Separated for too long: plant nutrition as the functional interface linking the plant-soil microbiome to plant performance

ABSTRACT: One of the central challenges in contemporary agriculture is to sustain productivity with reduced inputs while improving crop nutritional quality. In this context, reconnecting plant nutrition with the plant-soil microbiome represents a critical and timely opportunity. Despite increasing recognition of the microbiome's pivotal role in plant nutrition, this relationship is often conceptualized within fragmented, domain-specific frameworks rather than as a fully integrated system. Here, we argue that plant nutrition provides a robust, quantitative framework to reposition the microbiome within agronomy by linking microbial processes to measurable outcomes such as nutrient uptake, nutrient use efficiency, crop quality, and plant responses to environmental stress. We propose that nutrient acquisition should not be viewed as a purely physicochemical process, but as a biologically mediated outcome emerging from interactions among plants, microorganisms, and their environment, particularly in the rhizosphere. Evidence from isotopic, physiological, and ecological studies indicates that microbiome contributions to plant nutrition are measurable but strongly context-dependent, helping to explain their variability under field conditions and the limitations of simplified inoculant approaches. Finally, we advocate for integrative frameworks that explicitly connect microbial ecology, plant physiology, and nutrient dynamics across scales.