Introduction to Soil: Biological Properties (Part 3)

This is the third in a series of posts about fostering and maintaining healthy soil in your farm or garden.

As we’ve discussed throughout this series, healthy soils are living soils with high levels of organic matter. As Grace Gershuny puts it in The Soul of Soil, “The basic aim of ecological soil management is to provide hospitable conditions for life within the soil” (7). What kind of life lives within the soil, what do they do, and how can we build strong soil ecosystems? Let’s dig in and find out!

Soil Food Web – it’s alive down there!

For many people, the first creatures that come to mind when you think about life in the soil are earthworms and roly polies, or pill bugs. You might also think of moles and gophers, who are most often not welcome in our vegetable beds but who do serve a function in the soil ecosystem. There are many visible organisms that inhabit the soil, as well as countless microorganisms that we can’t see with the naked eye. 

In The Soul of Soil, Grace Gershuny goes on to say that “Soil organisms–from bacteria and fungi to protozoans and nematodes, on up to mites, springtails, and earthworms–perform a vast array of fertility maintenance tasks” (36). Our work as farmers and gardeners–really, as soil stewards–is to help these organisms do their jobs. 

Did you know that in every gram of healthy topsoil, there are billions of microorganisms (37)? And here you thought you were only growing and caring for vegetables, fruits, and flowers! So much of their work is invisible to us, happening at the microscopic level underground, but the results in the form of healthy plants are evident. 

If you think back to elementary school, you might recall a lesson on types of organisms in an ecosystem. There are producers, consumers, and decomposers, each serving vital functions to maintain a balanced and healthy ecosystem.

  • Producers: organisms that can produce their own carbs and proteins through photosynthesis. Most producers are plants, but there are also some specific bacteria that can make food out of the minerals and carbon dioxide available in the soil.
  • Consumers: organisms that consume producers and other consumers. You, me, and all animal life are consumers.
  • Decomposers: organisms that “perform the critical function of bringing the basic chemical nutrients full circle, from consumers back to producers” (37). Bacteria and fungi found in soil are the decomposers, serving a crucial role that makes the life cycle on earth possible. “Without them, life would grind to a halt as we suffocated in our own wastes” (37). Have you thanked a fungi today? 

Although most soil organisms are beneficial to the agro-ecological systems we create in our farms and gardens, some are harmful to plants. Soil stewardship aims to support the growth of the beneficial organisms and minimize the influence of potentially harmful organisms. 

As organic farmers and gardeners, we’re able to help our plants fight disease through preventative, long-term “healthcare” in the form of a healthy soil ecosystem. Trying to fix problems after-the-fact with chemicals can cause additional harm to the natural defenses in the soil, reduce overall soil health, perpetuate dependency on more chemicals, and expose people and other animals to toxins (Lowenfels and Lewis 24).

In future posts, we’ll explore in more detail some of the rock star soil organisms whose work is not only fascinating but crucial for healthy soil systems, including fungi, bacteria, and worms. 

Functions of the Soil Food Web

The organisms in the soil food web serve many important functions. For instance, as mentioned in the second post in this series, the living organisms in healthy soil access nutrients in rocks through chemical processes, make them available to plant roots, and then recycle these nutrients from decomposing organisms back into available forms every season.

In Building Soils for Better Crops, the authors write that “Soil organisms influence every aspect of decomposition and nutrient availability. As organic materials are decomposed, nutrients become available to plants, humus is produced, soil aggregates are formed, channels are created for water infiltration and better aeration, and those residues originally on the surface are brought deeper into the soil” (37).

As farmers and gardeners, we do a lot of work to prepare beds for planting, plant seeds and seedlings, irrigate, add supplemental nutrients, remove weeds, troubleshoot disease, etc.–but so much of the important work that helps our plants grow and produce nutritious food is happening within our soil. The microscopic work that is invisible to our human eyes can seem miraculous, but it’s measurable and it results from intentional and patient soil stewardship.

In this article on our blog, Linda Kincaid provides a summary of what was discussed at the 2018 EcoFarm Conference related to regenerative agriculture and carbon farming. Part of the article explains the role that some soil organisms play in capturing carbon in the soil. In future posts in this series, we’ll more deeply explore some of the topics in her article, including no-till farming.

Organic Matter

In the UCSC Farm article “Building Fertile Soil,” the authors write: “Think of a natural system, such as a forest or meadow: it thrives year after year by recycling available nutrients. Leaves fall and break down; grasses and flowers grow, bloom, and fade; animals die and decompose—all life adds organic matter to the soil. This is the cycle you’re trying to recreate in your garden.”

Organic matter includes the decomposing leaves, plant residues, compost, roots, and other once-living materials that are in various stages of breaking down. These materials provide both nutrients and structure to the soil.

Two key sources of organic matter in the soil are cover crops and compost. In a natural system, as mentioned above, falling leaves and the life cycle of animals, insects, and plants naturally build organic matter. In a garden or farm, we are speeding up that process and withdrawing nutrients from the soil whenever we harvest food and flowers. To make up for that removal, we have to add organic matter (and occasionally supplemental nutrients) back into the soil consciously.

Cover Crops

One way to introduce more organic matter into your soil is by planting cover crops. These plants are grown to cover and protect the soil from erosion and weeds, as well as contribute organic matter. Typically they are grown in the off-season of winter, but some fast-growing cover crops like buckwheat (Fagopyrum esculentum) can be planted during the spring and summer growing season to give the soil nutrient and structure boosts between other plantings.

A close-up photo of a garden bed filled with cover crops

Ideally, we don’t plant the same crop time after time in the same spot, and the same is true of growing crops that require significant amounts of nutrients, such as nutrient-dense vegetables. Planting the same crop or continually planting nutrient-demanding crops in the same location depletes the soil of the same set of nutrients over and over. 

Planting the same or similar crops in the same bed over time can also encourage the growth of harmful microorganisms and pests that become accustomed to that crop being available. 

Cover crops can serve as a break to the soil between plantings of more nutrient-demanding vegetable crops. They can add nutrients back to the soil, condition the soil structure, and they can also help reduce populations of harmful organisms and pests by removing their food source. 

Some cover crops, called leguminous cover crops, can also fix nitrogen and then release it into the soil when they break down. 

A few months after you plant your cover crop (depending upon the cover crop and time of year) and before they set seed, harvest the cover crop from your garden beds, chop it up, and either till the residue into the soil or make compost with it. 

To learn more about cover crops, read “Building Fertile Soil” and “Choosing & Using Cover Crops in the Home Garden & Orchard,” both produced by the UCSC Farm.


One of the best ways to add organic matter to your soil is by applying compost before planting. Fully decomposed, stable compost is called humus. In The Soul of Soil, the authors explain that “Humus is one form of organic matter that has undergone some degree of decomposition. There is no hard and fast dividing line, but a continuum, with fresh, undecomposed organic materials–manure, sawdust, corn stubble, kitchen wastes, or insect bodies–at one end, and stable humus, which may resist decomposition for hundreds of years, at the other” (Gershuny and Smillie 11). 

Fully mature compost, or humus, helps retain water in the soil; provides good structure and tilth in soil; holds on to nutrients to make them available to plants; can “moderate excessive acid or alkaline conditions in the soil”; brings soil temperatures up faster because of its darker shade; and can prevent toxic heavy metals from being available to plants (Gershuny and Smillie 14). Humus is a gardener’s best friend!

You can make your own compost, purchase it in bags from a garden center, or purchase it by the yard. Compost is #5 on our list of favorite soil amendments, available in the previous post in this series here.

Playing with compost during a Santa Cruz Permaculture Design Certificate course lesson on composting and soils. Photo by Steve Kurtz.

In your soil, you want a balance of living organic matter (e.g. plant roots), dead but active organic matter (e.g. recently harvested cover crop residue), and fully dead organic matter (e.g. humus) (Magdoff and Harold 30). These different kinds of organic matter serve different functions. 

For instance, the active organic matter that is decomposing but not yet fully humus provides a food source for organisms in the soil, thus keeping their populations active. For this reason, a healthy soil ecosystem with diverse microbial life requires more than just fully mature compost. Cover crops and the residues of past vegetable crops introduce this important active organic matter.

Measuring Soil Biology

To measure the organic matter in your soil, you can submit a soil sample to a lab. Instructions for how to test your soil at a lab like A&L Western Labs is described in the first post in this series.

You can also pay attention to what life you see when you’re digging in the soil. Earthworms are a good sign and so are mushrooms. A darker soil color can also indicate greater biological activity than soil with a light color. 

Most of the work of the soil food web occurs underground at the microscopic level. As a result, you may not be able to immediately assess the biological activity of your soil. Over time, you’ll recognize patterns that might offer insight into what microorganisms–good and potentially harmful–you have in your soil. 

Beyond lab results, the best way to become familiar with your soil is to get your hands in it often. There’s an old saying that the best fertilizer is the farmer’s footprints. In other words, the more time you spend in your garden or farm, the better your plants will grow because you will be paying attention to what they need. The same is true of growing healthy soil.

Preparing a bed for planting during a Santa Cruz Permaculture Design Certificate course lesson on soils. Photo by Steve Kurtz.

Learn More

Up Next: Increasing Biological Activity

Now that we’ve covered some basic soil properties–physical, chemical, and biological–we’ll go deeper into soil management practices. In our next post we’ll explore more strategies for how to increase the biological activity in your soil.

Want to study up even more? Our recommended resources and references are below.

This is the third in a series of blog posts about soil, so stay tuned for more information! You can also register for our Regenerating Watersheds & Soils weekend during our Permaculture Design Course. Dates and registration information is available on our website:


“Building Fertile Soil.” For the Gardener. Center for Agroecology & Sustainable Food Systems, University of California, Santa Cruz.

Gershuny, Grace, and Joseph Smillie. The Soul of Soil: a Guide to Ecological Soil Management. 4th ed., Chelsea Green Publishing, 1999.

Gershuny, Grace. Start with the Soil: the Organic Gardeners Guide to Improving the Soil for Higher Yields, More Beautiful Flowers, and a Healthy, Easy-Care Garden. Rodale, 1993.

Hemenway, Toby. Gaia’s Garden: A Guide to Home-Scale Permaculture. 2nd ed., Chelsea Green Publishing, 2009. 

Kincaid, Linda. “2018 EcoFarm Conference: Regenerative Agriculture for Crop Productivity and Carbon Capture.” Santa Cruz Permaculture, 2018.

Lowenfels, Jeff, and Wayne Lewis. Teaming with Microbes: The Organic Gardener’s Guide to the Soil Food Web. Revised ed., Timber Press inc., 2010. 

Magdoff, Fred, and Harold Van Es. Building Soils for Better Crops: Sustainable Soil Management. 3rd ed., Sustainable Agriculture Research and Education Program, 2009.

Martin, Orin. “Choosing & Using Cover Crops in the Home Garden & Orchard.” News & Notes of the UCSC Farm & Garden. Center for Agroecology & Sustainable Food Systems, University of California, Santa Cruz, 2012.

Martin, Orin. “Your Soil—A Primer, with Some Strategies for Sustainable Management.” News & Notes of the UCSC Farm & Garden. Center for Agroecology & Sustainable Food Systems, University of California, Santa Cruz, 2011.

Miles, Albie, and Martha Brown. Teaching Organic Farming and Gardening: Resources for Instuctors. Center for Agroecology & Sustainable Food Systems, University of California, Santa Cruz, 2005.

“Soil Cultivation: Fundamental Concepts & Goals.” For the Gardener. Center for Agroecology & Sustainable Food Systems, University of California, Santa Cruz.

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