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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.

Unhealthy plants create unhealthy soils

The popular narrative is that healthy soils produce healthy plants. 

This is correct but incomplete.

We need to ask the question, what creates healthy soils? “Healthy plants”, is the right answer. 

Without the contribution of plants, soil is just decomposed rock particles; sand, silt, clay.

Plants contribute the carbon, the sugars, the energy that serves as a fuel source, and substrate to develop microbial populations that build organic matter and mineralize nutrients and make them available to plants. The humic substances and humus clay complex are the result of plant contributions to the ecosystem.

Healthy plants create healthy soil.

The key adjective in this statement is ‘healthy’. Unhealthy plants do not create healthy soil. In fact, the opposite. 

Unhealthy plants create unhealthy soil. 

In this post a few days ago, Robert Kremer described how the root exudates of GMO crops can increase the virulence of soil-borne pathogens. But wait, root exudates are supposed to be a good thing, no?

The influence of root exudates on soil microbial communities is determined by the complexity and quality of the compounds they transmit through the root system, not only the quantity of exudates. 

Unhealthy plants will transmit simple carbohydrates, non-reducing sugars, amino acids, and other compounds in ratios that enhance the virulence of pathogens, by providing them with a ready food source. 

Healthy plants at higher levels on the plant health pyramid transmit more complex carbohydrates, reducing sugars, polysaccharides, enzymes, and complete proteins, as well as plant secondary metabolites. 

Unhealthy plants may also transmit some of these compounds, but in different ratios from healthy plants. 

The different ratios of complex carbohydrates, enzymes and secondary metabolites produce a different microbial community response in the rhizosphere. 

Unhealthy plants that transmit a lot of simple sugars favor the development of a disease enhancing soil microbial community. They increase the virulence of disease pathogens present in the soil. 

Healthy plants that transmit more complex compounds favor the development of a disease suppressive soil microbial community. They decrease the virulence of disease pathogens in the soil, and actually convert them to have a symbiotic relationship with the plant instead of a pathogenic one. 

While healthy plants create healthy soils, unhealthy plants create unhealthy soil. This is why focusing on optimizing plant health in the current growing season provides such big soil health rewards. 

GMO crops generally have different carbohydrate and amino acid profiles from their non-GM counterparts, which produces a different soil microbial community. 

2020-09-25T11:44:39-05:00September 24th, 2020|Tags: , , |

How GMO’s can influence soil microbiology

On several occasions, we have observed GMO corn crops and GMO corn stalk mulch produce a soil environment that enhanced disease, sometimes dramatically. Why would it be the case that GMO crops produce a disease enhancing soil environment, where non-GMO corn produces a disease suppressive environment?

Other research has identified that GM plants have altered carbohydrate and amino acid profiles in the root exudates, which seems to be a probable mechanism for producing an altered rhizosphere microbiome.

Robert Kremer and I approached this conversation in our podcast interview:

John: Earlier you mentioned the impact of genetically modified plants themselves, apart from glyphosate and AMPA. How do GMOs impact the soil’s microbial community?

Robert: Well, there’s not a lot of information. We found with soybean, for example, that genetic modification can have what are called pleiotropic effects—indirect effects due to the genetic modification that are in addition to the intended effect. In other words, effects that are in addition to the effect of making the plant resistant to glyphosate. And so there are things that can happen in the root system—with some of the early genetically modified soybean varieties, anyway—that even without being treated with glyphosate, the roots seemed to release a lot more carbohydrates or soluble carbon and amino acids. This is problematic because it attracts a lot of microbes that readily use this material, and many of those can be potential pathogens. So you have a potential problem not only with some root pathology, but it’s also possible to build up these segments of the microbial population and carry them over from year to year.

Another situation where we find these effects is in corn. Not in all varieties, but in many varieties that had been genetically modified to be resistant to insects using Bt, there was a side effect where some of the corn stocks would have a lot more lignin than others. Lignin is very difficult to decompose. That’s one of the reasons we sometimes see a lot of that residue being carried over for two or three years in the field—there’s so much lignin that it can’t decompose very fast.

And I think there are other situations that can occur. I had a Brazilian student here who looked at some of the nutrient composition. Some of the omega fatty acid ratios were changed in soybeans due to the genetic modification; that kind of thing. Now, I can’t say for sure if that has changed with some of the more recent cultivars, because I haven’t been looking at that very closely over the last few years. But, as you know, in our commodity agriculture, these varieties change almost from year to year. Some of the varieties that we were using fifteen years ago are not available anymore. So that’s always another problem. You just don’t know whether the effects of these newer varieties are any better or any worse unless somebody has a research program that’s addressing it.

John: Your first point is very intriguing. In essence, what you’re describing is that these crops and these plants may have the capacity to actually develop a disease-enhancing soil profile—which is interesting when you consider the long-term implications.

Robert: Right. That was a completely unexpected result that we had. And we were comparing it to some of the old non-GMO varieties like Williams 82 and Maverick, and they had much lower soluble carbon and amino acid release. So it was quite interesting, to say the least.

2020-09-21T20:35:48-05:00September 22nd, 2020|Tags: , , , |

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