Posts Tagged: armillaria

Oil and Fungal Evolution?

Like most of us, trees don't want to be eaten alive.

To prevent this gruesome fate, they developed extremely tough cell walls around 400 million years ago. For millions of years, nothing could break down lignin, the strongest substance in those cell walls. When a tree died, it just sank into the swamp where it grew. When the fossil record started showing trees breaking down around 300 million years ago, most scientists assumed it was because the ubiquitous swamps of the time were drying up.

But biologist David Hibbett at Clark University suspected that wasn't the whole story. An alternative theory from researcher Jennifer Robinson intrigued him. She theorized that instead of ecosystem change alone, something else played a major role - something evolving the ability to break down lignin. Through evolutionary biology research supported by the Department of Energy's (DOE) Office of Science, Hibbett and his team confirmed her theory. They found that, just as she predicted, a group of fungi known as "white rot fungi" evolved the ability to break down lignin approximately the same time that coal formation drastically decreased. His research illustrated just how essential white rot fungi were to Earth's evolution.

Fungi are still indispensable. The short-order cooks of the natural world, they have an unheralded job making nutrients accessible to the rest of us. Just like cooking spinach makes it easier to digest, some fungi can break down plant cell walls, including lignin. That makes it easier for other organisms to use the carbon that is in those cell walls.

"We all live in the digestive tract of fungi," said Scott Baker, a biologist at DOE's Pacific Northwest National Laboratory. If we weren't surrounded by fungi that decay dead plant material, it would be much harder for plants to obtain the nutrients they need.

To understand fungi's role in the ecosystem and support biofuels research, scientists supported by DOE's Office of Science are studying how fungi have evolved to decompose wood and other plants.

The Special Skills of Fungi

Fungi face a tough task. Trees' cell walls contain lignin, which holds up trees and helps them resist rotting. Without lignin, California redwoods and Amazonian kapoks wouldn't be able to soar hundreds of feet into the air. Trees' cell walls also include cellulose, a similar compound that is more easily digested but still difficult to break down into simple sugars.

By co-evolving with trees, fungi managed to get around those defenses. Fungi are the only major organism that can break down or significantly modify lignin. They're also much better at breaking down cellulose than most other organisms.

In fact, fungi are even better at it than people and the machines we've developed. The bioenergy industry can't yet efficiently and affordably break down lignin, which is needed to transform non-food plants such as poplar trees into biofuels. Most current industrial processes burn the lignin or treat it with expensive and inefficient chemicals. Learning how fungi break down lignin and cellulose could make these processes more affordable and sustainable.

Tracing the Fungal Family Tree

While fungi live almost everywhere on Earth, advances in genetic and protein analysis now allow us to see how these short-order cooks work in their kitchen. Scientists can sample a fungus in the wild and analyze its genetic makeup in the laboratory.

By comparing genes in different types of fungi and how those fungi are evolutionarily related to each other, scientists can trace which genes fungi have gained or lost over time. They can also examine which genes an individual fungus has turned "on" or "off" at any one time.

By identifying a fungus's genes and the proteins it produces, scientists can match up which genes code for which proteins. A number of projects seeking to do this tap the resources of the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), both Office of Science user facilities.

Understanding the Rot

Just as different chefs use different techniques, fungi have a variety of ways to break down lignin, cellulose, and other parts of wood's cell walls.

White Rot

Although fungi appeared millions of years earlier, the group of fungi known as white rot was the first type to break down lignin. That group is still a major player, leaving wood flaky and bleached-looking in the forest.

"White rot is amazing," said Hibbett.

To break down lignin, white rot fungi use strong enzymes, proteins that speed up chemical reactions. These enzymes split many of lignin's chemical bonds, turning it into simple sugars and releasing carbon dioxide into the air. White rot is still better at rending lignin than any other type of fungus.

Brown Rot

Compared to white rot's powerful effects, the scientific community long thought the group known as brown rot fungi was weak. That's because brown rot fungi can't fully break down lignin.

Recalling his college classes in the 1980s, Barry Goodell, a professor at the University of Massachusetts Amherst said, "Teachers at the time considered them these poor little things that were primitive."

Never underestimate a fungus. Even though brown rot fungi make up only 6 percent of the species that break down wood, they decompose 80 percent of the world's pine and other conifers. As scientists working with JGI in 2009 discovered, brown rot wasn't primitive compared to white rot. In fact, brown rot actually evolved from early white rot fungi. As the brown rot species evolved, they actually lost genes that code for lignin-destroying enzymes.

Like good cooks adjusting to a new kitchen, evolution led brown rot fungi to find a better way. Instead of unleashing the brute force of energy-intensive enzymes alone, they supplemented that enzyme action with the more efficient "chelator-mediated Fenton reaction" (CMF) process. This process breaks down wood cell walls by producing hydrogen peroxide and other chemicals. These chemicals react with iron naturally in the environment to break down the wood. Instead of fully breaking down the lignin, this process modifies it just enough for the fungus to reach the other chemicals in the cell wall.

There was just one problem with this discovery. In theory, the CMF chemical reaction is so strong it should break down both the fungus and the enzymes it relies on. "It would end up obliterating itself," said Jonathan Schilling, an associate professor at the University of Minnesota.

Scientists' main theory was that the fungus created a physical barrier between the reaction and the enzymes. To test that idea, Schilling and his team grew a brown rot fungus on very thin pieces of wood. As they watched the fungus work its way through the wood, they saw that the fungus was breaking up the process not in space, but in time. First, it expressed genes to produce the corrosive reaction. Two days later, it expressed genes to create enzymes. Considering fungi can take years or even decades to break down a log, 48 hours is a blip in time.

Scientists are still trying to figure out how much of a role the CMF process plays. Schilling and like-minded researchers think enzymes are still a major part of the process, while Goodell's research suggests that CMF reactions do most of the work. Goodell's team reported that CMF reactions could liquefy as much as 75 percent of a piece of pine wood.

Either way, the CMF process offers a great deal of potential for biorefineries. Using brown rot fungi's pretreatment could allow industry to use fewer expensive, energy-intensive enzymes.

A Close Collaboration

Not all fungi stand alone. Many types live in symbiosis with animals, as the fungus and animal rely on each other for essential services.

Partnerships with Rumens

Cows and other animals that eat grass depend on gut fungi and other microorganisms to help break down lignin, cellulose, and other materials in wood's cell walls. While fungi only make up 8 percent of the gut microbes, they break down 50 percent of the biomass.

To figure out which enzymes the gut fungi produce, Michelle O'Malley and her team at the University of California, Santa Barbara grew several species of gut fungi on lignocellulose . They then fed them simple sugars. As the fungi "ate" the simple sugars, they stopped the hard work of breaking down the cell walls, like opting for take-out rather than cooking at home.

Depending on the food source, fungi "turned off" certain genes and shifted which enzymes they were producing. Scientists found that these fungi produced hundreds more enzymes than fungi used in industry can. They also discovered that the enzymes worked together to be even more effective than industrial processes currently are.

"That was a huge diversity in enzymes that we had never seen," said O'Malley.

O'Malley's recent research shows that industry may be able to produce biofuels even more effectively by connecting groups of enzymes like those produced by gut fungi .

Termites as Fungus Farmers

Some fungi work outside the guts of animals, like those that partner with termites. Tropical termites are far more effective at breaking down wood than animals that eat grass or leaves, both of which are far easier to digest. Young termites first mix fungal spores with the wood in their own stomachs, then poop it out in a protected chamber. After 45 days of fungal decomposition, older termites eat this mix. By the end, the wood is almost completely digested.

"The cultivation of fungus for food [by termites] is one of the most remarkable forms of symbiosis on the planet," said Cameron Currie, a professor at the University of Wisconsin, Madison and researcher with the DOE's Great Lakes Bioenergy Research Center.

Scientists assumed that the majority of the decomposition occurred outside of the gut, discounting the work of the younger termites. But Hongjie Li, a biologist at the University of Wisconsin, Madison, wondered if younger insects deserved more credit. He found that young workers' guts break down much of the lignin. In addition, the fungi involved don't use any of the typical enzymes white or brown rot fungi produce. Because the fungi and gut microbiota associated with termites have evolved more recently, this discovery may open the door to new innovations.

From the Lab to the Manufacturing Floor

From the forest floor to termite mounds, fungal decomposition could provide new tools for biofuels production. One route is for industry to directly produce the fungal and associated microbiota's enzymes and other chemicals. When they analyzed termite-fungi systems, scientists found hundreds of unique enzymes.

"We're trying to dig into the genes to discover some super enzyme to move into the industry level," said Li.

A more promising route may be for companies to transfer the genes that code for these enzymes into organisms they can already cultivate, like yeast or E. coli. An even more radical but potentially fruitful route is for industry to mimic natural fungal communities.

For millions of years, fungi have toiled as short-order cooks to break down wood and other plants. With a new understanding of their abilities, scientists are helping us comprehend how essential they are to Earth's past and future.

 

Photo:

The evolution of white rot fungi most likely played a large role in trees beginning to decay about 300 million years ago. The fungus Schizophyllum commune is one modern example of a white rot fungus. Credit: Photo courtesy of Nathan Wilson

white rot fungi

After Flooding, Buried Trunks a Problem

A trunk "below grade", that is a buried trunk, is a problem for most trees.  Willows and other riparian trees along water ways that are inundated regularly can adapt to a change in soil depth around their trunks.  That's not true of most of our commercial tree species, and avocados and citrus are really susceptible to buried trunks/stems. they asphyxiate.  This can be a very common problem at planting when a hole is too deep and the new tree settles in the loosen earth and gradually the stem is buried.  Or, when the grower is doing the "right thing" and using an organic planting mix that gradually decomposes and the tree settles into the ground and the crown is covered by dirt.  The tree then starts looking bad -  leaves yellow.  The canopy defoliates.  All the while, the grower is putting on more water and more fertilizer and the tree looks worse and worse.  Remove the soil from around the base, and voila, in a few months the tree is happy again. If the dirt isn't moved, the stressed tree is now susceptible to root rots, both Phytophthora and Armillaria.  Those problems are a lot worse than just lack of air.

This suffocation is a common problem after flooding.  Dirt from higher up moves into lower positions, gravity moving dirt can move a lot.  It accumulates around the base of the tree.  The grower is preoccupied with other things that occur with flooding and does nothing.  A few months later, the trees start turning yellow especially when the weather warms up and they are more active and more water is being applied.  Flooding can also spread disease organism from other areas that are contaminated.  Oak root fungus is frequently spread in flooding waters, especially in the lower positions in little valleys.

Pulling that accumulated soil away from tree is important for tree health. It's something that needs to be done soon after the flooding incident, or any event that buries the tree trunk.

buried tree trunk

Name the Biggest TERRESTRIAL Organism

Have you ever thought about it? I'm sure a lot of you have…what's the biggest living thing on earth? If you're like me, you immediately think of animals like the blue whale. In this case, we're just talking about organisms that spend their life predominantly or entirely on land. Anybody thinking of the rhinoceros, or maybe the African elephant? Nope!

The answer to this question might surprise you. The largest terrestrial organism on the planet is actually a fungus! Not your typical, garden-variety mushroom, but a fungus, nonetheless. And while it is edible, it comes with a few problems. Its common name is honey fungus.

The soil is filled with living organisms, large and small. Bacteria are the most numerous soil organism – there can be more than a million in a teaspoon of soil! There are over 10 trillion types of soil bacteria!

There are “only” 100 billion types of soil fungi, but they play in important role in the life cycle within the soil. Fungi break down decaying plant material into nutrients that other plants can use to grow. They soak up water in water-logged soils. You might be familiar with seeing mushrooms growing on moist logs, or in soil with wet leaves.

Honey fungus is a bit different from many other fungi. It's not one that landowners will welcome because it can kill trees. In fact, it gained fame in the late 1990s as the “culprit” that was killing fir trees in the Pacific Northwest. (Fir trees are widely sought after as beautiful landscape plants,  Christmas trees, and for lumber used in building homes.)

Honey fungus is a parasite – Armillaria solidipes. Parasites are organisms that live off other organisms, sometimes hurting them. Honey fungus is widely distributed across the cooler regions of the United States and Canada. It is very common in the forests of the Pacific Northwest.

These fungi grow in individual networks of above and below-ground fibers called mycelia. Mycelia work in a similar fashion to plant roots. They draw water and nutrients from the soil to feed the fungus. At the same time, they make chemicals that are shared with other organisms in the soil. Sadly for the fir trees, the honey fungus can kill already weakened or stressed trees. The natural action of this fungus can be destructive in forests, leading to widespread die-off in timber stands.

One cool feature of the underground network of mycelia of all fungi is that they help hold soil particles together. Just like plant roots, mycelia work to prevent soil particles from blowing away in the wind or being taken away by running water. They are a very important part of the soil ecosystem.

Scientists have shown that Armillaria solipipes identify and connect to each other. That's right: when mycelia from different individual honey fungus bodies meet, either in or on the soil surface, they can attempt to fuse to each other. The fungi must be genetically identical honey fungi. When the mycelia successfully fuse to each other, they link very large fungal bodies together. This, in turn, changes extensive networks of fungal “clones” into a single individual.

The largest honey fungus that has been identified in North America is located in Oregon. It measures 3.4 miles across! Scientists also believe that this particular honey fungus may be over 2,000 years old. The next largest honey fungus is in the neighboring state of Washington.

While honey fungus is impressive in both age and size, it isn't always a favorite of scientists and landowners because of its parasitic nature. But it is the largest organism on earth, and scientists have had only a few decades of research to understand how mycelia fuse and communicate. Perhaps one day, research discoveries about honey fungus could lead to a new medicine (think Penicillin), or new ways to grow food – the possibilities are endless!

And this is the largest terrestrial organism. Who knows what lurks in the depths of the ocean?

P.S.

Armillaria solipipes is one of the many species that was once lumped as Armillaria mellea, oak root fungus.  So many woody perennials are susceptible to this fungus.  It turns out that avocado for whatever reason tends to be somewhat more tolerant of oak root fungus than many other trees.  Under stress, it too will succumb, though.

Amanita

Armillaria or Oak Root Fungus

Armillaria Root Rot

There have been a lot of new avocado orchards planted during the last few years. These often have been in old ‘Valencia’ orchards or lemons that had poor production. In order to save money, growers have just cut the trees at ground level and replanted the avocados near the stumps. Avocados have recognition of being resistant to Armillaria, but in this environment of high disease pressure, they can fail.

Armillaria root rot is common, yet is an infrequently identified and poorly understood disease. It is capable of attacking most species of trees and other woody plants growing in California. It is sometimes called “shoestring root rot” and the causal fungus is often referred to as the “honey mushroom.” Because oak is one of the preferred hosts, it is alsocalled “oak root fungus.”

If a tree undergoes a slow to rapid decline without any obvious reason, suspect Armillaria as the cause. Certain areas, such as drainage areas from chaparral or woodlands are likely areas for this disease. Old roots left underground provide a food base for continued fungal growth and survival.

General symptoms of Armillaria resemble those of other root disorders. These symptoms are disrupted growth, yellow foliage, branch dieback, and resin or gum exudates at the root collar. Trees may die rather abruptly without showing any decline symptoms. Avocados typically have a rather protracted death, but in citrus it can be rapid. Only rarely can the disease be diagnosed without examining the larger buttress roots and root collar of the tree. After carefully removing the soil, examine forthe presence of:

1) Rhizomorphs, or fungal ‘shoestrings’ attached to the wood under the bark. These may occur beneath the bark for some distance above the soil line in advanced cases, rarely they may radiate from the wood into the soil. Rhizomorphs may also grow out from the larger roots, resembling feeder roots in appearance. They are about the diameter of pencil lead and vary in color from black to reddish brown. The interior consists of white mycelial tissue.

2) Decayed areas of wood at the root collar or on the crown roots. Armillaria causes a white rot and the wood develops a stringy texture. Roots in advanced stages of decay may be soft, yellowish and wet.

3) Veined, white mycelial fans between the bark and wood where the cambium has been killed. Sometimes this fan (or fans) extends quite far above the soil line beneath the bark.

4) Soil remaining attached to theroots.

5) Characteristic mushrooms on the lower trunk or on the ground near the infected roots. These shortlived annual fruiting structures of the disease-causing fungus may develop during the fall or winter rainy season and may occur in small clusters or in large numbers. The stalk is typically yellow and 3 inches or more long. Usually a ring is connected to the stalk just below the cap. The cap is 2-5 inches across and often honey-yellow. It may be dotted with dark brown scales. The underside is covered with loosely spaced white or yellow gills radiating from the stem. After the disease has been identified, the grower should study the situation to determine the role Armillaria root rot has played in causing the decline or death of the tree. Frequently the fungus is only involved in a secondary manner by invading and destroying roots after the tree has been exposed to stress of some form, such as severe drought, water logging, or soil fill over the roots. The fungus can also act as a saprophyte feeding on dead wood. It is frequently involved in the decay of old tree stumps and roots.

Many oaks are lightly infected with the disease for years with no resultant damage except for isolated pockets of buttress root rot which are walled off by the tree and have no ill effects. Other infected trees show no damage until subjected to stress. Accumulating evidence suggests the type of root exudate that is produced influences the susceptibility of the tree. Certain forms of stress cause a shift in exudates that promote rapid development of the fungus and may hasten tree invasion and decay.

Spores are produced by the mushroom fruiting structures (mushrooms) and disseminated by air currents and introduced into new area. Once the fungus enters the cambium and bark tissues, mycelial fans develop during the parasitic phase of the attack. Subsequently, mycelium invades and decays the woody tissue of the roots and sometimes also the base of the trunk. Under proper conditions the fruiting structures form at or near the base of the infected tree, completing the life cycle.

Direct control of the fungus in a diseased tree is not possible with present technology. However, in many instances the fungus is incapable of causing severe damage unless the tree is first subjected to substantial stress. Thus, keeping the tree healthy and avoiding severe stress is one important approach in preventing loss of trees to Armillaria.

Drought and leaf defoliation are two major forms of stress that favor Armillaria. In dry years it is advisable, as in all years, to make sure irrigation scheduling is appropriate. Stresses such as defoliation from persea mite, soil compaction and physical injury can exacerbate the disease. Nutrient management may minimize Armillaria effects, although little research information exists on this subject.

The second most important means of minimizing Armillaria damage is to avoid or eliminate the fungus inoculum before planting. Trees planted in former orchards will quite possibly be exposed. Since these sites cannot be avoided, here is a suggestion that will be helpful: remove stumps and old roots from the old orchard to the greatest extent possible.

 

 

armillaria

Armillaria Root Rot

There have been a lot of new avocado orchards planted during the last few years.  These often have been in old ‘Valencia’ orchards or lemons that had poor production.  In order to save money, growers have just cut the trees at ground level and replanted the avocados near the stumps.  Avocados have recognition of being resistant to Armillaria, but in this environment of high disease pressure, they can fail.

 

Armillaria root rot is common, yet is an infrequently identified and poorly understood disease.  It is capable of attacking most species of trees and other woody plants growing in California.  It is sometimes called “shoestring root rot” and the causal fungus is often referred to as the “honey mushroom.”  Because oak is one of the preferred hosts, it is also called “oak root fungus.”

 

If a tree undergoes a slow to rapid decline without any obvious reason, suspect Armillaria as the cause.  Certain areas, such as drainage areas from chaparral or woodlands are likely areas for this disease.  Old roots left underground provide a food base for continued fungal growth and survival.

 

General symptoms of Armillaria resemble those of other root disorders.  These symptoms are disrupted growth, yellow foliage, branch dieback, and resin or gum exudates at the root collar.  Trees may die rather abruptly without showing any decline symptoms.  Avocados typically have a rather protracted death, but in citrus it can be rapid.

 

Only rarely can the disease be diagnosed without examining the larger buttress roots and root collar of the tree.  After carefully removing the soil, examine for the presence of:

1)      Rhizomorphs, or fungal ‘shoestrings’ attached to the wood under the bark.  These may occur beneath the bark for some distance above the soil line in advanced cases, rarely they may radiate from the wood into the soil.  Rhizomorphs may also grow out from the larger roots, resembling feeder roots in appearance.  They are about the diameter of pencil lead and vary in color from black to reddish brown.  The interior consists of white mycelial tissue. 

2)      Decayed areas of wood at the root collar or on the crown roots.  Armillaria causes a white rot and the wood develops a stringy texture.  Roots in advanced stages of decay may be soft, yellowish and wet. 

3)      Veined, white mycelial fans between the bark and wood where the cambium has been killed.  Sometimes this fan (or fans) extends quite far above the soil line beneath the bark.

4)      Soil remaining attached to the roots.

5)      Characteristic mushrooms on the lower trunk or on the ground near the infected roots.  These short-lived annual fruiting structures of the disease-causing fungus may develop during the fall or winter rainy season and may occur in small clusters or in large numbers.  The stalk is typically yellow and 3 inches or more long.  Usually a ring is connected to the stalk just below the cap.  The cap is 2-5 inches across and often honey-yellow.  It may be dotted with dark brown scales.  The underside is covered with loosely spaced white or yellow gills radiating from the stem. 

 

After the disease has been identified, the grower should study the situation to determine the role Armillaria root rot has played in causing the decline or death of the tree.  Frequently the fungus is only involved in a secondary manner by invading and destroying roots after the tree has been exposed to stress of some form, such as severe drought, water logging, or soil fill over the roots.  The fungus can also act as a saprophyte feeding on dead wood.  It is frequently involved in the decay of old tree stumps and roots.

 

Many oaks are lightly infected with the disease for years with no resultant damage except for isolated pockets of buttress root rot which are walled off by the tree and have no ill effects.  Other infected trees show no damage until subjected to stress.  Accumulating evidence suggests the type of root exudate that is produced influences the susceptibility of the tree.  Certain forms of stress cause a shift in exudates that promote rapid development of the fungus and may hasten tree invasion and decay.

 

Spores are produced by the mushroom fruiting structures (mushrooms) and disseminated by air currents and introduced into new area.  Once the fungus enters the cambium and bark tissues, mycelial fans develop during the parasitic phase of the attack.  Subsequently, mycelium invades and decays the woody tissue of the roots and sometimes also the base of the trunk.  Under proper conditions the fruiting structures form at or near the base of the infected tree, completing the life cycle.

 

Direct control of the fungus in a diseased tree is not possible with present technology.  However, in many instances the fungus is incapable of causing severe damage unless the tree is first subjected to substantial stress.  Thus, keeping the tree healthy and avoiding severe stress is one important approach in preventing loss of trees to Armillaria.

 

Drought and leaf defoliation are two major forms of stress that favor Armillaria.  In dry years it is advisable, as in all years, to make sure irrigation scheduling is appropriate.  Stresses such as defoliation from persea mite, soil compaction and physical injury can exacerbate the disease.  Nutrient management may minimize Armillaria effects, although little research information exists on this subject.

 

The second most important means of minimizing Armillaria damage is to avoid or eliminate the fungus inoculum before planting.  Trees planted in former orchards will quite possibly be exposed.  Since these sites cannot be avoided, here is a suggestion that will be helpful: remove stumps and old roots from the old orchard to the greatest extent possible.

 

Below:

Armillaria mushrooms and hyphal plaques under the bark

armillaria image

armillaria image 2

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