Microbiology Combined with the Root Metabolome Reveals the Responses of Root Microorganisms to Maize Cultivars under Different Forms of Nitrogen Supply

Plant–microbe interactions are key to nutrient-use efficiency. Root microbes are influenced by rhizosphere soil and plant cultivars. The impact of cultivar-by-nitrogen (N) interactions on the maize-root microbiome remains unclear, yet it is crucial for understanding N use efficiency in maize. This study evaluated the effects of maize cultivars and N forms, along with their interactions, on the diversity and composition of root bacteria and fungi. Additionally, we examined correlations between soil microbes and root metabolites. The maize cultivar Zhengdan 958 (ZD958) showed a positive response to the mixture of nitrate and ammonium N, resulting in increased in biomass, grain yield, shoot N content, grain N content, and root area. In contrast, the cultivar Denghai605 (DH605) did not exhibit a similar response. The diversity and composition of root bacteria and fungi differed between ZD958 and DH605. The N form primarily affected the community structure of rhizospheric fungi in ZD958 and rhizospheric bacteria in DH605, rather than endophytic microbes. A mixed N supply increased the relative abundance of Basidiomycota, which was positively correlated with ZD958 yield. For DH605, a mixed N treatment enhanced nitrification functions involving Bacteroidetes and Proteobacteria, while it reduced the effects of ammonium N supply. The dominant rhizospheric microbes in DH605 showed a stronger response to changes in root metabolites compared to those in ZD958. A mixed N supply increased the content of palmitoleic acid in ZD958 root exudates, facilitating the recruitment of beneficial rhizospheric microbes, which promotes maize growth. In DH605, a mixed N supply decreased the concentration of sphinganine, which is significantly correlated with Acidobacteria (negatively), Proteobacteria (negatively), Bacteroidetes (positively), and TM7 (positively). Our findings suggest that different maize cultivars respond differently to N forms, causing distinct rhizospheric microbial effects, and that root metabolites send metabolic signals to regulate and recruit key bacterial and fungal communities.