Cover crop carryover effects on fungal and bacterial communities in field soil and residue

Cover crops have a significant impact on their associated soil microbial community. The long term impacts of certain cover crops on the soil fungal and bacterial communities and how this affects root disease in subsequent crops is currently of great interest. Metagenomics sequencing technology is a robust and high throughput method for identifying majority of the microorganisms present in a community by amplifying and sequencing the DNA from environmental samples. In this project, amplicon sequencing was used to study fungal and bacterial communities in different cover crop treatments and their relationship with root disease in barley and soybean planted in the subsequent year. Root disease was assessed by destructively sampling the barley and soybean. DNA was extracted from field soil and residue during the cover crop growing season as well as in the subsequent year, and the associated fungal and bacterial communities were analyzed by sequencing the internal transcribed spacer region (ITS1), and the full length 16S ribosomal RNA gene, respectively. Amplicon sequencing found that certain cover crop treatments had an influence on the alpha and beta diversity of fungal and bacterial communities. Various beneficial and pathogenic microorganisms, including potential causal agents of root disease were differentially abundant in the cover crop treatments. The observed root disease was likely caused by Fusarium spp., in both barley and soybean, and was significantly different by cover crop treatment.