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The Soil’s Microbiome

Edible Evanston Work & Learn, June 2019

Tim Sonder, education chair


I’ve heard of a microbiome recently—I thought people have those?

Yes, the media is rightfully all abuzz about the human microbiome and especially the gut’s microbiome. We are mostly microbes (by cell count 10:1, although by weight just a few percent) and water and those microbes do much of the work of keeping us healthy. You will learn it is similar for the soil, and, even more importantly, that human nutrition is directly related to a healthy microbiome both in the soil and in the gut.

What is Soil and what is Dirt?

Dirt is non-living fine mineral particles, water and air, while soil (for farmers and gardeners) is a collection of living —and previously living— things interacting, extracting and exchanging needed chemical components incorporated into the dirt—those non-living materials.

What is healthy soil?

A soil with a range of microbes—bacteria, fungi, protozoa, nematodes and microarthropods—able to decompose and mineralize nutrients, control nitrogen cycling, hold water and air, and make nutrients available to plants and other organisms is good, healthy soil.

Aren’t all those critters bad?

There are pathogenic (bad) bacteria, fungal diseases, and nematodes. There are insects which harm our crops. But the majority of these living organisms are good and have co-existed in a balanced healthy way for millennium. Things get bad when we force the balance out of whack.

Give a little, get a little. Or maybe a lot.

It is said that 60 percent of the sugars and other products (especially amino acids) which plants make they purposely leak out of their roots. These exudates attract and feed symbiotic fungi and bacteria. This relationship is so close that for most plants the fungal hyphae—the strands of living tissue of the fungus—extend inside the plant root cells, forming symbiotic endomycorrhizae relationships with plant root cells. In this symbiotic relationship the fungi provide basic soil nutrients to the plant, while receiving photosynthetic products back from the plant.

Fungi can have an amazing reach and are among the largest living organisms on the planet. (The competition for that prize is apparently the aspen tree, but that’s another story.) These fungal hyphae, therefore, can reach way beyond a plant’s own impressive root structure and deliver nutrients and water from far away. And fungi are possibly the most powerful decomposers on the planet, able to extract nutrients directly from mineral rock, break down cellulose and woody lignin, and other complex molecules.

Mycorrhizal fungi are like fine root hairs, and can increase the surface absorbing area of roots as much as 50 times, thereby greatly improving the ability of the plant to access soil resources. Several miles of fungal filaments can be present in less than a thimbleful of soil. They release powerful organic compounds into the soil that help to dissolve nutrients like organic nitrogen, phosphorus, iron and other “tightly bound” soil nutrients.

Plants also have close relationships with bacteria. The most well-known is Rhizobia in legumes, which form root nodules and fix nitrogen from the atmosphere within the plant root. But there are many such relationships.

And while some exchange is going on while everything is alive, once bacteria and fungi die or are consumed and ground up and excreted by larger soil microbes, the elements that they contained also become available to plants.

Don’t I need fertilizers?

You need to make sure the microbes have everything they need. That’s what is meant by “feed the soil and not the plants.” Feeding plants with inorganic fertilizers does several bad things. First, these soluble chemicals tend to be toxic to many microorganisms. Second, even if they are not, they shut down the plant’s natural tendency to “ask for what it needs” by sending out specific exudates and therefore diminish the population of microbes right around the roots.

Your soil needs a varied diet of organic matter. Cover crops and the roots of plants you removed are great. Compost is the ideal organic matter, providing a range of predigested components (thanks to the microbes working inyour compost bin. An especially important component of compost is called humic acid (humus) because plays an important role in holding onto the available nutrients in soil and releasing them to plants “when called for.” That sounds anthropomorphic, but it’s chemistry—cation and anion exchange—e.g. the plant excreting elements like CO2 and water, creating an acid in the soil which releases those held nutrients.

Compost teas (which needs another class or two or three) can be used to both feed the microbes in your soil and boost their numbers. Mycorrhizal inoculants might help establish fungal communities.

I’ve got a lot of weeds, so what about, rototilling or herbicides?

Weeds c an be used as a sign about the condition of your soil. Most weeds thrive in disturbed soil, soil low in certain trace elements, or soil with a bacteria-dominant (instead of fungal dominant) microbiome.

A teaspoon of productive soil generally contains between 100 million and 1 billion bacteria. Fungus population numbers are smaller but they dominate the soil biomass when the soil is not disturbed. Bacteria, actinomycetes, and protozoa are hardy and can tolerate more soil disturbance than fungal populations so they dominate in tilled soils while fungal and nematode populations tend to dominate in untilled or no-till soils.

Rototilling is like blowing up a city with bombs and then running bulldozers over the landscape. It will take a long time to rebuild that city, and it will take a long time to reestablish the soil community, especially the fungal community in a tilled plot. If you tilled, you just did at least four things—brought dormant weed seeds to the surface where they can germinate; made the soil’s community bacteria-dominated; destroyed the structure which had allowed air and water to penetrate into the soil; temporarily released a lot of nutrients, providing a burst of fertility and a lot of runoff, followed by a lack of available nutrients. Just put a big layer of compost on top (or lasagna mulch if not available).

What about pesticides and biocides?

Here again a healthy microbiome in your soil will protect your plants in multiple ways. The mycorrhizal fungi trigger the plant to produce protective chemical against troublesome fungal attack, a wide-ranging community of fungi and bacteria on every surface of the plant protects the plant from having a bad actor dominate, as they all duke it out for balance, and the fatty acids the bacteria provide are used by the plant to build protective coatings on its leaves. Plus, the presence of all these organisms makes it less likely that fungal spores and such remain in the soil without being broken down.

So what do I do?

Um, as little as possible? Not quite, but sort of.

    Practice “No Dig” gardening to disturb the soil as little as possible.

    Apply living compost, as much as you can.

    Think before you attack things as posts or problems and look for an integrated solution which focuses on fostering the beneficial microbes and insects and prevention, like keeping your soil covered with either living and previously living mulch (e.g., understory cover crop or straw).

    And for more advanced measures:

    Balance what microbes you foster to match your needs: Brassicas (um, like the weeds they are related to) don’t form mycorrhizal relationships and thrive in bacteria dominant soil and tend to need more available nutrients. Trees like it heavily fungal, so love wood chips and hate turf grass, which is a bacteria-loving weed/plant.

    Read your weeds and learn what they tell you about your soil

    Apply compost teas



Understanding Soil Microbes and Nutrient Recycling

Mycorrhizal Planet: How Symbiotic Fungi Work with Roots To Support Plant Health and Build Soil Fertility, Michael Phillips - Chelsea Green Publishing - 2017

Teaming with Microbes: the Organic Gardener's Guide To the Soil Food Web, Jeff Lowenfels-Wayne Lewis - Timber Press - 2016

Understanding the Soil Microbiome with Nicole Masters – Podcast

Soil Science, Elaine Ingham

Soil Microorganisms: An Overview – Soil Biology,

All About Soil,

No Dig Organic Gardening - Charles Dowding