Rhizosphere bacteriome of Allium cepa after the application of chemical and endophyte-based fertilizer

The microbial community plays an important role in A. cepa productivity and soil fertility. In this study, we applied chemical (A2) and endophyte-based fertilizer (B) to A. cepa; where the use of B successfully improved productivity by the number of tubers and chlorophyll content compared to control (A1) and A2. We aimed to investigate how those fertilizers manipulate the rhizosphere bacterial community in A. cepa. The 16S-metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The application of A2 and B potentially enhanced the abundance of rhizosphere bacteria compared to the A1, possibly due to the increase in nutrient availability. Beta-diversity analysis showed that the B fertilizer did not highly change the bacterial community of indigenous rhizosphere bacteria, whereas the A2 fertilizer did. The endophytes themselves did not also greatly affect the original rhizosphere bacteria because they may enter the plant tissue and release the metabolites inside the plant host. The NGS data showed that the genus Aquicella was the most abundant in the rhizosphere treated with B and A1. Aquicella was discovered to boost plant resilience to contaminants by enhancing plant nutrition availability and encouraging plant root growth. Interestingly, Acidobacteria and Gemmatimonadetes decreased their population in the treatments of A2 or B. Overall, the use of B has a higher impact on plant productivity and soil properties without highly changing the composition of the bacterial community in the rhizosphere. Yet our metagenomic data support the hypothesis of phylogenetical conservation of bacterial communities concerning particular ecological conditions.