Crop rotation and fertilization shape the microbiomes of maize rhizosphere soil with distinct mechanisms

In agriculture, cropping and fertilization practices can significantly affect the soil microbial community, which in turn affects crop growth. Nevertheless, it remains uncertain how cropping and fertilization treatments influence the structure, function, and metabolic characteristics of microbial communities from bulk soil to rhizosphere soil. Here, a dual-factor experiment was carried out in the black soil of Northeast China, involving cropping (soybean—maize rotation and continuous maize cultivation) and fertilization (no fertilizer control, chemical fertilizer, and chemical fertilizer plus straw incorporation) treatments. After 10 years of experimentation, we collected the maize non-rhizosphere and rhizosphere soil and maize root samples, and conducted the quantification and amplicon sequencing of the 16S rRNA gene and ITS region, as well as metagenomic sequencing and metabolome analysis of soil samples. Our results revealed that fertilization exerts a greater influence than cropping practices on microbial community structures from soil to maize root by largely altering soil chemical properties, and on various metabolic genes and pathways. Crop rotation primarily mediated microbial community assembly by influencing specific functional groups. Compared to continuous cropping, crop rotation enriches beneficial bacteria, fungi and mycovirus, suppresses fungal pathogen abundance, and lowers fungal species diversity in the maize rhizosphere through balancing metabolites originating from a variety of plant and microbial sources. Crop rotation also imposes stronger homogeneous selections on the prokaryotic community than continuous cropping. In summary, cropping and fertilization treatments shape the maize root-microbiome relationships with distinct mechanisms.