The influence of management strategy on plant organ microbiomes in a corn-soybean-wheat rotation

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Michigan State University’s Kellogg Biological Station Long Term Ecological Research site harbors a set of plots in a three year wheat-maize-soybean rotation, providing an ideal location to conduct long-term characterization of these economically important row crops. The site has been maintained since 1989 with six replicate hectare plots for each of four management styles: conventional, no till, reduced inputs, and organic. Plants were sampled from three years of one rotation cycle. We analyzed the fungal and bacterial communities of leaves, stems, and roots throughout the growing season using fungal ITS2 and bacterial 16S rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all management styles for each crop. We identified core OTUs for each crop, and used network analysis to identify microbial hub taxa. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and that management strategy was less influential on community composition.