Comparative genome study finds ancestral fungus may have influenced end of coal formation; potential resource for biofuel production
|Scanning electron micrograph of wood being decayed by the white rot fungus Punctularia strigoso-zonata. (Robert Blanchette, University of Minnesota) Click to enlarge.|
Coal deposits—the fossilized remains of plants—were formed during a 60-million year period from around 360 to 300 million years ago. A team of 71 researchers from 12 countries, including researchers at the US Department of Energy Joint Genome Institute (DOE JGI), has proposed a new factor that may have contributed to the end of this Carboniferous period—named after the large stores of what became coal deposits.
The evidence, presented in the journal Science, suggests that the evolution of fungi capable of breaking down the polymer lignin, which helps keep plant cell walls rigid, may have played a key role in ending the development of coal deposits. With the arrival of the new fungi, dead plant matter could be completely broken down into its basic chemical components. Instead of accumulating as peat, which eventually was transformed into coal, the great bulk of plant biomass decayed and was released into the atmosphere as carbon dioxide.
We’re hoping this will get into the biology and geology textbooks. When you read about coal formation it’s usually explained in terms of physical processes, and that the rate of coal deposition just crashed at the end of the Permo-Carboniferous. Why was that? There are various explanations. The evolution of white rot fungi could’ve been a factor – perhaps a major factor. Once you have white rot you can break down lignin, the major precursor of coal. So the evolution of white rot is a very important event in the evolution of carbon cycle.—Clark University biologist David Hibbett, senior author
For their study, Hibbett and his colleagues focused on the Agaricomycetes. Agaricomycetes contains white rot fungi capable of substantial lignin decay as well as non-lignin-degrading brown rot and ectomycorrhizal species. Of the 31 brown rot and white rot fungal genomes that were compared for the study, 26 were sequenced at the DOE JGI, including a dozen that were done specifically for the study to flesh out representation of the fungal orders.
“The concept of the invention of an enzyme that can break down the ‘unbreakable’ is really great. The idea that a stable (inedible) form of organic carbon can become edible (and thus more difficult to bury over time), changes our perspective not only on global energy storage in the past, but on what it means for present day carbon sequestration and storage, in that sense this idea will have a big impact on our thinking about the past and the present.”|
—Kenneth Nealson, Wrigley Chair in Environmental Studies and Professor of Earth Sciences and Biological Sciences at the Univ. of Southern California.
The comparative analyses of 31 fungal genomes (12 of which were generated for this study) suggested that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species.
The researchers then used molecular clock analyses to track the evolution of the enzymes back through the fungal lineages. The idea is that just as the hands of a clock move at a defined rate around the dial, genes accumulate mutations at a roughly constant rate. This rate of change allows researchers to work backwards, estimating when two lineages last shared a common ancestor based on the amount of divergence.
Coal consists of the fossilized remains of plants—mostly lignin, which exists in cell walls as part of a tough matrix with cellulose, which is a carbohydrate composed of sugar subunits. The comparative analyses suggested that around 290 million years ago, right at the end of the Carboniferous period, a white rot fungal ancestor with the ability to break down lignin via enzymatic activity appeared.
Once white rot attacks and destroys lignin, the matrix collapses, and the cellulose is freed to be devoured by the white rot as food. Prior to that ancestor, fungi did not have that ability and thus the lignin in plant matter was not degraded, allowing these lignin-rich residues to build up in soil over time; once white rot became an ecological force, it destroyed huge accumulations of woody debris that would have otherwise escaped decay to ultimately be fossilized as coal.
So if not for the advent of white rot, large coal deposits may have continued to form long after the end of the Carboniferous period. This new study supports a paper published in 1990 by Jennifer M. Robinson that pegged the evolution of white rot as a potential contributing factor to the end of the Carboniferous period.
Because molecular clock analyses have substantial error, fungal fossils are needed for calibration. For this study, the molecular clock analyses were calibrated against three fungal fossils. Hibbett said that more fossils would help improve the age estimate; however, he noted, fungal fossils are rare and easily overlooked. Hibbert said that his group is interested in trying to reconstruct that ancestral white rot fungal genome.
We’re motivated to understand when this metabolic pathway responsible for lignin degradation came into existence. That’s why we needed to have that many fungal genomes in this study. Up until fairly recently, it was so much work to just get one genome at a time. Now we have comparative fungal genomics projects as we’re transitioning to a cool time with hundreds of fungal genomes.—Dave Hibbert
Igor Grigoriev, head of the DOE JGI Fungal Genomics Program, said that this paper is the first product of the Genomic Encyclopedia of Fungi, the DOE JGI umbrella project that focuses fungal genome sequencing efforts on DOE-relevant missions in energy and the environment.
As the head of the 1000 Fungal Genomes project, a part of the DOE JGI’s Community Sequencing Program portfolio, Joseph Spatafora, a professor at Oregon State University and co-author on the study, said that despite the goal of facilitating the sequencing of a thousand fungal genomes, two from each of 500 families, over five years, fungal genomics still has a long way to go.
There’s an estimated 1.5 million species of fungi. We have names for about 100,000 species, and we’re looking at 1,000 fungi in this project. This is still the tip of the iceberg in looking at fungal diversity and we’re trying to learn even more to gain a better idea of fungal metabolism and the potential to harness fungi for a number of applications, including bioenergy. It’s a really exciting time in fungal biology, and part of that is due to the technology today that allows us to address the really longstanding questions.—Joseph Spatafora
Biofuels. The ability of white rot fungi to decay lignin may ultimately be used to help address the challenge of freeing plant carbohydrates for conversion into biofuels via fermentation processes.
In addition, because enzymes from white rot fungi are able to break down complex organic molecules, they have been investigated for use in bioremediation operations that involve breaking down contaminants to remove them from the environment.
Our study was designed to reconstruct the evolution of lignin decay mechanisms in fungi, analyze the distribution of enzymes that enable fungi to break down lignin, and better define the evolution of the gene families that encode those enzymes.
The 12 new genome sequences could serve as potential resources for industrial microbiologists aiming to develop new tools for producing biofuels, bioremediation or other products, perhaps by using recombinant DNA methods or by selecting new organisms for fermentation.—David Hibbett
Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Otillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. de Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse, Chiaki Hori, Kiyohiko Igarashi, Joel A. Jurgens, Nathan Kallen, Phil Kersten, Annegret Kohler, Ursula Kües, T. K. Arun Kumar, Alan Kuo, Kurt LaButti, Luis F. Larrondo, Erika Lindquist, Albee Ling, Vincent Lombard, Susan Lucas, Taina Lundell, Rachael Martin, David J. McLaughlin, Ingo Morgenstern, Emanuelle Morin, Claude Murat, Laszlo G. Nagy, Matt Nolan, Robin A. Ohm, Aleksandrina Patyshakuliyeva, Antonis Rokas, Francisco J. Ruiz-Dueñas, Grzegorz Sabat, Asaf Salamov, Masahiro Samejima, Jeremy Schmutz, Jason C. Slot, Franz St. John, Jan Stenlid, Hui Sun, Sheng Sun, Khajamohiddin Syed, Adrian Tsang, Ad Wiebenga, Darcy Young, Antonio Pisabarro, Daniel C. Eastwood, Francis Martin, Dan Cullen, Igor V. Grigoriev, and David S. Hibbett (2012) The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes. Science 336 (6089), 1715-1719. doi: 10.1126/science.1221748
J. M. Robinson (1990) Lignin, land plants, and fungi: Biological evolution affecting Phanerozoic oxygen balance Geology 18, 607 doi: 10.1130/0091-7613(1990)018<0607:LLPAFB>2.3.CO;2