculture, with microbiomes at its core, is imperative. Realizing this vision requires synergy among scientists, farmers, industry, and policymakers to adopt microbiome-aware management strategies.