Understanding Soil Biology

Leonardo Divinci said that we know more about the heavens above our heads than the soils beneath our feet. How incredibly true!

The estimate is that we do not know a fraction of even 1 percent about the microbial life in our soils; their species, DNA, genetic sequencing, and what functions they perform. We have learned to count biomass, the total numbers of microorganisms, using a microscope and using the ‘direct count’ method, but clearly that does not give us an understanding of the functions and complex interactions. A single teaspoon of soil can contain anywhere from virtually no microorganisms to over 1 billion.

Consider that the most productive soils in the world can have bacteria species exceeding 1 million types. Fungi may well be into the tens and possibly the hundreds of thousands of different species with protozoa certainly in the hundreds and likely thousands and nematodes the same. Not only have we not discovered ALL the microorganisms in the various species, we have little information about the ones we have identified or named. While genetic sequencing, molecular profiling, DNA, and species profiling are ways to identify and group microorganisms, such raw analysis reveals little about their functions and complex interactions.

Observation in general is still the best teacher. We know that even within the same species there is a high level of duplication, i.e. organisms that do the same thing. Why? Because microorganisms respond to their environment. They are sensitive to pH, moisture levels, temperature levels, toxins, oxygen levels, CO2 levels, mineral presence, elevation, and the list goes on and on. As the soils move through these variables, so does the ability of these organisms to function. You will only find a small portion of them active at any given time. So to maintain a constant workforce, great diversity within the species is required so that someone is functional in all variables.

While we have learned a great deal, we are only beginning to scratch the surface into this unseen and mostly unnoticed world beneath our feet.

Some of what we do know:

  • Bacteria was likely the earliest life form on earth
  • They are prokaryotes, their DNA is contained in a single chromosome that is not enclosed in a nucleus
  • The three basic shapes (soil types) are coccus (spherical or oval), bacillus (rod shaped), and spiral
  • They divide by single cell division which is one cell divides and makes two cells, and so on
  • They can multiply faster than other microorganisms like fungi, protozoa and nematodes
  • Nature has designed the soil food web in such a way that the main food resources for higher organisms have the highest reproduction rate
  • In most cases bacteria need moisture to move about and transport the enzymes they use to break down organic matter. If soils become too dry, most bacteria go dormant

Bacteria are among the earth’s primary decomposers of organic matter, second only to fungi. Without them, we would be smothered in our own waste in a matter of months. Bacteria decompose plant and animal materials in order to ingest nitrogen, carbon compounds, and other nutrients. These nutrients are then held ‘immobilized’ inside the bacteria. They are released, or mineralized, only when the bacteria are consumed by another organism or otherwise die and are themselves decayed.

Each organism species, bacteria, fungi, protozoa, nematode, micro-arthropods, macro-arthropods (also known as shredders), earthworms, gastropods, and on up have a different Carbon (C) to Nitrogen (N) ratio. This allows for the nutrients held in one species to be released when eaten by another species. Bacteria are the most nutrient dense living organism on this planet with a general C to N ratio of 5:1. Fungi ratios average 20:1, protozoa 30:1 (just like us humans), nematodes 100:1, and micro/macro-arthropods upwards of 150:1. Bacteria and fungi are the decomposers. The predatory microbes are the protozoa and nematodes and they eat bacteria and fungi primarily. Shredders being micro/macro-arthropods tear apart the organic matter to get to their food sources, the fungi, protozoa and even nematodes. Earthworms will eat just about anything from organic matter, nematodes, protozoa, fungi and bacteria. Gastropods eat fungi, algae, lichens, fresh and rotting organic matter.

A protozoan with a C to N ratio of 30:1 has to maintain 30 Carbons and 1 Nitrogen in order to maintain its homeostasis. In acquiring the 30 carbons it must eat 6 bacteria (5:1). In doing so, it now contains 6 nitrogens but can only keep 1. The protozoa must excrete 5 nitrogen molecules back into the soil (as NH4-ammonium). Not only is the protozoa ‘mineralizing’ nitrogen, it is mineralizing P, K, Ca, Mg, S, Fe, Zn, Cu, B, Co, Mo, Mn, and many more mineral nutrients. This pattern is repeated over and over, many thousands of times a day by each of these active and functioning microorganism groups living in the soil.

With each group having a different Carbon to Nitrogen ratio that also dictates the type and kinds of food it can eat. Bacteria with a very close C to N ratio must eat foods that allow it to maintain its own vital ratio. Bacteria can decompose young, still-fresh plant materials (green) containing lots of sugars which are easier for them to digest. The more complex carbon compounds of other plants are left to the fungi with a wider C to N ratio. Bacteria produce enzymes that break organic matter down and they take in food (sugars, proteins, carbons, and other ions) directly through their cell walls which act as osmotic barriers; nutrients in - waste products out. Once inside the bacteria, the nutrients are locked up.

Bacteria play another very important role in the life cycle of a plant. In addition to helping decompose the plant, they play a major role in providing nutrients for the plant as it grows. As a plant grows, it releases exudates via the roots which are made up of photosynthetic sugars and compounds which are designed to grow specific microorganism groups within it rhizosphere or root system.

Plants have the ability to determine the biological groups within their root systems by the types of compounds they release through the roots. Plants that need to maintain higher bacteria to fungi ratios will exude simpler sugars and compounds that bacteria can eat and use to reproduce very quickly. Plants that need to maintain higher fungal populations than bacteria will release more complex carbon compounds that the fungi need to grow and reproduce. With these varied root exudates being released into the root system, microorganisms grow to the hundreds of millions per gram of rhizosphere soil.

If you are a predator such as a protozoa or nematode, you simply go where the huge food sources are, the root zone. As the bacteria and fungi grow rapidly, they are eaten by the protozoa and nematodes, releasing the mineralized nutrients in the form the plant can take up through the root system. Plants do not make enzymes strong enough to dissolve organic matter or complex mineral compounds in the soil. Plants can only take up ‘soluble’ nutrients. It is the microbes that produce enzymes strong enough to solubilize minerals and organic matter. Once taken into their bodies and retained as organic nutrients, the microbes then provide the ‘plant soluble’ form of nutrient that the plant will absorb through its own root system when these bacteria and fungi are eaten by predatory microbes. Nutrients in this form are far superior to anything that is in a synthetic or inorganic form.


Decomposition of solids can occur in two ways; aerobic (with oxygen) and anaerobic (without oxygen). There are 'good' aerobes and 'bad' aerobes just as there are 'good' and 'bad' anaerobes. Clostridium is an anaerobe, and can invade and destroy the inside soft tissue of decaying matter. By-products of anaerobic decay include Hydrogen Sulfide (rotten eggs), Butyric Acid (smells like vomit), ammonia (there goes your nitrogen turned from a solid into a gas – NH3 and back into the atmosphere) and vinegar. Escherichia coli (E. coli) are facultative anaerobes, meaning they can live in aerobic conditions if they have to but prefer anaerobic environments. They produce deadly and extremely harmful toxins as they process organic matter. Organic matter broken down in an anaerobic environment fosters pathogens and diseases and will produce poisons such as alcohols, and aldehydes which are extremely detrimental to beneficial organisms, plants, animals and humans.

For our agricultural soils, aerobic decomposition is the only correct method. Here again, we must take an active part in managing the biology so we achieve the desired outcome. Maintaining conditions that allow the beneficial aerobes to out-compete the harmful anaerobes is crucial. When it comes to biology, the group with the biggest numbers wins. 700,000,000 beneficial aerobes per gram of soil are always going to control and limit the 10,000 harmful anaerobes that might be present. However, the same is true in reverse. If we allow the conditions to favor the harmful anaerobes and their numbers are huge, the beneficial aerobes cannot compete.


Bacteria fall into four functional groups.

Decomposers-break down organic matter from simple carbon compounds like root exudates and fresh, green plant litter. Decomposers can also break down pesticides and pollutants by ‘immobilizing’ or retaining the nutrients in their cells. Actinomycetes are a large group of bacteria that grow as filaments, almost like fungal hyphae and decompose a wide array of substrates, but are especially important in degrading recalcitrant (hard-to-decompose) compounds, such as chitin and cellulose, and are active at high pH levels. In general, strands of 1 micrometer or less are actino-bacteria and not fungi. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes, such as Streptomyces that produce enzymes that include volatile chemicals that give soil its clean, fresh, earthy aroma. Cellulomonas carry cellulose breaking enzymes that they release only when they come in contact with cellulose, which constitutes half the mass of plant bodies.

Bacteria produce glues or slime layers that bind aggregates together as they restructure the soil particles. These glues are alkaline and tend to raise soil pH.

Mutualists-form partnerships with plants. Nitrogen-fixing bacteria are perhaps the best known here.

  • Rhizobium-fixes N inside the root nodules,
  • Frankia-has symbiotic relations with flowering plants to fix N,
  • Azosporillum-produces Auxins, ability to increase root hairs, fix N,
  • Azotobacter-free living N2 fixers, produces phytohormones and vitamins,
  • Azomanas-secrete alkaline slime, fix N,
  • Cyanobacteria-blue-green algae, get energy from photosynthesis,
  • Nirobacter-takes NH4 (ammonium) to NO2 (nitrite) in alkaline soils,
  • Nitrosomones-takes NO2 (nitrite) to NO3 (nitrate) in alkaline soils.

Lithotrophs or Chemoautotrophs- obtain their energy from compounds of nitrogen, sulfur, iron, or hydrogen so there are Sulfur-oxidizing bacteria, Phosphate-oxidizing bacteria, etc. These bacteria break down various mineral compounds to maintain their energy, cycle nutrients and degrade pollutants.

Pathogens-those disease causing groups that include Xymomonas and Erwinia and species of Agrobacterium, such as tumefaciens that cause gall or tumors to grow on stems of certain plants. Burkholderia cepecia is a bacterium that infects and rots the roots of onions. Some Pseudomonas species cause leaf curl and black spot on tomatoes. The list of pathogenic bacteria is a long one; including bacteria that cause citrus canker, disease in potatoes, melons, and cucumbers, and fire-blight of pears, apples and the likes. Anaerobic bacteria in high concentrations will eat beneficial bacteria and fungi.

Certain strains of soil bacteria Pseudomonas fluorescens have anti-fungal properties by producing phenazines, a very strong, broad-spectrum antibiotic that can correct ‘take-all’, a disastrous fungal disease affecting wheat, soybean, etc. Other Pseudomonas and Xanthomonas species can increase plant growth in several ways. They may produce a compound that inhibits the growth of pathogens or reduces invasion of the plant by a pathogen. They may also produce compounds (growth factors) that directly increase plant growth.


Fungi are microscopic cells that usually grow as long threads or strands called hyphae; Hypha for a single strand, Hyphae for more than one strand. A single hypha can span in length from a few cells to many yards. Hyphae sometimes group into masses called mycelium or thick, cord-like “rhizomorphs” that look like roots. Fungal forms include fruiting structures like mushrooms and individual fungus can include many fruiting bodies scattered across an area as large as a baseball diamond. All fungi are eucaryotes; organisms that have cells with distinct, enclosed nuclei.  Slender fungi, of 1.5 to 2.5 micrometers diameter, and also colorless, are usually disease-causing fungi in the category Oomycetes. Fungi with average diameters in the range of 2.5 micrometers, either colorless or colored, which may have randomly placed crosswalls, fall into the category of Ascomycetes, Hyphomycetes, or Deuteromycetes. Some of these fungal species cause disease, whereas other are neutral (no negative effects on plants), while most are clearly beneficial. Fungi with diameter greater than 3.0 generally fall into the category of Basidiomyctes. Colored Basidiomyctes tend, for the most part, to be beneficial, whereas those species that are not colored, or have narrow diameters, including a few genera of disease-causing Basidiomyctes are not.

Fungi lack mouthparts. Like bacteria, they produce enzymes that break organic matter down and they take in food (sugars, proteins, carbons, and other ions) directly through their cell walls via diffusion (osmosis)  and active transport; nutrients in - waste products out. Like bacteria, fungi should be viewed as living containers of fertilizer.

Fungi can be clear (hyaline), tan, gold, reddish, light brown, dark brown and black. The darker the color, the more melanin or humic acid materials the fungus has put into the cell wall. In general, the beneficial fungi will be dark colored-from tan to gold, to red to light brown, dark brown or black. There are some beneficial fungi that are clear. Fungi grow at the tips, so cytoplasm tends to be concentrated there and can grow up to 40 micrometers a minute. Compare this to the movement of a typical soil bacterium which may travel only 6 micrometers in its entire life.

Some fungi can produce crystalline materials on their surfaces. Oxalate, only one type of crystalline material made by certain fungi, has been shown to complex with many types of cations (positive charged nutrients) and anions (negatively charged nutrients), thus holding many types of nutrients on the fungal surface and preventing leaching losses from soils. Fungi are the major holders of Ca (calcium) that is added to soils. When fungi is eaten by fungal-feeding nematodes or microarthopods, a chelated form of calcium is released.

Fungi growing in anaerobic or reduced-oxygen conditions generally grow as a yeast form. When growing fermentatively, yeast tends to produce a broad range of plant-toxic materials, the most toxic being alcohols. Even tiny concentrations of alcohols (1 ppm or 1 microgram of alcohol per liter) will kill plants by dissolving the cell wall structure. Molds and yeast are fungi.

Fungi perform important services related to water dynamics, nutrient cycling, and disease suppression. Fungi are important decomposers and convert the hard-to-digest organic material into forms that other organisms can use. Fungi are the primary decay agents in the soil food web. They produce phenol oxidase, a strong enzyme that dissolves even lignin, the woody compound that binds and protects cellulose. These powerful enzymes are capable of dissolving all but the most recalcitrant carbon compounds and are released as new cells are put into place. Phenol oxidase enzymes are able to convert lignin, hard chitin shells of insects, the bones of animals, cellulose, and other tough organic matter into simple sugars and amino acids, yet they do not decay the chitin cell walls of the fungi.  The enzymes produced by fungi are decidedly acidic and lower the pH. Fungal hyphae physically bind soil particles together, creating stable aggregates that help increase water infiltration and soil water-holding capacity. Fungi are better than any other organism at tying up C (Carbon) and keeping it in an organic form. Fungi are the major decomposers of most complex carbon compounds such as humic acids.

When fungi die, their hyphae leave a subway system of microscopic tunnels, up to 10 micrometers in diameter, through which air and water can flow. These “tubes” are also important safety zones for bacteria trying to elude protozoa since protozoa are considerably bigger than the tunnels.

Soil fungi can be grouped into three general, functional groups based on how they get their energy.

Decomposers- saprophytic fungi convert dead organic materials into fungal biomass, carbon dioxide (CO2), and small molecules like organic acids. These fungi help increase the accumulation of humic-acid-rich organic matter that is resistant to degradation (humus) and may stay in the soil for hundreds of years – having great water and mineral holding capacity. They use complex substrates like cellulose and lignin in wood, and are essential in decomposing the carbon ring structures in some pollutants. The largest numbers of fungi are those that use non-living organic matter as their source of foods. These saprophytic fungi are aerobic organisms and extremely beneficial in helping to suppress, compete with, and inhibit disease-causing organisms in addition to all the functions they perform in organic matter breakdown, nutrient cycling, and soil building.

Mutualists- mycorrhizal fungi colonize plant roots. In exchange for carbon (sugars) from the plant, mycorrhizal fungi help solubilize phosphorus, nitrogen, micronutrients and water to the plant. One major group of mycorrhizae, the ectomycorrhizae, grows on the surface layers of the roots and are commonly associated with trees. The second major group is endomycorrhizae, which grows within the root cells and are commonly associated with grasses, row crops, vegetables and shrubs.

VAM (vesicular-arbuscular mycorrhizal fungi) may physically prevent the disease from reaching the root, may utilize the food that the disease organisms need to germinate and grow, may make inhibitory compounds that prevent disease organisms from growing, or may improve the nutrition of the plant by bringing mineral nutrients (phosphorus, copper, zinc, iron, nitrogen and water) from the soil to the plant. In the case of phosphorus the propensity of fungi to gather and transport it over distance is truly remarkable. This mineral is almost always chemically locked up in soils. Even when it is applied as fertilizer, phosphorus becomes unavailable to plants within seconds. Fungi have the ability to free it from its chemical and physical bonds. Some fungi trade nutrients for exudates, but most often nutrients are released as waste after they are consumed by other organisms or when the fungi die and are decayed. The nitrogen released by fungi is in ammonium form NH4+, which is the preferable form of N for most perennials. If nitrifying bacteria are present, this is converted in two steps to nitrate NO3-.

Pathogens are the third group of fungi. They cause reduced production or death when they colonize roots and other organisms. Root-pathogenic fungi such as Verticillium, Pythium, Rhizoctonia, cause major economic losses in agriculture each year. Smut fungi impact the flowers of cereal grains. Rust fungi cause disease on wheat, oats, rye, fruit and pines, Downy mildew (Plasmopara spp., Sclerophthora spp.), root rots (Phytophthora spp.), and white rusts (Albugo spp.). Botrytis or powdery mildew, a catch-all name for a group of fungi that infects different plants with the same results, produces an unsightly gray or white powdery fungal growth that covers the leaves, stems and flowers. Fusarium wilt on tomatoes, the first thing to suspect when a tomato’s leaves start to yellow from the bottom of the plant up, is caused by Fusarium oxysporum f. lycopersici, a soil-borne fungus that can survive for a decade or more in dormant stages. It enters the plant through roots and invades its water distribution network. Armillaria mellea (oak root fungus) which causes oak death is a tiny fungus taking down towering oak trees.

Pathogenic and parasitic fungi make use of various entry points into plants, including the stomata (an opening on the leaf surfaces that allows plants to breathe) and wounds.

Old Knowledge Becomes New!

Most people including farmers have little understanding about the life in their soils beneath their feet. It’s a world that formal education never taught and one that the chemical companies take an active part in destroying as its destruction requires higher uses of chemical fertilizer, insecticide, fungicides, herbicides, all the things that chemical companies want to sell you. Yet there are vast resources (biology) that are able and willing to assist the farming operations if we will simply learn to manage them. Properly handled, they have a tremendous potential for good; improperly handled, the pathogens and parasites cause an equal amount of headache and loss.

It is also a world that has made some remarkable discoveries in the past 30 years or so! However, virtually all the essential understanding of biology, soil, and plant interaction was known and understood very well 70 to 100 or more years ago. Yet our Universities choose to ignore the research and take money from private industry to fill their coffers in the pursuit of pushing chemical fertility as the future means of agriculture. As a result, many of the older generation of farmers and especially the newer generation of farmers never had an opportunity to learn about this.

Beneficial soil biology is much like a cell phone when it comes to crop residue decomposition in that few people really understand how it works. Very few people can relate the detail circuitry and electronic pathways that a cell phone goes through to send an electro-magnetic frequency to a cell tower then on to another cell phone half way around the world or right next door. But that doesn’t stop people from using them because the results are quite obvious, it works! The only thing in the soil that is going to degrade organic matter is soil biology, in the right species, types and population density, with the proper foods and resources to do the job. Do nothing and some organic matter is reduced. Manage the biology and a much greater amount of it can be reduced quicker and in ways far more beneficial to the soils and next years crop.

Just because we do not know all the details does not mean it doesn’t work. Some things are simply obvious. Soil biology and residue decomposition is one of those.

More to follow,
Ken Hamilton
Bio Minerals Technologies

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