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.

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?

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.

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