Unsung Soil Heroes, the Soil Food Web

Elizabeth Pearce @ SymSoil
8 min readMar 14, 2020


Sara Gaucher, PhD

When it comes to managing soil fertility and maximizing crop yields, chemistry is often the “go to”: add this fertilizer, apply that pesticide. There’s no doubt that our crops require specific chemical elements to thrive and produce, but it’s not the full picture. The missing piece is soil biology — how the soil microbe biome and related soil organisms (a.k.a. the Soil Food Web) work together to make nutrients accessible for plants and protect against disease. Understanding and harnessing these natural ecosystems is key to agricultural productivity and improved plant health.

The Cities Under Our Feet

We learn in school that human cities often establish near important resources like rivers or lakes. Similarly, beneficial microbial “cities” tend to form where they have easy access to food and water.

For microorganisms, that source is plant roots. It turns out that plants have a close connection with the soil microbe biome: after plants capture carbon dioxide from the atmosphere, they actually transfer 10% or more of that carbon into the soil. Some of these so-called exudates, like sugar molecules, attract microbes that have other resources the plant needs, like nitrogen and phosphorus which these microbes are willing to trade.

Some of the fungi, called mycorrhizal fungi, physically entwine within the root cells, forming an intimate, symbiotic relationship that benefits both the plant and the fungi. Even bacteria form similarly intimate connections with plants. And there are other microorganisms in soil called archaea, which are similar in size to bacteria but genetically distinct, that scientists are still learning more about.

Meanwhile, organisms that eat bacteria and fungi are drawn to the large populations that have now established around these plant roots. These include nematodes (microscopic worms) and protozoa (single celled organisms, 10–100 times larger than bacteria). And so this space, let’s call it Soil City, teems with life. In fact, these microbes may be tiny, but the weight of the microorganisms inhabiting an acre of soil ranges from 1–10 tons[1]! Scientists call the space inhabited by Soil City — the soil found within about a tenth of an inch surrounding plant roots — the rhizosphere (“rhizo” means root).

Kate Taylor — from Wikipedia
Diagram of amoeba engulfing a bacteria.

Other soil dwelling creatures make their home within and between the various Soil City (rhizosphere) communities. Most of us are familiar with earthworms — tubular creatures, typically a few inches long, that burrow throughout the soil. Arthropods — creatures with multiple pairs of legs and an exoskeleton, like millipedes and sow bugs — can be found scurrying around leaf litter. Take an even closer look at the soil — perhaps with a hand lens — and you may see other, “microarthropods”, like springtails and mites. Many of these creatures even ferry microbes like bacteria from place to place as they travel. That’s a good thing, because an inch is like 5 miles to a bacterium! These complex communities of organisms play a role in recycling the nutrients that feed plants, the next topic of discussion.

Recycling, Nature’s Way

Human cities have systems in place to deal with the items each member discards. In Soil City, one microbe’s trash is another’s treasure, and the whole system of resource management is based on recycling.

Let’s follow a leaf that dropped onto the soil from a lettuce plant — perhaps an outer leaf that matured past its prime and naturally dropped from the plant. Bacteria and fungi on the leaf surface begin to consume it, but it’s slow going at first as these microscopic creatures work to break into the tough outer leaf layer. We might see some arthropods — big guys like millipedes and sow bugs, little guys like springtails and mites — happen on the scene to make a meal out of some of the bacteria and fungi.

In doing so, the arthropods end up shredding the leaf into smaller pieces, a crucial step that speeds up the work of the remaining bacteria and fungi. Perhaps we see an earthworm emerge to drag a large piece down into its burrow for a meal. This bit of leaf is now under the soil surface and within reach of the larger soil microbe biome to use for food. In the end, all the elemental material that originally made up the leaf is now distributed within the soil in some form: within the bodies of the creatures that consumed it, throughout the soil where they poop, and in small bits of remaining leaf to be consumed in the future.

Unlike in human cities where we generally don’t appreciate poop from pets left lying around, plants make good use of the nutrients in worm, arthropod and microbe poop. It’s in a form plants can absorb directly through their roots. It’s also provided as a “slow drip” — tiny packets of nutrients scattered here and there throughout the rhizosphere, conveniently right next to the roots.

Meanwhile, the nutrients incorporated into the bodies of the creatures who ate parts of the leaf are now “locked in place”. Most of these creatures remain in the rhizosphere. This process is called immobilization. When a microbe dies, its tiny body decomposes and the plant root is there to capture those nutrients, too. Nutrients are also passed from one creature to the next — nematodes, protozoa, arthropods and earthworms eating bacteria; nematodes eating fungi; fungi eating nematodes. Each stage of consumption and digestion is followed by excretion of some nutrients, which the plants gladly take up.

A bonus in soils that contain materials like compost, clay particles, or biochar is that any extra nutrients beyond what the plants may need can “stick” to these materials and remain nearby for future use by plants.

While this illustration described decomposition of a lettuce leaf and incorporation into soil, a similar recycling process occurs for other types of organic matter such as compost or mulches. In contrast, when synthetic, water soluble fertilizers are applied to soil, the result is often a one-way trip: excess nutrients are washed deep into the soil and eventually to ground water where they are carried far away from where they entered the soil. There is just too much applied at once for the system to capture effectively.

Self-Policing Pest Control

Not all the inhabitants in Soil City are considered desirable for those of us who grow crops in the soil. Yes, there are types of bacteria, fungi, nematodes, and arthropods that seek to make a meal of living plants. It’s why pesticides were invented, after all. But a useful property of a healthy, functioning soil food web is that it can be largely “self-policing” when it comes to the bad guys.

Plants are no dummies: they can release exudates that preferentially attract beneficial microbes. The first line of defense for plants is the physical barrier set up by the “good guys” in a healthy soil microbe biome. With the space around their roots already crowded with mycorrhizal fungi and beneficial bacteria, there just isn’t much room for pathogens. The good guys got there first, and keep any “bad guys” from accessing nutrients that would otherwise allow them to grow strong and break in.

There is also active biocontrol in soils — beneficial organisms actively attacking crop pests and keeping them in check. Some of the microbes recruited by plants can release antibiotic compounds to combat pathogens. Others can stimulate the plant’s own immune system to resist attack.

Looking to slightly larger organisms, let’s take nematodes. Nematodes sometimes get a bad rap because a small percentage (10–20%) feeds on plant roots. But in healthy soil, the majority of nematodes don’t eat plants. Instead, they cycle nutrients from bacteria and fungi. What’s more, some of them actually feed on the larvae of insects like fungus gnats and thrips, which would otherwise mature to attack the crop. The result is an overall lower level of crop pests, bypassing the need for frequent applications of chemical pesticides.

How SymSoil Supports the Soil Food Web

There are many benefits to working with the soil microbe biome when growing crops. Nutrients are more efficiently utilized, and pathogens are better controlled, just by the system itself. This translates to fewer inputs required, which means less labor and cost. It’s better for the environment, too, by reducing runoff from fertilizers and pesticides that can pollute our waterways. High levels of biodiversity in soil also mean greater resilience — the ability of the system to recover from changes in moisture and temperature. Nurturing the biodiversity of our soils will pay dividends for years to come in the face of climate change.

SymSoil products are formulated to enhance and support the soil food web. For example, SymSoil Robust Compost contains a complex ecosystem of bacteria, archaea, fungi, protozoa, nematodes and microarthropods. It can be used to introduce these living components where they’ve been depleted previously from the soil to re-establish healthy microbial communities. SymSoil’s Fungal Infused Biochar provides a medium to more specifically enhance plant symbiotic fungi, the mycorrhizae, critical to nutrient management in plants.

The living component in our soils is increasingly recognized as a valuable resource to nurture and protect.

[1] Weil, R. R., and N. C. Brady. 2017. The Nature and Properties of Soils. Pearson Education Limited, Harlow, p. 494.

What is Robust Compost?

Robust Compost feeds plants the way nature intended with the complete soil microbe biome. Sometimes called Living Soil, Soil Food Web compost or biocomplete compost, the full spectrum soil ecosystem includes bacteria, fungi, archaea, beneficial nematodes, amoeba, flagellates and micro-arthropods. Often it has other types of life, including animals (earthworms) and it may contain diatoms and other algae, phages and other types of protozoa. Where healthy soil contains in excess of 10,000 species of life, Robust Compost has in excess of 1,000 species and includes at least 7 types of life. SymSoil® RC is Robust Compost, with over 2,000 species and 7% biochar, which acts as a soil conditioner as well as a tool to revive or reseed the soil microbe biome.

About SymSoil® Inc.

SymSoil is a leader in development of biological soil amendments for agriculture that restores the microbes that provide the right food to the plant roots, improving plant health, and making food more nutrient dense and flavorful, the way nature intended. SymSoil has products and services for growers using regenerative agriculture methodologies which improve profitability. Its flagship product, SymSoil® RC (Robust Compost) is a complex community of soil microbes, which includes in excess of 1,000 species, covering broad biodiversity of bacteria, fungi, amoebae, and other protozoa, beneficial nematodes and microarthropods. SymSoil was named one of 2019’s AgTech Companies to Watch. Accredited Investors can learn more about SymSoil as an impact investment here.

Originally published at https://symsoil.com.



Elizabeth Pearce @ SymSoil

We recreate the complete soil microbe biome to improve farmer profits. #RegenAg #ClimateAction #100KTrees https://www.100ktrees4humanity.com