Beyond Nitrogen Fixation: Multifunctional Roles of Common Bean in Organic Agroecosystems and Ecosystem-Oriented Breeding Strategies

Common bean (Phaseolus vulgaris L.) is among the world’s most widely consumed grain legumes and a foundational species for organic and low-input agriculture, yet its agroecological value extends far beyond nitrogen fixation and nutritional provisioning. This review reframes P. vulgaris as a breeding target defined by ecosystem function rather than by yield alone, synthesizing evidence on functional biology, biological nitrogen fixation, rhizosphere microbiome assembly and soil ecosystem engineering to identify the trait complexes that ecosystem-oriented breeding programs must select for. We examine the constraints limiting expression of these traits under organic management, including weed competition, biotic and abiotic stress, nutrient limitation, and the scarcity of cultivars and certified seed adapted to low-input environments, and evaluate the agroecological management practices, resource-use efficiency metrics and emerging technologies—spanning precision agriculture, phenomics, molecular breeding, genome editing and microbiome engineering—that can accelerate their genetic improvement. Central to this synthesis is a paradigm shift in breeding objectives: common bean is conceptualized as a holobiont whose performance emerges from coordinated plant–microbiome interaction, requiring breeding programs to select explicitly for nitrogen-fixation efficiency, root system architecture, rhizosphere recruitment capacity, nutrient-use efficiency and multi-stress resilience as heritable, ecosystem-oriented traits. We conclude by outlining priority breeding research directions integrating genomics, phenomics, envirotyping and rhizosphere ecology, positioning common bean breeding as a strategic lever for the transition toward regenerative, climate-smart organic agriculture.