Beneficial Fungi & Disease Prevention

When you use the word “fungus” do you only see ‘bad fungi’ or do you see some ‘good fungi’ too?  Do you imagine morel mushrooms, long white strands of mycelia under a dead log in the woods, or even penicillin? Or do you only see bad fungi that cause plant diseases such as anthracnose, botrytis rot, downy mildew, or fusarium rot?

Fungi are all of these and more. Fungi are microscopic; morels are the fruiting bodies of a much larger body of cells. The white strands under that dead log are masses of fungal hyphae called mycelia. Penicillium is a life saver. Yet bad fungi cause, on average, a 16% loss/year of agricultural production worldwide. (1) It’s no wonder you think of the bad fungi first!

The Roles of Fungi in the Soil

A tablespoon of healthy soil has 50 billion microorganisms. The mycologist David Hawksworth, states that “…the magnitude of fungal diversity was estimated ‘conservatively’ at 1.5 million species.” (2) Healthy soil is home to approximately 25,000 species of fungi; others are aquatic, some live in the guts of mammals, and some are leaf dwellers. But no matter where they are they are predominately good fungi.  Without them, we couldn’t grow any crops or digest our food.

Most soil fungi are good and help plants with nutrient and water uptake and protect plants from disease. Healthy soil also has bad, or disease causing, fungi but with good soil management they are kept in check by the good fungi, with help from beneficial bacteria, nematodes and other soil dwellers.

What Fungi Are in Your Soil?

There are 3 categories of fungi that live in soil.

  • Decomposers
  • Mutualists
  • Pathogens or parasites

The decomposers (or saprophytic fungi) turn organic matter into organic acids, fungal biomass, carbon dioxide, and plant-available nutrients. Decomposers can be found in many places besides your soil; in your compost bin, wood chip pile, on the forgotten yogurt in your refrigerator, or in a pile of dead leaves.  They prefer dark, moist environments and, because they’re microscopic, only their reproductive organs (or mushrooms) are usually visible. When you turn a pile of leaves, you’ll notice the bottom layers have white strands running through them. Those are mycelium, or masses of fungal hyphae. One fungal hypha is invisible to the naked eye, but when you’re seeing mycelium it’s comparable to the difference between an outhouse in rural Kansas and the mass of housing units in New York City.

Fungi decompose all organic matter through the use of enzymes:

“Fungi eat by secreting enzymes out of the tips of their hyphae. Instead of engulfing food like an amoeba or ingesting and digesting it like an animal, they dump enzymes onto food itself and after it breaks down into smaller molecules, they suck it back up through their hyphae.” (3)

The nutrients that are not needed by the fungi for growth are released into the soil and used by plants and other microorganisms. Decomposer fungi are responsible for plant-available nitrogen, phosphorus, and many trace minerals needed for strong growth.

The mutualists have a cellular relationship with plants. They bring nutrients and water to plants in exchange for carbon in the form of plant root exudates. Mutualists come in two distinct forms; ectomycorrhizal or endomycorrhizal.

Ectomycorrhizal fungi grow on the surface of roots. They extend the area available for nutrient and water uptake through their extensive hyphal network. They’re often associated with trees.

Endomycorrhizal fungi penetrate the plant root and extend their hyphal network into the soil. (Arbuscular Mycorrhizal Fungi) are a type of endomycorrhiza. They are able to supply the plant root directly with nutrients and water.

The pathogenic or parasitic fungi are what we usually think of when we say the word “fungus.” They include Phytophthora, Rhizoctonia, Pythium, Verticillium and others.  These fungi cause root rot, root and crown rot in shrubs, damping off in seedlings, sunken spots in plant leaves, cavity spot, numerous rusts, the list goes on. Most plant diseases are caused by pathogenic fungi, yet fewer than 10% of all known fungi colonize plants. (4)

These are the fungi scientists have studied the most because they affect our food supply. But they are not the majority of fungi in healthy soil. Beneficial fungi such as the mutualists and decomposers are found in soil alongside pathogenic fungi. They protect plants from diseases caused by pathogens as well as supplying the host plant with nutrients and water.

The Battle Between Good and Bad Fungi

In a forest where the soil isn’t disturbed, the good fungi will almost always win the battle. But in a farm field that’s tilled every year and synthetic chemicals applied, the fight may not be fair. That’s because the hyphae, of both good and bad fungi, are destroyed by conventional farming practices such as tillage. In a study conducted by Dipak Sharma-Poudyal, et al

“…results suggest that taxa more common in conventionally tilled systems can utilize fresh, mature plant residues that are turned into the soil with tillage as pioneer colonizers, and then produce large numbers of conidia that are not as affected by tillage as the mycelial life stage.” (5)

Fungi can survive for long periods in the conidia stage, waiting for the proper conditions to develop hyphae. Conidia of pathogenic fungi continue to infect crops. Because of those infections, conventional practices suggests you have to spray more fungicides, which decreases the fungal diversity. Plants become vulnerable to disease by fungi that have become resistant to your fungicides.

Botrytis and many mildews are resistant to almost all fungicides. The more chemicals sprayed on the fields the less diverse the microbial community. Lower diversity increases the prevalence of pathogenic fungi. It’s a vicious cycle.

How Can You Level the Playing Field Between Good and Bad Fungi?

Using regenerative  practices creates a better balance of microorganisms in your soil, and on your plants.  No-till farming systems create a greater diversity of microbial species so both good and bad fungi can co-exist. Using no-till and decreasing synthetics allows beneficial fungi to gain the upper hand. They use their protective mechanisms to keep pathogenic fungi away from your crops.

Even bad fungi have been proven to have benefits as insect parasites, creating hollows in dead trees for animal nesting, and trapping disease causing nematodes. There are so many species of fungi, and most have not been studied, that it’s sometimes difficult to determine the good from the bad.

Beneficial fungi will “…form protective webs and nets, often in conjunction with bacteria, around roots (and even on leaf surfaces, as leaves produce exudates that attract bacteria and fungi as well…)” to protect the host plant. (6) When beneficial fungi are given a chance to populate an area, they protect the host plant (their food source) in many ways. They not only supply nutrients and water to plants but also secrete enzymes that attack pathogenic fungi.

The mutualist fungi, including AMF, create conditions that are inhospitable for pathogenic fungi.  Soils that have a large diversity of microorganisms, including fungi, have been shown to suppress fungal diseases. Good fungi can out-compete bad fungi for nutrients, essentially starving them.  

Fungi - The Good and the Bad – In Balance

Good fungi and bad fungi will always be around. The key is to keep them in balance. If your farming practices take into consideration all the benefits of fungi you will find nature will help you.

Conventional farming practices decrease good fungi while attempting to prevent plant disease by bad fungi. Spraying fungicides and tilling in crop residue creates an environment more hospitable to bad fungi.

Good fungi need living plants to thrive, bad fungi are happy with the dead organic matter you tilled into the soil. Just under the surface in that field you’re leaving fallow all winter are bad fungi feasting. Decreasing tillage, not using fungicides or fertilizers, and using cover crops to feed your fungal allies will make a huge difference in the prevention of disease in your fields. It’s always easier to prevent disease than to try to bring back a diseased crop.

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  6. Lowenfels, Jeff, Wayne Lewis, Teaming With Microbes, Timber Press, 2010, pg 72
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