Changing a single plant gene alters the rhizosphere microbiome

“We report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.”1

Several growers have been reporting that different weed species are dominant the following growing season on soil where GM crops are planted, compared to soil with that same crop that is not GM.

Other growers have observed that disease expression is much higher following a GM crop than a non GM crop.

We understand that both of these changes can be produced by shifts in the soil biome. As biological populations shift, different weed species become dominant, and diseases can be either suppressed or enhanced.

A single gene change in a plant can produce a changed phenolic compound and sugar profile in plant sap and root exudates. This change in root exudates results in a changed microbiome in the rhizosphere.

A single gene change in a plant can produce a changed microbiome in the soil. What might this mean for breeding and GE?

Of course, few GE crops being used today only contain a single altered gene. Usually a number of genes are added or altered, along with a number of non-target changes that are also produced.

How might the soil microbiome differ between GE and non GE crops, and how does this influence the development of the soil microbiome?

How can we consider this characteristic to intentionally breed crops and select cover crops which shift the microbiome in a disease suppressive direction?

Is it possible that when we select for disease resistant crops the disease resistance mechanisms are largely or partially a result of a changed microbiome?

Can we deliberately breed crops  to produce a disease suppressive microbiome, as occurred accidentally with the selection of crown-rust resistant oats?

  1. Badri, D. V. et al. An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol. 151, 2006–2017 (2009).


2022-02-14T14:53:31-05:00February 15th, 2022|

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.

Whose opinion do you care about?

When we consider that some people have qualified opinions about some topics, and some people have qualified opinions about few topics, whose opinion do you choose to care about?

If you want to make a change on your farming operation how important is the opinion of your neighbors? The folks at church? The coffee shop? How important is the opinion of your family?

Does anyone in any of these groups have a qualified opinion about the changes you are trying to make?

If you care about their opinion, and their opinion is not yet qualified, how can you give them the necessary information to help them develop a qualified opinion?

Alternatively, are you able to ignore their unqualified opinion, and only rely on advisors who do have qualified opinions?

Being conscious and deliberate about whose opinion we care about can be very liberating.

Surround yourself with peers and advisors whose opinions you actually care about, and making changes in life or on a farm becomes much easier.

2022-02-02T05:57:23-05:00February 11th, 2022|

Vanished yield potential

How much yield is lost every year because we don’t apply the knowledge from the past?

Huber, McNeil, Zimmer, and others have reported regularly achieving 400+ bu per acre corn yields during the ’70s and ’80s. What happened? How was that yield potential lost? Why are we going backward? Why haven’t we made more progress?

From my podcast interview with Gary Zimmer:

John: What is something that you believe to be true about modern agriculture that is very different from the mainstream view?

Gary: When I was at Brookside, back in 1976, I visited a farm in northern Illinois that was growing 375-bushel corn, with a public variety of corn from the University of Illinois, on forty-inch rows. You could stick your hand in the ground clear to your elbow. Of course it got my attention.

In the ’90s, in Iowa, there was somebody who grew 400- to 500-bushel corn. That really opened up the doors to say that there’s much more potential.

This is why I find it offensive when people say, “How are we going to feed all these people?”

I say, “Forty percent of our corn goes into making ethanol, and we have the capability to double our yields. And we can do it with a cleaner method of farming.” It’s not that we can’t produce more food. And most people don’t even eat corn and beans. We can do a lot of things if we want to feed people. I think that conventional agriculture, or whatever you want to call it— modern agriculture—is shifting to a biological farming system.

2022-02-08T18:58:05-05:00February 10th, 2022|Tags: , , , |

Propagating Velvetleaf

Velvetleaf thrives in soil where unhealthy anaerobic fermentation produces ethane and methane.

Or, stated in a different way, soils where unhealthy decay/fermentation products have been applied.

One of the more effective ways to grow abundant velvet leaf is to flush wash water/waste water with strong antimicrobial cleaners into a liquid manure pit, then apply the liquid manure to the field.

A liquid manure pit mistreated with chemical cleaners becomes a smelly, stinky mess where manure does not digest and breakdown in a healthy way. A mismanaged manure pit will form a crust on top, and undecomposed sludge on the bottom.

Well digested liquid manure can be a valuable resource that smells good (or not at all), doesn’t stink, has no sludge or crust, and enhances healthy biology when added to soil.

This type of liquid manure does not stimulate velvet leaf growth because it does not add toxins to the soils.

The solution is to remove the cleaners from the manure pit, and add microbial inoculants that can speed up the conversion of the liquid manure to a liquid gold microbial tea.

When we change our manure management velvetleaf disappears from the landscape because the soil is no longer the environment it requires. You can read about how to change your manure quality here.

2022-02-16T07:39:40-05:00February 9th, 2022|Tags: , |

Stones of the field, minerals of the soil

At destruction and famine you shall laugh, and shall not fear the beasts of the earth. For thou shalt be in league with the stones of the field, and the beasts of the field shall be at peace with thee. ~ Job 5:22-23

Some other translations read “you shall have a covenant with the stones of the field”

What does it mean to be in league or covenant with the stones of the field?

Why would aligning with the stones of the field result in immunity to destruction and famine?

We know that stones influence and guide ground currents across the landscape. Medicine wheels and other arrangements of stones can produce a markedly positive effect on the local climate and crops by producing energy vortices or ‘acupuncture points’ for the earths naturally occurring ground currents.

However, when you dig deeper, the original Hebrew can also be translated as “you shall be in league with the minerals of the soil”.

And at once, the connection becomes clear. We know that soils containing abundant and balanced mineral nutrition produce crops that are resistant to diseases, are not consumed by insects, and produce healthy livestock which are immune to parasites, in addition to a list of other positive health attributes to long to mention.

Are you in league with the minerals of the soil?

2022-02-02T07:40:58-05:00February 8th, 2022|

Frost patterns expressing plant signatures

I have observed varying frost patterns on frozen surfaces most of my life, but I don’t recall many instances where frost patterns reflected the living organisms in the local environment so well.

The first photo is an outside view of a glass window in a homestead greenhouse on a cold winter morning.

The second photo is a selection of the greens that were harvested inside that greenhouse that morning.

Which of the plants vascular systems matches with which window pane?

What do these observations tells about information and energy being shared and perceived?

What frost patterns or other energy patterns have you observed?

Thanks to Nigel Palmer for sharing the photos.

2022-02-02T13:47:32-05:00February 7th, 2022|Tags: |

Farming from the soil up, or from the sun down?

Ecosystems are regenerated through the agency of plants, capturing energy from the sun and transferring it down into the soil.

Plants are the primary collectors of energy. They are the only way we have of bringing new energy into an ecosystem.

All other organisms simply convert the energy captured from photosynthesis.

Livestock are not the foundational organism to regenerating soil and ecosystems.

Fungi are not the foundational organism to regenerating soil. Neither are bacteria. Or actinomycetes, protozoa, or any other organism. 

These other organisms can be managed to develop an environment where plant energy collection jumps dramatically. Or they can be mismanaged in such a manner that photosynthesis declines in the landscape.

Optimizing sunlight capture increases yields and unavoidably results in regenerating landscapes.

Optimizing soil fertility to increase yields may or may not regenerate agricultural landscapes. With the approach being used in contemporary agriculture, the effect on landscapes has been negative, not positive.

Are you managing for most efficient sunlight capture?

Are you managing to optimize soil function, or sunlight capture?

2022-02-02T05:59:06-05:00February 4th, 2022|

A qualified opinion

“I’m not entitled to have an opinion unless I can state the arguments against my position better than the people who are in opposition. I think that I am qualified to speak only when I’ve reached that state.” ~ Charlie Munger

Propagating fear and division among family and friends does not serve us. It may serve someone, but it does not serve you, or I, or the good of community.

Perhaps we see this more clearly than before in this contemporary environment of  polarizing opinions, so strongly held they  divide families and communities.

Divisive opinions grew with Trump, transferred to a virus, and became ever more entrenched.

Collectively, we are tiring of the division, and ready to put it behind us. “Lets move on” is the prevailing sentiment.

It seems to me we should learn from this experience, particularly in the regenerative agriculture space.

We have the benefit of having a lot of facts and science in support of regenerative agriculture. There are also many facts and science that can be marshaled by advocates of contemporary agriculture.

Frequently, those with different perspectives are not even describing the same things, or discussing the same ideas, since they approach the discussion from very different world views.

What are the beliefs you have very strong opinions about? These might be beliefs about the usefulness of GMO’s, the benefits of anhydrous ammonia, the effectiveness of glyphosate,  the value of cover crops, the use of phosphorus fertilizers, etc. etc. etc.

How well can you articulate the opposing point of view?

Your ability to articulate the opposing point of view is likely to correspond to your level of empathy for those who hold a different view.  You now understand their perspective, even though you may not agree with it.

Developing empathy with those who hold a different point of view is a foundational requirement if we wish to intervene and facilitate a shift in perspective.

If you think glyphosate is great, or glyphosate is damaging, is your opinion a qualified one? Or are you depending on the opinions of others?

Asking ourselves and our colleagues to develop qualified opinions or acknowledge when our opinion is not yet qualified, can bring about a deeper understanding and openness with each other.

What are you qualified to have an opinion about?

2022-02-01T13:20:14-05:00February 2nd, 2022|Tags: |
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