Weeds and crops are never equally healthy in the same soil

As soil mineral balance and microbial populations improve, the domesticated crops we seek to grow become healthier, and the pioneering plants we often refer to as weeds become less healthy.

Different plants thrive in soils with different microbial profiles and different mineral profiles. The soils which are optimally balanced for our domesticated crops are not optimally balanced for the pioneering plants we call weeds.

When the crop becomes healthier than the weeds, diseases begin infecting the weeds and leave the crop alone.

Here is pigweed on the edge of a disease-free tomato field in 2006. I don’t know what this organism is. I do know the plants only survived a few weeks more, and the tomato crop remained disease-free.

A question for you: Should the organism that is causing this infection be called a ‘pathogen’ or a ‘pest’? Or does that label only apply when they infect our crop plants?

2020-06-24T07:06:08-05:00May 4th, 2020|Tags: , , |

Developing disease suppressive soil

Diseases and insects only become a problem when plants are unhealthy, lacking nutritional integrity and microbiome integrity. The tools of nutrition management and microbiome management are so effective, they have been and are used as management protocols for bio warfare weapons mitigation.

From the Regenerative Agriculture Podcast with Michael McNeill:

John: Michael, we’ve been circling around this topic of soil health and the impacts of tillage, herbicides, animal manures, cover crops, and so forth. At the beginning, you mentioned that there’s a correlation between soil health and the diseases that are present. You mentioned some work you were doing in Maryland—studying diseases as a weapon. What did you learn from that experience? And how does all of that tie into what we’re talking about?

Michael: Let’s say you want to use a fungal disease as a weapon—that you can get this disease introduced into the soil. Not only does it kill a crop this year—it’ll continue to kill it into future years. So hey, that’s a pretty good weapon—you shut down a people’s food supply. They have a problem.

Well, if you have good pseudomonas bacteria in the soil, they act as a policeman in the soil, if you will, and they’ll take out the pathogenic fungi that can arise. But if you use products like glyphosate—that’s an antibiotic type of product—you’re going to kill all the pseudomonas, and then you have no protection. And it’s very easy to get a huge population of fusarium going in the soil, which probably is a pathogenic fusarium—or pythium or phytophthora. You’ve lost the natural balance. If you have that balance, though, the pathogenic fungi are not going to do much to you. Your good bacteria will clean it right up.

John: So you can actually have a disease-suppressive soil where you don’t have challenges with those pathogenic fungi. I think I also heard you mention that you were working on developing solutions to those diseases as weapons. What were the types of solutions that you were working on?

Michael: There are all kinds of approaches. If you need a fast cure, of course you’ve got to look at chemistry and the fungicides and that sort of thing. But what you find is that if you get the soil contaminated, how do you fix it? Because if you put anything on it, you’re going to kill everything in the soil. Using a soil sterilizer is not necessarily a great idea. But there is microbial life in the soil that will hold everything in balance. And if you have the right nutrition available, everything will take care of itself.

I’ll use you as an analogy, John. If your nutrition gets pretty poor, you’re going to get pretty run down, and you’re going to be very susceptible to all kinds of diseases. Would you agree?

John: Oh, I think that’s just the story of the people who are trying to sell me supplements. (Sarcasm, I take many supplements, and believe they are important.)

Michael: That’s funny—but when that occurs, you can take this supplement or this drug to prevent the disease, but you’re still improperly nourished. You’re going to get another disease, and then you’re going to get another disease. But if you get your nutrition back and properly balanced, and everything is at the correct level, your immune system starts to function properly. A good share of your immune system is in your digestive tract—there are a lot of microbes working for you.

And the soil is no different. You get those microbes working for you, you’re going to stay healthy. The soil is going to stay healthy, and so are the plants.

John: Are you saying that when you manage the nutritional balance of the soil and the microbial population of the soil, that it’s possible to grow crops that don’t have disease?

Michael: Yes. When a plant is perfectly healthy, it’s very hard to get a disease to invade it, and an insect will not even stop to look at it. Why is that? It’s because an unhealthy plant cannot convert the sugars it’s produced into complex sugars—starches and lignin—which insects and diseases can’t use. They can use simple sugars and the nitrate nitrogen in the plant. The nitrate nitrogen is taken up by the plant, and it’s immediately converted into amino acids and proteins in a healthy plant. An unhealthy plant—a plant that does not have the right mineral balance to make all those processes and cycles work—will have a pretty heavy load of nitrate in it—a fantastic food for the insect. They can detect that, and they will land on that plant and feed on it. Disease and insects are Mother Nature’s garbage collectors—getting rid of the bad stuff, the weak plants.

The Agronomy of the future

Will not be based on chemistry but on biophysics and biology.

In the future, soil analysis will not be looking only at mineral balance and nutrient levels, but at the levels of amino acids, peptides, enzymes, carbohydrates, and other compounds that plant roots can absorb from the microbial community.

Agronomists will look at soil paramagnetism, redox, and electrical conductivity to evaluate a soil’s capacity to deliver to crop yields and quality.

Crop scouts will measure plant leaf redox and electrical activity to determine disease and insect susceptibility, and determine what treatments to apply to prevent possible infections.

The emerging knowledge of this space that is becoming more widely known is extremely exciting.

I posted a few weeks ago about Olivier Husson’s work on redox. His work is much broader and deeper than can be described in the referenced papers. He has been kind enough to appear on the podcast and to share his work in-depth in a six-hour-long webinar that we made available as a free online course on the academy that you can find here.

This will be the agronomy of the future. Enjoy.


2020-05-05T08:58:03-05:00February 12th, 2020|Tags: , , , , , |

The only thing that can not be overdone

Is balance. 

In regenerative and sustainable ecosystems anything can be applied to excess. 

Water can be excessive. So can oxygen. Or CO2. Or calcium, seaweed, biochar, humic acid, rock powder, liquid fish, crab shell, limestone, gypsum, manure, fertilizer, pesticides, and anything else you might name. 

You may have heard someone make a comment to the effect of “You can never apply too much of…(insert product here). 

You can be certain someone somewhere has done exactly that and suffered the consequences. Because there are always consequences of excesses. They are usually significantly worse and more difficult to deal with than deficiencies. 

2020-03-16T14:02:55-05:00February 11th, 2020|Tags: , , , |

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: , , , , , |

Bacterial resilience to antibiotics

Antibiotics were first discovered being produced by a soil-borne fungus. We have identified many different antibiotics that are made by plants and fungus, and even synthesized some on our own. Many of the anti-biotics we have developed are not necessarily labeled as such. Many herbicides and pesticides would be examples of an antimicrobial that is applied to agricultural soils. The case for glyphosate is now well established, and others are getting to be better known.

When we consider the widespread use of antibiotics on our soils and in livestock feed we might wonder about the implications for the microbial community in our soils. 

I found this excerpt from Stephen Harrod Buhner1 thought-provoking: 

Once a bacterium develops a method for countering an antibiotic, it systemically begins to pass the knowledge on to other bacteria – not just its offspring – at an extremely rapid rate. Under the pressure of antibiotics, bacteria are interacting with as many other forms and numbers of bacteria as they can. In fact, bacteria are communicating across bacterial species, genus, and family lines, something they were never known to do before the advent of commercial antibiotics. And the first thing they share? Well, it’s resistance information.

Bacteria can share resistance information directly, or simply extrude it from their cells, allowing it to be picked up but later by roving bacteria. They often experiment, combining resistance information from multiple sources in unique ways that increase resistance, generate new resistance pathways, or even stimulate resistance forms that are not yet necessary. Even bacteria in hibernating or moribund states will share whatever information on resistance they have with any bacteria that encounter them. When bacteria take up any encoded information on resistance they weave it into their own dna and this acquired resistance becomes a genetic trait that can be passed on to their descendants forever. As Gaian researchers Williams and Lenton comment…

Microbe transfer between local populations carries genetic information that changes species composition and thus alters the nature of each community’s interaction with its local environment2.

“The nature of each community’s interaction with its local environment” changes. One aspect of that:  as bacteria gain resistance they pass that knowledge on to all forms of bacteria they meet. They are not competing with each other for resources, as standard evolutionary theory predicted, but rather promiscuously cooperating in the sharing of survival information. “More surprisingly,” one research group commented,  “is the apparent movement of genes, such as tetQ and ermB between members of the normal microflora of humans and animals, populations of bacteria that differ in species composition.” Anaerobic and aerobic, gram-positive and gram-negative, spirochetes and plasmodial parasites, all are exchanging resistance information. Something that, prior to antibiotic usage, was never known to occur.

And, irritatingly, bacteria are generating resistance to antibiotics we haven’t even thought of yet. For example, after placing a single bacterial species in a nutrient solution containing sublethal doses of a newly-developed and rare antibiotic, researchers found that within a short period of time the bacteria developed resistance to that antibiotic and to twelve other antibiotics that they had never before encountered – some of which were structurally dissimilar to the first. Stuart Levy observes that “it’s almost as if bacteria strategically anticipate the confrontation of other drugs when they resist one.”4


With the growing understanding of how we have compromised our soil biology, we need to consider how we can regenerate that microbiome, add the organisms that have been lost, and recover those that are present but struggling. This is where microbial inoculants, diverse plant species, compost, and compost teas become important tools in agriculture management systems.


  1. Buhner, S. H. Plant Intelligence and the Imaginal Realm: Beyond the Doors of Perception into the Dreaming of Earth. (Simon and Schuster, 2014).
  2. Williams, H. & Lenton, T. Microbial Gaia: A new model for the evolution of environmental regulation. Gaia Circular, 2007 14–18 (2007).
  3. Wax, R. G., Lewis, K., Salyers, A. A. & Taber, H. Bacterial resistance to antimicrobials. (CRC press, 2007).
  4. Levy, S. B. The Antibiotic Paradox: How Miracle Drugs Are Destroying the Miracle. (Springer, 2013).


2020-03-16T13:45:20-05:00December 16th, 2019|Tags: , , , , |

What defines a pest?

What is a pest?

When a wolf succeeds in catching a rabbit for dinner, which of them is a pest?

Is a wolf a pest while it catches rabbits and deer? When it catches a  lamb?

Is a rabbit a pest while it eats clover, or only when it eats the greens in the garden?

Is a ladybeetle a pest while it consumes aphids in the fields, or only when they swarm houses in the fall?

Is the definition of a ‘pest’ completely human-centric? It seems we call these living beings pests only when they bother us, but not when they bother other organisms we are not personally invested in.

We have deeply interdependent relationships with bacteria, fungi, viruses, nematodes, insects, amphibians, reptiles, mammals and birds of every kind. Almost all of these organisms are quite benign in healthy ecosystems. When the ecosystem is degraded, they proliferate, and begin feeding on the animals or plants we have a vested interest in. Then we proceed to label them as a pest or a pathogen.

But if it is us that has mismanaged the ecosystem, are we the pathogen?

The environment/ecosystem determines the presence and proliferation of all these living beings.

If we are to be stewards of these ecosystems, we must acknowledge that it is our management of the environment that determines whether these organisms express themselves as a benign participant or as a pest.

If we want to accept responsibility and make a difference, it does not seem useful to label living beings as pests.

Labeling is a subtle subconscious shifting of responsibility. “I am not responsible for these pests! They invaded! From out there. They are out of control. The weather was awful, the season was wet/dry/hot/cold.”

Neither the wolf nor the rabbit is a pest. They are symbionts in the environment and are dependent on the greater ecosystems they are a part of to sustain themselves.

Neither spider mites nor fusarium is a pest or a pathogen. Nor are any other insects, nematodes, bacteria or fungi. They are simply present in the environment we have created for them. If they proliferate to the point of causing crop loss, it is because we have managed the ecosystem to create an optimal environment for them.

If we desire them to not be present to the point of causing economic damage, we only need to manage the ecosystem differently.

2020-05-22T07:14:59-05:00December 12th, 2019|Tags: , , , |

Are diseases present because pesticides were not applied in time?

Do people or animals get bacterial infections because they have an antibiotic deficiency?

Do plants get disease infections because of a pesticide deficiency? If not, why do we apply pesticides before the organism is even present?

Come to think of it, plants do absorb antibiotics synthesized by soil microbes, and they help prevent possible infections. Maybe plants do become infected because of antibiotic deficiencies after all?

In that case, what produces the antibiotic deficiency?

That would be dysfunctional soil biology. Which is likely dysfunctional because of all the pesticide applications the soil has been exposed to.

Perhaps killing the microbes that protect our crops isn’t such a good management strategy.

2020-03-16T13:46:02-05:00December 10th, 2019|Tags: , , |


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