Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines

Despite the crucial role of microbial communities in agroecosystem functioning, a clear picture of how nitrogen shapes rhizosphere microbial complexity and community structure across diverse maize lines remains elusive. To address this gap, we conducted 16S amplicon sequencing of the rhizosphere microbial communities across a diverse range of maize inbred lines (305 genotypes) and their F1 hybrids (196 genotypes) cultivated in both low-nitrogen (unfertilized) and high-nitrogen (fertilized) soils. Our findings reveal that N fertilizer treatment had contrasting effects on the rhizosphere microbial communities of inbreds and hybrids. N fertilization increased alpha diversity but decreased the abundance of Pseudomonas taxa in inbred lines, while the opposite was true for hybrids. The proportion of variance determined by plant host factors was also better explained under low-N, demonstrating that N fertilization reduced the influence of the host over the rhizosphere microbial community. Microbial networks revealed significant differences in the number of nodes and clustering coefficients between the rhizosphere microbial communities of inbred and hybrid maize, with these differences being further differentiated by changes in nitrogen levels. Overall, our study reveals the interplay among rhizosphere microbiomes, abiotic stress induced by low soil nitrogen, and plant host factors facilitating the identification of stable microbial communities in response to environmental stress. These findings contribute to the potential engineering of resilient microbial consortia highlighting the importance of the influence of plant genotype and the environment on the rhizosphere microbiome.