Laboratories in Ontario offer a range of DNA-based pathogen tests designed to identify issues in soil or other substrates. Some tests that they offer can identify a range of general pathogens in one test, while other tests can identify pathogens specific to certain crops. Because these tests can be expensive, it is important to understand the benefits and limitations of different tests.
Recently I submitted a soil sample from an area of a ginseng field that was completely destroyed by Cylindrocarpon root rot, which is caused by the fungus Cylindrocarpon destructans, and a separate sample from a healthy area of the garden nearby. The cause of the rot in the diseased area of the field was confirmed to be Cylindrocarpon destructans by plating at the University of Guelph – Simcoe Research Station. Samples were submitted for a DNA test that identifies multiple pathogens at once. Researchers at AAFC and in other countries had identified a ginseng-specific special form of Cylindrocarpon destructans in ginseng called Cylindrocarpon destructans f.sp. panacis, and the soil sample was also submitted for a PCR test (also DNA-based) that can identify this specific strain.
In both soil samples, the DNA test that identifies multiple pathogens showed no Cylindrocarpon destructans in the soil, despite the obvious presence of disease on every remaining root in the diseased portion of the field. On the other hand, the PCR test identified Cylindrocarpon destructans f.sp. panacis in both samples. It is not surprising that the PCR test would identify Cylindrocarpon in both the diseased and healthy area of the field because the tests are very sensitive and can detect even minute levels of a pathogen. The pathogen could easily have been moved to the healthy area of the garden by machinery or field workers but not at a level that caused visible disease symptoms. However, it is surprising that a broad-based DNA test did not identify the pathogen, even in a field completely destroyed by the fungus. This means that broad-based DNA tests established for a range of pathogens across many different crops may not identify the Cylindrocarpon strain that attacks ginseng, even if the species is listed as one the test can identify.
Does this mean that the broad-based tests do not work for ginseng? No. First of all, this is only one test and more research is required. Second, for some species like Phytophthora cactorum (the cause of Phytophthora root rot in ginseng) or Rhizoctonia solani (the cause of Rhizoctonia rot in ginseng), no ginseng-specific strains have been identified, and the tests can be very useful for identifying fields that are more at risk of developing disease or confirming their presence in a diseased area. However, growers need to understand the limitations of these tests. For some pathogens, specific tests may be required in addition to a broad-based test and it appears that Cylindrocarpon is one of those species. These tests will likely be improved over time and may be able to identify more crop-specific strains in the future.
It is also important to keep in mind that none of the available tests for soil pathogens so far can provide an accurate indication of the level of the pathogen in the soil. They just tell you if the pathogen is present or absent. There is no research that shows how much of a pathogen is required to cause economic damage to the ginseng crop on different soil types. However, even the presence of some species like Phytophthora cactorum in a field is a concern for ginseng.
Soil testing prior to site selection can be a useful tool for flagging issues in the soil, but growers need to talk to the laboratory to determine which tests are most appropriate for their specific needs. Once results come back it is a good idea to contact a crop specialist to help interpret the results. Some pathogens like Fusarium and Pythium are very common in the soil, and their presence in a soil test does not necessarily mean there will be a disease issue in that field.