Effects of cover cropping on beneficial and pathogenic microbial communities present in agricultural field soil and residue


Aiyer, H., Caldwell, C., & Foster, A. (March 5-6, 2021). Effects of cover cropping on beneficial and pathogenic microbial communities present in agricultural field soil and residue. Presented at the 2021 Plant Science Graduate Students’ Symposium (University of Saskatchewan).

Plain language summary

Harini Balasundaram (now Harini Aiyer) will give a presentation on her research for project J-001776 on two field research trials that were run from 2018 until 2021. These trials looked at the effects of cover crops on the soil microbiome in the first year and disease in barley and soybean in the following year. Much of this presentation is a focus on the details for the trial methods, a summary of disease and microbiome results and disease rating results. This presentation focuses on many of the details of Harini's MSc thesis that she will defend in summer 2021.


Fungal and bacterial communities in agricultural soil are significantly affected by the associated crops. Recent studies have focused on long term impact of cover crops on soil microbial communities and their potential influence on root disease. Amplicon sequencing can be used to identify the majority of the microorganisms present in environmental samples, and is more sensitive when compared to traditional methods. The main objective in this project was to use amplicon sequencing to study the changes in soil and residue microbial communities in different cover crop treatments during the growing season as well as in the subsequent year. Soil and residue samples were collected from 12 cover crop treatments in field trials set up in a randomized complete block design in Harrington, PE. Barley and soybean planted in each half of the cover crop plots in the subsequent year were destructively sampled to study root disease. Root disease, caused by Fusarium spp., was significantly different based on cover crop treatment for both barley and soybean. DNA extracted from the field samples served as the template for amplicon sequencing. The full length 16S ribosomal RNA gene and the internal transcribed spacer 1 region were used to study bacterial and fungal communities, respectively. Amplicon sequencing identified various beneficial organisms, such as arbuscular mycorrhizal fungi, and fungal and bacterial biocontrol agents, to be differentially abundant in the cover crop treatments. Pathogens amplicons were also common, including suspected causal agents of observed root disease: Fusarium oxysporum, F. sporotrichioides and F. graminearum. Preliminary results show that crops planted in the previous year have a significant impact on soil microbial communities. This may play an important role in root disease development in subsequent crops.

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