The effectiveness of microbial inoculants in fixing nitrogen

Soil biology can ‘fix’ and supply more nitrogen, and faster, than they are often given credit for.

The wheat field section on the right received an October application of AEA’s soil primer, which includes bacterial inoculants and stimulants. By March the following year, soil analysis reported an additional 80 units of N available for the crop.

To achieve these results, the soil must have adequate microbially active carbon, good gas exchange, and good moisture levels.

Soil microbial populations can regenerate quickly when given the right environment and support. Regenerating soil health can be accelerated to a few years, it is not a process that needs to take decades to achieve a significant turn around.

2020-05-28T07:05:35-05:00May 28th, 2020|Tags: , , , |

Direct absorption of molecules

The implications of plant absorption of large molecules and endocytosis are that the present mainstream model of agronomy based on measuring and managing nutrient ions is significantly incomplete, and can not be the basis for a regenerative agriculture without additional testing and management paradigms.

Bargyla Rateaver was one of the first, if not the first advocate for plant absorption of large molecules and endocytosis in North America that I am aware of. The Organic Method Primer she authored is under-appreciated for the encyclopedia of practical and agronomic knowledge it is.

Here are Bargyla’s thoughts on the subject, updated in 1993:

Direct Absorption1

Since the disastrous integration of manmade chemicals into agriculture, a huge structure of error has been built upon the false premise that “only ions can be absorbed”. Based on this, a measurement of soil and recommendation for soil have utilized the concept of “cation exchange” and the “CEC” has been the be-all of soil testing. Small structures such as ions are said to be “able to cross the membrane”. Discussions of the varied means for this fill textbook chapters on the subject of absorption.

We now know that this is all passé, an outdated formula promoted by the greedy minds of the chemical dispensers. There have been a number of investigators over the years who have documented that entire molecules were absorbed, but only small molecules. W. Flaig1 in 1968, speaking at the Vatican’s convocation on organic matter and soil fertility, entitled his work “Uptake of organic substances from soil organic matter by plants and their influence on metabolism”. In Japan, Satoshi Mori and Naoko Nishizawa proved that barley roots preferred to take up organic nitrogen compounds if offered these as well as inorganic forms.2

In the chapter on cover crops, we refer to Fritz Went, who saw in Amazon jungles that mycorrhizae absorb nutrients directly from decaying leaves on the ground. Nora M. Stark, who worked with him, in those early days before endocytosis was known, made the penetrating remark: “It is possible, that in extremely poor soils, mycorrhizae are important in supplying nutrients directly from litter to living roots”. She also mentioned that, in one case, she had “traced a hyphae from a dead fruit into a living feeder root cell”.3

Hainsworth notes, on pg 27, that carnivorous plants absorb digestion products of their prey apparently without reducing them to simple inorganic compounds.

We know now that whole molecules of any size can be taken into cells, and clusters of molecules that are particles, by endocytosis (and fluid phase endocytosis) via coated pits–extremely clever devices by an omniscient Creator: the cell membrane invaginates, trapping molecules on the clathrin-coated membrane surface, thereby forming vesicles to enclose such molecules and carry them through the cell, dropping them en route, and/or dumping unwanted or storage molecules in the vacuoles, finally returning to the cell membrane from which they came. (Plastic beads and bacteria enter via uncoated membrane regions; this takes energy. Large algal cells are taken up by fusion with the larger host protoplast, note L. C. Fowke et al.)

As there are hundreds of these coated pits and ensuing vesicles being constantly formed on cell membranes, the provision for cell absorption of compounds (and clusters of them constituting particles) is amply demonstrated; whole molecule absorption is not a small, erratic, exceptional, unusual phenomenon. On the contrary, those crowds of pits indicate that this is one of the Creator’s normal ways of circulating whatever cells need from one to another, from the environment to the cell’s interior metabolism4, or out of it to the environment, by exocytosis.

This new knowledge enables agriculture and horticulture to dispense, forever, with the theories of ion absorption. Long ago M. Dikkers told us that the plant deals with molecules, not ions.

It seems, however, that agricultural academia has either not yet caught up with the new research data, or minimizes it, or simply cannot bear to acknowledge that the monstrous pile of data accumulated throughout the world’s agricultural efforts can be wrong. One author, aware of endocytosis, nevertheless said it must be simply an adjunct to the usual ion absorption theory!

We are therefore the first to have introduced to agriculture the information and concerning the actual facts of how plants absorb through coated pits, distribute by smooth vesicles and exude via smooth vesicles, and the repercussions this implies for husbandry. It totally reverses dependence on the worthless Cation Exchange Capacity (CEC) tests, to which even organic growers still desperately cling.

We firmly believe that this discovery is the second great find of this century, second to only the disclosure/explanation of the DNA/RNA spiral, as it affects worldwide agricultural practice.

It seems that academia can afford to admit a previous error, if such does not impinge on financial benefits. In 1983 University of California researchers in San Francisco acknowledged that, although it had always been thought that a cell nucleus formed by highly complicated processes, it actually could form “spontaneously around any DNA in the cell. regardless of source, independently of genes”.

Such a nucleus had a membrane “identical to normal nuclear membrane…double layer of fat molecules pierced by many pores through which large molecules are transported”.

When confronted with his own microscopic view proving that granules can enter cells, Christopher Somerville of Michigan State University, expressed surprise. He looked at cells of an Arabidopsis thaliana hybrid, into which a plastic. PHB (polyhydroxybutyrate), made naturally by a bacterium, had been engineered. Small amounts of the plastic were made by the hybrid, in leaves, stems, roots. That the plastic occurred as particles, not ions, was undeniable, because the stained particles showed up as red dots. The dots would have had to be particles, as microscopes today are not yet able to show individual molecules (or ions!) sited in cells.

“The researchers expected to find PHB in only the cytoplasm of the plant cells, but it appears in the nucleus and vacuoles as well. That’s mysterious to us because these compartments are surrounded by membranes and it appears that the granules may be able to cross through”.5 Two strange aspects appear here: that there should be any doubt that the granules entered the cell, and that it should be surprising that they “crossed” the membranes of the cell organelles, when they must have first “crossed” the cell plasma membrane. The idea of ion entrance is implicit in the word “cross”, a concept the academic mind apparently finds almost impossible to forget; all relevant theories are based on it.

Obviously, the granules entered by endocytosis.

Much is known about this process in animal and human cells, but very little about it in plants, since there are only a handful of researchers around the world, who are working on it. Only three of them made it possible for us to show you electron micrographs depicting the stages in progress of molecules going into cells.

Plant cells differ from all others in having a cellulose wall, giving a plant rigidity; it is made of a meshwork of fibrils. It is apparently not difficult for items to pass through the cell wall, a mere tangle of microfibrils of cellulose, and there has not been any mass of data to prove or disprove this.

Inside this cellulose-mesh wall is a membrane. All living cells are surrounded by such a membrane, called in plants the cell’s plasma membrane.

No one seems to think a molecule has trouble getting through the cellulose mesh; it is confrontation with the membrane that was thought to pose all the problems. It is passage through this that has prompted so many scientists to devise explanatory theories.

In spite of all the theories, no one has ever seen the ions (such as K+), cited in soil tests, go through the membrane. Now we can track the progress of molecule masses by means of electron microscope pictures.

1 Inst, für Biochemie des Bodens der Forschungsanstalt für Landwirtschaft, Braunschweig, Germany.

2 Faculty of Agriculture, The University of Tokyo, Tokyo, Japan.

3 N. M. Stark “Mycorrhizae and Nutrient Cycling in the Tropics” in Mycorrhizae, Proceedings of the first North American Conference on Mycorrhizae, April 1969, ed. Edward Hacskaylo. Misc. Pubn 1198, USDA Forest Service, 1971.

4 Another very clever system is that of plasmodesmata, openings in contiguous cell walls, through which protoplasm (cytoplasm) is continuous from cell to cell, so that materials can move through these special, narrow passages.

5 BioOptions Vol 3 (3) pg. 2

1. Rateaver, B. & Rateaver, G. Organic Method Primer Update: A Practical Explanation : the how and why for the Beginner and the Experience. (The Rateavers, 1993). Page 21

The contributions of soil biology to plant nutrition

Have been known for decades, but have not gained traction in a business environment that offers no economic incentives to agribusiness for reducing or eliminating the need for applied fertilizers. Applied fertilizers produce an apparent magical response, and we are discovering that is indeed magical since it can not be sustained into the future.

Soil Microorganisms and Higher Plants is a classic, and worth reading if you desire to understand more of what soil biology can deliver, here are a few excerpts:

The biogeny of soil is the most significant indicator of its fertility. As soon as the activity of a microbial population begins in a rock, the first signs of fertility are manifested. The degree of soil fertility is determined by the intensity of the life processes of the microbial population.

It is impossible to solve problems of pedology, not to speak of agriculture and plant growing, without taking into account the microflora of soil. Plants are a very strong ecological factor, selecting certain species of bacteria, fungi, actinomycetes and other inhabitants of soil. As a result of wrong agricultural practices and crop rotation, the soil becomes infested with harmful microbial forms. By use of suitable plants in the crop rotation, one may change the microflora of soil in the desired direction and eliminate harmful organisms, in other words – restore the health of soil. Page 2 – 3

Increased accumulation of microbes in the root soil was first observed by Hiltner in 1904. He proposed the term  “rhizosphere”. In investigating the root system of various plants, Hiltner came to the conclusion that the accumulation of microbes in this area was not accidental and it was caused by the biological activity of the roots. Page 281

The microflora of the root zone is of great importance in plant nutrition. Growing near or on the roots, microorganisms, together with the plants, create a special zone – the rhizosphere. Soil in this zone differs in its physical, chemical, and biological properties from that outside the rhizosphere. The interactions between microbial species and between microbes and plants result in the formation of plant nutrient compounds. Substances present in the soil are subjected to a greater or lesser extent of processing before their absorption by the roots. The plants do not absorb those compounds which are characteristic of soil outside the rhizosphere but rather they absorb metabolic products of the rhizosphere. The rhizosphere microflora prepares organic and inorganic nutrients for the plants. Page 264

In the rhizosphere, iron, manganese, and other metals occur in combination with organic compounds formed by microbes. Amino acids, organic acids, and other metabolites of microbes form stable complex compounds. They are utilized by plants and used as a source of specific organometallic nutrients. These are found in greatest concentration in the rhizosphere and are preserved in the soil for long times. Page 281

Free PDFs of the book can be found on our reading list here.

2020-03-16T14:14:50-05:00February 27th, 2020|Tags: , , , , |

Can plants develop their own bacterial symbionts?

Our principle task as growers is to farm soil microbes. The larger and more vigorous a population of microbes we can grow in our soil profiles, the more nutritious and healthier our crops will become. Soil biology can supply all of a crops nutritional requirements when they are well managed and well supported.

A recent fascinating book that connects many dots in the historical research which have not come to mainstream attention is Herwig Pommeresche’s Humusphere. Translated from German, it is a treasure trove of references to European research on plant, soil, and microbial interactions which have been ignored in mainstream agronomy.

Here is an excerpt on the topic of remutation, how plants can develop bacterial cells from mitochondria and chloroplasts:


Recognizing that endocytosis takes place in plants is an important piece of support for the microbiological model of the cycle of living material, which includes microorganisms.

But there is also another area of microbiological research that seems to have completely lost the attention of the modern scientific community. It essentially represents the second half of the endosymbiosis theory developed by Lynn Margulis and the adherents of the Gaia hypothesis. This is remutation, postulated by Hugo Schanderl. In 1947, Schanderl1 had already succeeded in breeding and regenerating remutating, as he called it – living, viable microorganisms out of certain cell components, such as mitochondria and chloroplasts, from plant tissue after it died. These experiments showed that any living cell is capable of releasing new life after it has died.

Schanderl described every mutation in agricultural soil bacteriology as follows in 19702: “When a plant is buried, the soil is enriched with bacteria not only because a vast number of existing soil bacteria decompose and break down the plant corpse, multiplying tremendously in the process, but also because the soil is enriched with bacteria from higher plants as they break themselves down. Certainly, bacteria present in the soil also find abundant nutrients during composting, which allows them to multiply. But, as can be experimentally demonstrated, no bacteria need to enter from the outside whatsoever for decomposition to take place and a breeding ground of bacteria to arise.”

He continues in the same article: “A significant proportion of the bacteria regenerated from plant cell organelles present in cow dung return to the planting soil. Unlike artificial fertilizer, this kind of fertilizer is filled with life and enriches the soil with bacterial life, increasing it’s fertility.”

After more than fifty years of being ignored and denied by the sciences, the remutation model is now being indirectly confirmed by cellular and molecular research. Autonomous DNA that is independent of the cell’s nucleus has been found in both mitochondria and chloroplasts, which has led to acknowledgement of the endosymbiosis theory. In evolutionary terms, this also describes how ancient single-celled microorganisms relinquished their independence in favor of organizing into larger cells and, in a manner of speaking, were relegated into subordinate cell components.

Schanderl’s remutation model implies that all decomposing organic substances, as well as all seeds that are starting the development of new life, are most likely capable of reshaping their own cell components into autonomous microorganisms such that living plants can employ their help – if they reabsorb them from their surroundings – to carry on their metabolic processes. The question also arises as to what extent living cells are even able to absorb an exclusive diet of inorganic, water-soluble salt ions. Page 43-45

1. Rudloff, C. F. & Schanderl, H. Befruchtungsbiologie der Obstgewächse und ihre Anwendung in der Praxis. (1945).

2. Schanderl, H. Über die Isolierung von Bakterien aus normalem Pflanzengewebe und ihre vermutliche Herkunft. (1951).

2020-03-16T14:10:13-05:00February 26th, 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: , , , , |
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