Life in the Soil – Part III

In March of 2011, I toured a Shumei garden. It was then that I began to understand the principles of Natural Agriculture. It was enlightening to find people who share the attitude that natural processes must be the basis of agriculture.

My area of expertise is focused on organisms that live in the soil, and the processes these organisms perform in natural soils. Looking at what happens to these organisms in current conventional agricultural is depressing. We must understand what life forms are necessary in soil, how these organisms function, and what conditions are necessary for these organisms to do their jobs and benefit the soil. The more we maintain the proper conditions for the workers in the soil, and the better we mimic nature, the higher the quality of our foods becomes.

How does Nature grow plants? Conventional agriculture does things differently than the natural systems do. We need to understand how those differences influence and affect the soil and the quality of plants. We need to understand the damage conventional practices cause. We need to learn how to maintain our plant production systems as naturally as possible, realizing that short-term gain in yields costs too much to the long-term health and balance of the system. What are the constraints we impose? What are the sets of organisms that need to be there? How do these organisms behave in a natural system and how can we use them in our agricultural systems?


There is a very beneficial fungus in the picture above. We know this because of its wide diameter and color. Colored fungi are almost invariably beneficial. So the dark brown hyphae with the diameter of about 3.5 micrometers is very good, as is the tan-colored strand of slightly narrower diameter in the bottom left. There is a clear, colorless hypha a bit below midfield, but its diameter of five micrometers sets it in a beneficial category. Finally, there is a strand of fungal hyphae that is clear, narrow diameter, a bit out of focus, nearly parallel to the strand of brown fungus above center field. A narrow diameter and clear color almost always means that fungi are pathogenic, or disease causing. Thus, we can say something about the fungal community in this soil by observing its morphology.


In this particular case, the bad fungus is Pythium, which is a white rot fungus that can attack and destroy root systems. If we plant in this soil, should we be concerned about disease? No, because competition from the good fungi will prevent the bad fungus from growing. What if we had used a fungicide, meant to kill all fungi in the sample? All the beneficial, disease-competing fungi would have been killed in the soil, and most likely the disease-causing fungi would survive in the soil at a level deeper than the fungicide penetrates. If that happens, be very worried, because the disease will be able to destroy the plants in this system. By maintaining functioning beneficial organisms, in the proper balance in your soil, we can let the organisms do the work for us.

Below, to the left is an example of soil at a golf course in the United Kingdom. When we first started working there, massive weeds, insects, fungal diseases, root-feeding grubs and nematodes infested their soils. Then the proper biology was put back into the system. These nice white fungal hyphae started to grow, indicating that a good healthy food web had been reestablished. Disease, pests, and weeds were gone as well.

When fungal strands like this appear, it indicates that the soil is healthy. The soil is no longer bacteria dominated, and the ratio of fungi to bacteria has shifted from a strictly bacterial system to a well-balanced system—the proper amount of bacteria to fungi. When that happens, weeds, fungal diseases, and root and foliar diseases disappear. The soils no longer are compacted. Nutrient cycling is established, setting the stage for growing the grasses the groundskeepers want to grow. They do not have to use toxic chemicals anymore.

It only took about six weeks to create this conversion. So the life that is supposed to be in the soil can be put back very quickly. Can this kind of understanding of biology help the Shumei Natural Agriculture process?

In Tasmania, where the government is giving grants for people to test concepts that shift from conventional agriculture to more sustainable practices, an onion farm had been managed with conventional chemical practices for perhaps 60 years. The conventional field had two applications of herbicides already applied, but weed numbers remained very high. Roundup2 was not able to kill the weeds, as the genetic resistance to Roundup had been transferred to many plant species.

The field next to the conventional field, which had been previously managed by conventional means, two applications of compost tea3 were applied instead of Roundup, and no weeds to speak of germinated or grew there. Several thousand dollars were saved before the crop was even planted because compost and compost extract were used instead of the expensive herbicide and inorganic fertilizers. Onions were planted on the same day in both fields, and at the time, a third application of Roundup was applied because the weeds were clearly bad in the conventional field. A third application of compost tea was also applied on the biological field. Extremely few weeds were present in the biological field, and the onions were larger and roots deeper than in the conventional field.

The grower showed that when the soil in the biological field was not treated with organisms to suppress weed growth, the weeds were worse there than anyplace else. This proves that weeds were indeed suppressed by compost tea application, since without compost tea, the weeds were extremely dense.

What are composts and compost teas? Compost is made by the oxidative decomposition of a mixture of organic materials. Oxidative decomposition means that good levels of oxygen, or aerobic conditions, are maintained throughout the composting process. Aerobic microorganisms are allowed to grow rapidly enough to produce heat in the organic matter. This heat should be high enough for a long enough period of time to kill the pathogens, pests and weed seeds in the compost pile. The pile should be turned if the compost temperatures reach higher than 65 to 70 C (149 to 158 F) or if the pile smells bad, shows a layer of actinobacteria growth, or if moisture needs to be added into the pile. As the bacteria and fungi consume all the easy-to-use microbial foods within the pile during the composting process, the pile will cool back to ambient temperatures. Once cooling occurs, the pile is considered to be finished.

Finished compost can be extracted using water to pull soluble nutrients and beneficial microbes out of the compost. The extract then can be added to water to simplify spraying over a large area. Typically five to 20 liters (about 5.3 gallons) of compost tea per acre can be applied, depending on the concentration of organisms needed to change the soil’s biology.

Thus, by altering the biology in the onion field’s soil, weed growth was suppressed. If the biology in the soil is maintained such that adequate bacterial, fungal, protozoan, and nematode numbers are present, weed, disease, and pest problems will remain suppressed. Fertility will also be improved as nutrients are cycled by bacteria and fungi being eaten by protozoa and nematodes.

If we follow Nature’s principles and put the proper biology back into the soil, then onions will grow in a very healthy fashion.

Growers need to understand that different plants (weeds, crops, trees, and so on) have very different requirements for the balance of fungi and bacteria. We can all see that different plant communities occur in different places, but many people do not understand why this occurs. What allows this set of plants to do well here, but not over there? Why do these plants grow in this place now, but did not grow here 20 years ago?


To understand this, we need to first recognize and understand the normal course of plant community succession, why one type of plant community follows a different plant community. Succession starts with sterile, bare dirt. Everything on this planet was once sterile, without life, but then photosynthetic bacteria evolved and rapidly took over the planet, developing into many, many different species. Thus the earliest successional stage is strictly bacterial. But as these bacteria release wastes, true bacteria grow, saprophytic fungi appear, and then predators of bacteria and fungi develop. Not until a basic food web has been established can plants of any kind grow. The first types of plants are ones that put little energy into the root system, grow very rapidly for short periods of time, and produce high numbers of offspring, usually seeds. These plants thrive best with lots of bacteria around their roots, and not much fungal biomass. Thus, these plants prefer their soil to contain lots of nitrate and little ammonium.

But when green plants grow, the residues they leave when they die provide more fungal foods in the soil because of the lignin and cellulose that plants contain. This transition will begin to increase the amount of fungi in the soil to a point where the balance of fungi versus bacterial shifts only slightly to the side of fungi in the weedy species. Slowly but surely, the shift continues to occur and fungi catch up a bit with the bacteria, and then plant species shift as a result. True weeds phase out, and some early grass species, brassicas and wetland plants begin to appear. Eventually, these more fungal loving plants will develop a larger fungal component in the soil, with more species of fungi, creating a plant community shift to more vegetables and mid-successional. Nature keeps increasing that fungal component. Thus plant species shift to later successional grasses and plants that have more and more woody components, eventually leading to forest development.

Mature grasslands will give way to shrubs, vines, and bushes, which in turn will develop even more fungal dominated soil communities. These woodier, more fungal food containing plants put more fungal foods into the soil, shifting the soil balance away from bacterial food, increasing the fungal component more and more, and shifting plant species into conifer and old-growth forest systems. In the late stages of succession, bacterial biomass remains the same with respect to numbers, but its diversity keeps increasing. This is how Nature does it. Can we use this information in agriculture?

Part of the explanation for these shifts in plant species is that, early in succession, bacterial dominance generates a lot of nitrate in the soil, making it the predominant form of nitrogen. As fungi become more dominant, they shift the predominant form of nitrogen in the soil to ammonium, Nh4. In soils where bacteria and fungal populations are balanced, then nitrate and ammonium levels will be about equal. When the vegetation shifts to woody perennial plants, changing with the soil’s shift to fungal dominance, the predominant form of nitrogen will become ammonium, which is what trees require.

So Nature drives successional changes by increasing the fungal component of the soil more than the bacterial component. If we want to truly mimic Nature in our agriculture fields so to generate a successful crop with no weed, pest, or disease problems, we have to generate the same fungal and bacterial balance in the soil as that found in the natural system.

So why is not this planet covered entirely in old growth forest? Because disturbance re-sets systems to earlier stages of succession. A severe disturbance will set things back to very early stages of succession, while less catastrophic disruptions will push things back to intermediate stages.

If there is a fire, what happens to old growth forests? If whole trees burn and all the organic matter on and in the soil burn, succession may return all the way back to bare soil, with no plants at all. The system has to start again from the beginning. And of course, nature does exactly that.

If a pasture system is tilled, how far back in succession will the system be driven? This depends on how intense the disturbance is, how much of the life in soil was destroyed, and how much organic matter was lost. A rototiller will cause a great deal more damage than a moldboard plow because rototillers slice and dice and crush more organisms living in the soil, leaving only bacteria to rule, whereas moldboard plows only flip the soil surface over, leaving more organisms intact. When the first rainfall or irrigation occurs after rototilling, the soil will collapse and compact, because there was no life in that soil left to form the structure needed to build and maintain aggregate structures. Rototillers also press down on the soil at the depth of the metal blades, compacting the soil at that depth. Without any decent life in that soil, water is held at that compaction layer, causing anaerobic conditions to develop. This process, coupled with a lack of oxygen, set the stage for growing weeds, and only very early successional, disturbance-requiring weeds.

Be aware what is destroyed when any management practice is performed. Consider the effects of disturbance of any kind on life in the soil. Will that alteration result in succession going the way you want it to? How many of you have had experiences with a rototiller? After tilling, what comes back in abundance? Weeds. What if we disturbed the soil less, or not at all? Can we plant crops without disturbing the soil? Can we cause less damage?

Consider no-till methods, rolled cover crops, direct drilling, or planting into an existing living mulch, or permanent short-growing cover crop mix. Or as the practice of Natural Agriculture shows us, plant back into undisturbed soil where that plant was grown the year before.

If we have to damage our soils in order to prepare seed beds to grow our crops, then perhaps we could reduce the damage by coming back immediately after the disturbance and replacing the organisms we have killed. This is what Nature does, over time, to improve productivity in that soil. So, perhaps we can find ways to make these improvements more quickly.

By understanding what these organisms do in the soil, we could allow our agricultural soils to match what Nature does instead of destroying natural processes. When disturbances happen, we can use these principles to reduce the harm done, and more rapidly return our soils to healthy conditions to grow food for people.


Over the last 100 years of doing intensive chemical agriculture and intensive urban landscaping, humans have developed a very warped and incorrect view of how roots exist in soil. Then tilling, we fluff the surface layer of the soil, but we also push down on the earth below the plow blade, causing compaction at that depth. Because water will not move very rapidly from that fluffy layer into the compacted layer, an anaerobic layer develops. Then toxic, unhealthy bacteria grow, producing toxic materials and releasing major nutrients as gases. Plant roots will be restricted to just the top few inches. This is not natural. That is not the way plants are supposed to grow.


How far down into the soil do roots go? Over the last 100 years of doing intensive chemical agriculture and intensive urban landscaping, humans have developed a very warped view of how roots exist in soil.

The compaction layer and the black anaerobic layer are seen in the picture at left, above. They are the consequences of human management. As a result of this poor management approach, the roots of the plants have been killed at the anaerobic layer. The plants are forced to fight each other in that shallow layer of soil at the surface.

There are hundreds of papers in the arboricultural4 literature that suggest that trees only put their roots systems down about three feet into the soil, and then go sideways. Just like the tree in the picture above. Many, many examples of this type of root growth have been shown. But this does not mean this pattern of root growth is natural. What we see here is the same problem that humans impose in agricultural fields. Compaction was imposed on the soil by human management such as tilling to aerate the surface soil, but imposing compaction where the blades of the plow pushed down below the surface of the soil. People compact soil around houses or buildings to prevent the foundation from moving, but they pay no attention to the damage they are causing to the landscape trees. The tree in the above picture suffers from diseases, pests, and poor fertility because the roots are prevented from growing as deep as they should. But humans, instead of understanding the damage they cause, blame disease, pests, and poor growth on the soil being poor. When instead we should properly point the finger at ourselves for destroying the aerobic life that should be in the soil.

How far down can roots go? If you go out into natural systems and look at how far down roots of trees can go, the first thing to note is that those roots are not restricted to the top two or three feet of soil. Instead, tree roots can go from 100 to 200 feet deep, perhaps deeper. Go to a cave, and look for the roots of the trees growing through cracks in the rock down 50, 100, 200 or more feet.


If the soil has no compaction layer imposed on it by tillage, grass roots will easily grow four to six feet deep within a few months. The rye grass in the above picture was planted as seeds in healthy soil, and then dug up three and a half months later. Note that the roots were four and one-half feet deep in the soil. This is normal for grasses. Roots restricted to the top inch or two of soil are not normal, but the consequence of damage imposed by humans.

Nature sends messages to us about the harm caused by compaction and oxygen deficiency through diseases, weeds, and pests. We have to learn to listen, understand the message being sent, and take appropriate action.

How can productivity, nutrient cycling, soil structure, and all the other functions of a healthy soil be brought back? How do we get the organic matter back?

Most of us have seen the posters from the United States Department of Agriculture (USDA) telling us it takes a hundred years to build an inch of soil. But, we should understand that it is microbial life that builds soil structure. Without microbial life, we can never build soil and it will take forever to bring back healthy soil, with all its beneficial functions and processes. Soil functions and processes require soil microbial life. If we nurture the proper set of microbial life in the soil, then building soil happens continuously in a healthy cycle.


How fast can an inch of soil be built? Work done by James Sottilo shows how rapidly soil can be built. To get the same results in your systems, you have to do what he did. For example, take engineered soil. (Actually engineered soil is just dirt, as there was no life and practically no organic matter or foods for the organisms in it.) Engineered soil was spread in the park featured in the above photo. Before the sod went on. Then, the proper set of biology for the grass was applied, using compost tea. After the sod was placed, another round of compost tea with the proper biology was applied to the plot. Notice that the sod was compacted, because you can see the puddles of water forming on the sod surface. That was not healthy sod, and so we were not starting with good microbial life in the soil.

How rapidly can this problem be fixed? By doing exactly what Mother Nature would do, only faster. It might take Nature years to do this in the middle of a New York City park. But we can build soil rapidly by some simple management methods. We might question whether humans have the right to speed the process of succession. Nature would normally have to go through years of a weed stage of succession, given the damage that has been done to this park. But one way of looking at this is that humans did the damage and therefore they should restore the soil to its pre-damage state. We destroyed the grassland that was there before construction started, so we have the responsibility to Nature to return the system to productivity as rapidly as possible.


So, by applying the set of soil microorganisms that would have been present in a healthy grassland, we jump-started the successional process straight back to a healthy grassland system.

Note the dark brown color of healthy rich soil and the depth of the roots after just six weeks in the above picture. The root system is already down to six inches. Give this system a month or two months and those roots will be even deeper. There are no weed problems or root-eating insects, because we brought back the microbial components of a healthy soil system.

Take a look at these yards in a neighborhood of Boston in the picture, above to the right on page 21. The yard with the red circle around it is green and healthy and has not had any irrigation the entire summer. A year earlier, this yard looked like all the other yards in the neighborhood. How did this yard change from a dormant yellow patch of grass, full of weeds and disease, to a verdant patch of green? The owners of these houses were watering their yards of dormant grass and weeds in the late summer every chance they had. But the lawn that was not artificially watered still looks green and healthy. How can that be?

The answer is that after the owners had damaged their lawns so badly, we put the soil organisms and foods required for Nature’s nutrient cycling and soil building back into the soil.

Soil microbial life builds soil structure that will absorb and hold water. As such, in this lawn water use was reduced by between 50 and 70% as compared to the toxic chemical-maintained soil systems of the other yards. In the middle of a drought, it is important to reduce water use. You can also reduce your water bill by at least 50%, perhaps as much as 70%. Make sure the microorganisms you need to support the plant you want to grow are present in the soil. In that way, you can build the soil structure to hold water and nutrients.

Exactly what did we do to achieve this water-savings, and stop using inorganic fertilizers and toxic chemicals? We replaced the soil biology by applying aerobic compost in the fall of the previous year. The next spring, compost was applied in a liquid form three times. We had to make sure the right sets of organisms to support grass or flowers or shrubs or trees were present in each area to see all the problems go away.


By returning the right sets of organisms to the soil, we had no need of chemicals. Whether you work in agricultural fields, gardens, or lawns, the soil’s microbial life is what is important. This is exactly what you have been doing in Natural Agriculture. But we can reduce the time it takes for you to return to the microbial life that Nature had in the soil before these human-induced disturbances started.

If we start to understand the biology that is in our soil and if we know what our plants need, then we can increase the speed of recovery of our plant production systems and our planet.


2. Roundup: The Monsanto Company first brought glyphosate, an herbicide that kills a wide range of weeds and grasses, to market in the 1970s. Its brand name was Roundup. Because of relatively low toxicity, it was a desirable alternative to other herbicides. Later, Monsanto introduced Roundup Free, a range of crops resistant to glyphosate poisoning. This allowed farmer’s to kill weeds but not their crops, thus increasing Roundup’s sales and Monsanto’s profits. However, because of Roundup’s heavy use strains of glyphosate resistant weeds have naturally evolved. While glyphosate is used widely throughout the world and is approved by many regulatory bodies, both its long-term effectiveness and its impact on human and environmental health are still a major concern.

3. Compost Tea: Compost is decomposed organic matter that is used as a nutrient for plants. It is a key ingredient in organic farming. Making compost usually involves piling moist organic matter such as vegetable food waste, leaves, and dead plants and leaving it to decompose until it becomes nutrient rich humus. The process could take weeks or months. Compost is used in gardens, landscaping, horticulture, and agriculture. Additional benefits of compost are weed and erosion control, and warmth.

Compost tea is a liquid extracted from compost. It can be made by soaking compost in water for three to seven days. Its original use was to combat fungal infections on foliage.

4. Arboriculture is the planting, cultivation, and study of trees, shrubs, vines, and other perennial woody plants. It is both a practice and a science.

Part I
Part II
Part IV

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