Life in the Soil – Part I

Dr. Elaine Ingham earned her PhD from Colorado State University and is a leading researcher in soil microbiology and on the soil food web. She is also an author of the USDA’s Soil Biology Primer.


“Consider the fact that all the nutrients plants need are found in soil. They are present in excess in the rocks, pebbles, and particles of sand, silt, clay, and organic matter. Inorganic fertilizers are not needed, as the farmers and horticulturalists of Shumei Natural Agriculture have taught for many years.”

In her article Dr. Elaine Ingham lends scientific insight unto a spiritual practice of food cultivation. Dr. Ingham writes about what makes healthy soil, how the soil reveals its condition to those that understand how to read it, and then answers questions about building soil health.

In March of 2011, I toured a Shumei garden and began to understand the principles that embody Natural Agriculture. It was wonderfully enlightening to find people who share a similar attitude that natural processes must be the basis for agriculture. My expertise is focused on the sets of organisms that exist in soil, and the processes these organisms perform in natural soils. Looking at what happens to these organisms in current conventional agricultural systems is extremely depressing. We need to understand what life is necessary in soil, how these organisms function, and what conditions must be present for soil organisms to perform their beneficial jobs. The more we maintain the proper conditions for the workers in the soil, the better we mimic nature, and the higher the quality in our foods.

How does nature grow plants? Conventional agriculture does things differently than the way things are done in natural systems. We need to understand how those differences influence and affect the soil, plants 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?

The soil food web is comprised of the different organism groups in soil: bacteria, fungi (including mycorrhizal fungi), protozoa, nematodes, microarthropods, and larger organisms. These organisms interact to perform the functions needed by plants in the soil: disease suppression (around roots and around aboveground parts of plants), nutrient retention (so leaching loss of nutrients does not occur), nutrient cycling (making nutrients available to plants but mainly just in the root zone), decomposition of waste materials, and building of soil structure so roots can grow as deep as the plant requires.

Food web structure varies with season, climate, soil type, age of the ecosystem, etc. The existing food web will select for the growth of certain plants, and against the growth of others. Thus, defining health of the soil must be done relative to the desired plant. Is this food web healthy for this plant? To promote health, we need to understand soil as nature designed it. Plants have existed on this planet for at least the last billion years, meaning that the linkage between certain plants being selected by certain sets of organisms in the soil, and vice versa, has had plenty of time to develop.

To understand this system, then, we need to start at the beginning. The process of photosynthesis in plants uses sunlight energy to bond carbon molecules together and form sugars. Plants store sunlight energy by bonding one carbon from one carbon dioxide molecule, with another carbon from a second carbon dioxide molecule. Depending on what the plant needs, and its physiology, additional carbons can be bonded to the chain, storing energy in that sugar for future use. The sugar formed can be used to grow the plant, or it can be sent to the root system to escort nitrogen, in the form of an amino acid or protein, for example, to where the plant needs it. These sugars will bond with phosphorus, sulfur, magnesium, calcium, potassium, sodium, or any other nutrient in order to move those nutrients to where the plant needs that nutrient to continue growing.

All nutrients, except CO2 and sunlight, are provided to the plant through the soil. Soluble, inorganic forms of nutrients, move into the plant by simple diffusion into the roots, but the inorganic nutrients have to be converted from the ionic form, into carbon–bound forms once, inside the root, in order to prevent harm to the plant. Thus, once the soluble nutrient is inside the root, the plant uses enzymes to attach the nutrients to the carbon backbone of sugar from photosynthesis.

How many necessary nutrients are required for plants to grow? When I was a child, scientists talked about only three necessary nutrients: nitrogen, phosphorus, and potassium, or NPK. All that was needed to grow a plant, right? Wrong! By the time I was in high school, scientists realized more than NPK was needed to grow a plant. By then it was twelve important nutrients, including Na, S, Ca, Mg, B, C, O, Fe, and Zn. By the time I was in graduate school, the number of important nutrients jumped from 12 to 18. Today, scientists would say 42. And will we discover more necessary nutrients? Probably. Science continues to discover more essential nutrients all the time. In fact, probably all of the nutrients found in soil are necessary in some amount.

Consider the fact that all the nutrients plants need are found in soil. They are present in excess in the rocks, pebbles, and particles of sand, silt, clay, and organic matter. Inorganic fertilizers are not needed, as the farmers and horticulturalists of Shumei Natural Agriculture have taught for many years. But it is the organisms in soil that convert those nutrients in the sand, silt, clay, rocks, and pebbles from non–plant–available forms into plant–available nutrients. It is critical to have the organisms that perform these jobs present in adequate number, and balance, to be able to grow healthy plants.

If the beneficial organisms in soil are killed through inappropriate management, plants cannot get mineral nutrients from the soil. If plants cannot get mineral nutrients, then they will either die, or humans will have to take over providing those nutrients as inorganic fertilizers. Humans are not good at knowing what inorganic nutrients plants require at any given instant, and so we put on too much, in the wrong places, at the wrong times, and soil is harmed even more. Those excess nutrients also leach out of the soil and destroy soil further down the hill. Ultimately those excess inorganic nutrients harm water and destroy the quality of our ecosystems all the way to the ocean.

All agricultural soils, from young soils to ancient soil, contain all the nutrients needed to grow plants. Why is it, then, that you are told by fertilizer salesmen that your soil is poor, that it does not contain the nutrients needed to grow plants? Be careful, a trick is being played on you by people trying to sell you a product. Your soil has the nutrients in it, but if your plants show signs of poor fertility, what are lacking is the organisms to change nutrients that are present in the soil from a plant–unavailable form into a plant–available form. What you lack is the biology, the organisms, to convert the nutrients that are present in your soil into a form of nutrient your plant can use.

We need to have a full diversity of all these organisms in our soil. Each group of organism performs different basic functions. Disease, insect pests, and weeds are all actually messages from nature trying to tell you exactly what’s present or missing in your soil. Just because human beings have paid no attention does not mean that nature gives up trying to get our attention. Disease, weeds, pests, and poor plant growth are signs that you do not have the right sets of organisms present in your soil. However, you were taught by people who want to sell you a product, that you should pick up a toxic chemical to kill the organisms, or to fix the lack of nutrients. Neither of the chemical approaches fixes the problem in a sustainable fashion. Use a chemical and most likely you will need to use more chemicals. Perfect for the salesman. Not so good for your soil, your health, or your pocketbook.

When a disturbance occurs, such as a landslide, flood, or fire, all the organic matter that was present may be lost either as a result of being burned or buried deep in the earth. Regardless, nature immediately starts to build soil again. The first things that return after a catastrophic disturbance are photosynthetic bacteria. These bacteria gain energy from sunlight, fix nitrogen from atmospheric sources, and solubilize all other needed minerals from rocks, sand, silt, and clay. Photosynthetic bacteria do not need organic matter in order to function. Instead they release waste products, which are the organic materials that other organisms require. Lichens and algae will colonize as well, but all these organisms hold the mineral nutrients they solubilize in their biomass. Plants cannot grow yet, because no soluble nutrients are being released from the bacterial, lichen or algal biomass. Nutrient cycling has not yet begun to occur.

However, all these photosynthetic organisms release organic waste products, which give non–photosynthetic bacteria and fungi something to consume and grow on. As bacterial and fungal diversity increases, and more organisms become present to solubilize mineral nutrients from rock, sand, silt and clay, their biomass reaches a critical threshold that will support predator populations. When protozoa arrive, they can survive and flourish. Protozoa eat bacteria, and release plant available nutrients. With the arrival of predators, nutrient cycling begins. At first, only enough nutrient cycling occurs to maintain bacterial, fungal and predator populations. But as their numbers increase, eventually a rooted plant will be given the nutrients it needs, and plants will begin to germinate and grow.

To keep nutrients in soil and prevent them from washing away when plants are not growing, bacteria and fungi must be active and growing. Bacteria and fungi eat significantly different kinds of materials. Fungi are better at using lignin, cellulose, and other woody kinds of materials. Bacteria are better at using simple materials like sugars, structurally simple carbohydrates and proteins—not the more complex, woody things. Both bacteria and fungi hold the full range of nutrients necessary to support life in their biomass. So if you have a good soil food web, there is no need to worry about nutrients leaching from the soil.

But if your soil lacks diverse microbial life and living plants growing on the surface, then the soluble nutrients present in your soil will leach downstream to damage any ecosystem they encounter. Chemical fertilizer salesmen will tell you to put inorganic fertilizer on in the fall. But plants are not growing in the fall. As fall rains occur and the first few snowfalls melt, if there is poor microbial life in the soil, there will be nothing to hold that fertilizer. In that case, there is a crying need to add the required soil organisms to prevent leaching.

So, let us say you have a good level of bacteria and fungi in the soil. Nutrients are being held in the bodies of the bacteria and fungi. But now you put the seeds for your plants in the soil, and you want plant–available nutrients to be released. You want just the right amount of nutrients to be made into plant available forms to support your young plants, but not too much in order to avoid loss of those soluble nutrients. How does this work in the real world? How does nature make it work? Cannot we mimic this system, if we understand what it is?

Predators are needed to eat bacteria and fungi and release plant–available nutrients of all kinds. Protozoa and bacterial–feeding nematodes eat bacteria. Fungal–feeding nematodes eat fungi! Microarthropods eat fungi for the most part, and maybe a few nematodes and worms too.

Most people have heard about the bad nematodes that eat roots. Not until people start learning about soil life do they find out about beneficial nematodes. If a nematicide, or a nematode–killing toxic chemical is applied, all nematodes, not just the bad guys, are killed. We want the good guy nematodes to be left alone, because they make nutrients available to your plant. But we kill the good with the bad via the toxic chemical approach. And once killed, it will be bad guy root feeding nematodes that recover faster than the beneficial nematodes. This means if a toxic chemical is used, the exact things that you wanted to kill or suppress will actually be the first to come back. This helps the chemical pesticides sellers to make more money as they sell you more, and more, and more toxic chemicals. And all the while, as you spend more and more money, the problem is becoming worse. When pesticides are reused, the very organisms that suppress and control the problem organisms are killed. As the organisms that control the pest are lost, the worse the problem becomes.

Can we get rid of root–feeding nematodes? It is the good guy nematodes, the bacterial–feeding nematodes, the fungal–feeding nematodes, and the predatory nematodes along with microarthropods that suppress, inhibit and consume the bad–guy nematodes.

How did populations of root–feeding nematodes, or any other problem organism, increase in your soil? Nature builds soil, but disturbance destroys soil. Every time soil is disturbed, via plowing, digging, or compaction, some portion of the life in the soil is harmed. Consider the disturbances common in agriculture. When plows and tillage are used, fungi, protozoa and nematodes will be crushed, sliced to shreds, pounded into dust.

Can we replace the life killed by tillage, inorganic fertilizer, or toxic pesticides and herbicides? Where can we find the whole set of organisms required to make our soil healthy? The easiest and simplest source is good compost. The most important factors in making good compost are:

* Keep it aerobic at all times.

* Include plenty of good fungal and bacterial foods.

* Maintain good moisture levels through the entire composting process.

* Maintain adequate but not too high temperature for correct amount of time to kill weed seeds and human or plant pathogens.

If making worm compost, weed seeds have to be killed first by high temperature before adding to the worm bin, but then the beneficial aerobic organisms in the worms take care of the pathogens.

How do you tell if your compost is aerobic? It should smell like good forest soil. The just before rain smell is not what you want; actinobacteria make that material and while good for brassicas, it is not desirable for any other crops.

Anaerobic conditions result in the growth of the organisms that produce the bad smells. For example, only under anaerobic conditions can ammonia be produced. If in doubt about what the ammonia smell is, go to the grocery store and buy a bottle of ammonia. Open it, and carefully waft a little of the gas escaping from the liquid by your nose. If soil, compost, or lake or pond water smell like ammonia, then nitrogen, one of the most vital nutrients needed to grow plants, is being lost. The ammonia smell indicates that nitrogen is being lost as a gas.

Similarly, a rotten egg smell can only be produced when conditions are anaerobic. That smell occurs when any inorganic, soluble sulfur compound is reduced to hydrogen sulfide. Sulfur is needed by plants, and its loss as a gas can reduce yields. There are many other examples of toxic anaerobic compounds that harm plants, and most of these materials are only produced in anaerobic conditions.

Where do the organisms in compost come from? Both the beneficial and harmful ones come from the surface of the plant material put into the compost pile at the start. The conditions that develop in the composting process select for the growth of the beneficial (aerobic), or the harmful (anaerobic) microorganisms. The organisms that live in the habitats surrounding a living plant are present on that plant material when it is added to the compost pile, and they grow when conditions in the pile are right for them. If the conditions are not right, then the organism stays dormant or becomes dormant.

Thus, if you disturb your soil by tilling or digging in it, you need to replace the soil microorganisms that were damaged by the management you did. Is it unnatural to put back what we have harmed? As long as we make compost that contains the beneficial organisms of that place of its origin, that compost will maintain the set of organisms that should be present. We need to consider and discuss these things, especially because Natural Agriculture practice suggests that compost can be highly beneficial. When compost is considered to be bad, I suspect the reason it is considered bad, is because of a particular situation where the compost used was not really compost at all, but rather an anaerobic, smelly, black organic matter that would harm plants.

Part II
Part III
Part IV

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