Soil Food Web

Unseen beneath our feet, there dwells a teeming microscopic universe of complex living organisms that few humans ever consider. In one teaspoon of soil alone, there may he over 600 million bacterial cells. These bacterial cells exist in complex predator-prey relationships with countless other diverse organisms. This topsoil food web forms the foundation for healthy soil, healthy plants, and ultimately, a healthy planet.

The soil food web is the community of organisms living all or part of their lives in the soil. The food web has a basic set of expected organisms groups, but the numbers of organisms and different species in each group can vary significantly by plant and soil type. Photosynthesizing living plant material provides the initial energy to the soil food system through their roots. Living plant roots exude many types of complex high-energy nutrient molecules into the surrounding soil. Dead plant material is decomposed by bacteria and fungi, building up even greater numbers of these organisms and their metabolic products. As a plant grows, photosynthesis supplies much more than the individual plant’s carbohydrate requirements. It has been documented that plant roots can exude over 50 percent of the carbon fixed through photosynthesis in the form of simple sugars, proteins, amino acids, vitamins, and other complex carbohydrates.


Around plant roots, bacteria form a slimy layer. They produce waste products that glue soil particles and organic matter together in small, loose clumps called aggregates. Threading between these aggregates and binding them together are fine ribbon-like strands of fungal hyphae, which further define and stabilize the soil into macro aggregates. It is this aggregated soil structure, which looks a bit like spongy chocolate cake that effectively resists compaction and erosion and promotes optimal plant and microbial growth. Water and air are also stored in the aggregate pores until needed.


Mycorrhizal fungi are especially effective in providing nutrients to plant roots. These are certain types of fungi that actually colonize the outer cells of plant roots, but also extend long fungal threads, or hyphae, far out into the rhizosphere, forming a critical link between the plant roots and the soil. Mycorrhizae produce enzymes that decompose organic matter, solubilize phosphorus and other nutrients from inorganic rock, and convert nitrogen into plant available forms. They also greatly expand the soil area from which the plant can absorb water. In return for this activity, mycorrhizae obtain valuable carbon and other nutrients from the plant roots. This is a win-win mutualism between both partners, with the plant providing food for the fungus and the fungus providing both nutrients and water to the plant. The importance of mycorrhizae in plant productivity and health has often been overlooked. EXAMPLE Pines are not native to Puerto Rico and therefore the appropriate mycorrhizal fungi were absent in the soil. For years, people unsuccessfully tried to establish pines on the island. The pine seeds would germinate well and grow to heights of 8 to 10 cm but then would rapidly decline. In 1955, soil was taken from North Carolina pine forests, and the Puerto Rico plantings were inoculated. Within one year, all inoculated seedlings were thriving, while the un-inoculated control plants were dead. Microscopic analysis showed that the healthy seedlings were well colonized by a vigorous mycorrhizal population. While the benefits of mycorrhizae is not always as dramatic, it has been well documented that mycorrhizal plants are often more competitive and better able to tolerate environmental stress.


Compost in particular can improve soil nutritional availability and soil tilth because of its complex microbial population. Composts bring with them a wide array of bacteria, fungi, protozoa, nematodes and micro arthropods, along with the food resources needed to feed these organisms. However, not all composts have the same beneficial effects. There are many different types of composts, as determined by their original ingredients and their degree of maturity. The greater the diversity of food resources in the original composted material, the greater the diversity of microorganisms that can grow in that compost. Soil from potted plants may be composted in the fall and used again the following year. It is advantageous to leave the roots in the soil rather than removing them, fostering the presence of beneficial rhizoshperic organisms.


In general, the largest soil organisms are the first damaged by soil compaction and disturbance. These include earthworms and small insects, which are at the top of the soil food web and are essential to keeping microbial populations in balance. When these organisms are lost, an otherwise undisturbed soil will have the tendency to shift from being fungal dominated to being more bacterially dominated. This will alter nutrient availability and soil structure, effectively limiting the types of plants that can grow. Some species of anaerobic bacteria thrive in a soil deprived of oxygen and can produce chemical metabolites, such as alcohols, aldehydes, phenols and ethylene, that are toxic to plant roots and to other microorganisms. As compaction continues to eliminate pore space, plant roots have difficulty obtaining sufficient water, air and nutrients, placing them under considerable stress. This stress, added to the shift in beneficial organisms, will create a situation where plant pathogens may increase rapidly and cause serious problems. No-till gardening methods can be very useful in minimizing soil disturbance. When re-potting plants of any kind, minimal disturbance to the root structure and soil is essential.


Dr. Ingham and others in her field have found that plant roots, well colonized by a mixture of different bacterial and fungal species, are far more resistant to pathogenic attack. Mycorrhizal fungi form an impenetrable physical barrier on the surface of plant roots, varying in thickness, density and fungal species, according to the plant species, plant health and soil conditions.

This layer of beneficial fungi plays a powerful role in disease suppression, both through simple physical interference as well as through the production of inhibitory products. Some species of fungi that parasitize other fungi, such as Trichoderma, have been observed physically attacking and destroying pathogenic fungi. Dr. William Albrecht reported that Fusarium, a fungal species often maligned in its role in many plant diseases, could actually be one of the most common beneficial saprophytes in a healthy soil. He stated that the dividing line between beneficial symbiosis and parasitism could be very narrow. When Fusarium encounters a root that is poorly nourished or is under stress, it can become rapidly pathogenic.

In healthy soil, unaltered by the application of lethal agricultural chemicals, “microherds” groups of microbes colonize the root zone or the rhizosphere of the plant. Most are beneficial bacteria and fungi; they do not damage living plant tissue and are critical to making essential minerals available to the plant. These microbes retain large amounts of nitrogen, phosphorous, potassium, sulfur, calcium, iron and many micronutrients in their bodies, preventing these nutrients from being leached or removed by water runoff. Ideally, they out-compete pathogenic species and form a protective layer on the surface of living plant roots. It is usually only when the beneficial species of bacteria and fungi are killed by continuous soil disturbance and toxic chemicals that pathogenic species have an advantage.


As part of her research, Dr. Ingham has shown that herbicides, pesticides and fertilizers have many non-target effects. The most common pesticides are fairly broad spectrum; that is, they kill much more than the target species. Residual pesticides that accumulate in soil over many years may recombine and form new, unintentional chemicals that have additional and often synergistic negative effects. Out of the 650 active ingredients used to formulate most common agricultural pesticides, only about 75 have been studied to deter mine their effects on soil organisms. The remaining ingredients have never been studied for their effects on the whole system or on any non-target group.

Scientists don’t fully understand the effect of any in individual ingredient on soil life, much less the synergistic effects of the ingredients, or combinational effects with inert or soil materials. It is hardly surprising that a soil treated with numerous agricultural chemicals lacks a healthy food web. When inorganic ammonium nitrate fertilizer is applied to agricultural soil, ammonium and nitrate ions are rapidly released into the soil solution. Nitrate ions are negatively charged and can be quite mobile. The result is that a large percentage of these nitrogen-containing ions may move rapidly out of the plant root zone (rhizosphere) and into the groundwater. This produces not only reduced plant growth but also environmental pollution. Plants growing in unhealthy soil require additional fertilizers and pesticides, furthering the deadly spiral.


In return for the release of nutritional substances from plant roots, microbes themselves produce chemicals that stimulate plant growth or protect the plant from attack. These substances include auxins, enzymes, vitamins, amino acids, indoles and antibiotics. These complex molecules are able to pass from the soil into plant cells and be transported to other parts of the plant, with minimal change to chemical structure, where they can stimulate plant growth and enhance plant reproduction. They may also play a role in enhancing the nutritional composition of the plant. The types of molecules released are specific for a variety of plants grown under certain conditions, forming in effect a unique chemical signature. As these molecules are released into the rhizosphere, they serve as food and growth stimulants for a certain mix of microbes. Dr. Joyce Loper, of the USDA Agricultural Research Service, and other scientists have shown that for each plant species, this characteristic chemical soup stimulates the development of a select, beneficial company of root-dwelling microbes. This microbial population colonizes the root zone, producing certain chemicals that inhibit the growth of pathogenic species. These organisms are also instrumental in supplying the plant’s unique nutritional needs.


Plants require many different mineral ions for optimal growth. These must be obtained from the soil. Many nutrient ions are solubilized from the parent rock material in a process known as mineralization. Bacteria and fungi produce enzymes and acids necessary to break down inorganic minerals and to convert them into stable organic forms. Other nutrients are released through the decomposition of organic matter. In all cases, a healthy, diverse microbial population will develop with rapid decomposition of organic material and will facilitate the recycling of nutrients. Organic matter is also electrically charged and therefore critical to its ability to attract and hold many different nutrient ions. The higher the organic matter in the soil, the greater the ion holding capacity, resulting in reduced leaching of either an ions or cations from the soil.

There is much competition for nitrogen among soil organisms. Those organisms that have the best enzymes for grabbing nitrogen are usually the winners. Bacteria possess the most effective nitrogen-grabbing enzyme system, closely followed by many species of fungi. Plant enzyme systems do not produce enzymes that operate outside the plant and cannot compete well when there is strong competition for limited nitrogen resources. In a healthy soil, this does not mean that the plant will be deprived of adequate nitrogen. Bacteria require one nitrogen atom to balance every five carbon atoms, and fungi require 10 carbons for each nitrogen. Therefore, the predator organisms that eat bacteria and fungi get too much nitrogen for the carbon they require. Since excess nitrogen is toxic, is excreted as a body waste product back into the soil in a form that can be absorbed by plant roots. Nitrogen is not the only nutrient effectively stored and recycled by soil microbes. Carbon is the major constituent of all cells. When soils are depleted of organic matter and healthy microbial populations, the ability of a soil to hold carbon is destroyed and it enters the atmosphere as carbon dioxide, now recognized as one of the greenhouse gases that are responsible for breaking down the ozone layer.

There is little scientific evidence that bacteria and fungi simply die and decompose. If another bacteria or fungus uses the dead cells for a food source, there is no release of nitrogen. It is only when a predator consumes excessive amounts of nitrogen in the dead cells that it is released into the soil solution. It is this system of nitrogen cycling that has worked brilliantly for the past million years.


Mycorrhizal fungi will colonize the rhizosphere of any plant, given the right conditions. These fungi are as diverse as the stars in the sky, and many fungi are plant specific, some are not. We have had great success with MJ inoculated with SC-27, developed by Dr. Frank McKenna of Australia. We have also witnessed mycelium from fungi on MJ roots, visible to the naked eye, develop over time with no inoculation.

The problem with MJ, and so many plants, is that they are being grown outside of their native soil environment, much like the southern pines in Puerto Rico. Some plants adapt more readily to foreign environments than others and are less dependent on the symbiotic relationship that exists between plant and fungi. In nature, plants grow in the same soil season after season, developing a “relationship” so to speak with soil and its microscopic inhabitants.

It should be noted, that the regeneration of soil is beneficial to the cultivation of fungi and bacteria. (Composting old soil from pots) The benefits of organic cultivation simply cannot be measured. Try as we might, there is no improving on Mother Nature.

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