- Author: Ben Faber
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.
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.
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.
- Author: Jim Downer
All the media are full of stories about the impending El Nino effects and possible flooding rains in California. As I write this, it is the day before our first significant storm (Jan. 4) with a 100% chance of rain throughout Ventura county for tomorrow. Still long range forecasts for Jan and Feb show near normal or less than normal rainfall possibilities for the Avocado growing areas of California. The “real rain”, they say, will come in March. Although nobody can accurately predict the occurrence of rain, we are certainly due for an increased rain year based on statistical models and estimates of the El Nino effect by NOAA, JPL and NASA. If heavy rains are in the near future, nurserymen and growers will need to take measures to protect their operations from the many and disastrous effects of downpours. Physical displacement of soil as erosion and loss of soil are common during heavy rains. While runoff water should not leave agricultural properties, it has to move somewhere when rains come, so ditches should be cleared of weeds and other obstructions to permit efficient flow of water. Most operations will have already done this by now. So what can be expected when the rains come and after they leave? It will likely be a banner year for diseases both biotic and abiotic.
Many pathogens are splash inoculated from plant to plant or soil to plant, so it is imperative to prevent the development of flooded or puddled ground near growing areas. Now or between storms would be a great time to lay down additional gravel under container beds or other outside nursery areas. Keeping containers off soil, either with a gravel or fiber mat and gravel system is imperative when trying to control Phytophthora in nurseries. Compacted walkways and beds may become saturated this winter and create ideal sporulation conditions for Oomycetes or water molds which may then move in water flows to new areas of the nursery causing infections where never seen before. Consider boardwalks or additional gravel in known low spots and walkways so that workers don't move infested mud from one part of a nursery to another. For citrus and avocado growers it is vital to give water a place to go on flat or low lying areas. When we get the expected deluges, trees can suffocate from extended soil saturation and defoliate rapidly due to anoxic conditions.
For Phytophthora sensitive crops, it may be wise to increase the calcium by adding additional gypsum now to reduce sporulation and potential spread of disease. It is also wise to use preventative fungicides such as mefenoxam, and phosphorous acid to increase plant readiness for Phytophthora increases following wet weather.
This is also a great time for woody plant growers to prune any diseased or dead materials from plants ahead of winter rains because many Ascomycete canker fungi that cause disease in woody plants will have inoculum in dead twigs. This has been a banner year for Botryosphaeira fungi which have caused canker diseases in citrus, avocado and ornamentals at record levels due to drought stress. When rain comes, spores are splashed to new plants and can cause new infections. Since this is an El Nino year, it is warm, and warm rains are best for disease promotion. Remove inoculum now, cull and remove weak, diseased or dead plants ahead of the rains to cut down on disease spread. Even though it may be inappropriate to plant some crops now, it is always a good time to remove weak trees, plow diseased row crops and chip up the waste to be used as mulch.
With rains often come strong winds. Greenhouse and tunnel growers should consider the effects of wind this winter on their operations and possible crop loss from this damage. Tunnel houses used in berry and other production are at risk but other greenhouse materials such as polycarbonate sheeting can be detached by wind. Now is a great time to inspect and repair these structures or apply new sheeting as necessary. Wind can also move woody plants to rub against each other, causing injury to the main stem or fruit if tightly spaced. Trees that are blown over due to high winds can be damaged and devalued. Spend time now inspecting trellis systems and staking of woody plants to minimize damage that may be coming.
Outdoor nurseries that have planting media storage piles should start now to downsize these piles or provide new tarps in advance of wet weather. Greenhouse operations with media stored outside should ensure that bales are properly covered with new tarps to prevent saturation of the media. Media bales should be stored off the ground on raised pallets to avoid contamination with soil or mud flows.
The challenge of a wet and potentially stormy winter is to envision what excess water can do in your operation and then try to prepare. Flooding conditions create a time of potential pathogen movement and the best protection for plants is to keep them elevated above the mud and keep workers from spreading it with the movement of machinery or foot traffic. It is also useful to imagine invasion of soil from adjacent land owners who may have diseases or weeds not on your own property. Money spent now on infrastructure will prevent disease loss later this spring or summer.