Crop Diagnostics

 

The Diagnostic Process and Helping the Lab Help You

Prepared by Mardi Desjardins, MAFRI Crop Diagnostics Specialist (FPE)

The entire diagnostic process is based on finding the answer to one question, “What’s wrong with this plant?”. Answering this question happens through a process that involves the diagnostician going through a process of finding answers to a series of other questions. Whether there are problems with a crop, a tree or a garden, the diagnostic process will always be similar.
 

What happens when the sample arrives at the lab?

So just how does a diagnostician make a diagnosis? The key to making an accurate diagnosis is asking the right questions. Every diagnosis begins and ends by the diagnostician asking her/himself a series of questions and choosing the steps and procedures to follow in the attempt to find the answer to “What’s wrong with this plant?”. She/he will rely on information provided by the client, personal knowledge and experience, references appropriate for the situation and an assortment of lab procedures appropriate for the situation. Information provided by the client can affect the diagnostic process since missing or wrong pieces of information can result in the lab turning in the wrong direction during the diagnostic process.

1. The basic questions that most diagnosticians will use as they go through the thinking process are simple. Examples of the things the diagnostician will consider are:
       1. What is the crop or host?
       2. Is the crop/host being killed or just impaired in some way?
       3. Are many plants affected or just one or a few?
       4. Have I seen this before and if so, what are the possible causes?
       5. Can I determine the cause of the symptoms with a visual or microscope examination?
       6. Based on the information provided by the client and what we can see on the sample, are we likely dealing with a physiological problem, an injury, or a pathogen?
       7. What testing is most suitable for this sample?

Sometimes the questions are easily answered and the diagnostician can move quickly to a diagnosis. Sometimes the process is complicated and time consuming.

Every sample received by the lab is considered unique. It comes from a different environment from every other sample. Growth stage may be different from similar samples the previous week. Field histories can be very different. Condition of the sample can be very different from similar hosts received the same day. Although there can be similarities in symptoms of two seemingly identical host plant samples, each is given separate consideration as the diagnostician moves through the diagnostic process. Every sample has the potential to require different handling from every other sample of the same kind of plant.

What does it mean when a report refers to agar plate testing?

Of all the testing done in a diagnostic laboratory, agar plate testing is the most commonly used procedure when looking for fungi or bacterial pathogens. If agar plate testing has been done, it means that the diagnostic lab was looking for a pathogen. Sometimes the process will find a disease and sometimes not. If not, the test results may be an indicator that the cause is abiotic, not related to a pathogen. The testing takes time because the organisms must be allowed time to grow to a point where they can be identified and not all organisms on a test plate will be a disease. Plant diagnostic laboratories all use agar plate tests although not every sample will require it. It is used for many different pathogens and involves placing carefully prepared plant tissue or extracts from the tissue onto a culture dish containing an agar media. The dishes are incubated in conditions appropriate for the sample or suspected pathogen and results may be ready in a few days or can take many weeks to be completed. There is one common agar media, called Potato Dextrose Agar (PDA), used for attempting to isolate fungi from many kinds of samples and most samples with pathogens will be processed on this media. Sometimes PDA is not the best one to use and there are numerous recipes for media that the diagnostician can choose from. Currently our lab has 15 different media that are prepared at some point during each summer and used for isolation of pathogens. Every summer we come across something new or uncommon for which a new or different media recipe must be used. The test plates are always interesting and plates from similar samples can look very different, again an indicator of the uniqueness of each sample.

Different kinds of agar have different purposes. Top row of plates shows media for isolation of bacteria, bottom row shows media used for fungi.

These agar plates were both prepared from different wheat samples with similar symptoms and yet show different fungi, Fusarium sporotrichioides and Rhizoctonia solani in the plate on the left and Fusarium avenaceum in the plate on the right.

Helping the lab help you

The quality of the sample and information provided by the client are important in helping the Crop Diagnostic Centre to make an accurate diagnosis.

The quality of the sample itself is critical for the diagnostic process but information provided with the sample can be just as important. Field history such as crops grown over the past few years and chemicals used in the field in recent years sometimes provide important clues to help in the diagnostic process. If the sample contains too few plants, dried out plants or decomposing plants, diagnosis may be inaccurate or impossible. Also, it is always important to indicate the symptoms of concern. It may seem like the problem is self explanatory but sometimes what the client sees as the problem will be different from what the lab thinks is the problem.

The client can help the diagnostic lab produce an accurate result by providing sufficient sample material to work with, by getting the samples to the lab as quickly as possible, and by providing as much information with the sample as possible. A few leaves submitted as a sample may not tell the story so whole plants are preferred when ever possible. More than one plant or sample piece should be submitted whenever possible. When seedlings are involved, as many symptomatic plants as possible should be provided (at least 16 to 20) since if agar plate testing is required, four small plants may be required for just one test plate and multiple test plates are required for accurate diagnosis. Avoid shipping samples at the end of the week unless there is certainty that the sample will not be stuck in transit over the weekend. Pack samples to prevent crushing or drying out of the tissue. Some lab tests can be impossible or inaccurate if the tissue arrives at the lab in a dried or severely wilted state. Paper bags or paper envelopes are not suitable for packaging since they do not prevent drying of the tissue. On the other side of the spectrum, packaging of wet plants or packing plants with wet paper towelling is not advisable since it may lead to moulding of the plants while in transit. Providing the lab with adequate sample material and good information will help the lab to provide an accurate diagnosis.

One root of the word ‘diagnosis’ is derived from the Greek and means “coming to know”. Diagnosis involves looking for a pathogen or eliminating some of the suspects through testing or other means and analyzing the possibilities based on information gathered as well as drawing on experience. When submitting samples to the lab, help us help you by providing the best sample quality possible and providing any relevant information.

From the July 2010 edition of CROPS E-NEWS (subscribe)