Soil Microbiology & Agricultural Sustainability with Tarah Sullivan

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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 Tarah Sullivan. Dr. Sullivan is a soil microbiologist from the Department of Crop and Soil Sciences at Washington State University. Originally trained as a soil scientist at Colorado State University and then Cornell. Her current research at WSU addresses different aspects of how soil microbial communities assist in nutrient cycling and availability to plants. Microbial soil health is crucial to agricultural sustainability and Dr. Sullivan’s research seeks to understand microbial activities to increase yield and sustainability at the same time. She runs an active research lab, teaches both undergraduates and graduate courses and engages in outreach locally to increase understanding of these highly complex systems as she studies. Hello, Tara.

Tarah Sullivan: Hi, Drew.

Drew Lyon: So, soil microbiology. Lot of interest out there when I go talk to growers, there’s often at least one if not multiple questions about what’s going on in the soil. So, tell us a little bit about what you do, what your main projects are in your lab and what you’re focusing on right now.

Tarah Sullivan: The main focus of the research in my lab right now, is to understand how microbial communities in the soil and in the rhizosphere impact metal bioavailability. So that means whether or not a plant or a human or a fish or some part of the environment can actually take up the metal or the micronutrient. Is it useful to them or not? And how can we control the microbes that control that? So a lot of my projects are focused on different aspects of bioavailability and how the microbial community controls that. So I have projects ranging from contaminated sites, like the Bunker Hill Superfund site, up near Coeur d’Alene. Also, I have projects looking at Concord grapes and how we can use the microbial community to enhance iron nutrition to the grapevines. And then looking also at biostimulants. So this is a huge new area of the market is looking at products that will increase the activity of your microbial community. And we don’t really have, as scientists, we don’t have a good handle on how those work. So I have one student working specifically on how very specific biostimulants can alter the microbial community and how they function, and consequently, increase or decrease bioavailability to the microbial community. And then a huge aspect of my research right now is also focused on soil acidity in the Palouse and how that impacts soil health. And so that particular project has a lot of moving parts, a lot of different aspects of understanding what soil acidity does, understanding how that impacts soil health, understanding ways that it interacts with the positive microbial community or the beneficial microbial community, but also with the pathogens in soil, how that impacts biocontrol and pesticides and all these things all working together as well.

Drew Lyon: The whole soil microorganism, soil milieu I guess, is very complex and you hear, I hear a lot of people with what seem like very simple answers and yet it really isn’t that simple, is it? There’s a lot of things going on and you change one thing here and it changes something else. So how do you deal with all that complexity in this environment?

Tarah Sullivan: Well, that’s an excellent question and it’s a question we still address on a daily basis. A lot of soil microbial work, up until about 10 years ago, was done in looking at model systems because we knew the soil was extremely heterogeneous, extremely complicated and too much going on to really understand what one mechanism might be at work at any point in time. And so, a lot of scientists would sort of fall back to model systems where you have a single organism or you only have a pair of organisms, you have very set conditions, and you alter those conditions and look for interactions. Well, we’re beginning to really get a good grasp on the fact that those are not representative of what is actually happening in the soil and that we have organisms that we sometimes call “helper” organisms that may secrete molecules that are absolutely essential to the life of another class of organisms, and so those two can’t exist in separation from each other. So you can’t culture them in the lab; you can’t look at how these things may be actually influencing plant health. So, now the newest paradigm shift in soil microbial ecology and soil microbiology in general is to move towards the ‘omics right? So the microbiome, understanding the entire community all at once, the metagenome, so trying to understand all the genes that are present in soil, which ones may be functional at any given time, and then how that changes under different conditions. And it’s still not perfect, but we’re taking steps to try to improve the resolution and the quality of the data that we get. And that helps us understand how the community as a whole is working together over these highly dynamic and very complicated systems.

Drew Lyon: Sounds very interesting, but very complicated.

Tarah Sullivan: It is.

Drew Lyon: One other complicating factor, and you brought it up a minute ago is soil pH and the soil acidity. So here in the Palouse particularly, our higher rainfall areas we’re seeing a lot of acidification that has effects on nutrients availability, how plants grow; but it also affects the microbiology which also then affects all these other things. So what are you finding in that realm of how pH affects soil microorganisms?

Tarah Sullivan: Well, we just published a paper led by my post-doc Ricky Lewis, this year, that was specifically looking at how the soil is stratified. So by stratification I mean that the top 2 centimeters of soil are different from the 2 to 4 centimeter depths are different from the 4 to 6, 6 to 8, 8 to 10; so we know that soil is stratified naturally, in natural ecosystems, but understanding that stratification in agricultural systems is less well-described, specifically having to do with microbial communities. That’s really important in the Palouse because the acidification that we’re seeing is happening at a very discrete depth because that’s where the nitrogen fertilizer is being placed. So through nitrification and microbial activities in general, that nitrogen fertilizer’s placed and you get a zone of acidity that can go down as low as pH of 4 in many cases. So, understanding that stratification and not only how that stratification affects soil chemistry, which thereby affects soil health, but how that chemistry unpacks the microbial community was that first paper that we just got out, that talks about what we see in the Palouse. Many times, once you get below a pH of 5.5, roughly, you’ll have a decrease in rhizobia, which are essential for any sort of legume: chickpeas, lentils, anything like that, to function properly and fix the nitrogen. But also we see a huge shift in the microbial community from one that’s more or less balanced between bacterial and fungal communities to one that’s dominated by fungal communities. We also saw in some of the genetic work that we did that a lot of the organisms that are associated with contaminated sites, so for instance the Bunker Hill site or other mining sites, or things like that with lots of heavy metals, those species are very dominant in that super acidic zone in the Palouse soils. So they are species that actually indicate soil degradation and a decrease in soil health. What’s amazing about that is we’ll see, in the top two centimeters, where maybe liming has happened or soil health is still fairly stable, an even in the lower depths where soil health is stable, those species don’t dominate. It’s really strictly in that low pH zone of no-till soil specifically.

Drew Lyon: Interesting. So you have a zone with these organisms that are actually indicators that you have an unhealthy system going on there?

Tarah Sullivan: Exactly. It’s much like in macro-ecology. If you think about a jungle or a grassland, you’ll have keystone species, right? Organisms that tell you that the system is fairly healthy; there’s a great number of carnivores or different things like that, that ecologists will look for. So we’re beginning to start to understand, in very specific soil types, that there are species of microbes that can indicate either sort of healthy soils that are turning over nutrients and micronutrients in an efficient way and there are also organisms that indicate high metals or contamination or decreased soil health and productivity.

Drew Lyon: You know, there’s a lot of effort to try and develop tests to the able to tell whether your soil is healthy or not healthy, and this might be one of the things you might screen for? Is that– would that be correct or one way of getting at that?

Tarah Sullivan: Potentially. That’s something I’m actually really excited that my lab is also working towards is to understand how we can apply some of these techniques to really get a snapshot of soil health and maybe added into soil health tests. The species that we were finding in the acidified zone are similar to species that have been found in, like I said, mine tailings and things like that. So it would be the reverse of what you were looking for, if you found these organisms. You would say, “Oh no. Our soil health is not good.” The reverse of that would be to look for species that indicate soil health. The problem with that in microbial communities is that “species” is a very difficult term to nail down because there’s so much horizontal gene transfer. So that means these organisms, without necessarily having offspring, can pass on genes that are beneficial laterally. So, trying to define a species is, in many cases, much more difficult than to define a function. And so, in many cases, what I think probably is going to happen, in terms of soil health, is that we’ll have to lean towards functional genes and look at the genes that imply that the soils are functional and providing ecosystem services.

Drew Lyon: Okay. Another term you brought up earlier and that we hear a lot, or I hear quite a bit now in my reading is the “rhizosphere”. Can you tell us what the rhizosphere is and how microorganisms in the rhizosphere impact plant health?

Tarah Sullivan: Absolutely. This is a fun area of work where we define a textbook definition of the rhizosphere would be the “zone of soil that is under the influence of actively growing plant roots.” And that influence, and what is influenced is highly variable, right? So it can be soil chemistry, it can be soil carbon content, but also the active microbial community that’s feeding off of the root exidates. So that means the compounds that the roots are actively putting out into the soil. So we know that within the rhizosphere there are a lot of different chemicals and compounds that plants both actively and passively secrete into the soil. Those compounds can serve as signals or food sources for microorganisms. And in many cases, that is a much more stable environment than what we call the bulk soil. So the bulk soil is the opposite of the rhizosphere soil, in that there are no actively growing plant roots, and we know that microorganisms within the rhizosphere are different from those that we find in the bulk soil. And that those in the rhizosphere can provide a lot of plant growth promotion properties to the plant. So even if they’re not symbiotic, like the rhizobia that I mentioned earlier, they can be what we call associative, meaning they associate with very specific plant species because of those carbon compounds and those, in many cases, phenolics and even sometimes volatile organic acids, other types of nutrient sources and signals that might be contained in the rooting zone of that plant. So that could be everything from phosphate solubilization to even secreting plant phytohormones that increase growth and yield and other types of signals that can turn on or off plant defenses, which makes the plant actually more resistant to pathogen attack. So again, complex. [ laughs ]

Drew Lyon: That’s very complex; very interesting stuff, the interaction between the plant and the microorganisms in the soil. It’s all really interesting stuff. In fact, your lab sounds like it’s doing a lot of interesting work. What’s the thing you find most exciting right now, in your, going on in your lab?

Tarah Sullivan: Well, like I said, I think some of looking into the future and trying to understand soil health is a huge, huge forefront of soil studies and soil science in general. So one of the projects that gets me the most excited is understanding how very specific root exidates or root metabolites being exuded into the rhizosphere can very specifically recruit a microbiome that enhances plant health. So by that I mean, different– we know that different plant species have a different composition of root exidates and will therefore, recruit from the bulk soil, a very specific microbiome. So these are all the organisms functioning towards plant health, and what we’re trying to understand specifically with wheat, is that even all the way down to the genotype and variety, the root exidates are actually different.

Drew Lyon: Really?

Tarah Sullivan: And they will recruit a different microbiome. And working with Scott Holbert and some of the research that he started with looking at how certain wheat genotypes can suppress certain types of diseases, specifically rhizoctonia; we’ve also found that certain wheat genotypes, those genotypes that were suppressing the rhizoctonia were also more resistant to the aluminum that’s being solubilized because of the soil acidity problem. So, we’re now looking at the microorganisms associated with all these different genotypes of wheat to see if you can actually breed wheat to enhance the microbiome, which then enhances soil health, decreases soil pathogens, increases nutrient use efficiency and subsequently, decreases the chemical inputs. So it’s all intertwined. It’s this sort of trifecta of can we actually breed wheat, not just for yield, but for sustainable soils?

Drew Lyon: Very interesting concepts that didn’t even cross my mind when I started in agronomy twenty-some years ago. Really exciting stuff. Well thanks for sharing that with us today, Tara. If our audience has some questions, I think you put out an extension fact sheet a while back that’s one the Wheat and Small Grains website, is that correct? It discusses this in general, I think.

Tarah Sullivan: That’s absolutely correct. There will also be a review out in Advances in Egronomy later this year that’s all about metal bioavailability and the microbiome and then the paper that came out earlier. But yes, the extension site for Small Grains is already up and it’s got some nice figures to help understand how pH interacts with microbiome.

Drew Lyon: Okay. We’ll make sure we get those in our show notes. I appreciate having you on today, Tara. Thank you.

Tarah Sullivan: Thank you, Drew.

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 You can find us online at 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.

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