A Day in the Life of a Plant Diagnostician with Rachel Bomberger


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Show Notes & Resources Mentioned:

Contact Information:

Contact Rachel Bomberger via email at rachel.bomberger@wsu.edu
or by phone at 509-335-3292 or 509-335-0619.

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Episode Transcription:

[ Music ]

Drew Lyon: Hello, and welcome to the WSU Wheat Beat Podcast. I’m your host, Drew Lyon, and I want to thank you for joining me as we explore the world of small grains production and research at Washington State University. We have weekly discussions with researchers from WSU and the USDA-ARS to provide you with insights into the latest research on wheat and barley production. If you enjoy the WSU Wheat Beat Podcast, do us a favor and subscribe on iTunes or your favorite podcasting app. And leave us a review while you’re there so others can find the show too.

[ Music ]

Drew Lyon: My guest today is Rachel Bomberger. Rachel is the plant diagnostician for the W.S.U. Department Pathologies, Plant Pest Diagnostic clinic. The clinic a year around resource available to growers, industry, and the general public to help them identify and manage their plant health problems. The clinic works on all but one plant to test for fungi, bacteria, viruses, and nematodes. The clinic can also test soil for select pathogens and perform tests for special issues impacting Washington and the PNW. Hello Rachel!

Rachel Bomberger: Hi Drew! Thanks for having me.

Drew Lyon: Last time you were here, my guest on the W.S.U. Wheat Beat podcast, you introduced the clinic as a resource to growers and industry. But what really happens to a plant sample once it shows up in your clinic?

Rachel Bomberger: It’s a great question, Drew, to give some insight on what it’s like to be a diagnostician. So, when a grower or industry, someone sends a sample to the clinic, the first thing we do is actually an initial exam, very similar to like when you go to the doctor’s office. Where they take your temperature, your pulse, maybe measure your height. We kind of do the same thing. So, I’ll check the plant, you know, see what type of plant material is there. Generally, I ask for a whole plant sample, so I can check kind of head to toe, if you will, of the plant. But, sometimes I just get leaves or just roots. All sorts of things can end up in the mail on occasion. But, let’s say I have my sample, the first thing I do is start listing the symptoms. I examine looking to see, you know are there chlorotic leaves, necrotic roots. Do I see any evidence of leaf infection? It’s something like Cephalosporium stripe. Can I examine that a little bit further, see some of the classic or diagnostics symptoms, such, like I said for Cephalosporium stripe, where you see it discoloring the node? As well as things like eyespot. We can start checking different levels of the plant to see if we can see very typical symptoms and what’s going. So, that’s kind of the first step. Again, running through the symptoms and then from there seeing if I see any symptoms of certain typical diseases such as eyespot, Cephalosporium. And based on what I see there, that’ll kind of determine what testing I’m going to go on from there.

Drew Lyon: Do people often say, “I think this is, ‘such and such?'” Or is it kind of a blank page when they send it to you. In other words, “here’s a problem, I don’t know what it is, and you have to start from, basically, scratch.”

Rachel Bomberger:  It’s actually about 50/50. You usually a grower or industry member is pretty confident in what they have or they have a really strong suspicion of, “I suspect Rhizoctonia root rot.” And like I said, that’s about 50/50 chance that they’re right. I do get samples where the plant is just super bizarre. We have no idea what’s happening, but there is, on the submission form that you can find on my website, we do have a section called, “What do you think is wrong?” And this is the perfect place for a grower or the person sending in the sample to say, you know, “I think I have Rhizoctonia root rot,” “I think I have Cephalosporium stripe, ” “I think I have eyespot.” And then I can then check to make sure and see if my diagnosis and my exam is showing the same thing. And, any time you put that information, I do take that to heart and make sure that I can either confirm or, you know, negate that concern by saying, “I don’t see any of these symptoms.” So yes, a grower can absolutely put what they think is wrong and we’ll work to confirm or to relieve them that’s not a problem.

Drew Lyon: Okay, you mentioned your website. Just for our listeners, can you tell us what that website address is?

Rachel Bomberger: Yeah, it’s plantpath.wsu.edu/diagnostics.

Drew Lyon: Okay, we’ll make sure we get that in our show notes, so people can see that and use it. So, something comes in, you decide you need to do some further testing. What does ‘further testing’ include?

Rachel Bomberger: So, let’s say I’m examining a plant, and I’m starting to suspect root rot. You know, I’ve gone through that initial exam and maybe I’ve seen poor vigor or chlorotic leaves. Or, just kind of, what I like to call, “a sad plant.” What I might do then, is start to examine it under a microscope. And under a microscope, usually I can actually see damage to the roots, such as ‘spear-tipping’ or ‘rat-tailing’. Spear-tipping is where we see that the root has broken off at a sharp point and then what I call rat-tailing, because I’m a 90’s child, is where the cortex has sloughed off the root. This is pretty characteristic of a root rot pathogen. Especially, something like Rhizoctonia or Pythium. So, what I’ll do from that one microscope, so that’s kind of a larger microscope where I can put the whole plant. I’ll then take an individual root and put it under a fine compound microscope. That’s what you traditionally think when you see people looking into almost the binoculars to really see fine details. And for there, for things like Rhizoctonia and Take-all, I can actually see the structures of the fungal pathogens and confirm, based on microscopic observations, that it is that pathogen present. So, we can go from sample arrival to a diagnosis in two hours. Sometimes, I can’t find those structures that fit with the symptoms I’m seeing. Let’s say for Pythium root rot, you can’t always see structures on the roots. So, what I end up having to do, is take a selection of the affected tissue and then I go through a laboratory process where we surface sterilize to kind of kill any of – essentially like washing your hands. You’re getting of all, kind of the background microorganisms that associated with that root and then I put it onto laboratory media which really just kind of looks like weird jello. But, it allows fungal or bacterial pathogens to grow that way I can identify that structure from the roots. It can take anywhere from about 12 hours to 2 weeks, depending on the pathogen. Luckily, for a lot of the grain growers we can get results out anywhere from 12 hours to 3 days, is pretty average.

Drew Lyon: So, you can tell by how the pathogen grows on the agar what it is? Or do you have to do something after you get some growth to figure out what it is?

Rachel Bomberger: That’s a good question to make it sound a little less science-fictiony. There are patterns of growth that are distinctive for certain pathogens. And then, so that’s what we call hyphal growth. They’re kind of these thin, string-like strands that will grow from those pieces of tissue. But, usually what we’re going to end up using are kind of a fruiting body or a sexual structure, a reproductive structure. Because those tend to be a little more unique to the different pathogens, kind of like how flowers are unique to the individual plants.

Drew Lyon: Okay, so we’ve spent a little time talking fungal pathogens, which are fairly common pathogens. What about viruses? Those are mighty tiny things. How do you tell whether you have a virus infecting your plant?

Rachel Bomberger: Drew, those are pretty tiny. So tiny that even my lab microscope can’t see it, and I don’t really have a couple thousand dollars to throw down on a very fancy microscope that would let me see virus particles. So, what I do to test for viruses, during that initial exam, there are some pretty typical symptoms we associate with some of the viruses we have in our region. We call them ‘mosaics’ where they’re a little bit too regular pattern of different chlorosis or yellowing, or lighter green, symptoms. I’ll actually take that affected tissue and use it in what’s called an ELISA. If you want to be technical, ELISA is an ‘Enzyme Linked Immunosorbent Assay.’ Really just fancy technical language, but what it is, is I take that affected tissue, I grind it up in what we call ‘buffer.’ So, I kind of just liquified or made juice out of that plant tissue. And then, I’m going to expose it to different antibodies and antigens. And after some laboratory magic, we’ll actually see a color change in a test well that will indicate whether or not the sample is positive for a particular virus or negative. The great thing about this particular technology is if I receive that sample, your sample, by about 4 p.m., one day you’ll have your results by around 2 p.m. the next day, so it’s a really fast method of testing a virus.

Drew Lyon: Okay, so just a really quick reaction in that little well. Very good. What about bacteria? We have a few bacterial diseases out there. Is that as easy as virus or fungi? Or is it a whole different program.

Rachel Bomberger: On a scale of fungi to virus, it’s actually closer to the fungi side of that spectrum. We don’t have that many bacterial pathogens because we are a dryland growing area, but, those folks in irrigated areas do have bacterial pathogens that can show up usually through potentially infected seed sources, or maybe depending on what weeds or regrowth has been in their field, that can be a source of inoculum or the pathogen entering. But, with bacteria we follow a pretty similar set up or process for diagnosis where I’ll do the initial exam. And, my best friend is my microscope, so I usually start there after the initial exam and we’ll look for what’s called ‘bacterial streaming.’ I cut into the affected tissue and if bacteria is present, typically for most bacteria, you will actually see it stream out of the plant cells. This is isn’t always 100 percent. There are some bacteria that don’t reproduce that much, so we can’t see that streaming. So, what I’ll do instead is take some of that tissue again, we’ll surface sterilize it, and then put it on that funky science Jell-O to hopefully encourage the bacteria to grow and then we’ll work from there to start confirming which bacteria it is. Usually, this is based on color, how it grows, or does not grow on certain media, and we’ll work from there. Again, we only have a few that we really have to deal with in this area, so we have some quick tests.

Drew Lyon: Okay, so you’ve told us how things normally work. What happens if you have a fungi and you can’t get it to grow out on agar or you have a virus but you can’t I.D. it with ELISA, are there other ways to go about doing this? Or just throw up your hands and say, “I don’t know”?

Rachel Bomberger: I do that first, and then I go drink a beer and then the next day I come back to the lab a little bit more grounded. [chuckles] I’m very lucky that I’m located inside the same building as a number of plant pathologists, as well as Crops and Soils, horticulturists. So, I’ll go to my experts because I’m biased. I am a plant pathologist. I will start with first looking for disease, see what they think. If they confer that it does look like it is potentially a disease, then we’ll work form there, trying to see if there’s a new technique such as utilizing D.N.A or R.N.A to identify the pathogen. Or, if we start to think, “Well, maybe this isn’t a pathogen,” because about 50 percent of all plants sample that come into a clinic, and that’s any clinic, regardless of what state… When I worked in Nevada, we were a little bit closer to 60 to 40 percent, because most plants just have drought stress. But, most plant samples, most plant clinics experience about 50 percent biotic – so diseases, fungi, bacteria – and then 50 percent abiotic. So, these are things like weather related effects, chemical damage, are just all the sorts of things that can go wrong. I can kill a plant by looking at it. That would technically, I guess, be biotic since I’m living. But, just all the things that can also harm plants… So, if we can’t find a pathogen, a virus, or a bacteria, we start to look in there. You know, do the roots look like they have root rot, or do they have clubbing and twisting? Could it be aluminum toxicity? This is where we’ll start asking those broader questions. What was the pattern in the field? Is there any way that this could potentially be chemical damage? Could there be pH issues? So, we start digging deeper and maybe we need more testing. So, and this is different testing, so it might not include plant pathology, but could be soil test resources, analytical chemistry labs to figure out if maybe there’s been an herbicide issue. But, it always is kind of reaching out. That’s why I do suggest the clinic as a starting point, because we can start eliminating things. That’s the other beauty of diagnostics, is negative results do give us tons of data. If we can rule out all of the potential disease suspects, then we can start confidently moving in the direction of some of these abiotic issues that can be a little bit more ambiguous than a straight forward diseases issue.

Drew Lyon: I know you’ll bring, occasionally, a sample down to me to look at, you know, if you suspect might be an herbicide problem. And, a lot of problems, I think that what it looks like in the field is very instructive. So, drift issues tend to have a drift pattern. Freeze problems tend to occur in low spots. So, I think having that information is probably pretty valuable if people can include that in their notes to you. Maybe even include a picture, per say. Is there a way of attaching a picture with some of these samples? Or sending you a picture?

Rachel Bomberger: Absolutely! And, first of all, thanks Drew, for letting me bombard you all the time with those questions. But, yes! If you, you know, I only get a snapshot of what’s happening in just a few plants. So, any time, you’re welcomed to use the space on the sample submission form to detail that kind of field-wide information as well as photos. This is cliché, but photos, you know, can speak a thousand words. I can really understand what’s going on by seeing what’s in the field. The patterns, is it low spots or high spots? Is at margins? Is it only next to a certain field? You know, what’s going on kind of macroscopically versus microscopically. I’m also very lucky that some of the retired wheat breeders and scientists also, they have coffee across the hall from me every day at 10, so they’ve seen, you know, things that haven’t shown up for a couple of decades. But, so when I get things and none of my currently employed researchers know what’s going on, I am lucky that I get to pop across the hall and ask, “Have you seen this before?” Those usually end up being my favorite samples because it’s been something we haven’t seen for twenty, thirty years, but they knew it in a heartbeat.

Drew Lyon: Interesting. There is some value to having retirees come have coffee in the morning. So, we’ve talked a little bit about the plant pest diagnostic clinic. I guess once again, can you tell people how to find that information, and what forms they’re looking for on that site?

Rachel Bomberger: Absolutely, so we do have a website. Again, it’s plantpath.wsu.edu/diagnostics, or you can google ‘department of plant pathology’ plus ‘WSU.’ and there is a link to take you to the diagnostic web page. As well as our ever-popular Small Grains websites does include a link to take you. You are also welcome to email me. Give me call and I can email you the form directly. The form I’m referring to is the sample submission form. This is the space where I get to collect all of the data points – I sound really ‘sciency’ there – but, all of the information that’s critical for a proper diagnosis. You know, what variety is it? Where is the field located? How many acres are affected? What symptoms are you seeing? That seems really silly to say, but that can be a really important thing. Because the symptoms that I get really interested in aren’t always the ones that, you know, the grower or the client is having issues with. So, that also provides to make sure that I’m not just getting excited as a plant pathologist looking at something else that you’re not concerned about. And again, if you have a suspicion, again, growers are at least 50 percent right on what their biggest suspicion is on what’s going on. So, it does include space for you to put that information.

Drew Lyon: Okay, well I think this clinic is an excellent resource. Not every state has this resource available anymore. And so, we really appreciate your running of it and people should take a look at the site and if they have some needs, contact you, either through the website or by email. Thanks a lot, Rachel.

Rachel Bomberger:  Thank you, Drew.

[ Music ]

Drew Lyon: Thanks for joining us and listening to the WSU Wheat Beat Podcast. If you like what you hear, you can subscribe on iTunes or your favorite podcasting app so you never miss an episode. And leave us a review while you’re there. If you have questions for us that you’d like to hear addressed on future episodes, please email me at drew.lyon@wsu.edu. You can find us online at smallgrains.wsu.edu. You can also reach out on Facebook and Twitter @WSUSmallGrains. The WSU Wheat Beat Podcast is a production of CAHNRS communications in the College of Agricultural, Human, and Natural Resource Sciences at Washington State University. I’m Drew Lyon. We’ll see you next week.