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Disease Diagnosis with Rachel Bomberger

Posted by Blythe Howell | December 7, 2020

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Episode Transcription:

Drew Lyon: Hello. 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. In each episode, I speak 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 WSU Plant Pathology Plant Diagnostic Clinic. The clinic is a year-round 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 Pacific Northwest. Hello Rachel.

Rachel Bomberger: Hey Drew. I gotta say, third time around, you actually got “diagnostician” down pretty good. I was impressed! [ Drew laughs ]

Drew Lyon: I was wondering whether I was going to mess that up or not, but I got it down! [ Rachel laughs ] Thanks for noticing. So, looking back on this past year, maybe even back to when you started, what were some of the most frequent dryland plant issues that came into the clinic?

Rachel Bomberger: Really, root rots, for both wheat and the rotational crops, like peas, lentils and chickpeas were things that I saw the most frequently, and that would happen in the fall and even early spring to sometimes early summer. With wheat, we saw quite a bit of physiological leaf spot. And then the past few years, because we had some late-season moisture, we also saw quite a bit of ascochyta blight, unfortunately. These aren’t shocking things to get in with root rots, you know, ambiguous yellowing, unthrifty looking plants. This is when growers really want to utilize a clinic because we can help you figure out if it is nitrogen deficiency that you would fix with fertilizer application or is this something that is indeed a pathogen and might require pesticides in the future or possibly, even in season. Physiological leaf spot is another issue that would come in quite frequently to the clinic because we have fungal leaf spots like septoria and tan spot that can look really similar. And so, if you think you have a current season leaf spot you want to get a fungicide application on but if you have a physiological leaf spot that’s nutrient-based, so clinics really come in handy when you’re trying to make these “if” “then” decisions. You know if it’s a fungus, let’s apply a pesticide but if it is nutrient you don’t want to treat it with a fungicide. So it’s really the right time to utilize a clinic to get the best answer, that way we can actually get an appropriate management.

Drew Lyon: Yeah, I did seem to see and hear about physiological leaf spot this past year. Is there any, what the… biotic or environmental circumstances that tend to lead to that?

Rachel Bomberger: So with physiological leaf spot, often it’s associated with chloride deficiency, so when we have a lot of moisture that moves chloride down through the soil profile and away from the plant roots, that’s when we see physiological leaf spot. It also happens to be about the same time we would be expecting things like septoria and tan spot because we have that moisture, which fungi love. So, it’s kind of impressive and is job security, in some way, for diagnosticians that these pathogens in abiotic situations like to occur at the same time, or under similar circumstances.

Drew Lyon: Yeah, it seems like the different varieties… I mean, even physiological leaf spot between varieties looks a little different so, I know I’m always looking at it and saying, “is that physiological leaf spot or is that something else?:

Rachel Bomberger: Absolutely! A lot of these pathogens and abiotic disorders really depend on the variety, which always makes jobs fun, and is why everyone should remember to actually fill out their sample submission form. Extension agents, I’m also talking to you. [ both laugh ] They might be the worst. I get a lot of just, like, boxes in a plant and it’s usually from an extension office. I’m not going to name names…. Aaron. [ Drew laughs ]

Drew Lyon: So, these are the most common things but sometimes the more fun things are the rarer things. What were some of the rarer, more fun things, you’ve seen?

Rachel Bomberger: For sure, the rare ones are the head-scratchers and kind of, they perk up my… well, first they frustrate me because I often stare and it and go, “I’m not sure where to go with this.” But then they can be really exciting because you start tapping into other people’s expertise. Honestly, one of the most rare things in the clinic was stripe rust. We don’t get any stripe rust into the clinic because everyone knows what that looks like. So, I think I’ve got five samples in five years. Usually, it’s because I have to note to the grower that I also found stripe rust. You’re probably not shocked I found stripe rust. So that’s rare. But really the rarest thing I’ve dealt with is a bacterial leaf streak that’s also called black chaff. Now this is a bacterial disease and that is why it is so rare in our dryland cropping system, is bacteria rely on water to move throughout a field, so even though this particular bacteria is seed-borne, it relies on water, usually in the form of precipitation, or in irrigated fields, to move the bacteria around, to splash it around onto new leaves, to find that opening that it’s actually able to exploit and cause disease. So that was the rarest. I only found it one time. Most of the time it’s actually, kind of circling back to physiological leaf spot, it’s actually a genetic response to a particular stripe rust resistance gene. We call this, “pseudo black chaff” or “malinism” and it’s a good thing to see but it’s extremely alarming when you see dark purple or black looking plants in your field. The first thing you want to do is spray something, yank it out, or scream, maybe, but [ both laugh ] you can send it to the clinic and we can really quickly test to see it is indeed this physiological response and again, usually associated with a genetic marker for stripe rust resistance. Which you should feel warm and cozy about. And something that was rare this year also was I felt like we had an onslaught of wheat streak mosaic virus. Now, this virus is something we have in our cereal production region as well as our corn cropping systems. But this year I actually received samples and they came in fast and they came in furious. You know I had one sample come in that actually wanted testing for soil-borne wheat mosaic virus, and so I have the reagents, plus a few other virus — I call it my panel. I have my virus panel. I have one for wheat. So I decided just to just throw all the virus that I generally test in because it doesn’t take up much more time or much more reagents, so it’s easier just to test and go and it was positive for wheat streak mosaic virus! Ran it again just to make sure and then sure enough after reading into the situation a little bit more, there were circumstances that definitely help encourage this virus. Again, even though it’s something we have native, or excuse me, endemic to our system, we don’t see it all that often. But this year we sure did. I feel like once I found one wheat streak mosaic virus, I got, I think, 10 or 15 other samples that came in, and sometimes they would be fields that were entirely infected or multiple fields that had really wide-spread infection. That’s kind of the interesting thing about this virus is you can have either negligible amounts in your field or the entire field is infested. The reason this can be is the virus is spread by an area-fight mite, so those super, super tiny mites you can’t actually really see them with your naked eye. I see them under the dissecting scope and they look like little tiny carrots with little tiny legs so if it takes my microscope to see it, it would be pretty hard for a grower to see. But you can see distortion in the lower leaves caused by these mites. And what happens is they’re typically moving through a green-bridge event, so that means the mites are moving through a late-maturing crop, such as a late-maturing spring crop, into an emerging winter wheat crop. And so they’re moving from the dying plants to the nice, young, healthy-looking tissue. And we see the same thing with weeds so this is managing the green-bridge and managing your weeds are really important for keeping this disease low because it can be devastating. Just because we don’t typically deal with it doesn’t mean it doesn’t hurt when it does show up, unfortunately.

Drew Lyon: So wheat streak mosaic, when I was in Nebraska was just like an every year event. You get hail storms and you’re going to get wheat streak mosaic. But I hadn’t heard much about it since moving to Washington so anything in particular that happened this year, do you think, to cause you to see so much of it this year?

Rachel Bomberger: I think there were probably a couple of green-bridge events where that late-maturing variety was too close to maybe a recently planted field. That’s what I suspect might have happened. The other thing is if you’re near corn. Remember that corn and other cereals, they can also carry that virus. Eriophyid mite also around and is not controlled by insecticides. So it was probably just a bad storm of circumstance, I mean, that’s how disease works [ laughs] I mean we often have the host plant because we are growing it and the pathogen, but we just have those circumstances in the environment come together and that’s when we really see the disease take off. Yeah, it’s quite alarming! [ laughing ]

Drew Lyon: Yeah I’ve also heard, I think at least one of those instances I heard from the county person was a cover crop situation. So I think it had wheat or some small grain in the cover crop, so it was growing, purposely growing it over the summer not realizing this connection between the green-bridge moving it from one crop to the next.

Rachel Bomberger: Well, they probably won’t ever do that again! [ Drew laughs ] Wonderful learning experience! Unfortunately, that does happen. We have awesome growers in the PNW. I think a lot of that comes from a willingness to experiment and then just sometimes the circumstances aren’t great. [ laughs ]

Drew Lyon: But, like you said, we don’t see it very often so it’s probably not on the top of people’s minds.

Rachel Bomberger: Yeah I didn’t trust the result when I got it. I re-tested, I even grabbed new tissue to make sure — you know, because we use a pipette, maybe you dropped the positive control in somewhere, but no it was a very strong positive, unfortunately.

Drew Lyon: So, what have you found to be the most valuable tool when you’re making a diagnosis? It just seems like there’s a lot of different things out there and there’s a lot of different ways to try to figure them out. What’s worked best for you?

Rachel Bomberger: So I’m actually what you should say, “old school”. I love my microscope. I spend most of my day on the microscope. The way I kind of reconcile this in my brain is just like or a field rep goes out into the field and surveys for different patterns, different symptomatology on a large scale, I actually do the same thing on a much smaller scale with the individual affected plant. I’m looking for necrotic cell-tissues. If anyone has gotten a report from me for root rots, you’ll often see that I say that I found rat-tailing or rotted cortex, and that’s how I know that we have a root rot pathogen because you have something that’s damaging the outer layer of cells on the root and getting into the vascular tissue. So I go on kind of this microscopic pattern or scavenger hunt to try to see what’s going on. And a microscope is also my first stop because I can see if I’m not finding any of those symptoms that, those microscopic symptoms that would be typical for a pathogen if I’m not seeing it on that sample then that starts to make me make sure I want to go down another path, make sure that it’s non-abiotic and take another look at the sample submission form, see what they’re doing. There’s a lot of really cool tools being — I know you just had Karen Sanguinet in here who’s coming up with a lot of great tools. We have a lot of researchers coming up with great diagnostic technology. But, I always tell grad students and undergrads you have to be able to do these foundational techniques. You know, water-tissue floats. Culture, a really basic lab science or I’ve heard someone call it “barefoot” science because you can find out a lot of information and I find that I actually catch more issues that could be going on, so because I’m using the microscope and I’m actually observing the plant, I see that, you know, you do have root rot but you also have ascochyta blight or you have a virus but I also see that you might have aluminum toxicity because I’m looking at the plant. Sometimes when you’re doing these testing technologies you are only looking for a yes or no. Do you have pythium? You run a PCR and it tells you yes or no. I can get the same answer, you know, sometimes, viruses are different, but a lot of the time I can get the same answer in maybe tease out a little bit more by following that symptomology through the plant and examining it a little bit deeper. And again, I am super biased. I love microscopes. That is the only reason I wanted to go into science was microscopes. [ both laugh ]

Drew Lyon: They are pretty cool. There are some pretty nice ones out there these days.

Rachel Bomberger: Oh yeah! I have one that I found to be a really excellent tool and that was my colleagues. I’m really lucky that the clinic is right across the hall from Tim Murray’s office so he’s always been kind enough to let me pop in, ask questions, bat around a couple of ideas. So sometimes when we get really weird samples into the clinic, that’s when it takes extra brain-power to look at the sample and throw around a few ideas because once we have some ideas of what could be wrong, I can then go test and confirm what is or is not present. And I’m also lucky that I happen to be across from the hall from the lunch room where a lot of current and retired USDA scientists like to sit and eat lunch [ laughs ] So, folks like Bob Allen are there, Tim Paulitz is usually there and so if I find something really weird, I either get to go over and share it with them or tap their brains. Someone like Bob Allen, who’s worked in wheat for so long, he’s seen so many odd issues. Aaron Esser once sent me a sample where we had [ laughter ] black, an inch large, black lesion on the third node on every plant he sent me. So that screams that’s an abiotic problem because that’s too regular for a pathogen. But, Tim Murray, Tim Paulitz, myself, we had no idea what was going on. Bob Allen takes one look and says, “that’s frost damage” It was just a late-season frost, atypical symptomatology that we don’t typically associate, but it was frost damage! Sure enough! Checked with Aaron, checked with the grower, they had weather conditions that were conducive to that type of frost damage. So, microscopes and people who have seen a lot are really helpful. [ laughs ]

Drew Lyon: That is good. That is a real resource of being on campus and having a close proximity to knowledgeable people.

Rachel Bomberger: Absolutely. I’ve definitely popped down to your and Ian offices a couple of times [ laughs ] every week to make sure it’s not an herbicide or confirm that maybe!

Drew Lyon: So, what are some reliable resources for growers who are trying to make a diagnosis on their own or wish to at least get in the ballpark with what they have?

Rachel Bomberger: I think extremely highly of our extension specialists. I think our extension folk are fantastic resources because they live in the area, sometimes they’re even growing and experimenting on their own research plots, so I really think if you have a question, start with your extension agent and they, again, can come up with some ideas and then they can also send the sample to the clinic if they want confirmation. And I say, “if they want confirmation” because, I have to be honest, most of the time the extension agents are telling me what they think it is and I’m usually there to confirm or play tie-breaker. They’re usually right. [ laughs ] I’m really just there to help them ensure that it really was the right diagnosis. So, definitely start with extension agents. I think they’re great. I’m also biased but the Small Grains website has great information and is also an excellent resource to monitor ongoing issues. Our Timely Topics come out at such a fast rate when we’re responding to an issue. This year we had a significant frost event. I think four or five of us contributed to that Timely Topic to get it out in maybe 48 hours, it was some really speedy turn-around, so I think that’s a great place to make sure you subscribe to because you can see what’s going on in different regions. Maybe your neck of the PNW isn’t impacted, but other growers can get their answers solved. I also rely on the PNW Disease, Insect, and Weed Handbook and website. These are written by PNW extension agents and researchers for our area. That’s a really lovely thing, is they’re written by researchers who are from the PNW, so the recommendations are adapted to our region. Kind of along that thread, usually other university websites, their extension publications are also great resources. It’s also important to keep in mind that they are written for their area, like Drew, how many times have you used a Nebraska extension pub but said, “Make sure you don’t do x or y because it does not apply to this area.” So just read those with a little bit of scrutiny. If it doesn’t make sense for your region, your situation, it’s probably a good thing to avoid it but there’s great information and we have wonderful extension colleagues all across the country.

Drew Lyon: Yes, I occasionally look at a net guide from the University of Nebraska, and then they usually do require a little tweaking although —

Rachel Bomberger: Just a little.

Drew Lyon: The general biology and stuff, that’s the same everywhere but how you go about managing it can be different from region to region.

Rachel Bomberger: Yes. Excellent point. That was the point I was trying to get succinctly across.

Drew Lyon: Okay, so I’ve heard a little rumor that you might be thinking about moving on. I wonder if that’s true, what your next steps might be.

Rachel Bomberger: Yes. So, I potentially am thinking of leaving the clinic to actually pursue more extension education. Extension education was something I didn’t really know I had a flare for, if you will, or a passion for. I really enjoy bridging the gap between researchers and users, folks who are actually in the field dealing with the problems. That’s why I love diagnostics. I felt like I was solving problems in a real tactile, immediate way. And so through doing that, I’ve given a lot of presentations and I find that I truly enjoy getting to be a part of extension education even though it wasn’t necessarily a role of being a diagnostician. It was a natural fit and I really enjoy doing it. So, I am interested in pursuing extension education a little bit more fully.

Drew Lyon: Okay. Well, I know that at our Wheat Academy your sessions on diagnosing diseases in wheat was always very highly rated. So, I think highly of your skills in that area. We’re sorry to see you moving on but I’m sure you’ll find something that you will be very successful at in the future.

Rachel Bomberger: Thank you so much. And I hope so. Again, my goal is just to bring some energy and enthusiasm to talking about plant pests, plant diseases and really my goal is just to make folks engaged. That way when they’re walking in their field and they see something that looks a little matted, a little weird, they go, “Alright, cat vomit and snow mold look the same.” And so, they have their diagnosis. Right? [ laughs] We can make these moments really fun. So, thank you, Drew.

Drew Lyon: [ laughs ] Thank you, Rachel. Thank you for coming in and speaking with us today.

Rachel Bomberger: Alright. Thank you!

[ Music ]

Drew Lyon: Thanks for joining us and listening to the WSU Wheat Beat podcast. If you like what you hear don’t forget to subscribe and leave a review on iTunes or your favorite podcasting app. If you have questions or topics, you’d like to hear on future episodes please email me at drew.lyon — that’s lyon@wsu.edu –(drew.lyon@wsu.edu). You can find us online at smallgrains.wsu.edu and on Facebook and Twitter @WSUSmallGrains. The WSU Wheat Beat podcast is a production of CAHNRS Communications and the College of Agricultural, Human and Natural Resource Sciences at Washington State University. I’m Drew Lyon, we’ll see you next time.

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