John Kempf

The Rhizosphere Microbiome and Plant Health

Many times growers observe field outcomes we don’t have an immediate explanation for.

Why did that one section of the field with that early root disease not have any insect pressure later in the season?

Why does our crop not have any disease where we foliar fed last years cover crop, but disease is present where the same cover crop was not foliar fed?

Why does a field have greater disease pressure on one variety, but the next variety right beside it, not particularly selected for disease resistance, showed no trace of disease?

Why do GM crops seem to produce a disease conducive soil, where their non GM counterparts produce a disease suppressive soil microbiome?

Why does the relative health and photosynthetic efficiency of crops result in changed microbiomes in the soil?

Then, sometimes, we find a reference that connects the dots, and we learn some possibilities of what might have occured to produce unexpected results.

The Rhizosphere Microbiome and Plant Health is such a paper. Here are some condensed highlights from the paper:

– The microflora of most soils is starved. As a result,there is a fierce battle in the rhizosphere between the microorganisms that compete for plant-derived nutrients.

– Most soil-borne pathogens need to grow saprophytically in the rhizosphere to reach their host.

– The success of a pathogen is influenced by the microbial community of the soil in which the infection takes place.

– Every natural soil has the ability to suppress a pathogen to a certain extent. This phenomenon is known as general disease suppression and is attributed to the total microbial activity.

– Organic amendments can stimulate the activity of microbial populations in a conducive soil, resulting in enhanced general disease suppressiveness.

– ‘Specific suppression’ occurs when specific microorganisms cause soils to be suppressive to a disease. Specific disease suppressiveness is superimposed on the general disease suppressiveness of soils and is more effective.

– some soils retain their disease suppressiveness for prolonged periods and persist even when soils are left bare, whereas other soils develop suppressiveness only after monoculture of a crop for several years.

– Induction of suppressiveness by itself is remarkable, because for most plant species, successive monocultures will lead to a build-up of specialized plant pathogens .

– Nonetheless, development of disease suppressiveness in soils has been reported for various diseases, including potato scab, Fusarium wilt, Rhizoctonia damping-off , and take-all.

– Microorganisms that can confer suppressiveness to otherwise conducive soils have been isolated from many suppressive soils.

– Mechanisms through which rhizosphere microorganisms can affect a soil-borne pathogen have been identified and include production of antibiotic compounds, consumption of pathogen stimulatory compounds, competition for (micro)nutrients and production of lytic enzymes.

– Many beneficial soil-borne microorganisms have been found to boost the defensive capacity in above- ground parts of the plant. This induced systemic resistance (ISR) is a state in which the immune system of the plant is primed for accelerated activation of defense.

– Although locally plant immunity is suppressed, an immune signaling cascade is initiated systemically that confers resistance against a broad spectrum of pathogens and even insects

– In addition to plant growth-promoting rhizobacteria, beneficial fungi such as mycorrhizal fungi, Trichoderma spp. and other fungal biocontrol agents have also been found to induce ISR.

– As well as inducing systemic resistance, mycorrhizal fungi can also form a connecting network between plants that can convey a resistance-inducing signal to neighboring plants

– The microflora of most soils is carbon starved. Because plants secrete up to 40% of their photosynthates into the rhizosphere, the microbial population densities in the rhizosphere are much higher than in the surrounding bulk soil.

– From the reservoir of microbial diversity that the bulk soil comprises, plant roots select for specific microorganisms to prosper in the rhizosphere.

– Some plant species can create similar communities in different soils. Even within species, different genotypes can develop distinct microbial communities in the rhizosphere, suggesting that plants are able to shape the composition of the microbiome in their rhizosphere.

– Plants can determine the composition of the root microbiome by active secretion of compounds that specifically stimulate or repress members of the microbial community

– Furthermore, plant-associated bacteria produce and utilize diffusible N-acyl-homoserine lactones (AHLs) to signal to each other and to regulate their gene expression. Such cell-to-cell communication is known as ‘quorum sensing’

– QS-interfering compounds enable the plant to manipulate gene expression in their bacterial communities

– Recent evidence suggests that differences between plant genotypes in a single gene can have a significant impact on the rhizosphere microbiome. The production of a single exogenous glucosinolate significantly altered the microbial community on the roots of transgenic Arabidopsis.

– These results indicate that the plant genotype can affect the accumulation of microorganisms that help the plant to defend itself against pathogen attack. Indeed, differences have been found in the ability of wheat cultivars to accumulate naturally occurring DAPG-producing Pseudomonas spp., resulting in differences in disease suppressiveness.

– Specific wheat cultivars support specific biological control bacteria differentially, which further establishes that there is a degree of specificity in the interactions between plant genotype and the composition of their microbial community

– White fly feeding also led to significant changes in the rhizosphere microbial community. Although total numbers of bacteria were unaffected, the white fly- induced plants had higher populations of Gram-positive bacteria and fungi in their rhizosphere. The authors hypothesized that plants recruit plant-beneficial microbes to their roots in response to the attack.

Berendsen, Roeland L., Corné M. J. Pieterse, and Peter A. H. M. Bakker. 2012. “The Rhizosphere Microbiome and Plant Health.” Trends in Plant Science 17 (8): 478–86.

John Kempf2022-02-14T12:39:16-05:00February 14th, 2022|Tags: Disease suppression, disease suppressive soil, fusarium, GMO's, potato scab, rhizoctonia, soil borne pathogens, take-all disease|

Nutrition management for disease control

We have known how to prevent and reverse plant diseases with nutrition management for a long time. The information is not new, it has just been ignored or forgotten.

Fertilizers and trace minerals can be used to increase disease severity, or to reduce or eliminate disease entirely. Many fertilization practices today are known to increase disease. This knowledge should be foundational for every farmer and agronomist, but has largely been forgotten. Perhaps because it would eliminate the need for fungicide applications?

To illustrate how rich the literature is, here in as excerpt from the opening chapter of Soilborne Plant Pathogens: Management of Diseases with Macro- and Microelements published in 1989. For an up-to-date and more modern version I highly recommend Mineral Nutrition and Plant Disease.

Written by Arthur Englehard:

A large volume of literature is available on disease control affects provided by macro- and microelement amendments. Huber and Watson in 1974 in “Nitrogen Form and Plant Disease” reviewed and discussed the effects of nitrogen and/or nitrogen form on seedling disease, root rots, cortical diseases, vascular wilts, foliar diseases and others. They summarized work from the 259 references in four tables in which they list crops, diseases and citations. McNew in the 1953 USDA Yearbook of Agriculture discussed effects of fertilizers on soilborne diseases and their control. He reviewed briefly specific diseases such as take-all of wheat, Texas root rot, Fusarium wilt of cotton, club root of crucifers and common scab of potato. Many other diseases were mentioned, as well as how macro- and microelements effect host physiology and disease. Huber and Arny in “Interactions of Potassium with Plant Disease” summarized in three tables the effect of K (positive, negative, neutral) on specific diseases. They listed 267 references in the bibliography.

The Potash and Phosphate Institute is dedicated to research and education and celebrated his 50th anniversary in 1985. It is a source of information on the use of K and P in the production of plants and the effects on plant disease. The Institute promotes a systems approach to crop production; disease control is one of the factors in the system.

Leath and Ratcliffe described plant nutrition and diseases in forage crops production. They indicated that fertilizers affect pathogens in the soil and on the host, and also can affect the pathogenicity of an organism. Presley and Bird reviewed the effect of P on the reduction of disease susceptibility of cotton.

In 1983, Graham, in Australia in “Effects of Nutrient Stress on Susceptibility of Plants to Disease with Particular Reference to the Trace Elements” discussed under the heading “Macroelements,” the effect of six essential elements on disease; and under “Micronutrients,” seven essential elements and 15 others as having been reported to influence a host-parasite relationship. He gives 305 literature citations.

Another review by Huber entitled, “The Use of Fertilizers and Organic Amendments in the Control of Plant Disease” contains a wealth of information. He indicated how the severity of 157 diseases was affected by N in table 1. In table 2, a similar listing is given for nitrate and ammonium forms of N. The effects of P, K, Ca and Mg are given in tables 3, 4, 5 and 6 respectively. Tables for S, Na, Mn, Fe, Zn, B, Cu, Si and other elements are also presented.

A literature research of the CAB ABSTRACT database utilizing the DIALOG Information Retrieval Service and using some keywords: soilborne disease, macroelements, microelements, soil fungi, Fusarium, Pythium, and Phytophthora, yielded 1500 citations published during the past 14 years.

The Future

Obviously a virtual flood of literature is available regarding the effects of macro – and micro element soil amendments on the level of soilborne disease in plants. What is lacking is the correlation of the positive factors into integrated production systems. The biggest problem now is how to organize and comprehend the mountain of available and often conflicting data. We have entered an era in which computer-aided analysis and other sophisticated tools are needed to integrate information and develop systems approaches is to growing healthy, productive plants.

One of the most rewarding approaches for the successful reduction of soilborne diseases is the proper selection and utilization of macro- and microelements. Since virtually all commercially produced crops in the developed world are fertilized, it is extremely important to select macro- and microelements that decrease disease. This is an important and viable alternative or supplement to the use of pesticides which usually only gives partial disease control.

–

Remember, this was published in 1989. What other things have you heard about that deserve to be generally known, but aren’t?

John Kempf2021-02-16T14:49:42-05:00February 17th, 2021|Tags: disease suppressive soil, disease susceptibility, Don Huber, fusarium, phytophthora, pythium, soil borne pathogens|

Environment determines genetic expression

Prior to the human genome project, the popular expectation was that understanding the structure of DNA, and being able to edit or manipulate it’s structure would enable us remove the cause of degenerative illness.

As this project approached it’s concluding stages, it became obvious that DNA did not contain enough information to describe all the variability found within a given population. From this insight emerged the concepts of genetic fluidity and the science of epigenetics.

Epigenetics is the study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype. A foundational premise of epigenetics is that changes in environment result in changes of how an organism expresses itself.

“Heredity is nothing more than stored environment.” Luther Burbank

As farmers, we recognize this as an obvious truth. We know that we can plant the same seed in different fields with different soil types, and the crop will express itself differently. This effect is compounded as multiple generations are grown in different environments.

It is easy to recognize this process in plants, and also in animals.

We may not have appreciated enough how fundamental this process is in determining the pathogenicity or infectious capacity for the organisms we call ‘diseases’ or ‘pests’.

When we plant a blueberry plant into soil that is optimally balanced for alfalfa, we have placed it in an environment where it is unlikely to do well.

If we were to plant lambsquarter seeds into forest soil that is undisturbed, they will not even germinate, because they are not in the proper environment.

If we were to plant foxtail seeds into soil that is aggregated and well aerated, they also will not germinate, because they are not in the right environment.

Each of these examples is a case where the environment has determined genetic expression.

Soils can contain fusarium populations that are able to cause disease, but instead develop a symbiotic relationship with the plant, when there is a healthy soil microbial environment present. The DNA of the fusarium remains unchanged, but it’s expression is completely different.

Aphids will die in minutes, and become ‘candied’ when the sugar profile within plant sap they are feeding on changes. A change in the environment determines whether they live or die.

Not all insects in a given population serve as a vector for viruses. If an individual insect benefited from an optimal diet and environment, it will resist viral infections and not spread viruses from one plant to another. (Disease resistance is as real for insects as plants or animals)

Powdery mildew infections can decimate one variety, and leave another variety in close proximity completely untouched. The powdery mildew organism is present in both varieties, but one variety does not present a hospitable environment, and the organism never expresses itself as a ‘disease’.

We could continue this list until we included every ‘disease’ and ‘pest’ that is known.

The concluding point is simple: Every ‘pest’ requires a certain environment to be able to express itself. Change the environment, and the ‘pest’ ceases to be a problem.

If our crops are susceptible to disease or insects, it is because of our management practices that have created a hospitable environment. Change the environment with nutrition and microbial management, and you change the susceptibility.

John Kempf2021-02-12T12:23:33-05:00February 15th, 2021|Tags: disease resistance, disease susceptibility, fusarium, genetic expression, insect resistance, insect susceptibility, powdery mildew|

Soil glyphosate limiting manganese availability

We have observed many soils that do not deliver manganese well in spite of having large manganese reserves in the soil profile. In most cases, this is a result of manganese oxidation. Manganese oxidation can result from chemistry interactions, but a great deal of manganese oxidation occurs as a result of fusarium overgrowth from accumulated glyphosate applications.

Here are some thoughts Robert Kremer shared in our conversation on our podcast interview:

John: Coming back to the conversation about glyphosate and AMPA, how does glyphosate—and the accumulation of glyphosate and AMPA over extended periods—impact overall soil health?

Robert: We know that there are some indirect effects of continuous use of glyphosate on soil health, because we usually measure a lot of the biological parameters when we set up soil assessments. We see that there are some effects on some of the beneficial bacteria that are involved in plant growth promotion, such as producing plant growth regulators that stimulate root growth and other beneficial bacteria that will produce pathogen-suppressive compounds. We’re noticing that glyphosate tends to suppress those beneficial groups of bacteria, so that has an effect on subsequent plant growth as well. So we feel that there’s a problem there.

I briefly mentioned the effect on some of these microorganisms that are known to cause certain micronutrients to be immobilized, and therefore not available for plant uptake. One of these is manganese. And manganese, of course, is very important for the activity of many enzymes that are involved in many of our metabolic pathways. If it’s tied up, you may have poor photosynthesis. You may have poor amino acid formation because you don’t have enough of it to satisfy the needs of the enzyme.

We’ve found, for example, that fusarium that will colonize the roots of plants that are treated with glyphosate. Fusarium is a manganese oxidizer, so it will immobilize manganese. If it’s on the root system, manganese is not going to be taken up. And if it’s built up in the soil—whether there’s a genetically modified crop there or not—it’s going to remain in the soil. It’s going to continue to immobilize manganese. If you don’t have a lot of available manganese, that’s going to affect the overall soil health as well.

There are a lot of other things. Glyphosate may exchange with phosphorus in the soil, and then you have problems with either excess phosphorus, or, if phosphorus isn’t being taken up by the plants, it can become an environmental problem. We discussed the quality of the organic matter, because we basically just use two crops as the source of the organic residues being returned to the soil. If we don’t have the microbes there to decompose them, or if there’s not a diverse enough quantity of organic substances to help build up soil organic matter, then that will affect soil health as well, because—like I mentioned before—organic matter is one of the key indicators for good soil health.

John Kempf2020-07-20T22:09:29-05:00July 21st, 2020|Tags: fusarium, glyphosate, manganese, Robert Kremer|

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.

John Kempf2020-06-02T20:30:01-05:00June 3rd, 2020|Tags: disease suppressive soils, Don Huber, fusarium, oats, quality agriculture book excerpt, take-all disease|

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.

John Kempf2020-05-23T06:50:51-05:00May 26th, 2020|Tags: disease suppressive soils, Don Huber, fusarium, quality agriculture book excerpt, rhizoctonia, soil borne pathogens|