Nitrogen fixation, crop production and bacterial communities of common bean cultivars: a 77-year breeding perspective

Abstract Background and aims Common bean ( Phaseolus vulgaris L.) is an important food legume which contributes to sustainable agriculture by fixing atmospheric nitrogen (N). However, modern breeding programs have mostly focused on improving crop yield and agronomic traits, ignoring the crop’s capacity for effective symbiotic nitrogen fixation and interactions with microbial communities. We sought to investigate how genotype, soil N availability, and environmental conditions, affect plant growth, N fixation, and the composition of root-associated bacterial communities of 16 bean cultivars released over 77 years of breeding history. Methods Crop growth parameters of 14 pintos, 1 pink, and a non-nodulating navy bean R99 were evaluated in field trials conducted over two growing seasons under differing N soil fertility. The soil and root microbiomes associated with these cultivars were analyzed using 16S rRNA amplicon sequencing. Results The results revealed significant year-to-year differences in crop yield and SNF. While nodulation rates were consistent, N fixation efficiency declined under high soil N conditions. Cultivar-specific differences in microbiome composition were observed under N-limited conditions, with several taxa strongly associated with individual genotypes. Notably, modern cultivars showed reduced SNF, which was also more prominent under low N availability, suggesting potential trade-offs associated with breeding for high-input systems. The line R99 exhibited a distinct microbial profile and reduced Rhizobium abundance, indicating a complex genotype–microbiome interaction. Conclusion These findings highlight the importance of both genotype and soil environment on bean performance and microbiome structure and underscore the need for breeding strategies aimed at improving N-use efficiency in bean production.