Biocompounds in Soil Health and Sustainable Agriculture: Molecular Interactions, Microbial Processes, and Environmental Implications

Abstract

Biocompounds are important chemical mediators within soil-plant-microbe systems and play diverse roles in soil biological processes, nutrient cycling, and plant adaptation to environmental stress. Their presence in soil originates from multiple sources, including plant roots, plant residues, and microbial metabolism, resulting in a chemically diverse mixture of phenolics, flavonoids, organic acids, amino acids, peptides, polysaccharides, terpenoids, siderophores, phytohormones, and microbial secondary metabolites. This review examines the roles of biocompounds in soil health and sustainable agriculture, with particular emphasis on their molecular interactions, microbial processes, environmental fate, and ecological implications. The discussion highlights interactions of biocompounds with plant roots, soil minerals, organic matter, and metals, as well as their effects on microbial community structure, metabolic activity, nutrient transformation, and soil organic matter dynamics. Their potential contribution to plant adaptation under drought, salinity, temperature, oxidative, and nutrient stresses is also considered. Particular attention is given to adsorption, degradation, transformation, persistence, bioavailability, and potential effects on non-target organisms, which collectively determine the environmental behavior of biocompounds. Emerging approaches based on metabolomics, multi-omics, spatial analysis, microbiome engineering, Artificial Intelligence (AI), and precision agriculture offer new opportunities to investigate these complex interactions and develop more predictive approaches to soil management. Nevertheless, challenges remain in understanding compound mixtures, transformation products, field-scale variability, and long-term ecological effects. Integrating molecular, microbial, physicochemical, and field-scale approaches will be essential for translating knowledge of biocompounds into environmentally responsible strategies for maintaining soil health and supporting sustainable agricultural systems.