Posts Tagged: decay
Tree Decay
Proper pruning and tree care are important in most trees, including citrus and avocado. The question of what decay fungus is happening to a tree often comes up and a recent UC publication can help answer that question
Wood Decay and Fungi in Landscape Trees by Downer and Perry
The other question of what to do about the fungus is answered, as well. Check it out.
IDENTIFICATION AND BIOLOGY OF DECAY FUNGI
Many wood decay fungi can be identified by the distinctive shape, color, and texture of the fruiting bodies they form on trees. These fruiting bodies take several forms, depending upon the fungus that produces them, but most of them fit into categories commonly referred to as mushrooms, brackets or conks. They often grow near wounds in bark, including old pruning wounds, at branch scars, in proximity to the root crown, or near surface anchor roots. Some decay fungi, such as Armillaria mellea, produce fleshy mushrooms at the base of infected trees or along their roots, often after rain in fall or winter. All mushrooms and some bracket fungi are annual (i.e., appearing and disappearing seasonally), but many conks are perennial and grow by adding a new spore-bearing layer (hymenium) each year.
Decay fungi are divided into those that attack heartwood (causing heart rots) and those that attack sapwood (causing sap rots and canker rots). Further subdivision is based on the appearance of the decayed wood (i.e., white rots, brown rots, and soft rots) or location in the tree (the decay is called a butt rot if it is at the base of the trunk). Canker rots usually appear on branches or the trunk. When a fruiting body is visible on a tree, it is usually associated with advanced decay; the extent of decay may be far above or below the location of the fruiting body. Trees with extensive sap rot may show symptoms of decline, including increased deadwood and a thinning canopy with reduced density of foliage.
avocado tree decay
Wood Decay Fungi in Landscape Trees
Landscape trees provide welcome shade, fruit, homes for wildlife, and even a place for kids to...
This beetleās gut may hide clues to making better biofuels
Reposted from UC Berkeley Public Affairs
![A close up of a black shiny beetle against a green background.](https://news.berkeley.edu/wp-content/uploads/2019/03/Passalus_sp_BN.jpg)
The passalid beetle's unique gut architecture helps it transform decaying wood into energy-rich materials. (Graham Wise photo, via Wikimedia commons)
Decaying wood doesn't make the most nutritious food, but the long-horned passalid beetle has evolved to make the best of it. The guts of this forest-dwelling insect are adapted to take tough plant materials, like lignin and cellulose, and transform them into hydrogen, ethanol, methane and other energy-rich biofuels.
In a new study, researchers at UC Berkeley and Berkeley Lab describe how the architecture of the beetle's gut — and the beneficial microbes that inhabit it — help the beetle carry out such a transformation. This knowledge could help scientists engineer more efficient systems for producing bioproducts in the lab.
“We brought together a team of experts and used advanced molecular biology tools, together with spectrometry and tiny sensors, to discover that the beetle's gut is made of up specialized compartments — each with a distinct microbiome — that work together almost like a factory production line, using unique biochemistry to turn the wood into food and fuel,” said Eoin Brodie, assistant adjunct professor of environmental science, policy and management at UC Berkeley and senior author of the paper, which appears Monday, March 11, in the journal Nature Microbiology.
“The key innovation that nature has provided here is a way to combine biochemical processes that are otherwise incompatible,” Brodie said. For example, some of the compartments are optimized to carry out reactions that require lots of oxygen, while others carry out reactions inhibited by oxygen.
“It turns out that the beetle's gut architecture, such as the length and thickness of its gut walls, has evolved to suit its microbiome so that specific metabolic processes are favored in different gut regions,” said Javier Ceja-Navarro, a Berkeley Lab research scientist and lead author of the paper.
The shape of the gut also prevents certain compounds, like hydrogen, from escaping. These compounds help propel the production of products like acetate, which is a critical energy source, not only for the beetle itself, but also for its offspring.
“This beetle and its microbes have worked out what scientists around the world are hurrying to optimize – how to efficiently turn woody plant biomass into biofuels and bioproducts,” Ceja-Navarro said.
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
Joining forces to promote child health and wellness
According to current statistics, approximately 40 percent of school-age children in the U.S. are overweight or obese. This statistic is reflected in rising rates of diabetes, pre-diabetes, and heart disease risk factors. Nearly one-quarter of all children are pre-diabetic or diabetic at the time when they leave high school, a figure that has increased dramatically in the last decade. Dental problems, the other very common health problem of youth, carry the potential for current and future pain, infection, and tooth loss. Although low-income children and children of color are at particular risk for both conditions, risk is unacceptably high for all children.
It is important to note that these all-too-common conditions share the same critical risk factor: consumption of sugary foods and beverages. Unknown to many, over half of the added sugar consumed by children is ingested in liquid form—soda, fruit drinks, sports drinks, energy drinks, and other pre-sweetened beverages including iced teas and others. For teenagers sugar-sweetened beverages are the single largest source of calories in their daily diet. Further, research has demonstrated that liquid sugar is more highly related to obesity than added sugar coming in solid form.
To improve the medical and dental health of our children we need to help children and families find ways to reduce their consumption of sugar-sweetened beverages.
Fortunately research is being conducted to find effective ways to reduce children's sweetened beverage consumption.
- Reduce provision of sweetened beverages in the school, after school and childcare settings. UC ANR's Nutrition Policy Institute (NPI) has documented dramatic reductions in sugary beverage consumption after the enactment of state restrictions on the sale of highly sugared beverages in California schools and childcare. While much has been accomplished, more can be done to see that these kinds of restrictions are fully maintained.
- Offering children easy access to water stations and other free tap water sources in childcare settings, schools and recreational facilities provides a healthful alternative to sugary beverages.
- Encourage strong nutrition education programs for children. UC Cooperative Extension's EFNEP and statewide SNAP-Ed programs have been leading efforts to educate children on the value of a healthy diet including the risk of consuming too many sugary beverages.
- Similarly, educating families on healthy eating and on the benefits of reducing sugar-sweetened beverage consumption can support and reinforce the messages to children in the school-based programs.
A consistent message on sugary beverages delivered to families by dental and medical health practitioners, in tandem with other educational and community efforts, can substantially benefit children's health. As respected community members, dental and medical health practitioners are in a position to deliver consistent messages to families and also to work with community agencies and groups, including UC ANR and its affiliates, to initiate and support efforts to reduce children's and families' sugary beverage consumption. Our children deserve a healthy start.
For more information, see:
- Nutrition Policy Institute (http://npi.ucanr.edu)
- National Drinking Water Alliance (http://www.drinkingwateralliance.org/about)
- Dooley D, Moultrie N, Sites E, Crawford P. Primary care interventions to reduce childhood obesity and sugar-sweetened beverage consumption: Food for thought for oral health professionals. Journal of Public Health Dentistry, 16 June 2017. DOI:10.1111/jphd.12229.