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.

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. 

Disease suppression of wheat take-all disease

The presence of soil-borne disease infection is not correlated to the presence of an infectious organism, but to the absence of suppressive microbes.

Here is an example from Paul Syltie1 on wheat take-all disease: 

It is well documented that the fungus responsible for the take all of wheat Gaeumannomyces graminis var. tritici is attacked by soil bacteria, in particular by the bacteria in what are called take-all suppressive soils. These soils are unique in that the severity of the disease becomes progressively less as the cropping season continues. In some cases the disease may not even express itself whatsoever despite being present.

It is concluded by soil microbiologists that most soils express some degree of natural pathogen suppression. This occurs generally in soils by the mass of beneficial organisms overwhelming the pathogens at a critical time in their life cycle, robbing critical nutrients from them. Specific suppression occurs when select species or groups of beneficial organisms antagonize the pathogen at some stage of its life cycle.

Take-all in wheat or barley becomes less and less of a problem if the crop is grown in consecutive years. Both fungi and bacteria, such as friendly saprophytic Fusarium species, reduce pathogen numbers by competing for food supplies, and at the same time specific antagonistic microbes like fluorescent pseudomonads attack the G. graminis. The pseudomonads are especially effective when ammonium rather than nitrate fertilizer is used, resulting in a lower rhizosphere pH. This suppression likely occurs mostly in the rhizosphere, but also throughout the soil mass.

1. Syltie, P. W. How Soils Work. (Xulon Press, 2002). Page 111

2020-03-16T13:50:36-05:00January 6th, 2020|Tags: , , , , , |

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