WHITE ROT FUNGI: White rot fungi, like the "turkey tails" mushroom pictured here, can break down lignin--the molecule that helps make wood rigid and resist decay.
Image: Courtesy of A. Justo and D. Floudas
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A toughened crosshatch of carbon-based molecules is all that stands between plants and their total destruction at the hands of an array of microbes and fungi. Called lignin, the compound enables redwoods to tower and woody herbs to resist rot. As a result, lignin is the second-most abundant biological compound on the planet—and the bane of would-be biofuel-makers everywhere, blocking their best efforts to make fuels from the inedible parts of plants. It is also the reason for the vast deposits of coal laid down millions of years ago.
Now a new genomic analysis suggests why Earth significantly slowed its coal-making processes roughly 300 million years ago—mushrooms evolved the ability to break down lignin. "These white rot fungi are major decomposers of wood and the only organism that achieves substantial degradation of lignin," explains mycologist David Hibbett of Clark University in Massachusetts, who led the research published in Science on June 29.
By comparing 12 newly sequenced genomes of mushroom fungi with 19 existing genomes, the researchers determined that an ancestral white rot fungi (Agaricomycetes) first evolved the ability to break down lignin. The scientists then used so-called "molecular clock analysis"—a dating technique based on the hypothesis that genes accumulate mutations at a relatively regular rate like trees form rings that record their growth. Such an analysis suggests that an ancestral white rot fungi developed this lignin-degrading ability roughly 290 million years ago, a conclusion backed by comparison with the appearance in the fossil record of three other types of fungi (although the first definitive white rot fossil does not appear until roughly 260 million years ago) and the subsequent expansion and refinement of the arsenal of enzymes employed. The 60-million-year-long Carboniferous period—when the bulk of the world's coal deposits were laid down and atmospheric CO2 levels declined—ended roughly 300 million years ago.
The coincidental timing suggests the appearance of this ability to break down lignin helped slow the massive burial of organic carbon via nondegraded tree trunks and other wood, such as the lignin-rich fernlike plants known as arborescent lycophytes, now extinct. Previous explanations largely argued that such coal formation was a result of the Carboniferous's swampy conditions—after lignin-rich plants fell into these swamps, they simply were buried rather than broken down by fungi or microbes and turned to peat and then coal over geologic time frame. "They're not mutually exclusive," Hibbett notes, although more of the easily overlooked fungal fossils would need to be found to determine the truth.
How exactly white rot breaks down lignin remains unknown. The fungi releases reactive molecules and enzymes that seemingly tear the plant-protecting compound apart via "brute force," in the words of Hibbett. Once the protective lignin is out of the way, the white rot fungi feast on the cellulose, which comprises more digestible plant sugars. And subsequent evolution has given so-called brown rot fungi the means to work around lignin without attacking it directly. "They have evolved a way to get at cellulose and leave the lignin behind," Hibbett says, which results in the crumbly, brown logs littering temperate forests today—potentially coal in the distant future.
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15 Comments
Add CommentAh we must be careful when writing articles about science, and injecting bias into the article. This discusses an "evolutionary war" between woody plants and fungi. There is nothing to suggest there is any war or conflict, in fact, degrading wood may be beneficial in ways we have not bothered to investigate. Someone is simply perpetuating Charles Darwin's fears of unknown sickness, which has no pertinence to the way the world really works. This is the big problem with science is the blind man feeling the elephant metaphor. From this angle it feels like a lot of things. I do admit this article is interesting, and particularly I like the fact Hilbert mentions fungi dont get enough attention. However, lets wait until we have a clear "big picture view" before writing and injecting our bias into articles.
Reply | Report Abuse | Link to thisPoint taken, though I was more referencing the fact that woody plants prefer not to be decomposed by fungi. At least while still living.
Reply | Report Abuse | Link to thisAnother instance where mushrooms can help save the world.
Reply | Report Abuse | Link to thisjen007: If we waited until we had a "clear big picture view" of every scientific issue we could never write about anything new or interesting in science. And there have been numerous, well-documented evolutionary relationships that could fairly be described as "evolutionary wars", a category into which—given my limited understanding—this historic interaction between lignin-producing plants and lignin-digesting fungi seems to fit.
Reply | Report Abuse | Link to thisNot to rain on anyone's parade, but I read this theory years ago. It isn't a new theory. Maybe the researchers were unaware that this was an old theory. Or maybe the real point of this research was that they had found new evidence to support an old theory.
Reply | Report Abuse | Link to thisYou know how sometimes you read a theory and just know it has to be right? I remember years ago when I first read this theory I thought it was a cool idea that nicely explained why carboniferous forests didn't rot away like modern forsts. It was just too good an idea not to be right.
Hi hungry doggy,
Reply | Report Abuse | Link to thisI was one of the authors of the study, and we were certainly aware of the prior work suggesting that evolution of white rot fungi may have contributed to the decline in organic carbon burial at the end of the Permo-Carboniferous. The key paper, which we cited, is: J. M. Robinson, Lignin, land plants, and fungi: Biological evolution affecting Phanerozoic oxygen balance. Geology 18, 607 (1990). Robinson based her hypothesis (in part) on a handful of fungal fossils and evidence of function from contemporary ecosystems (Robinson also suggested that shifts in plant investment in lignin may have been a factor in the change in C burial, an idea that we did not address). She did not have detailed fungal phylogenies or molecular clock estimates (it was 22 years ago!). With our study, we were able to offer genome-based evidence that is consistent with the Robinson hypothesis, which I regard as a major insight.
Cheers,
David Hibbett
OK, this may be a dumb question, but if you want a biofuel from wood sources, why not just grind up the dried wood to a powder (i.e. make sawdust), and then mix that with other bio-oils to make a mixture that flows and burns?
Reply | Report Abuse | Link to thisNo need for fungi. Biomass pyrolysis transforms lignin into biofuels directly. See www.eprida.com. In fact pyrolysing Miscanthus is so efficient that it threatens to see refinery firms transform all agricultural land and forests into miscanthus monocultures. So exit food production and biodiversity. What is needed now is strong government and heavy international taxation on miscanthus to restrict pyrolysis to reasonable biomass sources.
Reply | Report Abuse | Link to thisThrilled to see my hypothesis put to test, and surviving!
Reply | Report Abuse | Link to thisEco_steve, the technology you're talking about wasn't available in the Carboniferous . . . though the accumulation of carbon in the lithosphere was (hypothesis) leading to ever-higher levels of oxygen in the atmosphere. This may have meant that wildfires were a much stronger ecological force. J. Lovelock, of Gaia fame, claimed that the hypothesized oxygen rise didn't happen, cause if it did, the terrestrial biosphere would have been cremated. There were some debates about this, and abundance of charcoal in fossil record suggests that fire was very active in the Paleozoic. But from a plant perspective, it's much better to have your remains rot than to have them burn. I loved working out this hypothesis. It's fun to think about evolution and biogeochemistry at the macro level -- kingdoms evolving and changing atmospheric composition.
p.s. the hypothesis being tested had its origins in a flight over the Amazon Basin after being immersed in discussion of Paleozoic biogeochemistry and Bob Berner's model results suggesting that atmospheric O2 levels approached, if not exceeded 30% in the Permian. Looking down over the great forest basin, I asked: "Why isn't this a coal swamp?" The question lead to years of rummaging around and tromping across disciplines, ending with the hypothesis that biodegradation processes have gotten better through the eons.
Reply | Report Abuse | Link to thisI think you are overstating the case for biomass pyrolysis Ecosteve. The process has been around in one form or another for thousands of years and on an industrial basis for centuries. Sure you can use fresh growth to produce fuel but that takes fuel. It is much easier to get the fuel in a concentrated form from fossil fuels. As we have seen from the corn ethanol boondoggle, people vastly overstate the benefits and efficiency so as to get the funding.
Reply | Report Abuse | Link to thisIf we could have great vats of scrap wood and weeds that were naturally producing fuel without the need for added heat, then we may be getting somewhere.
Them thar fungis may just learn us how!
Sorry but I just can't remain serious when talking about fungi. There are just too many bad jokes about "fun guys" and "fungus amungus".
Hi Dr. Robinson,
Reply | Report Abuse | Link to thisWonderful to see your comments here. I'd be interested to chat with you about this subject some time, off-line. You can find my e-mail address via the Clark University website. I hope to hear form you.
Best,
David Hibbett
Why don't we just shred the non-edible plant parts and use white and brown rot fungi in the process to convert to biofuels? Is there a bias against using biologic processes in engineering design or do they just not think about it? Considering many microorganisms as well as fungi act as chemical catalysts, I do not see why the use of organisms in processing is not more widespread?
Reply | Report Abuse | Link to thisif special attention is given to white rot fungi, u will realise that its ability to degrade lignin in wood can be borrowed buy pulp bleaching companies. this will help remove the brown lignin from the pulp and hence production of white paper withour use of things like sulphites which are not good for the environment
Reply | Report Abuse | Link to thisLignin degradation by white rot fungi is a peculiar process. Lignin is an irregular polymer with lots of cross-links. Fungi and bacteria can't bring it through their cell walls to pull it apart with enzymes. Instead, they secrete enzymes that in oxidize lignin extracellularly, breaking the big molecule into smaller fragments. This lets them access cellulose and other compounds in woody material that are more easily metabolized. Do a web search on "pulp and paper white rot fungi" and you'll find that a huge amount of research is going toward use of bioprocesses in lignin degradation. Commercial processors would love to have this work succeed, as the chlorine-based bleaching of wood pulp is produces organochlorines . . . nasty compounds, which nobody wants in their back yard. As I understand it, the totally chlorine-free alterantives are expensive. Do a web search on pulp and paper white rot fungi and you'll find there's a large, well funded community of researchers working on the problem. This research has been going on for decades. I'll bet there's an interesting science story behind its failure, thus far, to provide an a viable industrial process.
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