The Soil Food Web: Nature’s Way to Build Healthy Soils

The Soil Food Web: Nature’s Way to Build Healthy Soils

  • By Ralph Morini
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  • January 2019-Vol.5 No.1
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Soil is the foundation for life on earth. It provides habitat, recycles wastes, provides structural and nutritional support as well as air and water needed for plants, and ultimately, all life to thrive. Over the past 100 years, humans have departed from the natural practices that built the sustainable system we now call the soil food web and replaced it with more industrialized practices. Deeper tilling upset soil structure and displaced soil organisms. Natural soil amendments have been replaced with chemical fertilizers. The reduction in soil organisms weakened natural control of soil borne diseases and pests, leading to use of chemical pesticides. Herbicides replaced old-time weed management practices.


Despite dramatic increases in food production, there is growing concern about loss of topsoil, runoff-induced pollution, potential negative health effects of agricultural chemicals, the need for ever-stronger chemicals as organisms develop resistance to current remedies, and the loss of bio-diversity that pushes the world further away from nature’s healthy balance. It seems that modern agriculture is a short term success with negative long-term consequences.


The good news is that there is increasing recognition of the situation, a growing sustainable agriculture movement, and a developing understanding of what is required to achieve sustainability.


What is Healthy Soil?

Soil Composition Photo:


Conceptually, healthy soil is soil as nature evolved it over millennia. It is built on the community of plants and organisms that thrive in it and in turn enable each other to thrive. It consists of four major components: mineral and organic matter, air and water.


Of these, organic matter is the most important. This is because it impacts soil texture, structure, water movement and availability, and provides nutritional support for the organisms that comprise the living part of the soil food web, the basis of healthy soil.


The Soil Food Web


The Soil Food Web is the combination of organic matter and the community of organisms that decompose it in the soil. At the base of the web are bacteria and fungi which consume and decompose organic matter directly, converting nitrogen to plant-usable form and storing it in their bodies. Protozoa and nematodes prey on bacteria and fungi, releasing nitrogen to plants.


Larger organisms also play a role in decomposition. Arthropods —  including millipedes, springtails, mites, fly larvae, and beetles — break down organic matter while they themselves provide food for other beneficial arthropods. The community also includes insects, earthworms, and larger mammals like moles, mice, and rabbits that spend part of their time in the soil, plus birds and other predators that prey on them.


Food Web Function


The plants and organisms that make up the soil food web, combine with air, water and minerals in the greater soil ecosystem, to provide a life support system for plants. The relationships and interdependencies are many:

  • A community of organisms provides the decomposition function that recycles natural nutrients back into the soil, reducing soil organics to long-lived organic matter called humus.
  • Bacteria and fungi convert nitrogen from forms that plants are unable to consume, into ammonium (NH4+) and nitrate (NO3-) that are plant-accessible.
  • Bacteria and earthworms exude a slime that binds soil particles together, aggregating them into a structure that provides pore space for air and water passage through and storage in soil.
  • Fungi are the primary decomposers of the web. They grow threadlike structures called hyphae that in turn form mats called mycelia that can cover large areas when undisturbed. They release enzymes and acids that penetrate and break down tough chitin and cellulose plant tissue, and absorb plant nutrients into their cellular structure by osmosis (chitin is the substance in the exoskeletons of arthropods and insects). Fungal hyphae can transport nutrients over significant distances, and once inside the fungus, the nutrients are immobilized and not lost from the soil.

Mycorrhizal fungi attach to root systems and extend their reach

  • Specific fungi called mycorrhizae form symbiotic relationships with plants by either surrounding or penetrating root systems. They draw the carbohydrates they need from the host plant’s exudates while extending into the soil, sending moisture and nutrients that the root system wouldn’t otherwise reach, back to the plant.
  • Other types of fungi, living both below and above ground, provide benefits, including emitting toxins that kill harmful insects, improving seed germination and attacking soilborne disease carriers.
  • Protozoans, larger single-celled organisms, prey on bacteria and fungi, while ingesting organic matter. Their wastes “mineralize” the nutrients that have been “immobilized” by the fungi and bacteria, making them available to plants. Because bacteria and fungi live in the “rhizosphere” — the area surrounding plant roots —  the nutrients are accessible to plants. As much as 80% of the nitrogen needed by plants comes from wastes left by protozoa.
  • Nematodes, non-segmented blind roundworms, eat smaller microbes, also performing a mineralizing function. Because they are larger, they require more porous soil structure in order to travel, arguing for building and maintaining a good texture and structure. Bacteria attach to the skin of nematodes, which inadvertently transport the relatively immobile bacteria into new areas as they search for food.

Soil arthropods: Photo:

  • Arthropods, like flies, beetles and millipedes, are more visible because of their size, but their total bio-mass is actually less than the microscopic organisms. Most are shredders, increasing the surface area of organic material that is available to microbes, speeding decomposition. Some work on the soil surface, but many spend time below the surface, mixing and aerating the soil, taxiing microbial life into new areas and leaving waste products that add organic matter. Other familiar arthropods include mites, springtails, termites and ants.

Earthworm castings: Photo:

  • Earthworms are also shredders. They eat bacteria, fungi, protozoans, nematodes and the organic matter the organisms live on. They have gizzards that grind everything up as it passes through the worm’s body. Digestive enzymes of bacteria living in worm intestines release previously locked-up nutrients. Worm wastes, called castings, typically contain 50% more organic matter than soil not processed by earthworms. In addition, earthworms increase soil porosity, water holding capacity and organic matter. They break up hard soils, create root paths, bind soil particles together into aggregates and move nutrients and microbes through the soil.
  • The birds, reptiles and mammals that prey on other organisms of the web as well as plants growing from it, contribute by leaving wastes that become microbial food sources that are recycled into plant nutrients, move microbes residing on their bodies to other locations and at death, leave carcasses that are decomposed by soil life.

This summary isn’t all-inclusive, but illustrates the community of organisms that, combined with organic materials, form an interdependent system that works to build and sustain healthy soils.


Strengthening Your Soil Food Web


Start with an assessment of your soil condition by physically examining a sample. Dig a one foot square hole. Place the soil on a tarp and sift through it. Finding worms or their castings is a good sign and indicative of the presence of microbes. Similarly, the presence of centipedes, millipedes, beetles, spiders and springtails suggests a healthy food web.


Get a soil test: Submit a soil sample to your agricultural extension. Request data on pH, nutrients, % organic matter, soluble salt content and Cation Exchange Capacity. While preferred pH can be a function of specific plants to be grown, most soils want to be in the 6 to 7 pH range. Aim to build organic matter to about 5% of soil composition. Soluble salt content indicates whether over-fertilization may be harming soil organisms. Cation exchange capacity (CEC) indicates whether positive electrical charges carried by clay particles and humus are adequate to absorb negatively charged nutrient particles to prevent them from leaching away as water passes through the soil.


Add Organic Matter:

Compost can be purchased or home-made from yard and kitchen plant scraps. It is rich in a variety of microbes, and is composed primarily of humus, which is fully decomposed organic matter. The humus is light and loose, which helps aerate while holding moisture and nutrients until they can be released to plants. Guidance for backyard composting can be found in the article Basic Composting from the January 2018 issue of The Garden Shed.

Compost tea: Photo:

Actively aerated compost tea (AACT) is a much touted but somewhat controversial way to add beneficial microorganisms to soil. It is different from the compost or manure leachate long made by gardeners by suspending a bag of compost or manure in water for a period of time. Leachate is anaerobic, while AACT is aerated, which increases beneficial microbes. AACT is made by adding compost to chlorine-free water and pumping air through it for a couple of days, fostering aerobic bacterial growth. There are many retail AACT systems available and DIY building instructions on the web. Only a small amount of compost and a couple of days are needed to make enough tea to treat a typical home plot. The National Organic Standards Board of the US Department of Agriculture offers these recommendations to minimize pathogen risk and maximize benefits:

  • Use only potable water
  • Sanitize all equipment immediately after use
  • Use only hot compost that has reached a minimum of 131 degrees F for 3 days during decomposition
  • Avoid using additives, sometime suggested to increase microbe growth, to minimize pathogen risk
  • Don’t apply to edible plant parts including seed sprouts

Note that while many organic gardeners recommend applying AACT as a foliar spray to reduce disease, research has been inconsistent, probably due to variation in initial compost. Best use of AACT is to stimulate microbial activity in soil with adequate organic matter, rebuilding microbe activity in lawns that have been chemically treated and in compost bins. Its positive effects in these applications appear safe and well-supported.

Organic mulches can also help build the web. These include leaves, leaf mold, pine needles, grass clippings, wood chips, straw, seaweed, plant remnants and paper. Besides smothering weeds, enhancing appearance, moderating soil temperature, retaining moisture and reducing erosion, mulches provide a home for soil organisms and add organic material and nutrients as they decompose. Application rules are simple. Chop the material up and let it age. Install up to a 3″ thick layer for best results. Mulch to the drip line of trees. Keep mulch 3-4 inches away from tree trunks.


Minimize inversion tillage and compaction

Turning garden soil over annually is no longer recommended. It disrupts microbial populations by changing their depth in the soil, unnecessarily speeds up organic decomposition and destroys soil structure. Recommended practice is to add a couple of inches of compost to the soil surface and work it into the top 4-6 inches manually or with a chisel plow. Let the food web organisms finish the job.


Avoid Compaction. Wheel and foot traffic reduces porosity, affecting soil and air storage capacity as well as limiting food web organism diversity and abundance.

Cover crops in raised beds                Photo:


Cover crops offer an alternative to mulching during winter and fallow periods. They create soil cover and reduce erosion. Crops with tap roots reduce compaction and create pore space. Fibrous roots promote aggregation and soil stabilization while reducing leaching losses. Legume crops fix nitrogen. Typical cover crops are annual rye, clover, hairy vetch, and field peas. Plant them a month before frost; broadcast seeds and lightly rake the soil surface. In the spring, cut the cover crop before seed maturation and use the vegetation as a mulch; alternatively, you can compost the cut vegetation, or if immature, work it into the top soil layers 3-4 weeks prior to planting.

Reduce Pesticide Use: Broad spectrum pesticides harm beneficial insect populations. Increase habitat for beneficial organisms and add to bio-diversity to reduce the need for chemicals.

Manage Nutrients. Use organic amendments whenever possible. If you have to use chemical fertilizers, manage quantity carefully. Synthetic fertilizers deposit nitrate salts in soil that can harm soil microbes. The more chemical is applied, the more microbes die and the more chemical is needed. And so the destructive spiral begins.

Mulch grass clippings and leaves with your lawn mower and leave them on the lawn. For microbes to live in lawn soil they need to be fed. This is the logical way to do it.

Add mycorrhizal fungi to plantings. There are two types: Ectomycorrhizae surround roots of hardwoods and conifers and extend out from them. Endomycorrhizae, which penetrate roots and extend outward, are preferred by vegetables, annuals, grasses, shrubs, perennials and softwood trees. Buy the spores at garden centers as powders or solutions and follow application directions. Bare root transplants can be dipped or have the spores sprinkled on roots. Mix spores with seeds and into the backfill or on external roots on potted plants. The objective is to get spore-root contact, along with moisture to initiate germination.


Gardeners as Part of the Solution


Whether a commercial grower or a home gardener, if you’re accustomed to using synthetic fertilizers and pesticides, it takes a leap of faith to trust the natural solution. On the other hand, it is hard not to acknowledge the risks associated with the chemical-based approach. There is a growing population of successful agro-ecology practitioners who illustrate that natural practices work. They worked for millennia until human technology intervened. Given all that we have learned, using nature’s proven methods just seems like the right thing to do.



Teaming With Microbes, Lowenfels and Lewis (Timber Press,2010).

Natural Resources Conservation Service/USDept.Agr.”Soil Food Web” CSES-132P “The Soil and Me: A Perspective on Soil Health” “Soil Preparation”

PennState.Extension.”Managing Soil Health: Concepts and Practices”



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