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Biological Control: Applied Fungal Symbiosis in Modern Forestry Practices

This article is an excerpt from The Hidden Kingdom of Fungi: Exploring the Microscopic World in Our Forests, Homes, and Bodies by Dr. Keith Seifert, who spent more than forty years studying fungi on five continents. He did research on microscopic fungi from farms, forests, food and the built environment, to reduce toxins and diseases affecting plants and animals.


With endophytes running through branches and leaf tissue, epiphytes covering foliage, rhizosphere fungi surrounding roots, mycorrhizae connecting tree to tree in the soil, and saprobes processing the fallen debris on the ground, a healthy forest is a busy place. Keeping forests healthy is a long-term commitment. Forest ecologists and forest pathologists (sometimes called tree doctors) try to stay ahead of diseases that appear in the woodlots in their care, and treat or remove symptomatic trees before infections spread. Spruce budworm outbreaks, for example, occur in roughly thirty-year cycles in several parts of North America—the timing is not well understood, so careful monitoring is needed. Then, unless the area is bombed with chemical insecticides from a low-flying aircraft, entire forests can be destroyed as the voracious moth larvae devour needles or leaves.

In afflicted forests, however, some stubborn old trees do make it through multiple budworm epidemics. These trees should have the best endophytes, which might make high concentrations of mycotoxins to deter hungry larvae. Foresters have wondered if replacing the random mixture of endophytes in susceptible trees with carefully selected strains that produce lots of toxin might be a better way to protect the forest.

To look for such fungi, my colleagues and I traveled with some local foresters and a mysteriously taciturn man into the remote corners of the Acadian forest of eastern Canada. The four-wheel-drive jostled on heavily eroded tracks through cleared plantations, but the scouts knew the precise coordinates of the elite spruce—the tallest ones, with the straightest trunks and healthiest needles. The stranger in the suv was a sharpshooter with a high-powered rifle. After scanning the tall trees through binoculars, the chemist in the group, who was leading the effort, pointed and said, “That one.” The sniper shot, and a branch tumbled from the treetops through the foliage to the ground.

Acadian forest of eastern Canada (Source: Oregon State University)

Back in the lab, students and biologists went through the long process of isolating and purifying hundreds of endophyte cultures from the branches we’d collected and other specimens culled from nearby trees. With DNA sequencing, we recognized that many of the crinkled brown cultures that crawled out of the needles were Lophodermium, even though they made no spores. Several species of another asco called Phialocephala crept “out of other samples; sometimes, after several months in the refrigerator, they made a few spores. Cultures of both fungi made mycotoxins that inhibited or killed spruce budworm larvae in lab experiments, and others that slowed the growth of other fungi. We hoped that these endophytes would protect the trees from the caterpillars in the forest. The questions were how to get them into living seedlings and whether they would take up permanent residence as endophytes and reduce the losses expected during budworm epidemics. Early experiments with young trees were encouraging. The endophytes established in young endophyte-free seedlings and survived for several years. The same protective mycotoxins showed up in the needles.

Today, many conifers begin life in nurseries, gymnasiumsized greenhouses that shelter millions of seedlings in custom-designed containers that look like deep egg cartons. The seedlings are lined up on rows of tables under banks of fluorescent lights, with the hoses and pipes of the irrigation system running above them. The endophytes grow better in liquid broth in fermentation tanks than they do on agar, so the blobs of mycelium from the Petri dishes are blended into a slurry. To introduce the fungus into the seedlings, hyphal fragments are sprayed from the overhead irrigation system when the young needles are most receptive to colonization. Then the seedlings are planted out into the forest and the endophytes persist, penetrating new bud scars and colonizing needles as they appear each spring. The anti-insect metabolites build up inside the needles where they are needed. When the old needles fall to the ground and decay, the mycotoxins also break down. Hundreds of millions of spruce seedlings have now been treated with carefully selected endophytes native to eastern Canada. This is a long-term experiment; the people who set it up may not be working anymore when the trees mature and the next epidemic arrives.

The deliberate use of endophytes to reduce insect out-breaks is an unusual example of biocontrol but an instructive one. First, the treatment applied to seedlings is a much more focused strategy than spraying hundreds of square miles in a forest. It redirects or amplifies an existing mutualistic symbiosis in favor of desirable strains that produce potent mycotoxins. It is an intervention to ensure that planted seedlings will have an effective, protective endophyte population instead of a haphazard mixture of less helpful strains.

Different mycorrhizal connections in the forest (Source:

Second, this approach suggests that if we want to manage ecology for our own benefit, as we try to do in both wild and planted forests, we need to be aware of all the organisms that are present. The collection of microbes on the surface of and within the body of a host is called a microbiome. When the host is a living plant, the associated microbes are called the phytobiome. Trees are multispecies conglomerates called holobionts. To our eyes they seem to be individuals made up of cells of one species. But when examined more carefully, we see each one is assembled from many different component species. To improve how a managed forest works, we need to understand how tree phytobiomes form, how each component species changes over time and adapts when threatened, and how all the components cooperate to create something we regard as a tree. “Then, if necessary, we can tweak the holobiont to optimize its health and resilience. After all, the holobiont that we see as a tree is as much about fungi—the endophytes, mycorrhizae, epiphytes, rhizosphere microbes, and the pathogens—as it is about the plant that holds the pieces together. Simply put, tree huggers will always be fungus huggers—through all phases of a tree’s life.

When we think about trees and fungi, we tend to think only of forests. But whether the trees are naturally occurring or planted—in forests, plantations, or orchards—fungi are an integral part of the phytobiome. And trees and forests are as important for producing mushrooms, spices, and fruit as they are for producing lumber. The phytobiome is also important on farms, where understanding the beneficial and harmful influences of fungi may make the difference between producing enough food for our growing population—or not.”


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