Endophytic and Diazotrophic Bacterial Diversity in Pisum sativum Root Nodules Across Southwest China’s Rocky Desertification Gradients

Background: The adaptability of leguminous plant–rhizobia symbionts enables enhanced plant stress tolerance in environmentally stressed areas. However, how rock desertification (RD) severity affects the endophytic and nitrogen-fixing bacterial communities in Pisum sativum root nodules remains unclear. Methods: We systematically surveyed the microbial communities of P. sativum nodules across a gradient of four RD areas. We sequenced 16S rRNA and nifH amplicons, determined soil physicochemical properties, and performed bioinformatic analyses to relate nodule microbiome diversity to soil variables. Results: The dominant endophytic genera across all sites were Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium and Pseudomonas, with Rhizobium identified as the primary nitrogen-fixing taxon. Soil pH and total phosphorus (TP) showed significant correlations with the overall endophytic bacterial community, whereas total nitrogen (TN), TP, and soil water content (SWC) were associated with nitrogen-fixing taxa. Notably, P. sativum nodules from areas of slight rocky desertification (SRD) harbored higher endophytic bacterial diversity and enhanced carbohydrate metabolism compared to those from moderately rocky desertified (MRD) sites. Conclusions: This study sheds light on how bacterial communities within legume root nodules respond to RD stress, deepening our understanding of plant–microbe co-adaptation and informing microbial-assisted restoration strategies in karst desertification areas.