The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula

Compared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of <i>C. pilosula</i> by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of <i>C. pilosula</i>. There was a stronger interaction and stability of soil microbial networks after BOF treatments. <i>Microlunatus</i>, <i>Rubrobacter</i>, <i>Luteitalea</i>, <i>Nakamurella</i>, and <i>Pedomicrobium</i> were identified as effector bacteria, which were related to disease prevention and yield and quality increase of <i>C. pilosula</i>. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of <i>C. pilosula</i> in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of <i>C. pilosula</i> by changing the structure and function of the rhizosphere bacterial community.