The Department of Energy's mushroom research

Seal of the United States Department of Energy.
Seal of the United States Department of Energy. (Photo credit: Wikipedia)

OK, from the title I’ll bet you are thinking:

a. Mushroom clouds

b. Keep me in the dark and feed me ….

c. WTF

If you answered “c”, you might be close after reading the press release headline.

From the DOE/Joint Genome Institute

Adaptable button mushroom serves up genes critical to managing the planet’s carbon stores

The button mushroom occupies a prominent place in our diet and in the grocery store where it boasts a tasty multibillion-dollar niche, while in nature, Agaricus bisporus is known to decay leaf matter on the forest floor. Now, owing to an international collaboration of two dozen institutions led by the French National Institute for Agricultural Research (INRA) and the U.S. Department of Energy Joint Genome Institute (DOE JGI), the full repertoire of A. bisporus genes has been determined. In particular, new work shows how its genes are actually deployed not only in leaf decay but also wood decay and in the development of fruiting bodies (the above ground part of the mushroom harvested for food). The work also suggests how such processes have major implications for forest carbon management. The analysis of the inner workings of the world’s most cultivated mushroom was published online the week of October 8 in the journal, the Proceedings of the National Academy of Sciences (PNAS).

“Our hypothesis was that metabolic strategies and niche adaptations of Agaricus might not be present in the white-rot and brown-rot wood-decomposing fungi,” said senior author Francis Martin, Head of the ‘ARBRE’ Lab of Excellence at INRA, Nancy, France.

“Compared to genomes of these fungi, that we previously characterized, the Agaricus genome surprisingly has shown many similarities in gene composition,” added Igor Grigoriev, the study’s senior co-author and leader of the DOE JGI Fungal Program, “At the same time, our data also supported the view that Agaricus fits neither brown-rot nor white-rot classifications and that its adaptation to growing in a leaf-litter humic-rich environment is not typical of classic wood-degrading fungi.”

The ancient Romans used the word “humus” to designate soil and compost, the complex natural interaction of organic compounds from plant cell wall residues. Humus contributes the chemicals that drive the decomposition process through substances like humic acid that serve as a complement to fertilizer, adding organic matter to deficient soils and contributing to overall plant health to foster root vitality and stimulate the growth of beneficial microbial communities in the soil.

Agaricus is the ideal mushroom to study for adaptation and growth in humic-rich environments, noted Grigoriev and his co-authors. They surveyed the genomes and the transcriptomes—the subset of genes expressed under particular conditions— of two A. bisporus lines, a commercial strain and related wild variety. This analysis of Agaricus turned up several families of well-known sugar-degrading enzymes similar to the repertoire found in wood-decaying fungi. However, the enzymes in Agaricus such as heme-thiolate peroxidases and etherases predominate in the presence of humus-rich soil habitats, suggesting a higher ability to metabolize complex mixtures of derivatives of lignin and other polymers.

“The ability to use proteins prevalent in soil confers an advantage to Agaricus over other fungal scavengers,” said Martin. “To our knowledge, Agaricus had not been shown in nature to decompose wood,” said Martin. “Yet, we now see how Agaricus has adapted to growing in this ecological niche. Our understanding of the carbon cycling role of Agaricus in ecosystems is a prerequisite to modeling and optimizing carbon management for sustainable forests.”

Unlike brown-rot and white-rot fungi, A. bisporus is a very poor competitor on fresh non-degraded plant wastes like wood but competes well on partially decomposed litter on forest floors and grassland soils rich in humic substrates. The comparative analysis also revealed a dozen other genes that are dialed up during mushroom formation. “Key master switches may be manipulated to control fruiting body formation—the mechanisms triggering the complex cascade that leads from undifferentiated mycelia, the mass of branching, thread-like fingers, to the button mushrooms most commonly consumed” said Martin.

“Comparative genomics of fungi just got more interesting because the contributions of Emmanuelle Morin at INRA and the 42 co-authors, many of them at the JGI, that led to analysis of the Agaricus genome,” said John Taylor, Professor of Plant and Microbial Biology at the University of California, Berkeley and member of the DOE JGI Fungal Advisory Committee. “The most exciting discovery may be the expansion of these heme-thiolate peroxidases, the versatile catalysts that have an important industrial applications and seemingly allow Agaricus to live in humus, the lignin-rich residue of plants that pervade compost.” Such industrial applications include the breakdown of lignin-derived compounds in novel biorefineries to obtain novel high value chemicals.

Taylor further considered the implications of the findings as applied to climate trends. “If the peroxidases do degrade humus, there could be serious effects on the sequestration of soil carbon as soil warms.”

Martin pointed out that additional value will be accrued by making the gene map of Agaricus publically available: for identifying pathogen resistance traits and for highlighting wild germplasm collections benefiting the multi-billion dollar industry producing the button mushroom. “The genome sequence will expedite mushroom breeding for improved agronomic characteristics,” he said.

The DOE JGI is among leading worldwide contributors of fungal genomes to the public databases, having sequenced over 150 fungal genomes, providing a vital computational infrastructure for such large-scale comparative analyses. The Agaricus genome, originally proposed by Mike Challen, while at the University of Warwick, now at the Wellcome Trust Centre for Human Genetics, University of Oxford, UK., was sequenced under the auspices of the DOE JGI’s Community Sequencing Program (CSP), supported by DOE’s Office of Science. The CSP was launched in 2004 to provide the scientific community at large with access to unparalleled capabilities in massive-throughput sequencing, computational analysis and other genomic resources for projects of relevance to DOE missions in alternative energy production, global carbon cycling, and biogeochemistry. Sequencing projects are chosen based on scientific merit—judged through independent peer review.


The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit


Whatever happened to the idea that the DOE would do research on energy?

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Gene Selkov
October 8, 2012 3:46 pm

DOE has been funding biology research since its “conversion” from defence programs in early 1990s.

Steve Hoffer
October 8, 2012 3:52 pm

….Can’t…. quite….. understand…..
table mushrooms don’t grow on trees, but it might be possible to make them grow on trees, which would be bad. so we won’t do it?
I’m not sure they even understand what they found out enough to articulate it… Or it could be over my head.
I suppose the DoE could justify funding this. It does talk about storing carbon in forests. And it is the DoE’s job to be involved in increasing the cost of energy… apparently.

October 8, 2012 3:53 pm

I don’t remember at the moment which administration it was formed under, but DOE was a response to the 1974 oil shock. It’s original purpose was to get us off foreign oil dependency. So almost half a century later, how well has it done?

October 8, 2012 3:57 pm

DOo they really think that there is a major importance to the carbon effects of forest litter rot. Have they nothing else to do? They did work in references to carbon/climate change so that they will be funded in the next cycle. That’s what’s really important, is it not?

Gary Hladik
October 8, 2012 4:02 pm

“OK, from the title I’ll bet you are thinking: [snip]”
d. “Magic” mushrooms, which would explain A LOT of recent government energy policies.

October 8, 2012 4:03 pm

“If the peroxidases do degrade humus, there could be serious effects on the sequestration of soil carbon as soil warms.”

Oooh, we are warned of the possibility of a chance that there conceivably might be “serious effects”, although there is not a scrap of evidence to support that …
I weep for the mortal illness of evidence-based scientific thought, progressively being replaced by pseudo-scientific alarmism.
Here’s a protip for aspiring young scientists. If you have no evidence of serious effects, then STFU about serious effects. Yes, you will reduce your chances of fleeting scientificardashian fame, but you might actually achieve something …
… “Does this paper make my ego look big?” …

Craig Moore
October 8, 2012 4:07 pm

WhiteTail Foundation?

David Walton
October 8, 2012 4:10 pm

I guess the DOE has shifted the focus of their money (energy) wasting efforts.

John Game
October 8, 2012 4:25 pm

This is actually very good and useful research, even though John Taylor (who is himself and excellent scientist) is a little over the top when he tries to link it to global warming. Even if the warmists are right, I can’t see a three degree increase in temperature significantly damaging the activity of these enzymes. Most enzymes become more active as it warms, until its so hot that they degrade, but that’s not going to happen even if main-stream warmist scenarios do come to pass. – John Game, Berkeley, California.

October 8, 2012 4:29 pm

Cellulose decay and the way to do it is a very hot topic – as it could lead to cellulosic ethanol which would create a windfall of energy. This is a very timely and important piece of research, unless you are shilling for big oil.

October 8, 2012 4:31 pm

Also, shotgun sequencing genomes is pretty darn cheap these days…

Gene Selkov
October 8, 2012 4:36 pm

They are not young scientists, and even if they were, their bosses would know what politically correct stuff to add to all public communications in order to keep the funding flowing (that was not necessary under Clinton’s DOE, but increasingly became the norm when Bush took office, and even more so under Obama). That is utterly disgusting, but we have learnt to filter the crud out. The use of these PC semaphores (or lack of it) cannot be used to judge how good the science is.
Now, the evidence obtained from the genome (provided it was interpreted correctly) is never the same strength as you get from a wet lab experiment. But it can be a hint worth communicating.

October 8, 2012 4:54 pm

Fungi are very useful in a number of ways besides those mentioned in the article and attendant posts. They are also useful in creating highly sought after (and expensive) spalted lumber, which is used in musical instruments, high-end furniture, etc. . The process is relatively simple, but the trick is choosing the right fungi, and stopping the process at the right moment. The leading expert on the subject is Sara Robinson

Gene Selkov
October 8, 2012 4:55 pm
October 8, 2012 5:10 pm

Mushrooms really are an all-purpose biological miracle. Ever heard how they are growing mushroom packing crates that are biodegradable and use no woods pulp? And, are form fitting and even cheaper?
And I have to second their “magic” properties as well.

October 8, 2012 5:15 pm

Actually, this might be a good explanation for why CO2 levels always lag temperature rises and falls in the historical records. Higher temperature leads to more fungus rot leads to more carbon release.

Ian W
October 8, 2012 5:15 pm

Whatever is going to happen to these university research departments and all the little sausage carbon trolls they have turned out as MS and PhD grads – when they find out that carbon dioxide is just a trace gas used by plants for photosynthesis and has no important effect on temperatures. All of a sudden there’s no kool-aid – the cognitive dissonance will be painful to watch. Meanwhile the main-stream-media will do a volte-face and behave as if they’d faced that way all the time.

October 8, 2012 5:19 pm

They lost me at “forest carbon management”. Forests can manage their carbon perfectly well without us, thank you very much. Perhaps the Office of Science should have its budget put under the microscope.

October 8, 2012 5:23 pm

Willis said: I weep for the mortal illness of evidence-based scientific thought, progressively being replaced by pseudo-scientific alarmism.
Feynman called this kind of stuff Cargo Cult science, Willis!

October 8, 2012 5:25 pm

The Department of Energy you say? hmm…

October 8, 2012 5:49 pm

Sparks says October 8, 2012 at 5:25 pm
The Department of Energy you say? hmm…

They weren’t defined (or named) very specifically as to ‘purpose’ or function were they?
Clearly, their mission role could have been more specific had they been named either:
a) The Department of Energy Sinks
b) The Department of Energy Sources (or Sourcing even)

October 8, 2012 6:02 pm

I am reminded of Alexei Sayle’s “Government Eye-Poking Center” comedy skit.
“It is actually cheaper for us to poke a hundred people’s eyes out than it is to mine a single ton of coal. I think the figures speak for themselves.”

October 8, 2012 6:15 pm

I would have to akin this to similar public policies. Just like mushrooms, most of the public is fed excrement and kept in the dark. Just sayin – B

Steve in SC
October 8, 2012 6:40 pm

Wonder if this would qualify for Senator Proxmire’s “Golden Fleece Award”?

Tom J
October 8, 2012 6:50 pm

Perhaps the DOE could team up with NASA and show them how mushrooms could be used in Muslim outreach.

Chuck Nolan
October 8, 2012 6:59 pm

I believe the Energy Department should get back to the task of getting us off of foreign oil.
This is taking forever.

October 8, 2012 7:07 pm

John Game says:
October 8, 2012 at 4:25 pm
“This is actually very good and useful research, even though John Taylor (who is himself and excellent scientist) is a little over the top when he tries to link it to global warming.”
Maybe he’s in need of a career change and aspires to become a world class snake oil salesman.

October 8, 2012 7:08 pm

Tom J says:
October 8, 2012 at 6:50 pm
“Perhaps the DOE could team up with NASA and show them how mushrooms could be used in Muslim outreach.”
You have to find a way to turn them into clouds first.

October 8, 2012 8:48 pm

If (looking more like when) Mitt Romney becomes president, he’s targeted the DOE for the chopping block, and rightfully so.
Reading garbage such as this expensive report paid for by the 53% of Americans that still pay income taxes (jab, jab) reinforces my belief that the DOE is to money as mushrooms are to dead leaves, except mushrooms lead to tasty omelets, whereas DOE leads to HIGHER energy prices…
My brain and my wallet are hurting….
Mitt Romney can’t become president soon enough….

Mike Wryley
October 8, 2012 8:53 pm

Cellulosic Ethanol is another wet dream, not really stupid and moderately immoral like grain based ethanol, but the energy requirements to move large masses of low grade feedstocks to and fro, competition for arable land, probable abuse of land that should be left alone, all for a mediocre fuel, make it another candidate for green boondoggles.

Frank Kotler
October 8, 2012 10:19 pm

Oh goody! RoundUp-Ready mushrooms! I can’t wait!
DOE… wasn’t that the one Rick Perry couldn’t think of?

October 8, 2012 10:20 pm

While starting to read this I thought that there must be an alarmist aspect in here somewhere, and sure enough I found it, which Willis has highlighted.

October 8, 2012 11:03 pm

I must differ with the tone of this post. Whichever agency did this work they are on the right track.
“If the peroxidases do degrade humus, there could be serious effects on the sequestration of soil carbon as soil warms.”
Yes they do, and there is another fungus, Botrytis, that specializes in this. And probably more that we are unaware of. Unlike carbon theology, mycology is not a sexy career path and does not enjoy billion dollar funding.
The largest known organism on earth is a fungus beneath the Pygmy Forest near Mendocino, CA.
And you were wondering why CO2 follows temperature in the atmosphere?
My advice is NEVER underestimate the fungi.

October 9, 2012 12:36 am

Other than the de rigueur spurious link to global warming, this is useful research. Understanding how forests grow is all about how nutrients are tied up in “humus” (the correct technical term would be forest floor” and how they are accessed and released by the plants that grow there. Most of the nutrients tied up in dead organic matter (forest floor) are released by mycorrhizal fungi (fungi that live in symbiosis with the trees and take up nutrients and moisture for them) and decomposition is closely regulated. Saprotrophs like A.b. are also in competition for nutrients stored in the forest floor (including the Litter, Fibric and Humic (LFH) layers)) and how they interact with the mycorrhizal fungi and how they access nutrients could be very useful for understanding how to better manage forests. The work is very useful and making fun of the work, other than the nonsensical reference to global warming, is just ignorant. One of the worst things about the global warming hysteria is that almost all basic ecological research has to be tied to global warming in some way or other to be funded. I doubt that most authors believe their work is important for understanding global warming, but linking it to global warming is very important for getting funding. Another example of the stupidity that ensues when people try to do the right thing for the wrong reason.

Alan the Brit
October 9, 2012 1:48 am

Bovine faeces! I am staggered to see scientists indulging in this stuff, while very fascinating I am sure, do they not see that if the world was a year old for the sake of arguement, man would have arrived at around 11:40pm on New Year’s Eve! The world is a survivor, brutal, ruthless, savage, indifferent, living & surviving! Do they really think man can command it??? Me, I’m not so sure! Anyway off to hug a few bunnies, folks.

October 9, 2012 1:59 am

With mushrooms, it’s all in the timing. If they’re added to the omelet too early or too late the result is unsatisfactory. I find that beginning frying the mushrooms just before pouring the beaten eggs into their pan is the way to go . . . but it’s always a close-run thing.
Now that’s what the Department of Edibles should be studying . . . not how the damn things rot in the wild.

michael hart
October 9, 2012 2:39 am

I agree with BCBill. The authors are probably just trying to push every funding-button they can think of, and possibly a few they can’t.

Gary Pearse
October 9, 2012 5:26 am

I get this terrible image: very large number of monkeys with typewriters coming up with Hamlet. Climate science is a bit like that.

Mike M
October 9, 2012 8:06 am

Fortunately for me, my brain just seized up when I got to “forest carbon management”, (they don’t need no stinking badges to do that either), and I couldn’t read any further. It’s truly amazing, like some sort of mental self-defense against B S. Maybe when a special container for it overflows it automatically turns off the reading function?

October 9, 2012 10:48 am

Sorry BCBill, the minute researchers link anything to “carbon sequestration”, “climate change” and/or “global warming”, mega-points are deducted from credibilty. If they want their research to be taken seriously, they must divorce themselves from the pseudoscience BS.

October 9, 2012 12:09 pm

So they found that mushrooms, that degrade plant parts, have many similar genes to other fungi that degrade plant parts, mostly releated to degrading plant parts. Then they found that mushrooms, that make a fruiting body, have geens that are not like other fungi that make no fruiting body, and they think these genes might be related to makeing a friting body…
And it is iportant because of global warming?
If I had known being a researcher and getting published was that easy, I’d have gone into the field… Though I think I’d have studied the effects of fungi on grapes, and the variation in biochemical features in the fermentation products induced by variations in the cork composition… “Earthy notes” and “tannins” come to mind… Perhaps combined with a study of the effect of mushrooms on flavors of various foods in the presence of said grape fermentation products… And it is important because of how ‘global warming’ will impact upon it… or something…

October 9, 2012 12:37 pm

I just got back from a week-long expedition in the woods. I found an enormous number of red-belted conks which I plan on processing and making into tea/broth.
All of them were on fallen or dead trees and slowly breaking down the wood. I found a few other polypores as well that I was unable to identify. Some of them I suspect were some type of dyer polypore.

Chris R.
October 9, 2012 12:41 pm

DOE. Raised to the Cabinet level by one Jimmy Carter. If this is what they are doing now for research, I think they are definitely a candidate for a serious budget reduction. I believe the commentator John Stossel, quite seriously, put forward a deficit reduction program for the U.S. government stating that the EPA, DOE, and Dept. of Education should be eliminated. Research such as this lends a point to his observation.

Bruce of Newcastle
October 9, 2012 2:33 pm

I think we should store carbon in truffles. Temporarily, until dinner time. I also would like to store carbon in red wine, rum, nice cheeses and chocolate. To test this hypothesis I will conduct human experiments on a range of selfless volunteers dedicated to the betterment of mankind.

Tom Harley
October 9, 2012 8:30 pm

Reblogged this on pindanpost and commented:
some winners in comments … worth a read

October 9, 2012 9:18 pm

_Jim says:
October 8, 2012 at 5:49 pm
If there is a body called The ‘Department of Energy’ and they are studying and releasing research on mushrooms. Who’s studying Energy?
I have to post this, as to infer my current feelings on the issue!

george e smith
October 10, 2012 12:54 pm

Well since the Department of Energy, has so far not produced, or at least made available one lick of energy, it seems appropriate for them to research organisms, that can grow in the dark, and live of the sort of S**t that the DOE puts out.

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