Biodiversity and Habitat

biological activity in soil

Soil supports the growth of a variety of unstressed plants, animals, and soil microorganisms, usually by providing a diverse physical, chemical, and biological habitat.

The ability of soil to support plant and animal life can be assessed by measuring the following indicators:

Biological Activity Indicators including active fungi, earthworms, microbial biomass, potentially mineralizable nitrogen, respiration, soil enzymes.

Biological Diversity Indicators including habitat diversity and diversity indices for organisms such as bacteria, macro and microarthropods, nematodes, and plants.

What do plants, animals, and microbes need from soil?

Microbes need soil for:

  • Food. Most microbes need regular inputs of organic matter (e.g. plant residue) into the soil.
  • Space. Larger soil organisms such as nematodes and insects need enough space to move through soil.
  • Air. Most soil organisms require air, though some require a lack of oxygen. They live in low-oxygen micro-sites such as within soil aggregates. Generally, soil biological activity is enhanced by an increase in soil aeration.

Plants need soil for:

  • Support of the microbiological activity necessary for plant growth.
  • Support for, and minimum resistance to, root penetration.
  • Intake and retention of water in soil, while maintaining adequate aeration.
  • Exchange of soil air with the atmosphere.
  • Resistance to erosion.
  • Mineral and organic sources of nutrients.
  • In addition, farmers need adequate traction for farm implements to grow crops.

Animals and people need soil for:

  • Healthy plant growth.
  • Availability of nutrients essential for animal health. These are absorbed by plants, but are not necessarily essential for plant health.

All organisms need:

  • Low levels of toxic compounds.
  • Filtering of water and air.

At a landscape scale, a variety of soil environments are needed to support a variety of plants, animals, and microorganisms. (Lists adapted from Yoder, 1937, and Cihacek, 1996.

Diversity of soil and soil organisms

Each animal, plant, and microbe species requires a slightly different habitat. Thus, a wide variety of habitats are required to support the tremendous biodiversity on earth. At the microbial level, diversity is beneficial for several reasons. Many different organisms are required in the multi-step process of decomposition and nutrient cycling. A complex set of soil organisms can compete with disease-causing organisms, and prevent a problem-causing species from becoming dominant. Many types of organisms are involved in creating and maintaining the soil structure that is important to water dynamics in soil. Many antibiotics and other drugs and compounds used by humans come from soil organisms. Most soil organisms cannot grow outside of soil, so it is necessary to preserve healthy and diverse soil ecosystems if we want to preserve beneficial microorganisms. Estimated numbers of soil species include 30,000 bacteria; 1,500,000 fungi; 60,000 algae; 10,000 protozoa; 500,000 nematodes; and 3,000 earthworms (Pankhurst, 1997).

Cihacek, L.J., W.L. Anderson and P.W. Barak. 1996. Linkages between soil quality and plant, animal, and human health. In: Methods for Assessing Soil Quality, SSSA Special Publication 49.

Pankhurst,C.E. 1997. Biodiversity of soil organisms as an indicator of soil health. In: Biological Indicators of Soil Health. CAB International.

Yoder, R.E. 1937. The significance of soil structure in relation to the tilth problem. Soil Sci. Soc. Am. Proc. 2:21-33.

The Soil Food Web

Have you considered why a forest is a forest and a prairie is a prairie?


There is an incredible diversity of organisms living in the soil and they have food and dwelling preferences just like people do. In fact, throughout the whole composting process it is essential for you to remember to apply what you know about human beings to life in the soil. For example, there are individuals that function better in a temperate climate, while others prefer a humid climate. The same concept applies to the organisms we will be herding in the thermal composting process. The organisms living under a robust tree have different preferences from the ones that live under a healthy spinach plant.

Is a forest a forest because of the organisms that live in the ground? Or, are the organisms in the forest there because the trees are there?

The relationship is symbiotic, each exists because of the other and this, is the Soil Food Web.

“The soil food web is a community of organisms living all or part of their lives in the soil. A series of conversions of energy and nutrients, as one organism eats another, demonstrates the soil food web.” -Soil Biology Primer


Why is the soil food web important?

Remember: Anything your plant needs to live a healthy and robust life is already in the soil!   It is because of this fact that there are countless reasons why this food web is so important. At the most basic level, the soil food web is essential because it makes clean air and water possible. It also makes for robust plant life, which makes for healthy people and animals. When there is a diversity of organisms in the soil this directly reduces soil erosion, water runoff, sedimentation, soil compaction ( a condition that sets the stage for weeds), weed growth, water quality, organic matter, carbon sequestration, and plant fertility. Elaine Ingham said, ” You should not have to water in the summer if your plant biology is right.” SO AWESOME!!!


How does the soil food web do all these amazing things?

Essentially, the goal of plants and organisms is to grow and reproduce. There is an incredible diversity of soil organisms and each species plays a specific part in maintaining the food web.   For example, as plant roots grow deeper into the soil, bits of the plant root slough off and certain organisms consume these parts. Additionally, when roots slough off, the plant releases a liquid known as exudate (not dissimilar to how we bleed when we skin our knee) and organisms feed off this as well.

As a whole, soil organisms breakdown organic materials (manure, plants, other organisms, and even pesticides). Organic matter is the warehouse for soil life because in it are the nutrients that both plants and organisms need. Through breaking down OM, the organisms store nutrients in their bodies and those nutrients are eventually released into the soil through their waste or through their being consumed by others. Plants absorb these waste products and thrive.


What is in soil organic matter?

Soil Organic Matter from

Living organisms in OM are bacteria, fungi, nematodes, arthropods, protozoa, earthworms, and the roots of living plants

  • Fresh Organic Residue, also known as detritus, residue, organic matter and dead plant material, is comprised of any organic substances (plant, animal, and organismal) that have recently been added to the soil and have just started to decay.

Decomposing Organic Matter is composed of:

  • active fraction organic matter: that which can be used as food to microorganisms
  • labile organic matter: matter that is easily decomposable
  • root exudates: soluble sugars, amino acids and other elements that are the “blood” of the roots of plants, such as sap
  • particulate organic matter (POM) or light fraction organic matter (LF): Both POM and LF have definite size and weight definitions.
  • lignin: hard to degrade compound that is the fibrous structure of older plants. Straw, pine needles, and palm fronds have a lot of lignin. This means it will take more time for organisms to break it down. Fungi use the carbon ring structures of lignin as food.

Humus refers to:

  • recalcitrant organic matter: matter that few organisms can decompose, such as those with a lot of lignin
  • humified organic matter: the bits that are the leftovers of what the organisms couldn’t break down. It could be that this material cannot be decomposed because it could be wrapped up in soil aggregates or it is to chemically complex for the organisms to consume. Humus is what improves the water and nutrient holding capacity of soil.

It’s a good idea to familiarize yourself with the soil organisms you will be herding. By understanding their functions and preferences you will be able to have greater success in microherding. By default, when you begin looking at your soil samples, you might find that you would like to know what the organisms do, what they like to eat and how they behave. YouTube is a great resource for being able to watch the organisms in action.

How do seasons effect the soil organisms?

From experiencing the winters here in Iowa, I know that when its cold I don’t feel like doing much other than hiding inside my nice warm house and sleeping a lot. Organisms are not much different when it’s cold out. The reason why we put food in the fridge is so that it doesn’t rot as quickly, well the cold keeps the organisms from being as active. In the same way, when temperature are high and there is lots of moisture, organisms are flourishing. If you think about the areas of the world that have the most parasites, well, these areas typically never get cold and the organisms just keep growing and evolving.

This is not to say that organisms don’t exist in the extreme cold, hot, dry, or wet places. Not too long ago it was discovered that bacteria, known as hypothermophiles, were living in the Yellowstone Park hot springs. Since then, bacteria have been discovered thriving in the thermal vents on the ocean floor and inside molten lava. They’re everywhere and that’s a good thing. The combined benefits of a balanced system with diverse organisms results in pristine environments. Yep, that’s what we’re going for.