Soil Health Assessment for Crop-Specific Production: Linking Soil Microbiomes, Pathogen Risk, and Crop Nutritional and Phytochemical Quality

Soil degradation is one of the greatest threats to sustainable agriculture, yet current soil health assessment frameworks largely rely on physicochemical indicators and may insufficiently account for crop-specific biological requirements and microbiome functions. Increasing evidence indicates that different crops require distinct combinations of physical, chemical, and biological soil properties and recruit differentially enriched rhizosphere microbial assemblages that regulate nutrient cycling, disease suppression, plant performance, and nutritional quality. This review critically examines current concepts of soil quality and soil health and highlights the need to shift from generalized toward crop-specific soil health assessment. We synthesize the principal physical, chemical, and biological indicators of soil health, with emphasis on soil microbiomes, beneficial microorganisms, soil-borne pathogens, molecular diagnostic approaches, and representative sampling strategies. Using publicly available FAOSTAT and EPPO datasets as an exploratory European case study, we describe continental crop production patterns and the geographical occurrence of major plant pathogens to illustrate how regional crop production and pathogen records can provide context for crop-specific soil health assessment. We further assess evidence linking soil properties and plant-associated microbiomes with crop nutrient composition and bioactive phytochemical accumulation. Collectively, this review proposes a crop-specific conceptual framework that integrates ecological, biological, and agronomic processes to support the interpretation of soil health measurements and provides a basis for future empirical validation.