Episode 81 | The Role of the Soil Microbiome in Reducing Nutrient Loss

Lizzie French
Soil Biology Manager
Waypoint Analytical, Inc.

Mick Goedeken
Regional Agronomist
Waypoint Analytical


May 2026 Podcast - Episode 81
Title: The Role of the Soil Microbiome in Reducing Nutrient Loss

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Todd Gleason: This is episode 81 of the Illinois Nutrient Loss Reduction Podcast. I'm University of Illinois Extension's Todd Gleason. Today, we'll explore the role of the soil microbiome in reducing nutrient loss with a couple of folks from Waypoint Analytical. We'll learn about it and Elizabeth French and Mick Goedeken, as we explore the biome and how it interacts with the ecology of the soil. Let's start with Elizabeth French. She goes by Lizzie. Hi, Lizzie, thank you for being with us. Tell me about yourself, please.

Lizzie French: Yeah, I am Dr. Lizzie French. I live currently live in Laramie, Wyoming, but I spent a good chunk of my adult life in the Midwest. I got a biology degree at Indiana Wesleyan and then went to grad school at Purdue in the Botany and Plant Pathology Department. I started working on projects with tomato pathogens, but then I got really interested in all the other bugs that were out there in the soil and really ended up focusing on more on just the soil microbiome as a whole, how it interacts with the plant, and how that ends up impacting plant health and soil health. And I liked it so much, I stuck around a couple more years and did a postdoc in a different lab at Purdue, and then ended up moving into the industry. Worked with Nutrien for a few years on soil biology and how we can use it to make agronomic decisions and then moved over to Waypoint about a year and a half ago now, and have, yeah, been loving it. Really enjoying the, the work that I've been able to do with them, looking at soil microbes and how we can help make agronomic decisions, understanding, you know, having that fuller understanding of what's going on in the soil.

Todd Gleason: Mick Goedeken is here, too. He's a regional agronomist with Waypoint Analytical. Hi, Mick, thank you for being with us. Thanks for joining the Big 10. I see you are at Nebraska or a Nebraska fan, so we have the U of I along with Purdue. We're only 90 miles apart, so we're kind of close. You're way out there in what we call the Western Corn Belt. Tell me a little bit about yourself, please.

Mick Goedeken: I'm Mick Goedeken. I have a master's degree in soil fertility. I started out my professional career in the soil testing world and then I decided to move around a little bit and I've experienced retail agriculture, I've experienced wholesale agriculture, the seed industry, and then I worked in research, and then I most recently before joining Waypoint 2 years ago, I actually worked for Orthman Manufacturing and was their agronomist for Orthman Manufacturing covering the entire globe. So now having joined Waypoint, I have a territory that is from Idaho to Ohio, so it's a much smaller than the entire globe and lots of my counterparts call me the Corn Belt agronomist. I cover the 3 labs in Grand Island, Nebraska, Champaign, Illinois and Atlantic, Iowa. So I am the support system, agronomic support system for those 3 labs and then I also support the sales efforts and try to learn from Lizzie as much as I can.

Todd Gleason: Lizzie, on that point, tell me about Waypoint Analytical, what is this organization?

Lizzie French: Yeah, Waypoint Analytical, we are one of the largest ag soil testing networks in North America. We've got 7 different ag labs across the US, and we run probably 2 million plus soil samples in a year. But we also offer, you know, tissue testing, water testing, manure, fertilizer, pathology testing, you know, kind of disease diagnostics, nematodes, and now soil biology testing as well for looking at more the, more the good guys in the soil, not just the bad, the pathogenic organisms.

Todd Gleason: We're here today to talk about the soil microbiome. Can you tell me what that is and why it's important?

Lizzie French: So, the soil microbiome is everything, all the living organisms you can't see in your soil, right? So you've got bacteria, you have fungi, you have viruses, protists, nematodes. There's, you know, thousands of different species of organisms and, you know, if you pick up just a spoonful of soil, there's going to be billions and billions of these tiny microscopic organisms living in your soil, making up that soil ecosystem and doing a lot of really important jobs in the soil that we don't always think about just because we can't, we can't see these organisms. You know, they're really important for nutrient cycling, uh, you know, mineralization of nutrients, breaking down residues, uh, building up soil structure, all of, you know, all really important things that we need to happen in our soils from both from a production standpoint and a conservation standpoint, right?

Todd Gleason: Mick, I'll bet when you talk to producers, maybe even to some of the folks in your lab, they ask you, "Hey, why is it that this soil microbiome thing you're talking about is important to us?" Can you put it in terms that I can understand as a farmer, uh, who's just wanting to know what N, P, and K might look like on my soils?

Mick Goedeken: So for years, as producers or agronomists, we've focused on the chemistry aspect of the soil and getting the soil chemistry correct and then we started looking at the physical properties and saying, "Okay, now this biome portion is bringing everything, so we have the biological, the physical, and the chemical all into, in included in it so that we can see exactly what that soil can do for us and make us more efficient." Uh, some of the things that the, the biome test allows us to see is how much, how many microbes are out there that can help facilitate keeping nitrogen in an available form. You know, nitrogen is a very complex cycle and is biologically driven. If we have the wrong microbes in there, we're going to cause a lot of denitrification. Well, we don't want denitrification to happen. So if we know more about our soil, we can know more how to treat that soil and how to apply our nitrogen more efficiently.

Todd Gleason: Lizzie, this is about the biology, the mechanics of the soil, really the ecology of the soil itself and how it works together. Uh, what do you think creates a, a healthy soil, across the Corn Belt?

Lizzie French: Really like Mick was saying, it's those three components together, right? You need to have the soil structure that allows you to have good air infiltration, good water infiltration. That interacts, you know, the soil biology plays a role in that where you've got, you know, microbes producing these sticky glues that help kind of build that soil structure. You need the chemistry, you know. You have to be able to grow a crop. That's, that's what soil health is in production agriculture, right? You got to be able to grow a crop and you want your grand-kids to be able to grow a crop too, right? So you need to have the chemistry there to be able to, to grow that crop. Uh, and then yeah, like I said, the biology piece interacts with all of that. So you need to have a healthy, thriving community of microbes that are able to cycle those nutrients into available forms that are helping to build that soil structure. And all of those things affect each other. So they kind of, you can't really pull them apart to understand them. You have to look at them as, as a whole to be able to really get an idea of the whole system. And so really, you know, when you're talking about the Midwest, corn and soy, having, you know, sufficient levels of the nutrients that you need to build those crops, having solid soil structure and then having high, high levels of soil biology that are able to then, you know, make those nutrients available, keep that soil structure where it needs to be.

Todd Gleason: We will, get to making the nutrients available or and or keeping them in place, probably both, actually. But, how is it that you measure a microbiome? What do, what happens? And, are there good things and bad things about it?

Lizzie French: Yes, so there are lots of ways to measure. Um, you know, the thing most people are probably familiar with is something like, like the Haney test where you're getting a respiration metric. That is really kind of a 40,000-foot view of how much overall microbial activity do I have, you know, are they living and breathing? Uh, and that's, you know, that is a great high-level metric. It doesn't tell you specifically what those microbes are doing and what they're capable of doing in your soil. Uh, what we've done with our test is we're looking at the DNA of the microbes in the soil. So you can think about, you know, when you do a, a nutrient extraction, you have a specific process where you're separating out those nutrients and then you're able to kind of analyze them on an, on an, on an instrument. We're doing the same thing, but we are getting those, finding the microbes in the soil, taking their DNA, and then we're able to specifically look at that DNA and say, "Okay, how many of you are nitrogen fixers? How many of these microbes in the soil can solubilize phosphorus? How many of you are mycorrhizal fungi that are going to help bring, you know, essentially essentially extend the root system and help those that crop acquire more nutrients?" So that's what we're really able to answer using that DNA analysis is kind of who is it that's there and what are those microbes actually capable of doing in the soil.

Todd Gleason: On the microbiomes, uh, are they capable of keeping uh, nutrients, particularly nitrogen, phosphorus, in place? And if that is true, do they lock them in place so that they're not usable by the plant as well?

Lizzie French: That's a great question. So, uh, you know, microbes need nitrogen and phosphorus, too, for their survival, right? So one of the ways that they help to keep it in the soil, well, there's, there's two ways. So we'll talk about the first one. The first one, they keep it in their biomass, so as part of their body, they're keeping nitrogen and phosphorus. When those microbes are growing, yes, they, they do temporarily lock up those nutrients so that they're not available. But microbes have much faster life cycles than we do, or that plants do, right? So that, you know, within a, a short amount of time, you know, days, weeks amount of time, that those nutrients that have been kind of vacuumed up into the microbial biomass become available again as they go through their life cycle, um, and you, you know, you have other organisms in the soil like protists that are kind of tiny little lions keeping the population of the, of the antelope in check on the, you know, soil savanna, right? So they're able to go out and eat those bacteria and make that nitrogen available again for the crop. So that's the first mechanism that they can use to keep nutrients in the soil. The second one is, which most people are probably more familiar with, is through building up organic matter. So that microbial activity, um, a lot of that microbial biomass, those dead microbes become part of the organic matter. Those microbes are important and they break down residues, they keep that carbon in the soil, a lot of those nutrients are kind of locked up into that carbon. And so as, and, you know, the soil organic matter we really want it to be dynamic, active, um, you're building up new organic matter as you're mineralizing some to be able to make new nutrients available. So it's this cycle that microbial activity keeps going where it's able to then retain those nutrients in the organic matter, make them available again for the crop.

Todd Gleason: Mick, you're an agronomist, you're also a farmer. When you talk to producers after they've, um, maybe taken a look at what their soil biome is like with Waypoint Analytical, how do you tell them about deploying that biome? And what practices will help them to do so?

Mick Goedeken: The best way I can describe it is we take the information that, that is in that biome test and we can manage our individual fields more successfully is the way that I would look at it myself. Uh, you know, if I know a field has a lot of phosphorus mineralizing bacteria in it, that's going to make phosphorus more available, then I can be assured that I can manage that phosphorus more efficiently in that field. If I don't have that, then how do I get to there? And I'm a true believer that a lot of the bacteria that we need in our soil, it's there. We just haven't fed it the right way to get it to where we need to get it to. And so then maybe it's a practice where we change what we're doing so that we can build the, build the bacteria there.

Todd Gleason: So Lizzie, you, you're maintaining that it's important to understand how the soil biology interacts with, I guess, the fertilizer management. I think that's right. Uh, so can you improve biolog- the biology to manage that fertilizer? Mhm. And how do you do it? Um, what are the biggest opportunities you think?

Lizzie French: Mhm. Yeah, so from a big picture perspective, right, just anything, any practices you can implement, you know, this part is, is you know, I would I would say it maybe gets re-branded every 10 years or so, but it's still it's the same, it's the same principles of you can boil it down to, you know, you need your microbes need food and they need housing. And if you think of that, you know, from a soil health perspective, that's uh, you know, protecting your soil structure, so minimizing tillage as much as possible, that's going to prevent you from breaking up all of those nice fungal networks that spread out throughout the soil and help your crop get to nutrients, and it's going to help, you know, protect the soil structure, protect the housing for those bacteria as well. You and then you need to feed them, right? And whether that is through organic inputs, like manures, composts, all of those things provide carbon to the soil for those microbes to live, uh, cover crops, just keeping a living root in the soil for a longer period of the year, where you're able to then feed that soil biology longer. All of those practices are going to build up those populations of microbes overall, uh, and help you do more with the fertilizer that you're adding. Because you're able to then, you know, soak up that fertility into that microbial biomass that you're feeding, you're able to, you know, you've got populations of solubilizing organisms and mineralizing organisms that are going to help, you know, if, if those, say phosphorus is getting tied up in your soil, you have that microbial activity that can help kind of bring it back into solution, um, versus, you know, if you if you have low, lower levels of biological activity, that is, um, you know, you'll need to apply more fertility to get the same result in your crop.

Todd Gleason: How important, Lizzie, are conservation practices in in this soil biome, in this whole ecology of the soil and its health? Uh, you mentioned cover crops. I'd also like to know about kind of reduced tillage kinds of things. Maybe waterways, the kinds of things that move water uh, through and out of the soil. It could be even tile. Uh, you, you tell me what's important.

Lizzie French: Yeah, so all of the above. I would say. Um, you know, the tillage, again, it's, you don't see huge increases in soil biology as a result of reducing tillage, but you maintain what you have. You don't end up losing. And then adding in other practices like cover crops or um, application of organic inputs is going to build that soil biology. Waterways is an interesting one. Like I mentioned, I live in Wyoming, so we have the opposite problem of not enough water to keep our micro- our to keep our microbes and our crops happy. Um, but yes, in the, in Illinois, in the Midwest where you have too much water sometimes, and you need that tile drainage, that's actually a really important component of managing, uh, you know, a part of the soil microbiome, a part of that nitrogen cycle that leads to nitrogen losses, right? So nitrification, denitrification, uh, those are both processes that are that happen entirely because of microbial activity. So you have the microbes that are taking that ammonia, converting it to nitrate, you know, if you have a lot of rainfall, that nitrate can end up leaving through your waterway, it can end up getting denitrified by another group of organisms that are going to take that, and, um, convert it back into air, essentially, and so you've completely lost your nitrogen out of your soil that way. Um, and those are all microbes that, you know, you can manage through tile drainage, through practice, you know, like applying a nitrification inhibitor on your nitrogen, splitting your nitrogen application so that there's not so much food for the microbes to then go chew up and get rid of at one time. There's lots of, you know, things that you can think about from a nitrogen management perspective, especially when you, you know, you can see one of these reports and see, "Oh, you know, I have a really high potential to lose nitrogen, you know, given the right environmental conditions, so I need to think about how I'm going to be protecting that nitrogen investment that I'm making on that field."

Todd Gleason: I do want to narrow this down a bit. So, we could talk about the Corn Belt from Western Illinois up through parts of Iowa, even into Minnesota. There's a large portion of that part of the Corn Belt which has similar soils, relatively speaking. Uh, how, how should maybe they manage, uh, their soil biome, do you think? And Lizzie, why don't you start for me?

Lizzie French: I would say this is always a tougher question, right? It's much easier to answer this question for like say the South Plains of Texas because, you know, they really, the the soil there needs all the help it can get, whereas, uh, you know, in the, in the area you just mentioned, you know, Illinois to Minnesota, tend to have, yeah, those really nice like high organic matter, really good soils. So in my mind, the, um, and, and we typically see when we look at those soils, relatively high levels of overall soil biology, even in, you know, conventionally managed fields, just because you got a lot of food there for your microbes if you've got, you know, 4 or 5% organic matter, you're going to have a lot of biological activity. Um, and so, I would in those cases, definitely the, you know, the conservation piece is important because if you're not keeping that soil where it is, you're not going to have that, you know, microbial activity and good healthy soil forever if you're not doing what you can to conserve it.

Mick Goedeken: How about I jump in there and add Yes, please do. Because, because that region that you're that you're discussing experiences a lot of compaction. Yes. And when it comes to microbes, compaction is an enemy. Yes, absolutely. And we don't we don't give compaction enough credit for what it does to to the plants. And if you think about I I wish I had time to go through my presentation on corn roots and the push power of corn roots because corn roots don't have a lot of push power when that corn plant is little. And most of our compaction is at a 6 to 8 inch level across anywhere in the world, but especially in that area, because we end up going into the field when it's not ideal conditions, because we farm on a on a calendar system, unfortunately. And so we'll make passes where we shouldn't, and we create compaction, and when we create that compaction, it hurts the soil biome. It really does. And so managing that compaction is, is something that needs to be done. And, you know, we talk about reducing tillage and I did work in the strip-till world, and I'm a fan of strip-till as long as it's a straight shank, and that we're getting below that compaction layer and actually breaking that compaction layer up. Those are things that are very important.

Todd Gleason: When we talk about the soil biology and the interaction and fertilizer management, as we've been doing some, how, how can you or a producer improve the biology to reduce fertilizer needs?

Lizzie French: Yeah, again, so improving your soil biology in terms of specifically for nutrient cycling, um, you know, it's still the similar practices. Those microbes are there, they might not just be at the level that you need them to be to be able to provide those benefits, and so implementing those conservation, soil health practices is going to help build up those levels. Um, if you have, you know, a soil biology test in hand and it's telling you that you already have high, good levels of soil biology, then that's also a point for you to trigger to think about, "You know, if I have decent levels of organic matter, I have high levels of soil biology, maybe I want to consider dialing back that nitrogen fertility a little bit, cause I can pretty confidently say that you will not see any, you know, you're likely not going to see a yield loss if you have, you know, if you have that organic matter to mineralize, you have that soil biology, you're, you're probably going to, you know, and, and I, I hate to make a hard and fast recommendation for how much to dial back, just because that does depend, you know, heavily on how much rain you're getting, things like that, but, um, that is definitely something to take into consideration when you're thinking about fertility, especially in the environment we're in with, with how the cost of fertility at the moment, um, this type of information can help you feel more confident about your decision to, to dial back on fertility if you have that capability to provide, um, you know, provide those nutrients from your soil and from your microbial activity."

Todd Gleason: What is it that you would like to leave with farmers? What, what kinds of things should they understand about the soil biome, the test that you provided at Waypoint, how they might deploy it? And Lizzie, I guess I'll start with you.

Lizzie French: Um, you know, I would start with that, you know, whether, whether you've realized it or not, you've been farming your microbes this whole time, and, uh, you know, they're they've always been a part of the agricultural system whether we, we recognized what they were doing or, or we didn't. And they're a huge component and it's a big blind spot if you don't know, um, where you're at as a system in terms of, of your levels of soil biology. So, no, I would encourage folks to, um, just to take, you know, take a look, try, you know, just one or two samples across a, across a field that's got maybe some variability in, in yields where you can maybe try to understand, "Hey, is this low yielding area on my field that maybe is normally on a high, a high yielding field, is that a, a biological limitation or is there something else going on there that, um, that you might be able to identify with this type of testing?" Uh, and just be able to, to think through better how to use the fertilizer you're applying most efficiently when you have all of the information available about your field.

Todd Gleason: And finally, because Mick, this is in your direct wheelhouse, are there things farmers should consider before getting a soil biome test?

Mick Goedeken: Uh, yes, consider learning from what you've done, and consider learning and don't be afraid to change, because when you do this biome test, you're going to learn some things. Not every field's the same, a blanket treatment of your entire farm doesn't work. If we start managing field by field, I think we can improve efficiency a lot.

Todd Gleason: Anything I didn't ask that I should have, or any other final comments from either of you?

Lizzie French: Oh, the last thing I remembered, you know, we talked a lot about conservation practices and soil health, the other big thing that we did not talk about from a soil biology perspective was pH. If you have an- if your soil is very acidic, your soil health practices are not like, they might help a little bit, but you're going to be, you're still going to be limited by that pH in terms of your biological activity. That is one of the biggest drivers, um, of soil biology in the soil, and so if you're, if you've, you know, your soil has become acidified over time, that's, that's your first step, you need to manage that first, and then you can work on the other, the other components to build up soil, soil health.

Mick Goedeken: So Todd, remember when we said everything was related, right, early on? Yes. So pH is the driver for biologicals, it's also the driver for the chemistry and the efficiency of that chemistry. Yeah. And so once again, we just tied everything all together again.

Todd Gleason: Mick Goedeken and Lizzie French are both with Waypoint Analytical. Enjoyed us here on the Illinois Nutrient Loss Reduction Podcast. This has been episode 81, "The Role of the Soil Microbiome in Reducing Nutrient Loss." Our program is produced in conjunction with University of Illinois Extension's Rachel Curry, Nicole Haverback, and Luke Willing. I'm Todd Gleason.