European Journal of Sustainable Agroecosystems

Background: Legume-based cropping systems underpin biological nitrogen fixation and phosphorus mobilisation, yet the metabolic dialogue occurring in the rhizosphere that governs these processes remains incompletely understood at a mechanistic level. Rhizosphere metabolomics, the untargeted and targeted profiling of small molecules exuded by roots and transformed by associated microbiota, has emerged as a powerful lens for dissecting how legumes recruit beneficial microorganisms and regulate nutrient cycling efficiency (NCE).

Objective: This review synthesises peer-reviewed evidence published mainly between 2015 and 2026 on rhizosphere metabolomics in legume systems, with the specific aim of mapping how root-exuded metabolites mediate symbiotic nitrogen fixation, phosphorus solubilisation, and interspecific nutrient exchange in legume-cereal intercropping, and of identifying methodological and conceptual research gaps.

Sources of literature: A structured search was conducted across Scopus, Web of Science, PubMed, and supplementary grey literature (FAO and international agricultural research reports), yielding 118 studies retained for qualitative thematic synthesis after a PRISMA-style screening process.

Major findings: Flavonoid and isoflavonoid exudation reproducibly triggers rhizobial nodulation gene expression and host-specific Nod-factor signalling; organic acids (citric, malic, oxalic, gluconic) and phosphatase-active bacterial taxa jointly govern rhizosphere phosphorus solubilisation; and arbuscular mycorrhizal fungi (AMF) mediate reciprocal nitrogen-phosphorus-carbon exchange in legume-cereal intercropping, with carboxylate exudation acting as a key regulatory node. Reviewed evidence consistently shows that legume rhizodeposition reshapes microbiome assembly toward nutrient-cycling-competent keystone taxa, although the direction and magnitude of these effects are highly species-, soil-, and context-dependent.

Research gaps: Persistent limitations include a scarcity of field-scale validation relative to pot-based studies, lack of standardised metabolomics protocols across laboratories, limited attention to underutilised legume species, and immature frameworks for integrating metabolomic, metagenomic, and metaproteomic data streams.

Conclusion: Rhizosphere metabolomics offers a mechanistic bridge between plant physiology, microbial ecology, and agronomic nutrient-use efficiency in legume systems. Realising its translational potential for sustainable intensification will require standardised multi-omics pipelines, field-representative experimental designs, and closer integration with policy frameworks promoting biological nitrogen fixation as an alternative to synthetic fertiliser inputs.