Changes in the diversity and predicted functional composition of the bulk and rhizosphere soil bacterial microbiomes of tomato and common bean after inorganic N-fertilization

Abstract

Although previous studies have shown that nitrogen (N) fertilization may negatively affect bacterial diversity in bulk soil, information regarding N impacts on the microbial structure and function of both the bulk and rhizosphere soil bacterial microbiome (bacteriome) is less abundant. In this study, tomato and common bean plants, two globally important vegetable crops, were grown in soils fertilized with urea, ammonium, or nitrate for four consecutive fruit harvests. 16S rRNA gene amplicon sequencing and 16S rRNA gene-predicted functional analyses were performed on bulk and rhizosphere soil samples. Correlation analyses were used to examine the links between changes in the composition, structure, and predicted functionality of the bulk and rhizosphere soil bacteriome with variations in soil properties. All of the tested N-fertilizers decreased the bacterial richness and altered community composition and predicted functionality of the bulk and rhizosphere soil bacteriome of both plants. The magnitude of these effects was dependent on the soil component (bulk and rhizosphere) and type of N-fertilizer and was controlled by the N and C soil content. For both plants, decreases in bacterial diversity due to N-fertilizers were more pronounced in the rhizosphere than in bulk soils and higher in the fourth than first harvest. These results suggest that the recruitment of bacteria by plants is affected by N-fertilization. The present findings should facilitate expanded studies to identify soil-plant-microbiome interactions in N-treated soils with potential consequences for plant growth in agricultural systems.