Life in the Soil – Part II

Having briefly explained how we replace the complex set of organisms that need to be in soil, let us make sure to cover all the important points regarding a healthy soil food web. If all of the soil microorganisms are in the proper balance, disease will be suppressed because plants put out specific exudates to grow exactly the right bacteria and fungi around every part of the root system, protecting all the roots.

What is an exudate? Exudates are mostly sugars from photosynthesis, a little bit of protein and some carbohydrate. If I sent you into your kitchen and asked you to make a recipe of mostly sugar, a little bit of protein and a little bit of carbohydrate, what would you end up making? Cakes and cookies. Thus, root systems of plants release different cakes and different cookies depending on which bacterial or fungal species the plant wants to have working for it at any point in time. The plant may put out one type of exudate in order to grow those bacteria and fungi that prevent the growth of fungal diseases. In another part of the root system, the plant may put out foods that grow those bacteria that solubilize iron because the plant needs more iron. Because there are billions of bacteria and miles of fungal hyphae around that root, the plant is protected from disease organisms. No disease causing organisms can survive in that root area because there is no space left and no food left for something un–friendly to consume.

Predators are attracted to the root system, bringing nutrients and eating the harmful organisms, as well as the other bacteria and fungi present, and thus releasing plant available nutrients. Like pizza delivery guys, predators deliver precisely the nutrients your plant needs right to the surface of the root.

Is not nature amazing? If we just get the proper microbial life back into our soil, then there is no need to apply inorganic fertilizers. Hopefully, you begin to understand that the management you have been doing in Shumei Natural Agriculture has a scientific basis.

So soil amendments are not needed if you have the right sets of organisms in the soil to do the work. Think about the fact that your plant puts out the foods to grow billions of bacteria on every bit of its surface and supports miles of fungal hyphae growing around its root system. Bacteria and fungi form a castle wall to protect your plant from disease and pests.

How many species of bacteria and fungi are in that wall? Every species of bacteria or fungi grow best in one particular set of conditions. One species grows best at zero degrees, one grows best at five degrees, another grows best at ten degrees, and so on. Some species grow better at low moisture, while others grow best at higher moisture. Each species also needs different levels of calcium, or CO2 concentration, or iron, or boron, and the list goes on and on. There are an unfathomable number of factors that will cause one species to do better and another one to die out.

When you start thinking about all those factors, how many species of bacteria are needed in soil? Research is being done at many institutions all over the world, such as the Center for Microbial Ecology at Michigan State University, Cornell University, Auburn University, UC Davis, and so forth, using DNA analysis to determine that there are a million species of bacterial in one acre of woodlot soil in Michigan, along with five hundred thousand species of fungi, thousands of species of protozoa, and hundreds of species of nematodes. And that is just in one wooded acre in Michigan. Imagine other woodlots in Colorado, or California, each with its unique cast of millions of species from all these different organism groups.

If we destroy that life, how can we replace it rapidly and easily? The answer is: Make compost. If your soil lacks anything, you can put it back with good compost. If you do not disturb your soil, then the life in that soil will not be lost. If you disturb your soil, then you may need to help remediate the damage that you have done. The goal is to help nature’s organisms get back to the proper balance so that the natural nutrient cycling processes can occur at the rate they need to occur.

Disease suppression depends on having all these species functioning, so that every second of every day, the roots, leaves, flowers, fruits, and stems are protected by this castle wall, no matter how environmental conditions change.

With this massive set of organisms growing on all surfaces of the plant, and all these organisms needing the proper balance of nutrients in their bodies, nutrients will be taken up, held, sequestered, and retained. These nutrients will not leach or be lost through water movement, because the bacteria and fungi are glued and bound to plant surfaces, organic matter surfaces and sand, silt, and clay surfaces.

But then, how are all these nutrients turned back into plant available forms? When bacteria and fungi are eaten by predators, nutrients are released in plant available forms. Given that plants are most demanding of nutrients in the springtime, most predators need to be most active during that time.

How does your plant make sure that this nutrient–cycling system is rapidly providing all the nutrients that the plant needs? When your plant needs lots and lots of nutrients, it puts out lots and lots of cakes and cookies through its root exudates so bacteria and fungi grow rapidly and take up all available nutrients from soil water, organic matter, soil particles and rocks. Beneficial predators are attracted into the root system, which then eat the bacteria and fungi and release plant available nutrients right there at the root surface.

When the plant’s growth slows down and it does not need as many nutrients, an example would be when the plant starts to make seed, then the plant directs more of its energy to the flowers and the seeds. When that happens, less energy is being released in the soil, so fewer cakes and cookies are released, the bacteria and fungi no longer grow rapidly, and the protozoa lose interest in the root system. The protozoa, bacteria, and fungi may go into dormant phase as the soil nutrient cycling system slows down.

Another really important function these organisms perform is to build soil structure. Fungi produce threads, or strands, as they grow. A dead brown leaf can be decomposed by fungi rapidly, and within a few days that leaf changes from mostly cellulose and lignin to fungal biomass and humus. Bacteria cannot use dead brown leaves as food, because their nutrient concentration of everything from nitrogen to zinc is too low.

When fungi start to consume plant material, however, they release sugars that bacteria can use. So leaf decomposition is a two–step process. Fungi have to come first to start breaking up the leaves, and bacteria can then scavenge the sweets that the fungi do not use.


The beneficial fungi we want to see always look like strands or threads of uniform diameter tubes growing from their tip. Fungi can be black, tan, red, golden, or clear, and can be narrow, under two micrometers, or wide, greater than three micrometers.


Bacteria are much smaller than fungi, on the order of one to five micrometers. They can be round, rod–shaped, corkscrew shaped, and C–shaped. Each of these shapes can have small diameters or very wide diameters. Some species can move under their own power, although at least half of bacterial species cannot move by themselves. Bacteria can clump in various patterns; such as chains of individuals, filaments that grow around themselves, colonies, picket fence patterns, V–shaped pairs, or just as chains connected end to end.

We train people to identify these different organisms in soil. A sample can easily be analyzed for microbial populations in five to ten minutes, once you get good at identifying organisms.

There are great videos of roots growing through soil showing the castle wall of bacteria and fungi surrounding the root. As the root develops root hairs farther along its length, protozoa arrive to start nutrient cycling processes for the plant.

When roots grow through soil, the soil needs lots of spaces, hallways, airways, and passageways so the root can grow without expending energy to push its way through the soil. A better aggregated soil makes it easier for the root to reach the sites, nutrients and water it needs.

Soil aggregates, which are clumps of smaller soil particles bound together, are built by all of the organisms in soil working together. Sand, silt, and clay are pulled together by bacteria that ooze glue–like exudates to bind the particles together. Aerobic bacteria make copious amounts of glue to hold themselves on to surfaces so they do not wash away from their food source. The bacterium then glues some organic matter into place, then some silt and clay, then more organic matter, then a sand grain, and so on. This process creates a soil micro–aggregate.

A macro–aggregate that can be seen with the naked eye requires fungi to bind its particles together, just like rope around a group of packages, or micro–aggregates, made by the bacteria. As all these material get pulled together, airspaces appear between the aggregates in areas that were once filled with bits and pieces, creating space for oxygen and water to move very easily through the soil.

How many of you see water puddling on the soil’s surface in the springtime or after a rain? Through these puddles, nature is trying to send you a message. Puddles indicate areas where there’s poor soil structure and the needed bacteria and fungi are not present. No hallways and passageways are available to allow good infiltration of water or air or roots. Compaction layers are likely present and soil life is lacking. Learn to read all the messages that nature is trying to send. How do you prevent puddles or compaction? Put organisms back in that soil.

Once micro– and macro–aggregates are built, larger organisms need to move the particles around and form larger spaces. Protozoa, nematodes, and microarthropods rearrange the macro–aggregate furniture and make bigger spaces appear. Does soil have feng shui? Absolutely, and it is built by the organisms that live in the soil. No life: no feng shui.


The name of the above nematode is Alaimus, and she eats bacteria, then releases the nutrients previously held in the bacteria’s bodies in a plant–available form. How do we tell that this is a nematode, and how do we figure out she is Alaimus? We identify organisms based on morphology. The mouthparts show us that this is a bacterial–feeder. We want to know whether we have enough of these beneficial nematodes in a teaspoon of soil. Thus, we may need to scan through several drops of a slightly diluted soil looking for these organisms. Typically, all this scanning work is done under a microscope at 400X magnification. This low magnification is easy to work with, making the soil analysis process quite easy for people to learn and master.


A root crosses the lower part of this picture, while the top area is occupied by a ciliate. Note the hairs coming off the ciliate’s body. These are cilia, for which the group of organisms is named. Within the root, note that you can see quite a number of different cells, and so it is easy to distinguish it from a hypha of a fungus. There are aggregates made by bacteria all around the root; note the little round bacteria and the rod shaped bacteria in high number.

The color of the aggregate tells something about conditions in the past. The tan color denotes fulvic acids, while the dark brown to nearly black color denotes humic acid formation. These are both highly condensed, very beneficial foods for aerobic fungi. These forms of organic matter are a way to save foods in complex forms so no microbes attack them too quickly.

The ciliate indicates that the sample is, or recently was, anaerobic. In the past, this soil may have been in good shape, based on the humics, fulvics, and aggregates, but the material is or recently was anaerobic, indicating that the soil may cause harm to plants. The presence of the ciliate says that attention needs to be paid, and immediately, to this agricultural field to establish a better set of organisms, or face probability of diseases and pests or poor fertility.

With all of these organisms, we need to understand the balance of each organism for each plant, climate zone, soil, and condition. The relative biomass of fungi versus bacteria seems to be an important determinant of pH, nutrient retention, and soil structure, while the balance of protozoa and nematodes indicate whether nutrients will be cycled rapidly enough to maintain nutrient concentrations in the root zone.

Consider how the nutrients needed by an old growth tree come to be in the root zone of such trees. No one applies inorganic fertilizer to old growth forests. Yet, the increase in biomass and nutrients stored in plant biomass is greater than that of any agricultural field. If nature manages to grow old growth forests where more carbon, nitrogen, sulfur, phosphate, and so on are sequestered each year, than are removed from agricultural fields in crop yield, and yet no additions of N, P, K, or any other nutrients are needed, then we need to pay attention to how these old growth systems manage to do this.

The secret is to have the right balance of biology in the soil to hold and release nutrients in exactly the right ways.

The largest organism on this planet, or at least the current winner, is in Washington State. Paul E. Stamets1 has shown this fungal individual is possibly 20 miles wide, and goes from a couple inches below the soil surface to as deep as 25 feet, creating a single individual fungus the size of a herd of blue whales. This organism holds and retains nutrients in the soil on a massive scale. But come springtime, the microarthropods, flying squirrels, earthworms, and other predators in the old growth forest system wake up and feast on that fungal tissue that grew without predators all winter long. These predators almost entirely consume the fungal tissue, almost wiping it out. Think of all the nutrients released and cycled! But come fall again, when the predators go to sleep, the fungus grows and reaches the same size, and sometimes growing even larger.

Trees, on the other hand, do not release the nutrients they take up until they are decomposed. Those nutrients are stored in the tree’s wood, branches and roots and will not be released to be cycled for hundreds or even thousands of years.

So, from where do all the new nutrients for old growth trees come? Nobody is out there putting inorganic fertilizer into that forest and yet each year, old growth forests increase the nutrients held in old growth tissue. Each year, more plant material continues to be stored in that forest than in any agricultural crop we harvest. How is this possible?

Where do the nutrients constantly come from? Both bacteria and fungi have the ability to solubilize nutrients that are in the soil’s parent material, sand, silt, clay, and organic matter. There are thousands of years’ worth of mineral nutrients in sand. All minerals that plants need are in rock, except for nitrogen. Nitrogen gas is found in the atmosphere, carbon, drawn from carbon dioxide in the atmosphere, and energy, which is sunlight.

Bacteria and fungi have the enzyme systems to pull these plant–unavailable forms of nutrients from rock and convert them into their own biomass. Then bacteria and fungi are eaten by their predators, resulting in the release of plant–available nutrients. Bacteria and fungi contain the most concentrated forms of N, P, K, Ca, Fe, Zn, and other nutrients of any organisms on the planet, so they hold and retain nutrients in an organic form. Predators release those nutrients in a plant available form.

Fungi in an old growth forest hold nutrients and then are almost completely eaten by predators in the spring and summer. When the predators go to sleep in the dry, dry summertime, or in the cold, cold winter time, the fungi start to re–grow. Come next spring the fungi are completely re–established, and ready to go again. Think of how dynamic a forest is! We need that fast a cycling system in our agricultural fields, and we can get it just by improving the soil microbial life in them.


1.  Paul E. Stamets (b. 1955) is an American mycologist, author of numerous books and papers. He is a strong advocate for bioremediation and medicinal mushrooms. He is on the editorial board of The International Journal of Medicinal Mushrooms, and is an advisor to the Program for Integrative Medicine at the University of Arizona Medical School.

Part I
Part III
Part IV

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