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

Authors: Yurgel, Svetlana; Miklas, Phillip; Porter, Lyndon

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/25/2025
Publication Date: 2/21/2025
Citation: Yurgel, S., Miklas, P.N., Porter, L.D. 2025. Nitrogen fixation, crop production and bacterial communities of common bean cultivars: A 77-year breeding perspective. PhytoFrontiers. 1-17. https://doi.org/10.1007/s11104-025-08257-x.
DOI: https://doi.org/10.1007/s11104-025-08257-x

Interpretive Summary: Common beans are an important food crop that can naturally take nitrogen from the air and use it for growth, thanks to a partnership with helpful soil bacteria. This process, called nitrogen fixation, helps reduce the need for chemical fertilizers. However, most modern bean breeding has focused on increasing yield, not on how well the plants fix nitrogen or interact with soil microbes. In this study, we looked at 16 types of common beans developed between 1945 and 2022. We grew them over two years in fields with different levels of nitrogen in the soil. We measured plant growth, nitrogen fixation, and the types of bacteria living around the roots. We found that nitrogen fixation was lower when soil nitrogen was high, even though the number of root nodules stayed the same. Some newer bean types were less effective at fixing nitrogen, especially in low-nitrogen soil. Each bean type also had a unique set of root bacteria, showing that genetics play a role in shaping the plant’s microbiome. These results suggest that breeding programs should focus not only on yield but also on improving how beans work with soil bacteria and use nitrogen efficiently.

Technical Abstract: Background and aims Common bean (Phaseolus vulgaris L.) is an important food legume which contributes to sustainable agriculture by fixing atmospheric nitrogen (N) through symbiosis with rhizobia. However, modern breeding programs have mostly focused on improving crop yield and agronomic traits, ignoring the crop’s capacity for effective symbiotic nitrogen fixation (SNF) and interactions with soil 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 of16 common bean cultivars released over 77 years of breeding history (1945–2022). Methods Crop growth parameters of 14 pintos, 1 pink, and a non-nodulating navy bean R99 were evaluated in field trials conducted over two consecutive growing seasons under differing N soil fertility. Additionally, 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 as percent of seed N derived from the atmosphere (% NDFA). 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 bacterial amplicon sequence variants (ASVs) strongly associated with individual genotypes. Notably, modern showed reduced SNF, which was also more prominent under low N availability, suggesting potential trade-offs associated with breeding for high-input systems. The non-nodulating 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 common bean production.