Functional Stability of the Common Bean (Phaseolus vulgaris L.) Nodule Microbiome in Semi-Arid Regions

Common bean (Phaseolus vulgaris L.) is a strategic crop whose sustainable production depends on symbiosis with nitrogen-fixing bacteria. However, the composition and functional potential of the nodule microbiome in varieties adapted to semi-arid regions, such as northern Mexico, remain poorly documented. Therefore, this study evaluated the influence of host genotype on nodule-associated bacterial communities in three improved varieties (Pinto Bravo, NOD1, and Jamapa) under conventional management, using high-throughput sequencing of the V3–V4 regions of the 16S rRNA gene. Alpha and beta diversity analyses showed no significant differences among varieties, indicating a similar nodular microbiome regardless of genotype. At the phylum level, Proteobacteria and Bacteroidota predominated, suggesting a conserved microbial core. At the genus level, Rhizobium was the most abundant taxon, while non-rhizobial genera such as Acinetobacter and the JC017 lineage were also detected. Functional prediction using PICRUSt2 revealed conserved metabolic profiles, with dominant pathways associated with amino acid biosynthesis, carbon metabolism, aerobic respiration, and fatty acid biosynthesis, indicating metabolic redundancy linked to tolerance to osmotic, thermal, and oxidative stress. The results suggest that under semi-arid conditions, the symbiotic interaction is governed by mechanisms at the host species level (P. vulgaris), which ensure the recruitment of a functional core microbiome, whereas intraspecific variation among improved varieties may influence the recruitment of specific accessory taxa.