151: The Role of the Soil Microbiome in Soil Health

Soil is alive and we want a lot of life in the soil. According to Deborah Neher, Professor in the Department of Plant and Soil Science at the University of Vermont, healthy soils have three components. These are a range of different pore sizes to help with structure as well as balance water and air; balanced pH and nutrients; and organic matter to hold moisture and nutrients as well as provider microbes. Soil structure is created by mineral particles, bacteria, fungi, and plant roots. What determines a good quality soil depends on the ecosystem – a forest has different needs than active farmland.

Bacteria and fungi are the life forms most associated with soil health. Some tests show the number of fungi and bacteria and their ratio to one another. However, they are not showing what is in the soil and there is still limited research on what these fungi and bacteria are doing. Often bacteria are associated with negative health factors. But there are many good bacteria that promote plant growth by producing nutrients or making nutrients more available. Others provide biological control. And others convert nitrogen in concert with legumes. Fungi can also be good and bad. Their structure is like linking pipes so they connect plants. This can help cope with drought conditions by pulling water from faraway sources.

Deborah also touches on how to properly compost to kill off pathogens and weed seeds. Through research, she found that the process is more complicated than knowing the nitrogen to carbon ratio – the type of carbon matters! Her lab tried the same nitrogen to carbon compost “recipe” in three different production methods: windrow, aerobic static piles (ASP), vermicomposting. Each final product had completely different fungal and bacterial communities. Listen in to learn what kind of carbon is best for disease suppression.

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Transcript

Craig Macmillan 0:00

I'm your host, Greg McMillan and our guest today is Dr. Deborah Neher. She's a professor in the Department of Plant soil science, the University of Vermont. And today we're going to talk about soil health. Welcome to the podcast.

Deborah Neher 0:10

Thank you. It's a pleasure to be here.

Craig Macmillan 0:13

Before we get rolling, I understand you grew up on a farm, you have some background in agriculture.

Deborah Neher 0:16

I do. I grew up as a fourth generation family farm in Northwest Kansas, where we grew wheat and sorghum and had some livestock. And as far as my educational background, I have formal education in environmental science, as well as plant ecology. And I did my PhD at UC Davis in plant pathology. Since then, I've kind of merged to the ecology and the agriculture and I consider myself a soil ecologist. So my area is biology, but I work in soil.

Craig Macmillan 0:44

That's awesome. Because there's a lot of life in the soil. And we're about talking about everybody's interested in healthy soils. We have government programs now about topic. We have conferences, we have articles, we have books, but this is one of my favorite questions. When I talk to people about this topic I started with, what is your definition of a healthy soil?

Deborah Neher 1:03

That's a great question. And I know there's a number of definitions that are out there. But as a biologist, I want to first emphasize that soil is alive, and that we want a lot of life in the soil. A healthy soil would be one that's porous, that we have a number of, you know, range of different pore sizes, which give the soil structure and this also helps balance air in the water and soil. We need a chemically balanced soil, one that's valid for pH as well as nutrients in the soil. And then we need the biological part. And that's usually relates to organic matter, living plants. And plant roots are an important piece of that, too. Organic matter is kind of unique on the surface of organic matter, it's got these negative charges, and that attracts nutrients that have positive charges, like magnets, you know, opposites attract, yeah. But in addition to that nutrient holding capacity, it also brings in the microbes, and that's really a source of the microbes into the soil. Plant roots are also a source and support of the microbes in soil. So healthy soil, it's porous, it's chemically balanced, and it contains organic matter.

Craig Macmillan 2:10

The actual parameters for that are probably going to vary depending on the ecosystem, right? So what are the challenges for us? But how do I know like, how do I what do I manage? What do I look for? And obviously, I think, from what I can see, for different crops, I think the ranges are still kind of being figured out. I think what most people would like as well, I've got a five on this variable, do I need a 10? Or am I okay? And it doesn't seem to be that simple.

Deborah Neher 2:33

It is not that simple. It's really unique site by site, you know, one number can't really be applied to everything. When you get a number, you have to think well, what's good for what? And so a number for a good agriculture system might be a different number or a bad number, say, for a forest system, or for a functional wetland. So we have to really think about what is the the type of ecosystem? And what kind of land management practices are we interested in? That really depends and also what types of soil we're on, you know, what is good on a sandy soil might be different than if it's in a clay soil, heavy clay soil, for example.

Craig Macmillan 3:12

Exactly. And so today, I want to focus on the microbiome aspect of this. And we do you have a number of different types, classes, find ones even of organisms, bacteria, fungi, actinomycetes, silicates, nematota, there's probably others that I'm forgetting. But today, I want to focus on the bacteria and the fungi, because those are two things that you can send to you send a sample to a lab, and you will get some measures of those. And it's like, okay, cool, but what are they doing? Right, so what role do different kinds of bacteria play in the functioning of a healthy soil?

Deborah Neher 3:44

A great question. And I'll just start with, I think we have to be really careful not to over generalize and say all bacteria are alike, or all fungi are alike. Because there are such a broad diversity. There's 1000s of 1000s of species, and different species do different things. And I also like to think of microbiome kind of like an orchestra, you need all the different players and working together. You don't just want specialists and soloist, you need the whole ensemble, right? If we go back to bacteria, there's a lot of different bacteria there are people often think about pathogens, that's the first thing on the mind is the bad guys. But there's a lot of beneficial bacteria, as well. There are bacteria that we call them plant growth, promoting bacteria, they're producing chemicals in the soil that are stimulating plant growth, the plant might perceive them as kind of like a plant hormone, perhaps or it could be converting a nutrient that makes it more available to the plant. There are some bacteria involved in biological control. For example, there's a bacillus subtilis that's a known as a biological control. And they can do that by just through their own natural defenses. You know, they're going to antagonize or compete with other microbes. There are also bacteria that are involved in nitrogen fixation, that are associated with legumes in the nodules of the legume, they create like a little factory in there, where they're converting nitrogen gas from the atmosphere, and converting that into ammonium, which is a form that the plant can take out. And one thing we have to be careful in bacteria is not to think they're all alike, as I mentioned, and even, we go well, then let's get down to family or maybe get down to genus, but you even have to be careful. Not every species within a genus is the same. For example, there's one called Pseudomonas and there's one species of Pseudomonas Pseudomonas syringae. That's a pathogen. There's another species of Pseudomonas Pseudomonas fluorescence, that's a well known biological control. Now, fungi, fungi have equally different, you know, variety of lifestyles or things they do. There's also fungal pathogens, there's those that are decomposers mycorrhizae. That's a popular topic these days, that's a type of fungus. The cool thing about them is they're like a big plumbing system, they have this body structure that's like long pipes. They're called hyphae. And they can connect between different plants and go long distances. So they can be helpful to help plants say cope with drought, for example, because they can pull water from a great distance and pull that into a central use. I also mentioned the that an important attribute of healthy soils, I think, is aggregate structure. And these aggregates are really a composite of not only the mineral particles of soil, but it links in the bacteria that produce sugars on their outside their sticky, helping those hold together. And the fungal hyphae, which act like threads that weave these together and then plant roots to they're really working in concert with that soil to help provide this structure. Aggregate stability is I think, an excellent indicator that we can measure of soil health.

Craig Macmillan 7:04

Is that's related to bulk density?

Deborah Neher 7:06

Ah, good question. Indirectly, aggregateability can be related to bulk density. Usually, if you have more aggregates, you actually have lower bulk density. Okay, because an aggregate is going to have open spaces, it's going to have a balance of air and water. So bulk density would be just thinking about the solid particles per unit volume. So if you fluffed those up with more spaces and voids, within that aggregate, you'll have less bulk density.

Craig Macmillan 7:36

Is there is there a way that I can can measure or investigate aggregates?

Deborah Neher 7:41

Yeah, that's a good question. As far as aggregate stability, there are some really fancy advanced methods that organizations like NRCS, the Natural Resource Conservation Service do and if you're a soil scientist you get into there's also some really simple things that you could do. The simplest one I ever saw was taking an egg carton and in the base of those putting clumps of soil and then adding a little bit of water into each of those and see how much that disintegrates once you add water. If it just all crumbles and become small particles, you do not have very good structure. It should stay fairly intact when you're dripping that water on there.

Craig Macmillan 8:22

Interesting interesting. I'm just thinking about clay so we have a lot of a lot of vineyards are in clay, clay, gravelly clay, loams, etc on the Coast California and and other places. And how hard it is the water to go in to those clay soils. So I'm thinking about like dropping putting water on a chunk of clay and and just seeing it kind of get slimy.

Deborah Neher 8:44

Yeah, clays are tough clays are really tough.

Craig Macmillan 8:47

Are there ways to at least get a sense of how much life there is in this the soil? I mean, I know that that like, oh, that's got to have this or that. But other kind of metrics that are ways of investigating or anything that I can do. So for instance, I've been looking at some lab reports recently where they give us a total bacteria to active bacteria ratio, and they give us some ranges, then they actually will give us some actual identifications of particular nematodes that are found total funded active. Okay. So I've been trying to figure out kind of how to interpret that. But then I'm also curious, so how do you cope with that kind of thing? Is this a gene sequencing thing? Or is it a mass based thing or you pour the reagent on and it turns blue?

Deborah Neher 9:29

Great question. And I've worked with some of the methods, those measures that you're talking about are really, I think, defined as total and active bacteria, total and active fungi, right? Those methods, at least when I've used them involve a stain, kind of a fluorescent stain that you put on. And then you're actually making those into onto microscope slides and using the microscope so you have to spend time behind the microscope and you're counting, you know the number of cells or the number of hyphae that are crossing, you have a grid there, a grid pattern, and you're counting it. And that allows you to be quantitative. It's a laborious method, I would say it is the gold standard, if you want to actually get an estimate of total microbial biomass and activity, however, it's very tedious and very laborious. Another approach that people have used is one that's called PLFA phospho lipid fatty acids. That one is an easier method to get an estimate of biomass and activity. These are giving you some estimates. But this is where I say we have to be careful about overgeneralizing because this tells us nothing about who is there or what they're doing. We just knows there's a lot of them. And that's step one. Sometimes we hear a generalization about what about the ratio of fungi to bacteria, for example, and it's been touted that we want to strive for a higher ratio of fungi to bacteria. I'll tell you this concept really comes it from literature and science that was done in the 1980s. Really, the focus was on the effect of cultivation and tilling the soil. That's what it's really representing. Because when we go and cultivate and till soil, in fact, that's probably the most destructive thing we can do to the soil biology, you're just like ripping their house in their habitat into shreds. You're wrecking that pore structure. But anyway, so in cultivation, when we have highly tilled soils, that tends to favor bacteria. I mean, if you think about it, lots of threads, you know, for the hyphae. If you're slicing through there with knives, you're breaking those up. So that's deleterious to fungi. It's also deleterious to earthworms and also deleterious to other micro arthropods and larger organisms. So with cultivation, it's known that those tend to be fairly bacterially dominated soils. And so the thinking is, then if you go with a reduced till, or no till you're going to have more fungi. And so you'll start to see that ratio increase that, you know, tells us something about cultivation. I guess being trained as a plant pathologist, my first thing is we need to know at least who is there? Are we talking about pathogens? Or are we talking about beneficials? If all of those and most of them are pathogens, we don't want them? That's not necessarily a good thing, if all those fungi are pathogens, like ferrocerium or verticillium, or yeah, so we need to know who they are. That's the tip of the iceberg, right?

Craig Macmillan 12:38

You're working on related work, you actually do go down to the species level, when you do figure that out to describe the community in whatever system it is you're looking at. How do you actually do that?

Deborah Neher 12:47

Traditionally, we we use agar plates, and we try to culture these organisms. And it took very specialized media, some organisms grow faster than others. So we put things on there biocides to try to inhibit the ones we didn't want and allow the ones we did want, we call that a selective or a semi selective media. But then we learned only about 10% of microbes can live on a petri dish. So we were just looking at a subset of these organisms that did well. And consequently, we are missing a lot. But that's where the molecular techniques have come in, and helped us discover all those organisms that are not able to be cultured on a petri dish. There are techniques where you can take a soil and you can extract the DNA out of that. And then we use a series of steps, we call it amplicon sequencing, we put out what's called a primer on there, and it's going to copy a specific region of that DNA. And it's usually a region that's highly variable between species. And then once we extract that DNA, we can go through a process called a PCR Polymerase Chain Reaction just makes lots of copies. And then we can look at the sequence and there's databases that have sequences, and that helps us match to who is there, you know, the technology keeps improving, the longer the pieces we have, the better resolution we're gonna have. If they're short pieces, we may only get to family or genus longer pieces, that technology keeps improving. So we'll get more species.

Craig Macmillan 14:27

Do you think this kind of technology is going to find its way into the commercial realm? Or is this a strictly an academic thing at the moment?

Deborah Neher 14:34

Oh, I think definitely. And the price keeps coming down. So it's getting cheaper and cheaper to do. What I mentioned is who is there? What technology we still have to develop is what are they doing? That's a different kind of technique, and that's still at the academic level, and uses some different methods where we actually have to look at the genes and link them into a function. Are they fixing nitrogen? Are they producing say an oxidative enzyme. Antibiotic? What are they doing that part's academic. As far as who is there? I think this is where we have to understand their ecology, we need to know who and a little bit what they're reflecting, or is knowing that say, a lot of E. coli is there, that might be telling us do we have a contamination problem, you know, for example, if we know that's it, then we can prepare like a probe, a little tag that says, I want that organism and we can actually go fishing for it, pull it out and quantify it and say, this is how much we have. And then we could develop a model and say, once you're above a certain threshold, this could be risky. But we have to link it to say, a land management practice, or some known contaminant or something about land management, so we can help interpret what that means.

Craig Macmillan 15:52

So it sounds like to me, at the practitioner level, or at the industry level, we have some broad categories of things that we can find out. But there's a lot behind the curtain, we are guessing a lot. And so what's your advice, if I'm in that kind of situation where I have some information, but I don't have the kind of maybe I would like from a science standpoint, it's gonna be very important, obviously. But you've said different microbes do different things, what's kind of my best bet in terms of how I should proceed, or their techniques or things changes maybe, or the things that I might look for. So for instance, you talked about pathogens, I should be taking the top, I should be taking the top of the plant the plant part and evaluating it in relation to the soil health. So I might, for instance, have a high, I don't know, total active fungi, but maybe they are deleterious. And so I should be looking at the plant, seeing how the plants reacting that just simply what I'm getting out of the analysis, because it's kind of like what you want kind of what the grower wants, this is my take what a grower wants to say, okay, I'm gonna take a sample of soil, and what set it off? And then I'm gonna get a report back, and they're gonna tell me, yes or no, do this. Right. That's kind of where we're at at the moment. And so do you have any advice for how I can work with that? I guess I'm looking for some help on like, okay, gonna report back what I do next thing is just kind of kind of fishing for something here.

Deborah Neher 17:14

I think the first step is you always want to be scouting your plants. Do you see some kind of symptom? How well is it growing? Is are those leaves yellowing? Do I see lesions? Above ground? Is there something below ground? I mean, I think that's step one. So am I expecting there to be a problem? Those are some factors that we'll look at, is it a disease or not? Or is it an insect? You know, it could be that kind of thing. So we need to see, are there lesions are there root nodules? Are there something that doesn't look very healthy? That's step one. And I was gonna say for sure, if that's the case, then I would send a sample could be soil, or it could be part of the plant that has the symptoms into say, maybe a plant diagnostic clinic, but a lot of land grant universities have these available to growers that would help you identify a disease. There is interest in just general microbial activity, because everybody's trying to increase the activity and the diversity, etc. Commercially, there's limited types of tests available. The ones that are available are going to do like you said, the active and total bacteria or fungi, there are some estimates of respiration, which is another measure of activity, right. And there's another method that's fairly new. It's a per manganite method. It's a different chemistry method, a different way of looking, I can get your reference for the, you know, at the end, this per manganite method is is really linked in with management practices, and has been shown to really link nicely with that rather than just respiration. The problem with respiration is that you don't know who is respiring is it fungi, bacteria, it could be the plant roots itself, too. So it's really difficult to interpret. That's the really hard thing is it's so general, you don't know where it's coming from. On the beneficials and looking at the overall community. There are not very many commercial labs available yet. This is something I really would like to see. And I keep pushing it. One of the challenges is trying to get enough people that are trained to actually run these tests. Yeah, yeah. Like I've worked with some nematode communities, and I don't look at just pathogens but beneficials and there just aren't enough people in the world trained to do that. However, I keep if we can narrow down a particular like a dozen or a couple dozen organisms that are really like sentinel species are really tell us something important. Then we could develop molecular probes to those that specifically pull those out and help us interpret it. But that is still really at the research phase. Those are some of the things I'm going to do. But I need more people like myself so that we can accomplish this faster and maybe in my lifetime.

Craig Macmillan 20:12

Yeah, that's, that's a whole nother show the state of science and encouraging scientists of the future. You know, you don't even think of like little Jenny at age 10. Hey say, Jenny, what do you want to be? I want to be an ecologist, you know, it's not very normal and get that all the time. But we need more kids like that. Right? Right. Because nematodes are incredibly fascinating. They are just mind blowingly fascinating. Before we before we talked about that, or if we have time to talk about that. I wanted to get to compost recipes. You've done some interesting work where you studied different compost recipes, including what the manipulations of the windrose were, and then what the impact was on soil and fungal communities coming out of that. What kinds of things did you learn?

Deborah Neher 20:56

Sure, let me just tell you how I got started on compost. Yeah, so there was a year, a couple years here, I'm in Vermont. So there were a couple of years here that we had some major epidemics called early blight, or late blight, and these affect solanaceous, crops, potatoes, tomatoes, it was just bad year bad weather for this particular epidemic. So the farmer said, What do I do with my disease plants? Well, the extension agent said, throw them in the landfill. And I'm like, you know, the idea is you want to have keep the organic matter and the nutrients on your farm, we're not throw them in the landfill. So I said why if you compost these properly, you should be able to kill those pathogens and those weed seeds. So I set up a demonstration project. And we demonstrated that, okay, it works. Now the catch is you've got to really do a particular type of composting, it's got to be really monitored, it's what we call a thermophilic composting. It's got to reach high temperatures, and it says high temperatures that really helped kill the pathogens and weed seeds. Okay, that part is pretty well defined guidelines for that are, you know, outlined by the National Organic Program. And those work, the thing that it doesn't do is tell you what comes after the composting, they tell you the guidelines how to reach the thermophilic. But you don't want to stop there. Because if you let that cure and mature, you're going to have a lot of recolonization by beneficial microbes, and micro arthropods that are going to help you manage diseases. But you got to let it you got to be patient and allow this recolonization it happens naturally. These rules that are guidelines that are developed by say National Organic Program tell you use a carbon to nitrogen ratio of say 25 to 40 to one, so that many units of carbon two per unit of nitrogen, but they don't tell you what kind of carbon and carbons come in different flavors. There's carbons that are like carbohydrates that are like sugars, starches, they're really easy to decompose. And there are those that are like lignans and cellulose that are more difficult to decompose. We took some recipes where we could keep carbon to nitrogen ratios constant, but just changed the type of carbon, we follow the recipe. But what we found is you get completely different outcomes, that the type of carbon will completely change the micro, the bacterial and the fungal communities. So they're very unique. So as I say, recipe matters. You really need to think about what are you putting, hay, are you putting softwood you know, wood chips you puting some hardwood bark? What is it? As far as disease suppression they found out, you know, including some wood chips in that the bark and they're generally support a product that has more disease suppressive qualities.

Craig Macmillan 23:56

Okay. Is there a reference or a compendium or a book, for instance, that might have some more need to have information about these techniques. So people can try different things.

Deborah Neher 24:10

I have a peer reviewed scientific articles that outlines the actual research. But I've also just summarized a very large comprehensive chapter on disease suppression and using compost for disease suppression that just came out in a new book called The A Composting Handbook that was published in December 2021. And that is now available for purchase. I think it's about 1000 page book. So it's very comprehensive. So I've got a chapter that's almost 40 pages long in there, but it includes tables of which kinds of pathogens can be managed with compost, which kind of diseases you know, that's that's one of the features that I think will be useful to people that want to use composting.

Craig Macmillan 24:55

And I'll put a link to that in the in the show notes.

Deborah Neher 24:58

Great.I have one other thing I wanted to do. mentioned that I tried it, because you mentioned about the process and what's going on in the windrows. So we tried another thing, there's different means of achieving this thermophilic pile, you can have a windrow, where you can be turning it or you might keep it if you're trying to save land space, you have aerobic static piles. ASP is another method, just forcing oxygen into that. And then so those are two methods. And then there's a type of vermi-composting, working with earthworms that can also be used. Now, the thing with earthworms if you get too hot, it'll kill the earthworm when we're trying to do compost that can be meet qualifications for certified organic, it has to be shown and demonstrated that you've reached the temperatures. Long story short is we came up with the same recipe and tried curing it three different ways through the windrow the ASP or the vermi-compost. Start the same recipe, different curing process, completely different fungal and bacterial communities. So when people say, oh, just throw stuff together, I'm like, No, you really need to think about designing that compost. It leads me to think that eventually we need some designer compost, some that are made unique for different applications. And there's also a need to have a little bit more standardization and labeling of these products. So a consumer knows what they're getting. If you're gonna pay more, you want to know you're getting something better. Yes. You know, than if you're going low bid.

Craig Macmillan 26:37

Yeah, exactly. And in the in the vineyard world, I've been very pleased to see the composters, at least in our in a separate press California, you know, being able to demonstrate their techniques and give you the analysis and allow you to compare products pick like well, what I'm looking for here is I'm looking for nitrogen in some form. Okay, here's an analysis of nitrogen, because I'm less interested in and I'm more interested in carbon in some form, what kind of books organic carbon, so we fortunately, we're getting some of that, you know, so we're getting there. But obviously, there's way more work to do, like you said, designer products for particular situations, particular paths. And it's exciting. I think we got a long way to go. But we're doing really well. And I think people just generally interested in compost has a really good thing. And they're interested in, in learning more, I think is there. I think a long time ago was a hay compost is good. Like that was it. You know, compost is good. And then as time has gone on, we've got more experience, we've learned, hey, I need to be a little bit more sophisticated than that. So we're kind of out of time. But is there one thing regard to soil health that you'd suggest to our listeners, if you want to prove the health of their sauce?

Deborah Neher 27:43

Well, I think to me two biggies for really improving soil health is you want to keep plants in the system, and especially perennial plants, and that applies very much to vineyards. That's, that's good and also to reduce the tillage. So if we can keep the ideas, keeping plant roots in there all the time, and reducing the tillage that's going to really favor a more robust, active, resilient soil community and thus better soil health.

Craig Macmillan 28:13

That is good advice. I think there's a lot more to talk about, which I would love to do. We'll see if we can do that in the future of there's so much going on here. Where can people find out more about you?

Deborah Neher 28:23

Well, I will provide some links, you know, that will be available to you at the podcast site, some links there. I also have a personal web page that I make available, my various references as well. If you just search by name on Google, you'll find me everywhere.

Craig Macmillan 28:40

Yes, I noticed that. And yeah, I've got we will have a link to the lab, the near lab webpage as well, some other things and then a ton of links to various articles, podcasts, chapters. You've done a great job of getting out there. I really appreciate that a lot of folks do work kind of in a closet. And you very much had been doing some extension work and getting the findings out there.

Deborah Neher 29:01

My father would always ask me, well, what good is this for me? So it always kept me thinking I owe everything I learned in do I need to come back around and think about the application.

Craig Macmillan 29:13

I want to thank our guest, Dr. Deborah Neher, Professor of Plant and Soil Science at the University of Vermont.

Transcribed by https://otter.ai