Soil metagenomics of soybean double-cropped with wheat

Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops. The soybean cyst nematode (SCN) (Heterodera glycines I.) is widely distributed across all soybean production areas of the US, being the major soybean yield-limiting factor, especially in the Midwestern US. Double cropping cropped soybean is commonly planted following winter wheat. We previously reported double-cropping soybean fields with reduced SCN counts compared to fallow at both R1 stage (beginning of flowering) (-31.8%) and after soybean harvest (-32.7%). Literature suggests that enriched microbial communities could be correlated with the suppression of SCN in fields previously planted with wheat. To test this hypothesis, three field locations with noted SCN suppression were selected for a metagenomics study. Ten subplots were selected (5 wheat and 5 fallow) from each location. A total of 90 soil samples were selected: 3 fields x 2 treatments x 3 timepoints x 5 replications. Three DNA markers targeted distinct microbial groups: bacteria (16S V4-V5), fungi (ITS2), and Fusarium (ttef1 ). Amplicons were sequenced using an Illumina MiSeq platform (300+300 bp paired-end). Sequencing datasets were processed in R using the DADA2 pipeline.