Water DNA Tests: Pros, Cons and Interpreting Results

This post was written by S. Jandricic and A. Wylie.

Overhead boom irrigation

This is the fourth article in a series about water sanitation. The goal of this series is to get you reflecting on your own irrigation system before you are faced with a problem.  The first post covered where problems are likely to occur in your greenhouse ; the 2nd covered the types of pathogens found in water and the 3rd covered where and how to sample your water.

Once you’ve got your water sample, this post will cover why water DNA tests are useful, and how to interpret the results. This is the next step towards identifying and then treating your water issues to prevent unnecessary fungal or bacterial disease in your greenhouse crops, and potentially save you thousands of dollars in crop losses or fungicide applications.

These posts make good refresher resources, so make sure to bookmark them!

Why Should I Get a DNA Test on My Water?

Sampling from all points along your water system – from your pond to your misting lines – can help narrow down sources of contamination in your greenhouse using DNA tests.

if you’re testing your water, it’s likely because you either a) have an undiagnosed disease problem in your greenhouse already, or b) you want to head off any issues that could be caused from your cistern, roof water, or water lines. Even with disease symptoms present, It can be REALLY difficult to nail down which pathogen is the culprit (and which fungicide will work), without a DNA test.

Overall, DNA tests are the gold standard, for many reasons:

  • DNA doesn’t lie. It’s surprising how much symptoms from one disease look like another sometimes; even an expert with years of experience can make a mistake when it comes to diagnostics from just signs and symptoms. Especially diseases that cause root rots. With DNA tests, you can be sure.
  • They can screen for multiple pathogens. One of the DNA tests available, the DNA multiscan®, does just that – scan for multiple pests at one time. This test can point towards a disease issue you might not have even considered. You can choose to look specifically for fungi or bacteria or both.
  • Multiple samples can determine WHERE a problem is coming from. If you take samples from multiple points along your water system, and disease issues are only detected in one area (e.g. a secondary holding tank), or are especially high in one area, this can narrow down the source of the problem (see our Case Study, below, for an example!). This can potentially save you thousands of dollars in crop losses and unnecessary fungicide application by eliminating recurring disease issues at the source.

Interpreting Results:

Despite the benefits of DNA analyses, as with any tool, they aren’t perfect. They require some know-how (or asking experts) to provide correct interpretation of results. You still need to be an investigator of sorts, and use your DNA results, PLUS other pieces of information, to come to the right conclusions.

An example of the output from a DNA multiscan test. It’s often useful to run the results of your DNA lab tests past a disease expert, as some fungal species have beneficial strains, and “high” loads of a certain pathogen don’t always mean it’s the main culprit.

Here are some things to keep in mind when interpreting a DNA test, including DNA multiscan® results:

  1. Look for specific pathogenic species on the results output. For example, positive test results for “Fusarium” on DNA results – without indicating an actual species – are likely false leads, since there can be beneficial or non-disease causing species of Fusarium. You want to look for specific species known to cause disease, e.g. Fusarium oxysporumPositive DNA tests results for an actual pathogenic species from your water and/or a diseased plant, paired with matching disease descriptions of symptoms in your crop (from an accredited source), together, strongly suggest a specific culprit.
  2. Be cautious of “low” versus “high” pathogen loads on DNA Multiscan results. Although it can be tempting to go down a the list of positive results on a DNA scan and assume that the results that came back at the highest levels are the true culprit, it doesn’t always works this way. Some pathogens are often present at low levels (like Pythium) without causing disease, and other pathogens cause significant disease at very low pathogen loads. For example, whenever I see a positive result for Thelaviopsis (black root root) – high or low – from a plant or water sample in a greenhouse that grows susceptible crops, I immediately tell the grower to put on a preventative fungicide application. Black root root produces resting spores that are hard to kill and are easily spread, and can cause infection at even low levels.
  3. Be aware that DNA analyses CAN’T tell you if pathogen is alive or dead. They just pick up DNA fragments (sort of like crime-scene tests). So you may need more than just a DNA tests to go on (more on this below).
  4. Understand that DNA tests CAN’T directly tell you if your treatment is working or not, because of point #3, above.  Testing your water BEFORE and AFTER water treatment may show differences in pathogen loads, but without knowing if the pathogens survived the water treatment, that’s not much use. 
  5. Know that DNA analyses CAN be paired with more specific tests to help determine water treatment efficacy. For example, if you run a DNA multiscan on your water, and multiple pathogenic species come back positive on the test, you may want to ask the lab to try to “plate” or grow suspected pathogens pre/post water treatment on specific media.  Plating makes sure a specific pathogen found in your recirculating water is actually alive, and has the potential to cause issues.

Case Study: DNA multiscan® to the Rescue

One of the most powerful aspects of DNA analysis is to help you determine what you ACTUALLY have, versus what you THINK YOU HAVE.

For example, a greenhouse in Ontario had a yearly problem with a certain percentage of their poinsettia crop wiling and dying starting in mid September. Because poinsettia commonly are susceptible to Pythium aphanidermatum and Pythium ultimum, the growers naturally assumed assumed this was the problem. They applied the appropriate chemicals. When this didn’t fix the problem after several seasons, the growers thought they might have a fungicide-resistant Pythium strain.

To be sure WHAT we were facing, we had multiple symptomatic plants tested individually across the entire crop, to give us a good sample size to make conclusions from.

Root rot diseases caused by different pathogens are notoriously hard to distinguish from each other based on symptoms alone. When dealing with a plant that’s yellowing and wilting, its always a good idea to get a DNA multiscan test done to positively identify the cause.

Surprisingly, the DNA multiscan® results yielded that ONLY Fusarium was present in all 12 samples. Fusarium oxysporum in poinsettia is rare, but not unheard of (and actually is affecting poinsettias more and more). The test showed NO evidence of more common pathogens in poinsettia, like Pythium or Phytophthera, and follow up trials with Fusarium-appropriate fungicides showed results. (This last step was important for identifying Fusarium as the causative agent, as there are some strains of Fusarium oxysporum that are actually be beneficial).

Although this testing was expensive ($250 per sample, 12 samples), it ultimately saved them thousands of dollars over the years since in crop losses and unnecessary applications of the wrong fungicides.

Further, this greenhouse was then able to use DNA multiscan ® of their water to determine WHERE the Fusarium inoculum was coming from.  After testing all areas, we ultimately found the potting line that used recirculating water was the culprit, as the water was sometimes re-used between crops that had different susceptibility to Fusarium. After fixing this sanitation issue, they’ve never spent another cent on fungicides in their poinsettia crop!

Where to Get a DNA Multiscan® and Other DNA Analyses:

The following labs in Ontario can provide DNA results for water samples:

A & L Canada Laboratories Inc.

Greenhouse Analytical Services | SGS Canada

SGS Canada Inc.

The University of Guelph’s Agriculture and Food Laboratory

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