Exploring Multifunctional Microbial Genes From the Rhizosphere of Allium ampeloprasum Under Different Fertilization Systems

ABSTRACT The diversity and environmental degradation caused by overreliance on chemical fertilizers in crop production have facilitated the development of alternatives to ensure agricultural sustainability. Previous studies have examined how fertilization affects functional genes in microorganisms in the root zones of cereals and legumes. However, the impact of fertilization on the functional genes of the vegetable rhizosphere remains underexplored. Therefore, this study aimed to identify the multifunctional genes associated with the A. ampeloprasum rhizosphere that are influenced by chemical fertilizers and biofertilizers. We extracted whole DNA from the soil samples of the A. ampeloprasum rhizosphere amended with chemical fertilizers and a biofertilizer. The mined DNA samples were analyzed through shotgun metagenomics sequencing to obtain functional genes of agricultural importance. Our findings revealed taxonomic groups with 43 functional genes with plant growth‐promoting traits associated with fixing atmospheric nitrogen, solubilizing phosphate, producing phytohormones, and others. A greater prevalence of these genes was observed in the plot treated with biofertilizer (G2), with 22 genes compared with 11 genes found within the plot treated with synthetic fertilizer (G1) and 10 genes in the bulk soil plot (G3). Our microbiome analysis at the class taxonomic level revealed the prevalence of Actinomycetes, Alphaproteobacteria, and Acidimicrobiia. Our α diversity analysis results demonstrated that, compared with G1 and G3, G2 presented greater within‐sample functional gene diversity. Compared with those of the other samples, β diversity analyses revealed partial differences in the microbial functional gene composition in the biofertilizer‐treated soil (G2). These results indicate that biofertilizer application maintains a stable, functionally diverse microbial gene pool associated with stress tolerance, nutrient solubilization, and nutrient cycling, thereby supporting sustainable agriculture. This, however, highlights the potential of biofertilizers as sustainable soil amendments that can preserve microbial functional diversity without disrupting community diversity.