SRP500629 PRJNA1098361 Differences in endophytic bacteria within peanut pods under different planting modes Peanut continuous cropping severely limits the improvement of both yield and quality. Crop rotation is thought to be a powerful solution to address this issue. However, there is currently limited research on how specific rotation methods affect peanut yield and how they influence the colonization of endophytic bacteria within pods. Based on five years of continuous cropping trial data, three different cropping systems (WF, annual summer peanut and winter fallow; GM, annual summer peanut and winter ryegrass; CR, summer peanut rotated with maize and winter wheat) were employed in this study to systematically analyze and evaluate the effectiveness of crop rotation in mitigating peanut continuous cropping obstacles and its underlying mechanisms. Through comparative analysis of peanut yield, peanut quality, and changes in endophytic bacterial communities during different developmental stages of peanut pods under different treatments, the results demonstrated that CR significantly increased peanut pod yield by 33% compared to WF. In terms of peanut kernel nitrogen content, the CR treatment increased it by 6.8%, and the GM treatment increased it by 1.4%. LEfSe and LDA analyses revealed that compared to WF, CR increased the colonization of beneficial bacteria such as c_Actinobacteria, p_Actinobacteriota, and o_Corynebacteriales within the pods during the developmental and maturity stages while reducing the colonization of potential pathogenic bacteria such as c_Gammaproteobacteria and o_Burkholderiales. Appropriate crop rotation practices can effectively enhance peanut yield and quality, improve soil environmental quality, and promote the colonization of beneficial endophytic bacteria within pods.