B. Biology & Ecology

Soil is designed to be as alive as possible

Biology of Soil

Key Facts

from NRCS


I.     Soil is alive!

A.   In most ecosystems, more life and diversity lives underground than above.

B.   Energy flows from the sun, through plants, and through many trophic levels of soil organisms.

C.   Soil organisms can be divided into six groups: bacteria, fungi, protozoa, nematodes, arthropods, and earthworms. Each group of organisms plays important roles. Even within each group, there is great diversity in form and function.

D.   The rhizosphere is the interface between plant roots and the soil environment. It is the location of much soil biological activity and plant-microbe interactions including symbioses, pathogenic infection, and competition.

E.   Soil organisms are part of a living system.  Ecosystem characteristics largely determine the structure of soil communities. Weather determines daily and seasonal variations in biological activity.

1.   The types of species present and their level of activity depends on micro-environmental conditions including temperature, moisture, aeration, pH, pore size, and types of food sources.

2.   Arid systems have few earthworms, but have termites, ants and other invertebrates that serve similar functions.

3.   Grasslands have near equal amounts of fungal and bacterial biomass, or may be dominated by bacteria. Coniferous forests may have 100 to 1000 times more fungal biomass than bacterial biomass.

II.      We need soil organisms for the services they provide. 

They play critical roles in plant health and water dynamics.

A.   Soil organisms are an integral part of the cycling of nutrients through the environment. They drive:

 1. Decomposition,

2. Mineralization  (E.g., protozoa and nematodes excrete excess nitrogen into the soil when they eat nitrogen-rich bacteria and fungi.)

3. Storage and release of nutrients,

4. Degradation of pollutants before they reached groundwater or surface water,

5. Carbon cycling, carbon sequestration, and soil organic matter transformations,

6.   Nitrogen cycling (N fixation, denitrification, nitrification).

C.   Soil biological activity substantially affects soil structure including the size of soil pores, the stability of soil aggregates, and the existence of macropores. Soil structure impacts how water flows over, into, and through soil and how much water is held within reach of plant roots.

1. Large, burrowing invertebrates (e.g., earthworms, ants, termites, beetles) create macropores that allow rapid flow of water into or through soil.

2. Even tiny arthropods produce fecal pellets that are mixtures of soil and organic matter. These became stable soil aggregates.

3. Fungi and bacteria produce substances that help bind soil particles together and stabilize soil aggregates.

4. Soil organic matter can be physically protected from degradation within stable soil aggregates.

D.   Plant pest dynamics depend on the whole mix of organisms in the soil. Some organisms prey on or compete with disease-causing organisms. Some bacteria release plant growth factors that directly increase plant growth.

E.   In arid lands, biological soil crusts seem to be important for all the purposes listed above. They help fix nitrogen, stabilize the soil surface, affect water flow, and prevent the establishment of some exotic plant species.

F.   Mycorrhizal fungi help plants acquire nutrients from the soil and they help stabilize soil aggregates.

G.  Resilience is the ability of a soil to recover its functions after a disturbance such as fire, compaction, tillage, etc. The mix of organisms in the soil partially determine a soil’s resilience.

III.    Management affects soil organisms

A.   We know that land management practices change the soil community. The link between specific changes and soil function is less clear.

B.   Soil biological crusts are very sensitive to trampling.

C.   Reducing tillage tends to result in increased growth of fungi, including mycorrhizal fungi.

D.   Soil compaction, lack of vegetation, or lack of plant litter covering the soil surface tends to reduce the number of soil arthropods.


Soil Biology Quick Facts

  • The tips of small plant roots move through the soil with a twisting screw-like motion.  Mature trees can have as many as 5 million active root tips.
  • A single spade full of rich garden soil contains more species of organisms than can be found above ground in the entire Amazon rain forest.
  • Although the soil surface appears solid, air moves freely in and out of it. The air in the upper 8 inches of a well-drained soil is completely renewed about every hour.
  • The plants growing in a 2-acre wheat field can have more than 30,000 miles of roots, greater than the circumference of the Earth.
  • The wonderful "earthy" smell of newly plowed ground is believed to result from chemicals produced by micro-organisms.  One of these chemicals, called geosmin, is produced by actinomycetes, organisms that have some properties of both bacteria and fungi.
  • Soil can act as either a sink or a source of greenhouse gases.  An estimated 30 percent of the carbon dioxide, 70 percent of the methane, and 90 percent of the nitrous oxide released to the atmosphere each year pass through the soil.
  • It takes about 4,000 to 6,000 pounds of crop residue per year to maintain the content of organic matter in a soil.
  • Modern farming practices that minimize soil disturbance (plowing) and return plant residues to the soil, such as no-till farming and crop rotations, are slowly rebuilding the Nation's stock of soil organic matter.
  • Of the carbon returned to the soil as plant residue, about 5 to 15 percent become tied up in the bodies of organisms and 60 to 75 percent is respired as carbon dioxide back to the atmosphere. Only 10 to 25 percent is converted to humus in the soil.
  • “We know more about the movement of celestial bodies than about the soil underfoot.”
    ---Leonardo Da Vinci, circa 1500's
  • “Every time you take a step in a mature Oregon forest, your foot is being supported on the backs of 16,000 invertebrates held up by an average total of 120,000 legs.” 
    –Dr. Andrew Moldenke, Oregon State University.
  • Even in agricultural soils, more than a thousand arthropod legs support your every step.
  • One cup of soil may hold as many bacteria as there are people on Earth.
  • Bacteria and actinomycetes are exceedingly tiny. Yet, because of their tremendous numbers, they make up half the living biomass in some soils. 
  • The weight of all the bacteria in one acre of soil can equal the weight of a cow or two. 
  • Actinomycetes have cells like bacteria, but grow as long filaments like fungi. Like fungi, they help degrade tough materials, but unlike fungi, they prefer high pH (over 7.0). 
  • A teaspoon of farm soil may contain tens of yards of fungi. The same amount of soil from a coniferous forest may hold tens of miles of fungi.
  • Nematodes are amazingly diverse. Twenty thousand species have been described, but it is thought that 500,000 species may exist. Five thousand soil species have been described.
  • Earthworms move from lower strata up to the surface and move organic matter from the soil surface to lower layers.  Where earthworms are active, they can turn over the top 6 inches of soil in 10 to 20 years.

Bacterial-Fungal ratio succession in soils:

From comment made by Doug Weatherbee here.

...it might be helpful in understanding Dr. Ingham’s work to know that there is an underlying ecological pattern of the relationship of soil microbiological population mixes to the above ground plant population mixes. For me a fundamental part of permaculture is identifying ecological patterns. Once you get the patterns, you can analyze and understand many ‘different’ locations, plant populations, etc.


If you’ve ever been to an old growth conifer forest and looked at the forest floor you’ll see lots of fruiting fungi in the form of mushrooms. Dig into that old growth forest soil and you’ll see kilometers of mycelium strands (no wonder Paul Stamet who lives in the Pacific Northwest USA old growth forest country sees fungi as key to ecological restoration). In contrast, if you go to a drylands environment you’ll tend to not see fungi fruit (mushrooms) or visible mycelium strands in the soil. Or similarly, I think most of us would be surprised to see mushrooms growing in tilled agricultural farm fields. Why is this?

Its because there is an underlying ecological microbiological pattern to all soils which is at its base the ratio of fungi to bacterial biomass in the soil. Over the past several decades soil microbiologists have been able to pin down a pattern of soil microbe and plant changes through time and space that they call “succession.” I think understanding microbial/plant succession is vital for any permaculturalist. Microbe/plant succession is a continuum. If you start on the extreme left of the continuum you get very “early” successional soils and plant communities where weeds (in the biological sense of weeds: annual, fast growing, tons of seeds, nitrate loving plants) thrive. A key to understanding why the weeds thrive is that the soil microbe population is bacterial DOMINATED. The fungi to bacteria biomass ratio is 8-10 more bacteria than fungi. The bacteria produce a sugar substance loosely called bacterial slime that is alkaline (slime is for protection, transport corridors, etc.) The slime drives the soil alkalinity here. So these bacterial dominated soils have a high ph. Without going into the details of microbial nutrient cycling, let me cut to the chase and say that the alkaline soil conditions results in a bunch of specific bacteria converting microbial cycled soluble Nitrogen into Nitrate. This process is called nitrification. And the bacteria that do it require high (alkaline) ph for the enzymes they use to convert Nitrogen into Nitrate to work. Weeds love high Nitrate levels. They’ll out compete “higher successional” plants any day if there’s tons of Nitrate in the soil.

If you move to the right on the succession continuum you get a tighter fungi to bacteria ratio. In a soil where the fungi to bacteria biomass ratio is more balanced, lets say 1 to 1, you’ll find that “higher” level plants thrive and out compete the weeds. Higher level plants means in the context of the successional pattern and include annuals like tomato, cucumber, pepper,corn, etc. All these plants like to have their Nitrogen in two flavours: Nitrate and Ammonium. In soils that have a more balanced mix of bacteria to fungi the soil alkalinity is more neutral. This because fungi, as part of their ‘eating’ secrete acids as well as enzymes. The extra fungal biomass means extra acids being generated in the soil resulting in a soil ph change. As the ph moves closer to 7 (neutral) the nitrifying bacteria I mentioned above can’t as easily convert Nitrogen into Nitrate. Just a note, the soluble Nitrogen I originally mentioned above is actually Ammonium. So, if less Ammonium is being converted to Nitrate, the Ammonium to Nitrate balance is changing. Weeds like high pulse levels of Nitrate. When they don’t get it, they are on a diet and can’t thrive. In contrast the tomatoes and peppers do well with a bit of both Nitrate and Ammonium. Its important to understand, that the soil microbes are responsible for this. If we leave an area alone, the plants that grow will tell us the story of the fungi to bacteria ratio in the soil.

If we move more to the right on the successional continuum we get ever increasing fungal biomass and ratio dominance. In a healthy vineyard soil you might see 3-5 times the fungal biomass compared to bacteria. A fruit orchard, 5-10 times fungi. A healthy old growth conifer forest 100-1000 times as much fungi to bacteria. Think about the plant systems we just moved into, they’re perennials. As we jumped from annuals to perennials we jumped into a fungal dominated soil. As the soil gets increasingly fungal dominated we get more and more fungi secreted acids entering the soil, resulting in an increasingly lower soil ph (acidity). When the soil ph drops below a nuetral 7 and becomes acidic, those nitrifying bacteria I mentioned above can’t convert Ammonium into Nitrate. The enzymes they use to do this just don’t function in acidic soils. So, the form of soluble Nitrogen in the soil becomes ever increasingly Ammonium. As we move into more advanced (in terms of succession) Perennials we get a greater love of Ammonium as the desired plant Nitrogen food. If you give any organism its preferred food it will out compete other organisms that have different preferred foods. Broccoli, for example, likes a more Nitrate rich soil with a fungi to bacteria ratio of .3-.7 approx (bacterial dominated). Chances are slim that you’ll find a ‘natural’ growing broccoli plant in an Ammonium rich old growth forest in California. Likewise, chances are slim that you’ll find a confer thriving in a tilled broccoli field. The soil fungi to bacteria ratios are different and give a competitive advantage to different above ground plants groups.

When thinking about your field ask yourself some questions about the type of grasses you WANT to grow and the types of plants that seem to thrive there. Do you want to grow perennial grasses but lots of high seed yielding annual weeds thrive there? If so, you’ve got a bacterial dominated soil. Most of the time, we do need to move our soils along the successional continuum pattern and get more fungi in there, especially if the soils have been farmed (chemically or often organically). Farming practices of tilling, chemical ferts, pesticides and evening dumping manure on fields either kill fungi or overfeed bacteria. Both result in bacterial dominance.

But here’s the rub. If I live in an old growth conifer forest in say Oregon, USA, and I want to grow a veggie garden I’ll most likely need to make my soil more bacterial. I mention this to point out that understanding the successional continuum pattern and what your specific soil microbe population is in relation to the plants you what to grow is always the first step. Getting fungi into many soils is often the first answer, but not always. Then once we’ve got the right fungi:bacteria ratio for the plants we want to grow, we need to look at the other members of the soil food web (ciliates, flagellates, amoebae, nematodes, micro/macro arthropods) and ensure their numbers and diversity are OK. But, first step, is the fungi-bacteria ratio.

There's a dialogue related to this page in the Integral Permaculture FB group (click icon to go there)

There's a dialogue in our FB group about this subject (click icon to go there)