Genetics Provide Valuable Insight into Mysterious Decay Fungi

Valuable insights to developing effective biological control agents for protecting conifer trees from root rot have been discovered.

Pine log extensively colonized by Phlebiopsis gigantea showing fruiting structures from which spores are released. Photo: Robert Blanchette and Benjamin Held, University of Minnesota.

Pine log extensively colonized by Phlebiopsis gigantea showing fruiting structures from which spores are released. Photo: Robert Blanchette and Benjamin Held, University of Minnesota.

An international team of 41 scientists from eight countries, including USDA Forest Service Forest Products Laboratory (FPL) researcher Daniel Cullen, unraveled the longstanding mystery as to how the Phlebiopsis gigantea fungus rapidly colonizes wood to the exclusion of other invading microbes.

Daniel Cullen, FPL research microbiologist

Daniel Cullen, FPL research microbiologist

The devastating conifer pathogens in the Heterobasidion genus cause substantial economic damage to conifer roots in the Northern Hemisphere, by infecting stumps and wounded trees.  Another common and benign fungus, Phlebiopsis gigantea, is able to rapidly colonize conifer wood and prevent Heterobasidion species and other pathogens from taking hold.

Recently reported in the prestigious open access journal PLOS Genetics, “These findings pave the way for our deeper understanding of the complex and multifaceted biochemical pathways by which wood-degrading fungi metabolize wood and its constituents,” according to Professor Robert Blanchette of the University of Minnesota.

The unusual ability of Phlebiopsis gigantea to rapidly colonize freshly cut conifers has been known for decades. How the fungus tolerates and degrades the resins that conifer trees use as part of their defense against all invading microbes was poorly understood until now. By identifying the key Phlebiopsis gigantea genes and enzymes involved in resin metabolism, more effective biocontrol strains can be developed. This knowledge will also be valuable in advancing the industrial bioconversion of woody biomass into useful products, including bioenergy-related products.

Scanning electron micrograph of a radial section of pine wood with Phlebiopsis gigantea filaments visible during attack. Photo: Robert Blanchette and Benjamin Held, University of Minnesota.

Scanning electron micrograph of a radial section of pine wood with Phlebiopsis gigantea filaments visible during attack. Photo: Robert Blanchette and Benjamin Held, University of Minnesota.

FPL assistant director Ted Wegner observed that “This important body of research provides a fundamental science base for developing commercially viable and environmentally preferable ways of protecting conifers from root rot as well as opening the door for new commercially viable and environmentally preferable forest biomass conversion technologies.”

Within its genome of 30 million base pairs, Phlebiopsis gigantea was predicted to harbor 12,000 protein-encoding genes. The team of researchers identified specific genes involved in the degradation of pitch and novel enzymes produced by Phlebiopsis gigantea that could be of value in the industrial bioconversion of woody biomass. For example, utilization of freshly harvested conifer wood for bioconversion or for paper manufacture can be complicated by the resinous materials. The enzymes and enzymatic processes employed by Phlebiopsis gigantea may lead to the development of new approaches for the reduction or elimination of troublesome resins that interfere with pulping and papermaking processes and products. According to Cullen, “While commercial applications may be years away, the research findings offer considerable promise in reducing the costs of pitch deposits in paper manufacture.”

Regarding the economic importance of controlling Heterobasidion root disease, Professor Sarah Covert of the University of Georgia stated that “Heterobasidion root disease is one of the most costly conifer diseases in the entire Northern Hemisphere.”

The complete report can be found at

Pulp NonFiction: Fungal Analysis Reveals Clues for Targeted Biomass Deconstruction

Without fungi and microbes to break down dead trees and leaf litter in nature, the forest floor might look like a scene from TV’s “Hoarders.” Dan Cullen, research microbiologist at the FPL, is part of an international team of scientists studying the genomic make-up of two fungi species that are especially talented when it comes to clean-up.

Phanaerochaete chrysosporium and its close relative Ceriporiopisis subvermispora can selectively break down the cell wall components cellulose and lignin—the number one and two most abundant biopolymers on Earth. Both fungi species are found all over the world and are of interest to bioenergy researchers because they possess enzymes that can break down plant biomass and could therefore be useful for accelerating biofuels production.

In a study published online in the Proceedings of the National Academy of Sciences, the team presented a comparative genomic analysis of the two white-rot fungi, whose genomes were generated and annotated at the Department of Energy’s (DOE) Joint Genome Institute (JGI). The study revealed substantial differences among the sets of genes involved in lignocellulose degradation, providing further insight into the mechanics of how white rots do their dirty work.

“The fact that we have such a large group of people involved in this project is a clear demonstration that there’s certainly interest in enzyme discovery,” said Cullen, study senior author and long-time DOE JGI collaborator.

Cullen and his colleagues compared the fungal genomes to learn more about the basis of C. subvermispora’s ability to selectively break down lignin. Understanding this process is of longstanding interest to the pulp and paper industry. According to the American Forest & Paper Association, approximately $175 billion worth of forest products such as pulp and paper are produced annually, and account for five percent of the Nation’s GDP.

Kent Kirk, a former FPL researcher who is considered a leading figure in the study of lignin degradation by fungi, provided perspective on how the current research could impact the pulp and paper industry. “This grew out of fundamental research by the University of Minnesota and FPL where they applied the concept of ‘biopulping,’ the partial decay of wood by lignin-degrading fungi to decrease the energy required for mechanical pulping. Cerioporiopsis subvermispora quickly became the ‘biopulper’ of choice.”

Kirk described how wood chips treated with the fungus for two weeks required 30% less energy for pulping than untreated chips and how outdoor trials were repeatedly successful at the 50-ton scale. “The technology has not yet been commercially adopted, but as energy costs continue to rise, it should be increasingly attractive for implementation,” Kirk said.

Analyzing the diversity of wood-decaying fungi and cataloging enzymes involved in lignocellulose degradation is one of the goals of the DOE JGI Fungal Genomics Program led by Igor Grigoriev. “We are in the process of conducting functional comparative genomics of more than 20 such fungi sequenced or currently being sequenced at the DOE JGI,” he said. “This should provide us a better understanding of the diverse and complex mechanisms of lignocellulose degradation in fungi, the influence of these mechanisms on carbon cycling in the forest ecosystem, and ultimately lead to improvements in biopulping.”

Cullen sums up the collaborative work of the DOE JGI team and their interest in these fungi, “In this particular case, one would come away thinking more about the role of white-rot fungi in the carbon cycle. Lignin is a recalcitrant compound in forest ecosystem biomass and very few fungi have the capability to degrade lignin. Even fewer fungi have the ability to selectively remove lignin at such an efficient rate. C. subvermispora is one exception in its ability to do just that.”

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By Rebecca M. Wallace, FPL Public Affairs Specialist