Dr. Laura Kavanaugh, chief science officer of Advancing Eco Agriculture, talks about third-generation DNA soil testing, which can provide greater understanding of how soil is functioning and greater applicability of that knowledge for farmers
Acres U.S.A. Can you discuss your background — your context and how you became the chief science officer at Advancing Eco Agriculture?
Kavanaugh. I have an unusual path. I actually started out as an engineer, and my first job out of college was at the Johnson Space Center, working on the space shuttle program. I did that for over 10 years. As that was winding down, I went back to school to get my Ph.D. at Duke — their program in genetics and genomics. I studied fungal genetics and how DNA jumps around between species.
After I graduated, I went to work for Syngenta for over 10 years, and that’s where I started the journey into GMO development. It was an awesome experience because I could connect with all kinds of crops and growers all over the world.
But in that process, I just came to decide that GMO approaches were not a long-term solution. We spent time calculating how long we thought GMOs would work until nature overcame them, and then tried to make increasingly more complicated systems so it would take nature longer. But in the end, nature is always going to win.
I decided, well, that’s not it. I started looking into soils and the interactions between plants and microbes. And not only does that help produce the healthiest plants, with the most nutrients and an immediate crop for the farmer, but there’s so many important long-term impacts. We don’t really talk about these much. I don’t quite understand why; maybe our thinking needs to be a little bit more long-term.
Soil microbes create water retention, so they’re hugely important in resistance to drought. They hold your soil, so you don’t have huge amounts of erosion. There’s a picture from the Smithsonian of a person standing on a road, and the farmland is about six feet below them because it’s eroded away. It’s so powerful because it’s hard to see erosion on a daily, human basis; but erosion is hugely impactful to farms. And there’s environmental pollution — all of our fertilizers are running into waterways, and we have these big red blooms.
Acres U.S.A. Can you explain a little bit more how you came to think that, long-term, this wasn’t going to work — that nature is going to win?
Kavanaugh. Sure. When you’re using glyphosate, for example, you quickly start to see these glyphosate-resistant weeds. You’re spraying millions of plants with this chemical that is designed to kill them, and it does kill almost all of them. But the ones that mutate and are able to survive — and the ones that just by random accidents survive the spraying — those are the ones that are going to propagate.
Nature is always experimenting. That was so interesting when I was studying genetics — DNA intentionally has mutations as it’s being copied. They’re very low level, because it can’t tolerate a lot, but they’re always being perpetuated in the natural system, and that gives the system the ability to adapt. Even though you might have a super successful system, nature is so dynamic that you always have to be experimenting so you could be ready for the next thing.
In the example of glyphosate and weeds, there’s going to be some mutation in some weed somewhere that, just by accident, is able to survive an application, and then that weed is going to perpetuate. It’s going to become the new progenitor, and that becomes a bunch of weeds. Over the course of time, when you spray billions of billions of plants, nature’s eventually going to overcome that. The companies try to stack traits, so there’s more than one thing to overcome; that might last longer, but they’re going to always be overcome by nature.
Acres U.S.A. Was any of your research into the difference in exudates from GMO plants versus non-modified plants?
Kavanaugh. No, it wasn’t. My experience of this whole space — GMO plants — is that it’s not the GMO thing you’re putting in. I don’t know that it’s really such a terrible thing to do a little tweak like that, because nature is always doing that by itself anyway. But GMOs are driven to operate in a very conventional system, and in those systems, we’re constantly doing for the plant what nature would do if we didn’t intervene.
What we see, at least in my experience of biotech, is that we’re not interested in what the plant’s doing to feed microbes because we’re feeding them anyway — we’re giving them all their nutrients — we’re giving them all the protection with our chemicals — we’re doing all that for them. So exudates are not something we’d research. We were perpetuating the plants in greenhouses, where there’s really not fertile soil anyway; these plants are selected to be successful in a conventional system.
Acres U.S.A. So, your concern with GMOs isn’t so much the modification itself as the conventional system GMO crops fit into.
Kavanaugh. Yes, although these biological systems are so complex that you can always have unintended consequences. There’s regulation in the industry, and you try to test and make sure there’s nothing really weird happening, and yet it’s so complicated that it would be hard to say there’s never a possibility of unintended consequences.
It could be all kinds of things. The expression rate of the genes can be changed. With Bt, you’re taking a gene from one species and putting it in a totally different one. How does it function in that new one? How does its presence in this new species affect how that species operates? You can’t test plants under every stressful situation or encounter situations that might be out in the environment. So, there are of course opportunities for unintended consequences.
We don’t really understand the depth of complexity in a plant, so there’s just no way we could fully hope to know what these changes might impact.
Acres U.S.A. Your current work with AEA is in developing DNA testing protocols. Can you give just a brief overview of the differences between different types of DNA testing — first, second, third generation, etc.?
Kavanaugh. Sure. First-generation sequencing was super intensive. It involved gels and stuff, and the person won the Nobel Prize for figuring it out. DNA testing was very slow until the DNA sequencers came out, which are part of the second generation. That hugely advanced the whole field. But the limitation of that technology is that it can’t produce very long pieces of DNA.
Second-generation DNA sequencers make a copy of the DNA. They’re not actually directly reading the sequence — A, C, T, G, etc. — they’re making a copy that’s fluorescent, and then the sequencer can measure fluorescence. It’s ingenious, but because it’s making these copies, the length of each strand is very limited, and it limits what we can derive from the information.
So, if I am sequencing a human — one known species — I know that one human DNA has three billion base pairs, and a second-generation sequencer gives me maybe 250 base pairs. It’s a very hard puzzle to put together, but it can be done — that’s the Human Genome Project.
But when you look at soils, there’s not just one species in the sample, like with the Human Genome Project — there’s millions of different species in any piece of soil that’s not totally dead. Now you not only have puzzle pieces from a single species — you’ve got puzzle pieces from thousands and thousands and thousands of species that you’re trying to put together. The second-generation technology doesn’t work well in that space.
So, somebody came up with this ingenious method within second-generation technology that allows us to look at one single gene and determine the species based on some of the mutations within that one gene. That’s a process called 16S sequencing, and it works really well for bacteria, but it doesn’t work well for other higher-order organisms that don’t have a single gene that you can pick out really well that is common across a species.
So, second-generation technology, because of the limitation of the size of the strand we can look at, is really focused on looking at bacteria. There are ways to look at fungus too, but that’s a separate step; most of the time you’re just looking at bacteria.
Second generation was a great leap forward to start to understand the bacteria in soils — and bacteria are usually the main component — 60 to 70 percent of the species in soil. But there’s a huge component of higher-order species that are not visible in that method. That’s where this new third-generation technology has come in. It allows us to directly measure DNA. It’s not relying on a copy, so it’s able to see really long pieces of DNA, and when you start to look at long pieces, you can identify what species they came from just from one piece.
Acres U.S.A. So, you’re able to look at the entire gene genome of a bacterial cell or the entire genome of a fungal cell.
Kavanaugh. You still can’t see a whole genome — those are very, very large — but if you get a piece of DNA that’s 500 bases long, that’s pretty unique to a certain given species. It can be identified, whereas shorter pieces can’t. Also, you can do the assembly of the puzzle better.
So, now we start to get better assemblies of more species. And actually, you can combine the two technologies to get even better assemblies. The second-generation technology is very powerful in that it can produce a lot of data — millions and millions of little short reads — and when you combine those together via third-generation technology, you get more complete genomes of a lot more species, and all of those go into databases, and we can then measure the fragments that we get out of the soil and compare them to what’s known and figure out what’s there.
With third-generation technology we can also see higher-order organisms in addition to bacteria, and to me that’s really important. Fungi, algae, micro-arthropods, even worms — the whole food web. You’re starting to see all of those things, and now you become limited by what the database knows. We estimate we have 1 to 5 percent sequenced compared to what’s present. You might have less clarity on exactly which species, but you still have a lot of information, and you’re starting to see a lot bigger view of what’s really present.
As time goes on, as we continue to increase the databases, we increase our ability to interpret the data better.
Acres U.S.A. Right. And I’m sure this is where AI comes in.
Kavanaugh. Yes, AI is really important in trying to interpret the data because you’re getting large volumes now. It’s very hard for a human to interpret. We’re starting to try to see patterns across different fields and different crops. This is our new frontier, really.
I think people get too wrapped up in trying to identify the one microbe that’s going to do everything. We have that mentality in farming — I’m going to put this chemical on, or that treatment, and it’s going to fix everything. But the soil is really about diversity; it’s really about a complex community of microbes and fungi and higher-order soil-food-web organisms that are present.
Also, how much are those diverse microbes actually interacting with the plant root? Hypothetically, you could take a seed and plant it in a very fertile soil, and if the plant has been selected over generations to not really look to microbes as partners — because it’s been bred to be fed fertilizers — it isn’t going to be very interactive with the microbes.
This is where regenerative farming is so powerful. We go back and we start to reconnect the microbes and the plants, and we want to find those plant seeds that have a lot of native microbes on them ideally — or we can add them, potentially, with a seed treatment — and we want plants that are genetically predisposed to interact with microbes. And then we need to have a lot of microbes in the soil and on the seed.
But if you can’t measure those microbes, you can’t manage those relationships. DNA sequencing is just another tool in our regenerative toolbox to demystify this whole regenerative farming thing.
I think it’s so hard when we talk about microbes, because it feels like voodoo to people. They see this goopy, weird stuff, and they think, “How is that going to make my plants grow better?” People have come to not think of the soil as a living thing, so they don’t know how important microbes are.
Through sequencing, I really want to change this idea that soil microbes are this mysterious voodoo thing and make it scientific — to measure how well plants are interacting with roots.
Acres U.S.A. What will a third-generation DNA report look like? You submit a sample; what kind of information comes back to the farmer?
Kavanaugh. At a high level, it’s going to tell farmers how well their microbes are interacting with the plants they have in the field and how much diversity and microbial life is in their soil.
We already know that those are going to be very strong indicators of water holding capacity, insect resistance, pathogen resistance, etc. There’s going to be those levels of indicators. As time goes on, we want more understanding of how to link exact numbers. This will take some time, but what’s most important to me is that you measure this and then we tell you what to do about it.
This is the powerful thing and why I’m so excited to be doing this — this is the first time I’ve seen DNA sequencing coupling really tightly with economic understanding. When I give a farmer a measurement, I don’t want to just give them a measurement back; I want to say, “This is what we’re seeing, and so you should do XYZ.”
I think farmers have a lot of questions about applications and how they affect the microbes in the soil. We want to start answering those kinds of questions by having a lot of data. “I have this issue. I’m fearful of losing my crop. I have to spray something; which one of my options should I choose?” This kind of testing can help the farmer choose the one that works and that least impacts long-term soil health.
Acres U.S.A. Right. So, this is a tool that could be used in addition to a sap test.
Kavanaugh. Yes. The sap test is going to tell you what you should do right now for these issues — to compensate for the nutrients. And then DNA testing helps you understand whether microbes are moving in a direction that’s going to continuously improve plant health, if you steward the land in a particular way. I see the microbiome as more of a long-term indicator. But both are actually quite valuable.
Acres U.S.A. The test result that a farmer gets back — I assume you’re developing some kind of score? It’s not going to have a list of the 10,000 different species of bacteria or whatever; but will it include some kind of percentage of fungi to bacteria to protozoa to nematodes, that kind of thing?
Kavanaugh. That is what we are moving toward. I want this to be something farmers can interpret and understand. I’ve seen a lot of reports, and I’m not trying to be negative of anyone who’s done work in a space in the past, but I think a lot of the data that’s produced isn’t necessarily actionable by the farmer, or even understood by the farmer.
We need to present this information in ways such that people can get an intuitive sense of the health of their soils. We’re trying to find that sweet spot between too much information that’s not informative and being too basic.
But in general, our focus is on diversity in the soil. It’s not focused on specific species, because we just don’t have enough knowledge right now. The focus really needs to be more on diversity and overall magnitude of the life in your soil.
Acres U.S.A. How much of a difference in results will a farmer get if, say in an orchard context, they take a sample from soil that isn’t touching a tree root versus if they took soil that was right up against the root of the plant?
Kavanaugh. That will certainly make a difference. We know that each individual plant — and this would be true for any cover crops in the row, any other plant — it recruits a general community that’s unique to that plant. If you’re right up against a root, you’re going to see a much richer community, ideally, because the plant and the microbes are in this dance of nutrient exchange.
We need to look at the bulk soil because we need to have a baseline of how much life is in the soil. But to me, the key to farming is really knowing how well your plants are interacting with that community of microbes. Many things affect that, but at the end of the day, that’s the bottom line in terms of plant health.
All the nutrients are in the soil, and I know that the microbes are there because they know how to extract it and exchange it in this barter system of the plant. So I’m not really as concerned about soil chemistry. I think we’re going to see that the microbes know what they’re doing; we don’t need to compensate so much for nutrients. In the long term, nature’s been here for millions and millions of years, and the reason that we’re still all alive is because nature’s so good at this.
We need to reconstitute that system, and these microbial measurements are going to help us really see that bottom line result in the right direction.
Acres U.S.A. What form factor do you envision for the testing equipment for this third-generation technology? Is it going to be standard centralized lab equipment — the farmer takes a sample and puts it in the mail — or is it equipment that soon, or in the longer term, will be on-farm?
Kavanaugh. I would love to see this pushed down as close to the farm as possible, but right now the technology isn’t quite ready to release on the farm. I’m also uncertain how much farmers want to do that. Farmers tend to want to grab a sample and send it off to someone else. They have so many things to do that they don’t want to be able to do everything themselves. I think it’s something we’ll have to test in the market to see what customers really want.
The computational piece is actually the most challenging piece. Farmers won’t have the computational capacity to analyze it on-farm, but they could potentially upload the data to the cloud or something. I can see this offering potentially moving in that direction in 10 years or so.
Acres U.S.A. Similar to testing bulk soil versus soil right up against a root, if you collected a sample and tested it immediately in the field, how different would the results be compared to if that same sample were sent in the mail and tested a few days later? How much of that soil life dies or changes in that period of time?
Kavanaugh. That’s an excellent question. Certainly, you’d never go wrong by doing it quicker and faster. We’re setting up our lab right now. My vision is to rapidly expand that into many labs. Ideally, you grab your sample and drive it over and get it analyzed.
But you can stick samples in the freezer, and that does a good job of suspending things. That’s been tested quite a bit and demonstrated. But you don’t want to leave them frozen for a long time.
Acres U.S.A. At least you won’t have to send these samples over to the Netherlands.
Kavanaugh. Right, exactly. The idea is to make the delivery really fast; we want to increase the speed at which people get their data back — it doesn’t do a farmer much good to get data in a month or six weeks.
We want to reduce the cost of these tests, and we want this to be accessible to a much broader community of people. Right now, some of the testing drives a number of people out of the market. Our key thing is to make this accessible, because it’s so important, I think, in helping people transition their mentality to see that soil is a living thing, and that life in that soil is your best friend. Then they don’t have to go see a Ray Archuleta demonstration — as great as that is — they can just get the result from their own field.
I’ve just sat in awe of the data I see sometimes. Just to get in your mind that the sample that came from your field or your garden — that there’s thousands and thousands of species in the soil.
Acres U.S.A. Can you give a hypothetical comparison of what you’ve seen on these tests between a conventional corn or soy field and a good regenerative operation? How big a difference are we talking about?
Kavanaugh. It looks hugely different. I mean, I can’t even get DNA out of conventional farming soil, in most cases. From what I can tell, it’s dead. There’s just nothing in there.
Acres U.S.A. Literally — like, you don’t get any DNA data?
Kavanaugh. Right. I can’t extract DNA from it.
Acres U.S.A. That’s incredible. That needs to be more widely popularized.
Kavanaugh. When we do samples for people, that will be one of the things they see — that we couldn’t even get any DNA out of this.
But, even over the course of one or two years, that can shift drastically. This is why this type of measurement will be so impactful for people.
Acres U.S.A. Yeah, that’s great. Is there anything else about this type of testing that that farmers should know?
Kavanaugh. I guess the biggest thing is that biological testing has been missing from the equation. There are tech companies measuring soils because they see the potential application in farming; in this case, though, we’re moving from a farming perspective and adding the technology.
I think it’s going to become so beneficial to farmers — it’s very practical. We actually have the tools to move the regenerative system forward. But we’re not just taking this and throwing it over the fence to a farmer to figure it out. We’re going to be walking alongside them and providing recommendations for practical ways to move that system.
