Agricultural management affects root-associated microbiome recruitment over maize development

Abstract

Diversified cropping systems provide yield benefits that may result from enhanced nutrient availability via the root microbiome. We hypothesized that root-associated microbial communities in diversified and conventional systems would differ most during high plant nitrogen demand, reflecting microbiome-derived benefits, and that these effects would be greatest nearest the root. We compared maize bulk soil, rhizosphere, and rhizoplane prokaryotic and fungal communities in diversified and conventional systems at four plant developmental stages using amplicon sequencing. The greatest differences between systems in root-selected prokaryotic community composition occurred within the rhizoplane during vegetative stage 11 (high nitrogen demand). During this period, the rhizoplane of maize from the diversified, compared with the conventional, cropping system hosted higher abundances of bacteria implicated in complex organic matter decomposition (Verrucomicrobia and Acidobacteria). In contrast, fungal root-associated communities differed most between cropping systems during vegetative stage 4 (low nitrogen demand) and became more similar over time. Unexpectedly, prokaryotic rhizosphere communities, unlike rhizoplane communities, did not always differentiate from bulk soil communities, indicating value in differentiating between root compartments to understand root_microbiome_management interactions. For example, the diversified system rhizosphere and bulk soil prokaryotic communities were not well differentiated compared with the conventional system, indicating the possibility of a camouflage effect.