The Carbonifungerous Period

This story is already on most of the science news sites I read so I thought about leaving it to them, but how could I deny you the pleasure of reading my words. If; however, you prefer reading a professional science organization cover it, here is the article from the National Science Foundation, who helped fund the study.

Study on Fungi Evolution Answers Questions About Ancient Coal Formation and May Help Advance Future Biofuels Production

We burn a lot of coal. Historically around half of all the electricity here in the good ol' US of A has been produced with coal power. That coal was deposited/produced during the carboniferous period. Get it CARBONiferous, so like, lots of coal.
 
Anyhow, a new study publish in the June 29 edition of Science is suggesting that maybe a big contributor to the end of coal deposits is the evolution of rot fungi. But Science isn't free so you only get a link to the entry summary.

Endless Rots Most Beautiful

The study is part of an ongoing endeavor to help categorize and decipher the early evolution of fungi. It is believed that one and a half million species of fungi exist on earth, but only about 5 percent of those have been categorized. To help identify the diversity of fungi and uncover a fuller picture of their roles in the overall ecosystem of our planet, studies like this are becoming more prominent.

The team of 71 scientists designed their specific study 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," lead scientist David Hibbett.

White rot fungus decay on wood

To do this, the team compared the genome of 31 fungi, focusing on the Agaricomycetes. In the process twelve new genomes were sequenced for the first time, specifically for this study. In addition they traced the mutation rates on the genes responsible for lignin decomposing enzymes in order to trace the evolution of the ability.

The team's study determined that the earliest multiple lignin-degrading enzyme producing Agaricomycetes lived roughly 300 million years ago. This is right around the end of the Carboniferous period, which suggests a possible connection between the ability of fungi do break down wood, and the decrease in deposits of non-decomposed woody debris into the ground. With trees getting decomposed instead being buried, the large deposits that eventually became coal ceased. And thus an entire geological time period was brought to a halt by the evolution of  a group of fungi.

Aside from the pure scientific discovery entailed, the scientists involved with this study hopes that by  sequencing these genomes, we may uncover new tools of industrial biology. "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," again, lead scientist David Hibbett.

So if you think about it, this group of fungi may be responsible for causing fossil fuels to be in limited supply and simultaneously be a key to creating renewable biofuels.


Photo Credit: Robert Blanchette

Fungal Word Friday

Basidium

Spore-bearing Basidium

A small club-shaped structure that bears four spores (typically) at the end, it a distinguishing characteristic of basidiomycete fungi.

Mycorrhizal Metal Mosh Pit

Wow, two mycorrhizal posts in a row. You would think that maybe the symbiotic relationship that is necessary for most plants to live might be important.

Populus alba branch

It should come as no surprise that in many places around the world, soils are becoming polluted. With 6 out of the 10 most highly polluted locations containing large amounts of heavy metal contamination, finding ways to deal with that particular problem are of great interest. Unfortunately, since we can't degrade heavy metals, we need to find ways to remove them from the soil.

This is where plants come in. An increasing amount of  focus has been put into a reclamation process called phytoremediation. Simply put, this is the uptake and accumulation of heavy metals into plants, which can then be removed, making for less contaminated soils. This process is more cost effective and more popular with people than machine centric traditional methods.

Typically plants used for this are small shrubs and as such are only capable of extracting an equally small amount of heavy metals, which means it takes a lot of time and replacement plants to get the job done. Recently studies have been done with larger shrubs and trees in hopes of creating a larger sink for the metals. One of the most popular trees for this is  the poplar tree.... Popular Poplar. Because of this tree's relatively quick growth and tolerance to heavy metals it is a key species for study. But, how can we make it better? How about a little arbuscular micorrhizal fungi? Namely, Glomus intraradices.

A team of Italian Scientist has just published a study, which is turn part of a larger study looking to improve phytoremediation, looking at the effects that this fungus had on leaf protein expression in the presence of heavy metals.

Effects of Heavy Metals and Arbuscular Mycorrhiza on Leaf Proteome of a Selected Poplar Clone: A Time Course Analysis

Using a clone that was previously selected because it demonstrated a natural tolerance for copper and zinc, the scientists set out to determine how much of a difference was demonstrated by presence of the fungi. The team grew their clones in a glasshouse with polluted and non-polluted soils and with or without G. intaradices inoculation. At several different intervals (4, 6, and 16 months) they took leaf samples and tested for leaf protein expression.

Their results showed that while in the short term fungal colonization caused a decrease in protein expression that outdid even that of growing the plant on polluted soils, after the initial growing season things evened out, and by the end of the 16 month period the Mycorrhizal fungi helped the poplar grow to the same extent as the tree in healthy soil. The one caveat is, even with the Fungus, leaf bio mass did not reach non-polluted soil levels.

A key lesson (besides the influence of mycorrhizal fungi on leaf protein expression) that this study demonstrates is the importance of long term and repeated sampling. If the study had only included the 4 month point sample it would appear as though the fungus had just as much of a negative effect as the poor soil, while subsequent samples illustrated quite a different and more complex tale. This observation is noted by the scientist in the study, I just wanted to add my voice.

When we do any kind of science it is always vital that we don't account a single point of data as evidence for or against a hypothesis, but that we vigorously seek to exhaust the possible variables that could change our outcomes.



Study: Guido Lingua, Elisa Bona, Valeria Todeschini, Chiara Cattaneo, Francesco Marsano, Graziella Berta, and Maria Cavaletto
Photo: Wikimedia user MPF

Mycorrhiza Symbiosis: It's not just for Ascomycetes anymore.

A mycorrhiza is the symbiotic bond between fungi and the roots of vascular plants. This important mutualistic relationship is found in over 90% of plant families. Without it they would be unable to absorb vital nutrients from the soil and their fungal partners would be left without  constant access to those tasty carbs that make life worth living.

Sheathed ericoid mycorriza on Vaccinum myrtillus

So basically: the plant absorbs light, photosynthesizes it, passes some sugars on to the fungus coating its root system; and in turn the fungus absorbs nutrients and minerals from the soil that the plant is unable to uptake on its own and exchanges them. Barter system!!

Anyway, as mentioned, while the vast majority of plants depend on this relationship only a very small portion of fungi are known to join in this inter-kingdom partnership, most notably those in the ascomycetes order Helotiales. But the world is going all wibbly because some basidiomycetes have taken a liking to blueberries.

A new study conducted by scientists from the Czech Republic and Norway have isolated a basidiomycete that forms a mycorrhizal sheath with the European blueberry(Vaccinium myrtillus) root system.

Novel Root-Fungus Symbiosis in Ericaceae: Sheathed Ericoid Mycorrhiza Formed by a Hitherto Undescribed Basidiomycete with Affinities to Trechisporales

In previous studies there have been tentative relationships between basidiomycetes and plants but until now the levels in studies have not been significant enough to differentiate between  true mycorrhizal cooperation, and saprotrophic or necrotrophic contamination.

Our intrepid heroes however managed to isolate this potentially new species (They are currently referring to it as "Sheathed ericoid mycorrhiza" from natural samples and synthesize it in vitro. In the lab they got it to form sheath clamps onto the root system, verifying that the fungus was indeed able to form symbiosis with the V. myrtillus. This demonstrates the first true evidence that a non-sedacinoid basidiomycete is capable of forming a mycorrhizal relationship with plants.

Unfortunately the team was unable to verify it into a new species as of yet. They were however able to isolate it into either the Trechisporales or Hymenochaetales orders. Both found in soils samples but until now unproven to be mycorrhizal fungi.

This type of study shows that even well studied areas, such as the mycorrhizal relationships between plants and fungi are continually turning up new and novel ways that adaptations can occur.



Photo and Study credit: Martin Vohník, Jesse J. Sadowsky, Petr Kohout, Zuzana Lhotáková, Rolf Nestby, and Miroslav Kolařík.

Death of Mice and Men

In a small village in the Yunnan province of China in the 1970's over 300 healthy people died.  Then in 2005 scientists attributted another series of Sudden Unexplained Deaths (SUD) to potentially deadly mushrooms in their diet. Over the next few years five more outbreaks of these mass deaths were linked to the specific mushroom Trogia venenata, the weird thing is that at the time this mushroom was not known to be toxic.

Trogia venenata

Now the same group of researchers that observed the correlation of these deaths to T. venenata has tested their effects on mice in controlled laboratory settings.Want to guess what happened?

Death of Rats

That is correct, they all died.

Hypoglycemia and Death in Mice Following Experimental Exposure to an Extract of Trogia venenata Mushrooms

Within 30 minutes of exposure all of the mice exposed to extract of T venenata started showing signs of toxicity. Within 3 hours of feeding 70% of the test mice were dead, the rest followed in the next few hours. Those mice in the control group, (fed extract from L. vinaceoavellanea instead of  T. venenata)  lived throughout the seven day observational period.
The team then went on to measure the toxicity levels and found that mice started dying at around 370mg, this is the equivalent of a human eating 150g (5.2 oz).
So remember, eating the wrong mushroom is not just deadly to rodents...




Death of Rats Artwork: Kit Cox http://www.fantasyartists.org/KitCox

Jewels of the Fifth Kingdom

I feel like a treat, so here is Jewels of the Fifth Kingdom (part one). A series of photos set to music, all done by David Fischer.

Discover Magazine : How the fungus that can punch through Kevlar becomes a cereal killer

A very cool article over on Discovermagazine.com about how Magnaporthe oryzae does its thing to rice.
*Hint: it takes advantage of last weeks Fungal Word Friday.

Anyway, check it out:
How the fungus that can punch through Kevlar becomes a cereal killer

Fungal Word Friday

Ascus

The sexual spore containing bag or capsule in ascomycete fungi.

 

Ascus of Saccharomyces cerevisiae containing four spores.

If you want good wine you better know your yeast.

We all know that yeast are important to the fermentation process of alcohol, but what else do they contribute to the drink?

A single species, Dekkera bruxellensis, is responsible for the identifying aroma of near half of the red wines, and is of course an important part of the flavor as well.

 Dekkera bruxellensis

There can be a downside to this yeast though, D. bruxellensis also produces a phenol which can make your wine taste like medicine and lead it it becoming undrinkable.

But this detrimentous event can be avoided to some extent by learning the ins and outs of D. bruxellensis. Researchers at the Lund University in Sweden have worked alongside the Centre of Genomic Regulation in Spain have now sequenced the yeast's genome.

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.
 Mind you this is the abstract, the full texts costs. but here is the ScienceDaily article related to it.
Knowing Yeast Genome Produces Better Wine

According to Professor Jure Piskur of the Department of Biology at Lund University, “We now know a lot about how Dekkera bruxellensis acts in the aroma formation process during wine production. Wine producers can use this knowledge to their advantage.”
And, "At the end of the day this could lead to more new and interesting wine tastes and greater financial savings for the wine industry."

So, next time you open a bottle, be it corked or capped, remember that it is the work of these researchers that helps insure you taste wine and not cough syrup.

Reference work: Piskur J, Zhihao L, Marcet-Houben M, Ishchuk OP, Aerts A, LaButti K, Copeland A, Lindquist E, Barry K, Compagno C, Bisson L, Grigoriev IV, Gabaldón T, and Phister T. “The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties” International Journal of Food Microbiology (2012)

Pleated Ink Cap Mushroom

This past week I found this little mushroom in on of the potted plants on my balcony.

That evening all that remained was a husk.
After a keying it out I have determined it to be a pleated ink cap mushroom (Coprinus plicatilis).

Rogers Mushrooms: Coprinus plicatilis

A Fermentor's Phylogeny

We all appreciate those select few yeasts capable of creating that wonder of wonders, ethanol. And a select few it is, only around 25 of the 1500 yeasts out there are capable of this amazing feat. Among those are the clade Scheffersomyces. Funny enough not a lot of time has been put into detailing exactly how these little moonshine stills are related to each other.
Sure they have been studied to see who is who of making booze, but as much effort has been put into just the who is who part of that statement.
But that is changing.
A study done at the Department of Biological Science of Louisiana University aims to put these little yeasties into thier place on the family tree.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039128

In this study Hector Urbina and Meredith took samples of yeast from several decaying wood and lignicolous insect guts and put them through a wide series of identification tests. Biochemical Analyses, yup. Morphological characterization, check. And most impressive sounding Multilocus Phylogenetic Analyses, done and done.
And as will happen when a team studies yeasts taken from wild samples(In this case from decomposing trees and insect guts.) New and species have been found. This is not a surprise with few species we have identified in the vast fungal knigdom, but as always it is good to learn more.
Based on the types of wood each strain the proposed species names are: Scheffersomyces virginianus, found the Quercus virginiana, Scheffersomcyces quercinus isolated from Quercus niger, and Scheffersomyces illinoinensis gathered from the substrate species Carya illinoinensis.

 S. quercinus, budding cells (a-b); S. virginianus, budding cells (c-d); and S. illinoinensis, budding cells (e-f)

All three of these new species produce xylose reductase and have been placed in the taxa, which indicates an enhances enzyme efficiency in fermenting D-xylose into good ol' ethanol.
While we have not yet managed to bio engineer any yeasts into taking adavantage of this abundant source of renewable carbon. If we can continue to discover new strains that are eager to make a little fungal white lightning we are sure to keep trying.


Photo and study credit:
 Hector Urbina, Meredith Blackwell
Department of Biological Sciences, Louisiana State University

Yeast on Yeast Violence Around the World

A study in the June 12, 2012 issue of the International Journal of Systematic and Evolutionary Microbiology have isolated three strains that represent a new yeast species.

 S. fodiens

Saccharomycopsis fodiens (as the research team proposes the species be named) specimens were recovered as part of independent collections from flower associated beetles in Australia, Costa Rica, and the Galapagos Islands.
The wide spread, yet isolated distribution of S. fodiens lead the researchers to propose that its dispersal may be linked to human factors.
Another interesting character of the species is that it when grown in the presence of other fungus and yeasts it feeds on them... Cannibals! Well not really, since they are consuming other yeast species, but still yeast on yeast violence. It does this by forming short protuberances(seen in picture) that penetrate the vitim cell causing death.
Saccharomycopsis fodiens sp. nov., a rare predacious yeast from three distant lacalities.


Just further evidence that no matter what you are or where you live, there is a species of fungus that can and will eat you.

Study and photo credit :  Marc-André Lachance, Carlos A. Rosa, Enrique Javier Carvajal, Larissa F.D. Freitas, Jane M. Bowels

Fungal Word Friday

Appressorium

An appressorium is a flat hyphal organ that uses turgor pressure to breach host cells.

 Hyaloperonospora parasitica generateing an appressorium.

Photo credit: Emmanuel Boutet, 2002

Mushroom Moving Madness

When most people here the word mushroom they don't even think about fungus they think about food. And to be fair mushrooms often make a mighty tasty food so I don't blame them.
Mushrooms are a major player in the food industry around the world, so obviously a lot of them get shipped out from mushroom farms everyday. How many, you may ask? Tons and tons.
Here is a nice video brought to you by the company Havatec, whose mushroom machine handles up to 20 tons of mushrooms per hour!



This one machine automatically does the harvesting, sizing, cutting them all to the same stem length and then filling and weighing crates that it stacks and prepares for shipment.

That's pretty impressive if you ask me.

The Many Uses of Myrothecium verrucaria

Myrothecium verrucaria is a common Deuteromycete found all around the world and is quite the potent cellulose decomposer and potential plant pathogen.

Because of that ability it has been tested by the United States Department of Agriculture to control invasive weeds such as kudzu. It is very fast acting, seeing degradation of health in the kudzu vine within twelve hours of application.
M. verrucaria also capable of killing specific plant parasitic forms of nematode, without harming the roots they infest or the free living nematodes in the area.
So this little Deutero-dude can be used as an herbicide, simultaneously it can be used to protect plants from parasitic worms. Talk about flexible! 
Oh, but it appears there is more that this little fella can do. A recent study published in PLoS ) One describes a novel "white" laccase (A form of the laccase with a max spectral absorption of 600nm) produced by M. verrucaria that is capable of decolorizing a wide range of dyes.
 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038817
 In this study, the team of Dan Zhao, Xi Zhang, Daizong Cui, and Min Zhao isolated a unique form of laccase that when purified was capable of rapidly (In four out of the twelve dyes tested it only took 10 minutes!) removing the dye pigment.
Laccases are actually already used to decolor dyes in several textile processes, and the wide range of dyes that the particular form produced by M. verrucaria leads to yet another potential area that this fungus is capable of useful application. 
So we now a single species capable of being a , pesticide, herbicide, and dye remover(dyeicide?).  Oh and laccases such as the ones produced by M. verrucaria are also used as preservatives in drinks such as beer and juice. I am starting think the uses may in fact be unlimited.
Oh, and less you think this Fungus is all friendly, remember the cellulose decomposing capabilities I mentioned? It doesnt, mind using those skills to break down cotton...

So there you have it, one species, capable of giving us so much and at the same time taking the very shirt off our backs.

Chytidiomycosis and the Frogs that Lived

By now anybody who is remotely involved in biology has heard about the massive loss of amphibians around the world. And that one of the causes is fungal infection. The notorious amphibian Chytrid fungus (Batrachochytrium dendrobatidis, Bd) is a major culprit, leading to sporadic death in some species populations and up to 100% death in others.

 Batrachochytrium dendrobatidis

Chytridiomycosis, the infection name, hits the amphibian in stages. Upon first contact to amphibious skin, zoospores give rapid production to sporangia which then produces more zoospores. Those zoospores reinfect the host, causing a cascade of infection. This leads to a reddening and eventual sloughing of skin over the body, convulsions, lethargic changes in behavior and eventual death.

Luckily there have been some cases of treatment options for Chytrdiomycosis. Reid Harris of James Madison University found in 2009 that coating certain species with the bacterium Janthinobacterium lividum seems to offer protection from infection. Applying the chemical chloramhenicol to infected specimens of Archey’s frog (Leiopelma archeyi) cured them of the disease. And even use of Rooibos tea in water has been found to ward off chytridiomycosis in certain posion dart frogs.

In the June 07 online issue of PloS One journal, a study by Laura A. Brannelly, Matthew W. H. Chatfield, and Corinne L. Richards-Zawacki at the Tulane Univesity demonstrates that there are some species of Amphibians that are even resistant naturally to infection.

Field and Laboratory Studies of the Susceptibility of the Green Treefrog (Hyla cinerea) to Batrachochytrium dendrobatidis Infection

Their study was based on the observation that while amphibians around the world were succumbing to Bd there has not been a noticeable impact on the populations of southeastern United States.

With this in mind they chose a common amphibian from the region, the green treefrog (Hyla cinerea) and ran tests to determine the susceptibility of the species. They gathered frogs from a local wildlife area and found an absence of Bd. The team then went about inoculating them in the lab with strains of the fungus both from the region and more virulent strain from the Philippines.

While they were able to establish infection, the team found that some specimens cured themselves over the study, and those that maintained infection showed no clinical change in body condition over the 26 week experiment.

Their clinical evidence, along with the absence of Bd found on collected specimens of green tree frogs from other collections has lead the team to conclude that H. cinerea is not susceptible to the fungus that has been wreaking havoc on the amphibians of the world.

So, even facing a fungal based Amphibian Apocalypse in the rest of the world, you will always be able to retreat to the deep south to enjoy the chirping of frogs on a balmy summer night.

Phot Cred. Johnson ML, Speare R via. Wikimedia

Fungal Word Friday

Stipe

 A stipe is the stalk, or stem of a mushroom or toadstool. Seen here is the mushroom of Pluteus readiarum. The thin white stem is the stipe.

















Photo by Michael (inski) (Pluteus readiarum Stevenson (38218)) [CC-BY-SA-3.0 (www.creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

Introduction

This blog is going to be dedicated to Fungi. Be it interesting articles or studies I come across, or pictures I take.  I have a BS in Biology with an emphasis in Natural History but have a special interest in the Fifth Kingdom. I want to start out light, so I give you Paul Stamet's wonderful TED talk: 6 ways mushrooms can save the world.