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Forage legumes for disease suppressive soils

How often do you see rhizobium nodules the size of golf balls? I have only observed them on sun hemp.

The nitrogen fixation process of rhizobium bacteria in legume nodules has a reducing effect and shifts the soil microbial community in the direction of disease suppression. Forage legumes should be a part of our crop rotations and ecosystems for more reasons than just supplying nitrogen. Because of their reducing effect, they also increase manganese and iron availability from the soil reserves which are present in the oxidized form that plants don’t utilize.

2020-07-27T06:55:28-05:00July 27th, 2020|Tags: , , , , |

Oats, a very effective disease suppressive cover crop

Many have observed the plant performance improvements of crops being grown after oats. It is fairly common to observe not only an increase in disease resistance, but also a yield increase because of the increased manganese availability, which increases a plants (and animals) reproductive performance.

But there is another very important point hidden in this dialogue. Before crown rust was a significant challenge, oats did not have a reducing/disease suppressive effect. The plant secondary metabolite profile of oats changed once they were bred to be resistant to crown rust. This change in the metabolite profile resulted in a changed profile of root exudates, which converted a plant with a former oxidizing effect on the soil redox environment – a disease enhancer, to a reducing effect, or disease suppressive.

This means we need to consider the possibility that some plants which currently have an oxidizing effect, such as modern wheat, can be shifted to having a reducing/disease suppressive effect when we change the plant metabolite profile. We know we can change the plant metabolite profile significanly based on how we manage plant nutrition. Breeding is not the only pathway, and certainly a slower pathway, to developing crops which produce a disease suppressive microbiome.

From our interview:

John: You spoke briefly about the use of crop rotations and that 85 percent of the effect, in terms of disease suppression, happens from the prior crop or the prior cover crop. What are some particularly useful crops or cover crops that have a very strong disease-suppressive effect?

Don: Again, that’s going to depend on your disease and your overall soil biology. For instance, if you’re dealing with take-all, Gaeumannomyces graminis—the root and crown rot of cereal crops—you’ll find that brassica species have a suppressive effect. Perhaps the best cover crop overall is oats—another cereal crop. When we bred crown-rust resistance into oats, this also gave us an oat crop that provided disease control—take-all control—for our wheat and barley.

The reason is that crown-rust-resistant oats also produce a glycolcyanide root exudate that suppresses the manganese-oxidizing organisms. If you suppress the manganese-oxidizing organisms, you also suppress the manganese oxidation by the pathogen that is required for virulence. So you’ve increased the manganese availability for the plant—for its own resistance.

The shikimate pathway is a pathway that gives tolerance or resistance to take-all, because that’s where the lignotubers are formed. Lignification and callousing—all of those materials are produced through the shikimate pathway. And manganese is a very critical component in that pathway—at six or seven different steps in the pathway. If you inhibit the availability of manganese—if you have a good, strong mineral chelator that ties up manganese—you’re going to increase take-all, because you reduce the functional availability of manganese for the plant in its own defenses.

A plant like rye is very efficient in the uptake of manganese and other micronutrients. Rye takes care of itself with its resistance to take-all pathogen, but it doesn’t do anything for a subsequent crop. It does very well, with very little disease pressure, because it’s very efficient in taking up manganese and other micronutrients. If you have triticale, which is wheat-rye cross, if it doesn’t contain that section of the rye chromosome that is responsible for micronutrient uptake, then the triticale will be as susceptible to take-all as a wheat crop.

You don’t get a crop-rotation benefit out of rye like you do from oats. The root exudate of oats has a very strong antimicrobial compound against the manganese-oxidizing organisms that make manganese less available. You’ll see that effect—that change in the soil biology—carry on for two or three wheat crops after an oat crop. Subsequent crops will have very little take-all. Oats probably has the most dynamic effect in this regard.

Brassica species—canola or mustard—also produce quinolones and some other materials that have a similar ability to reduce take-all as the glycoprotein in oats. Following canola, you’ll see an increase in some of the other diseases. It’s not just influencing one particular disease. If you’re using Roundup-ready canola, genetically engineered canola—where you’re adding a very strong mineral chelator, because that’s how glyphosate works, by tying up those minerals in the physiology of the plant—if you’re growing Roundup-ready canola and applying glyphosate, it’s going to move out of the root exudates and change that soil biology. Then you may see a reduction in take-all, but you see a very dramatic increase in Fusarium root rot, as well as Fusarium head scab and the toxins of that particular plant pathogen. So, you’re changing the dynamics of the system with the particular management tools that you use. 

Managing soil borne pathogens

For soil-borne pathogens, there is no correlation between the presence of the organism in the soil and the expression of the disease in the crop. Infections severe enough to produce crop loss are correlated with the absence of suppressive organisms more than the presence of the pathogen.

Soil colonizing organisms are usually dependent on crop residue for nutrition and generally have higher nutrition requirements. Soil inhabiting organisms have much lower nutritional requirements and remain present in the soil more or less constantly.

Both groups can be effectively managed with cultural management practices to prevent any infections from occurring. From the podcast interview with Don Huber.

John: That’s a very impressive statement. We can manage disease and pathogenicity based on how we manage our soils, from a cultural perspective. That’s a very, very important perspective that I think we don’t commonly hear in agriculture.

You mentioned a number of different management tools: crop rotations, using cover crops, tillage, the impact of moisture, etc. Earlier you spoke of the differences between soil-borne pathogens and soil-inhabiting pathogens. It’s fairly well understood that we can use crop rotations to manage soil-inhabiting pathogens. Are you suggesting that it’s also possible to use these tools to manage and suppress soil-borne (colonizing) pathogens?

Don: Very definitely. Most of our soil-borne (colonizing) pathogens have very limited genetic resistance. We rely on those management techniques to control them. Sometimes we don’t recognize it as much as we need to, but soil-borne pathogens have a much more limited relationship as far as population dynamics. We may measure the population of spore load and other things for organisms like Fusarium, but the organism is there in a high-enough population that regardless of what we do—if we didn’t have the other organisms associated with it—it would take our crop.

Soil colonizers colonize only as long as they have a nutrient base to function with. So we can either extend the time between susceptible crops—which we typically do with most of our potato pathogens, for instance—we see them building up in two or three crops and we want to break that population down. Same thing with anthracnose on corn. It’s a soil colonizer. Cephalosporin on wheat. All of those organisms survive in the residue. Many of them even produce an antibiotic, so they slow down residue degradation to extend their lifetime in the soil—so that other organisms aren’t able to colonize that food base.

This is quite different from Rhizoctonia or Fusarium—many of the Basidiomycete-type pathogens are very excellent soil inhabitants. They don’t require the base of nutrients that many of our colonizers do.

How the form of nitrogen influences disease suppression

Nitrate and ammonium nitrogen have dramatically different impacts on soil biology and possible pathogens. Some pathogens are enhanced by nitrate and suppressed by ammonium. Others are the exact opposite. Most (but not all) soil-borne pathogens are enhanced by the presence of nitrate. This corresponds to the impact of reduced vs oxidized environments, since ammonium is the reduced form of nitrogen, and nitrate is the oxidized form of nitrogen. In general, reduced environments are very disease suppressive, and oxidized environments are disease enhancing.

I have had many discussion about this topic with Don Huber, inlcuding this one on a podcast interview.

John: What are the impacts of nitrogen and nitrogen applications on developing disease-suppressive soils?

Don: Most of your soil organisms are hungry for two things. One of them is nitrogen. The other is carbon. When you change either of those nutrients, you see tremendous stimulation of a lot of organisms in the soil, depending on what your source of nitrogen is.

One of their primary pathogens on a lot of vegetable crops in Florida is Fusarium oxysporum. It’s a vascular Fusarium. Growers can get pretty much complete control by using nitrate nitrogen and calcium. If they can stimulate nitrification, or if they apply nitrate nitrogen, potassium nitrate, or calcium nitrate—and also use some liming (lime = an oxidizer) to get their pH up—they have fairly effective control of Fusarium wilt diseases.

With tobacco, where we use fumigation to control some of the soil-borne diseases, you should have at least 30 percent of your nitrogen as nitrate nitrogen. If you don’t—if the plant is taking up all ammonium nitrogen—you can get into a carbon deficit because the plant detoxifies the nitrate or the ammonium nitrogen by combining with photosynthate from photosynthesis; that provides the carbon base for those amino acids. Then the nitrogen is translocated as the amino acid. If you don’t have enough nitrate nitrogen present to buffer against an ammonium source—if you’re going to get fumigation, because our soil fumigants tend to knock out nitrifying organisms—or if you don’t get nitrification there, it stabilizes in the ammonium form. It can be a drain on the carbon and the energy availability until that ammonium is detoxified and utilized by the plant.

John: I’m thinking about your description of how many soil-borne pathogens—soil-borne fungi such as Fusarium and Verticillium, for example—are dependent on oxidizing manganese and limiting manganese absorption by the plant. If that were the case, what would be the impact of adding ammonium to such an ecosystem—where you have a reduced form of nitrogen? What would the impact of the ammonium be on these soil-borne pathogens?

Don: On that group of pathogens, you will see a tremendous reduction in disease—with the ammonium nutrition. I wrote a chapter in one of the annual reviews on the impact of the form of nitrogen. You’ll see a tremendous benefit in different organisms by the form of nitrogen that the plant is predominantly supplied with. If you modify the environment so that those soil microorganisms make those conversions, you’ll see that the form of nitrogen will be available for the plant.

So, it’s important that you have both the management tools as well as the form. Most of our soil’s nitrification takes place very rapidly, so you need to do something to inhibit nitrification. We can do it biologically—we can modify the speed of that reaction so that we can increase the amount of nitrogen in nitrate or ammonium. When it’s taking ammonium nitrogen, you have a reducing environment. That reducing environment is favoring manganese-reducing organisms so that there will almost always be an increase in manganese availability for the plant—when you predominantly use an ammonium form of nitrogen. The more rapid, oxidative form is the nitrate source of nitrogen.

Developing disease suppressive soil

Diseases and insects only become a problem when plants are unhealthy, lacking nutritional integrity and microbiome integrity. The tools of nutrition management and microbiome management are so effective, they have been and are used as management protocols for bio warfare weapons mitigation.

From the Regenerative Agriculture Podcast with Michael McNeill:

John: Michael, we’ve been circling around this topic of soil health and the impacts of tillage, herbicides, animal manures, cover crops, and so forth. At the beginning, you mentioned that there’s a correlation between soil health and the diseases that are present. You mentioned some work you were doing in Maryland—studying diseases as a weapon. What did you learn from that experience? And how does all of that tie into what we’re talking about?

Michael: Let’s say you want to use a fungal disease as a weapon—that you can get this disease introduced into the soil. Not only does it kill a crop this year—it’ll continue to kill it into future years. So hey, that’s a pretty good weapon—you shut down a people’s food supply. They have a problem.

Well, if you have good pseudomonas bacteria in the soil, they act as a policeman in the soil, if you will, and they’ll take out the pathogenic fungi that can arise. But if you use products like glyphosate—that’s an antibiotic type of product—you’re going to kill all the pseudomonas, and then you have no protection. And it’s very easy to get a huge population of fusarium going in the soil, which probably is a pathogenic fusarium—or pythium or phytophthora. You’ve lost the natural balance. If you have that balance, though, the pathogenic fungi are not going to do much to you. Your good bacteria will clean it right up.

John: So you can actually have a disease-suppressive soil where you don’t have challenges with those pathogenic fungi. I think I also heard you mention that you were working on developing solutions to those diseases as weapons. What were the types of solutions that you were working on?

Michael: There are all kinds of approaches. If you need a fast cure, of course you’ve got to look at chemistry and the fungicides and that sort of thing. But what you find is that if you get the soil contaminated, how do you fix it? Because if you put anything on it, you’re going to kill everything in the soil. Using a soil sterilizer is not necessarily a great idea. But there is microbial life in the soil that will hold everything in balance. And if you have the right nutrition available, everything will take care of itself.

I’ll use you as an analogy, John. If your nutrition gets pretty poor, you’re going to get pretty run down, and you’re going to be very susceptible to all kinds of diseases. Would you agree?

John: Oh, I think that’s just the story of the people who are trying to sell me supplements. (Sarcasm, I take many supplements, and believe they are important.)

Michael: That’s funny—but when that occurs, you can take this supplement or this drug to prevent the disease, but you’re still improperly nourished. You’re going to get another disease, and then you’re going to get another disease. But if you get your nutrition back and properly balanced, and everything is at the correct level, your immune system starts to function properly. A good share of your immune system is in your digestive tract—there are a lot of microbes working for you.

And the soil is no different. You get those microbes working for you, you’re going to stay healthy. The soil is going to stay healthy, and so are the plants.

John: Are you saying that when you manage the nutritional balance of the soil and the microbial population of the soil, that it’s possible to grow crops that don’t have disease?

Michael: Yes. When a plant is perfectly healthy, it’s very hard to get a disease to invade it, and an insect will not even stop to look at it. Why is that? It’s because an unhealthy plant cannot convert the sugars it’s produced into complex sugars—starches and lignin—which insects and diseases can’t use. They can use simple sugars and the nitrate nitrogen in the plant. The nitrate nitrogen is taken up by the plant, and it’s immediately converted into amino acids and proteins in a healthy plant. An unhealthy plant—a plant that does not have the right mineral balance to make all those processes and cycles work—will have a pretty heavy load of nitrate in it—a fantastic food for the insect. They can detect that, and they will land on that plant and feed on it. Disease and insects are Mother Nature’s garbage collectors—getting rid of the bad stuff, the weak plants.

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