Diverse crop rotations influence the bacterial and fungal communities in root, rhizosphere and soil and impact soil microbial processes

Diverse crop rotations can improve crop productivity but impacts on the interaction of soil nutrient cycling and the soil and root-associated microbiomes are not well understood. Here, we analysed 16S rRNA and ITS DNA amplicons of soil, rhizosphere and roots from two Canadian long-term field experiments, wheat grown in Saskatchewan and corn grown Ontario. Together with soil biogeochemical analysis, we determined that long-term diverse rotations and cereal monocropping affected the composition of soil organic matter, nutrient cycling and selected bacterial and fungal microbiomes. Differential abundance analysis identified 27 bacterial amplicon sequence variants that were more abundant in the soil and rhizosphere of monocropped corn that were classified as Ktedonobacteria and Actinomycetales. Both wheat and corn samples showed significant variation in the abundance of several saprophytic Sordariomycetes. Monocropping increased lignin by 56% in corn and 25% in wheat, demonstrating shifts in soil organic matter composition in the two systems, although no differences in amino sugars were observed. Depending on sample type, soil total lignin and phosphatase enzyme activity were correlated (p < 0.05) with variation in bacterial and fungal community composition along with available N in corn and β-glucosidase in wheat. Our results indicate that over the long-term, reduced cropping diversity altered soil nutrient cycling and soil, rhizosphere and root microbiomes corresponding with reduced yields in the monocropped corn and wheat systems.