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Thesis Format



Master of Science




Thorn, R. Greg


American ginseng (Panax quinquefolius L.) is a perennial herbaceous plant cultivated for its medicinal properties. Growers report that when ginseng is replanted in a field previously used to cultivate ginseng, it soon succumbs to disease, known as ginseng replant disease. I examined changes in composition in the ginseng mycobiome throughout cultivation in a newly planted garden and beyond (i.e., 3–14 years post-harvest) with a third-generation metabarcoding approach (Pacific Biosciences, single-molecule real-time sequencing). Amplicons of about 600 nucleotides from the nuclear ribosomal internal transcribed spacer (ITS) region and translation elongation factor 1-α gene were chosen to help discriminate between closely related fungal species. The ITS data showed community variations in fungal plant pathogens Fusarium oxysporum and F. solani over cultivation, and traces of Ilyonectria mors-panacis in ginseng garden soil. The mycobiome data generated provides insight into the dynamics of ginseng garden soil during ginseng cultivation and beyond.

Summary for Lay Audience

American ginseng is a perennial plant farmed in regions of Southern Ontario, Canada. For several thousand years, ginseng has been used in traditional Chinese and Indigenous medicine for its health benefits. Because of high demand, wild ginseng was over-harvested, resulting in it becoming endangered. To meet global market, ginseng was developed as a commercial crop. However, growers soon noticed that replanting the crop in a field where it had been grown before led to root rot. This disease syndrome was given the name ginseng replant disease (GRD). GRD became a challenge for the North American ginseng industry as the condition can persist for decades after the first ginseng harvest. Suitable land to grow new ginseng crops has become limited and new sites come with unknown crop histories. The exact cause of GRD is unclear but has been attributed to harmful soil bacteria or fungi. The type and number of harmful fungi can influence plant health by causing disease. Previous researchers who investigated American ginseng have found that a variety of harmful fungi became more abundant after a second planting of ginseng. I studied the fungal communities of ginseng garden soil throughout cultivation, from the newly planted garden to harvest year and beyond (i.e., 3–14 years post-harvest). I chose sequencing targets that provide more resolution to identify closely related fungal species in soil. Of these species, many were harmful fungi that increased in abundance years after harvesting of ginseng. However, as these increased, so did some beneficial fungi that may help protect the plant from disease. I also found that variations in species abundance was able to separate the soil fungal communities of a replant garden (i.e., second planting of ginseng) and former ginseng garden (i.e., garden stage between harvest and a second planting of ginseng) from a newly planted garden at its harvest year, that could be used to develop a diagnostic test for soils prone to GRD. However, more testing should be completed to include bacterial abundance and soil chemistry throughout ginseng garden soil and beyond harvest.

R_Rajsp_OTU_Table.pdf (1256 kB)
Table D4: List of Fungal OTUs.