World's largest fungus fruiting body discovered

Mycologists in China have discovered what may be the world's largest fungal fruiting body. It is a kind of bracket fungus, of the species Fomitiporia ellipsoidea, and forms a structure of about 10 meters in the longest dimension, and weighs up to half a metric ton. (Photos at BBC News website)

Bracket fungi thrive on dead wood, forming shelves or 'brackets' projecting perpendicular from the wood surface, instead of standing on stalks like classic mushrooms. They also have pores rather than gills, as openings for the dispersal of spores.

The size of this fruiting body is however dwarfed by the immensity of the world's (potentially) largest organism, also a fungus, called Armillaria ostoyae, whose underground mycelium covers an area of 965 hectares! Fruiting bodies like brackets and mushrooms are only the visible part that has emerged from the ramifying network of nutrient-gathering hyphae in order to accomplish sexual reproduction and spore dispersal. In the case of this newly discovered individual of Fomitiporia, scientists attribute its large size to the perennial nature of its growth, and the long time that it has been allowed to grow undisturbed.

Sources

• BBC News article by Matt Walker
• Dai YC, Cui BK (2011) Fomitiporia ellipsoidea has the largest fruiting body among the fungi. Fungal Biology, in press, doi:10.1016/j.funbio.2011.06.008

No more bananas by mid-century?

Four varieties of banana (Wikimedia Commons)

They can see it coming. Most bananas sold today belong to the Cavendish variety, which is grown in extensive monoculture plantations around the world. The plants are virtually sterile, and are propagated by transplanting suckers or cuttings. The cultivar Gros Michel, which was the predecessor to the Cavendish, was wiped out in the early 20th century by a fungus called the Panama disease, Fusarium oxysporum f. sp. Cubense, which as the names suggest showed up in the Caribbean. A new strain of this fungal pathogen has emerged in recent decades to attack the Cavendish variety, which is now under threat. The new strain, called Tropical Race 4, has spread through the Asia-Pacific region, and has yet to hit Latin America, that other bastion of banana agriculture, but it's only a matter of time.

Possible solutions include genetically-modified strains of the Cavendish banana plant, or increasing the genetic variety of bananas in cultivation. Preserving genetic variation in crop foods is now an important concern, given the susceptibility of Green Revolution-style monoculture projects to pathogens. Seed banks around the world store varieties of important crops like the potato and rice as an insurance policy, as traditional cultivars are being abandoned for 'modern' high-yield plants. There is also a thriving trade in so-called 'heirloom seeds' among gardening enthusiasts and smaller-scale farms.

Will such measures be enough to save the banana? Time will tell, but the days of the big, starchy, and seedless Cavendish may be numbered. (Another fun new fact: India "grows and consumes more bananas than any other country in the world." Who knew?)

(via Gawker)

"Primitive" fungi discovered... in a pond!

The microbial world is ubiquitous (there are microbes everywhere!) and vast (there remains so much to be discovered). Basic discoveries are made on a fairly regular basis, and new taxonomic groups of microorganisms are routinely identified when people sequence DNA from the environment.

We don't necessarily have to go to exotic locations like hot springs or the deep sea to discover something new. A new group of "primitive" fungi has recently been described from samples taken from a variety of locations around the world, including a pond in Devon near Exeter University in the UK, where the scientists worked.

This group, called the cryptomycota (not capitalized, because it's not yet officially described according to the rules of taxonomy), has characteristics which make it apparently a 'missing link' between the fungi and other eukaryotic microbes. Sequences of a number of genes place it as a sister group to the rest of the fungi; that is to say, on the family tree of the fungi, it branches off at the very base of the tree.

Although the term "primitive" is often used for groups that fall out at the base of phylogenetic trees, like the cryptomycota, it's important to note that they don't necessarily resemble the ancestors of these groups in every respect. That is to say, just because one branch of your family split off many generations ago from your own lineage, it's not true that this branch more closely resembles your great-great-grandparents. Likewise with other living organisms.

However, in this case, the cryptomycota are called a 'missing link' precisely because they have some characters which were presumed to be present in the ancestors to fungi. They have flagella, which are absent in all 'true' fungi except the chytrids. In fact, chytrid fungi were originally not considered to be true fungi, because they had a flagellated stage in their life cycle. Aside from the cryptomycota, the chytrids are the next-most-basal group of fungi. Furthermore, in every intro biology class we learn that fungi have a chitinous cell wall. These are lacking in the cryptomycota, and presumably also lacking in the precursor to fungi, because it's a feature that's unique to the 'true fungi'.

Fluorescence microscopy image of cryptomycota. Flagella are labeled with an antibody (red), the nuclei with a fluorescent stain (blue), and the ribosomal RNA labeled with an in-situ hybridization probe (green). Via BBC News.

As before, it's important to point out that the term 'missing link' is often misinterpreted. Just as the word 'primitive' has commonsense connotations of being somehow worse off than the 'advanced' species, the same goes for 'missing links'. In the context of systematics, what it refers to is the fact that some species retain traits that are present in ancestral species (either known from fossil evidence or inferred by reconstruction), and their having a mixture of 'derived' and 'primitive' characters provides additional confirmation for how we reconstruct the phylogenetic relationships of these related species.


Also notable is how these fungi were identified. It's fairly routine now to study microbes from the environment without needing to culture them in the lab. Sequences of a well-known gene, such as the ribosomal RNA genes, can be produced from DNA extracted from the environment, and then compared with known sequences in databases, to see 'what's out there'. Novel sequences identified in this way can be related to actual cells under a microscope, by labeling them with probes that specifically target these unique parts of their ribosomal RNA, a method called in-situ hybridization. That's what's shown above in the micrograph, where the probe labeled with a green fluorescent molecule demonstrates that these peculiar flagellated cells were the mysterious fungus-like sequences that the scientists kept finding in environmental samples.

So the lesson here is: There's plenty out there waiting to be found, even in stagnant nondescript ponds! As DNA sequencing gets cheaper and labeling techniques become more convenient, I'm sure that we'll be hearing much more news like this, about cool new microbes that many years ago would have been impossible to identify or classify.


Sources:

Jones et al. "Discovery of novel intermediate forms redefines the fungal tree of life." Nature (published online: 11 May 2011) doi:10.1038/nature09984

BBC News

Zombie ants in news, and musings on science reporting...

Markings on fossil leaves appear to be the 'death grip' of ants infected by the so-called zombie fungus, Ophiocordyceps. The fungus causes the infected ants to move to a position on nearby vegetation and die immobilized there, such that the sprouting fruiting body of the fungus will more efficiently spread its spores over yet more ants. This grip leaves distinctive markings on the leaves, which were recognized by a group led by David Hughes (disclosure: I have met David and heard him talk about his work).

Having this fossil evidence allows us to be able to give a minimum age for the history of this fungal life-style. Despite advances in the study of molecular evolution, fossil evidence is still the most direct way to pin a date on events in the history of life. Earlier hopes that the rate of changes in nucleotide or amino-acid sequences could provide an objective 'molecular clock' (first proposed in the 1960s by Emile Zuckerkandl and Linus Pauling - yes, that Linus Pauling) turned out to be premature, because rates of molecular evolution are not generally uniform across species and even in single lineages over time, and therefore need to be calibrated, typically against the fossil record.

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On the topic of science reporting: The Guardian newspaper article linked above is better than most newspaper science reporting, however, it still illustrates a few sticky points that nag at me when I read about science in the news.

Chief among these is the lack of citations. That is disconcerting, especially to someone in an academic setting where proper attribution is always emphasized. Science reporters are quite uneven in how they cite things: some simply omit any mention of where the research they describe is going to be published (or has been published), some state the journal name and leave it at that, and only in a few cases is a full citation (or in this article: a link to a PubMed record) given. Here, however, note that the PubMed link is to an earlier paper on a related topic, but not about the issue being directly reported. The article says that the scientific report is published in Biology Letters, but a quick search in the journal's website turned up no hits. Hence I can only conclude that it's yet to be published, and the reporter was privy to a prepublication preview.

Unfortunately, this affects blogging, too. I'm happy to highlight interesting papers and newspaper reports on biology, but without having seen the original paper, if new research is being presented, it is hard to assess the quality and reliability of the work, and whether it really is worth being blogged about. Worse yet, the reporter may have distorted the actual conclusions, or misrepresented the facts, ... the list goes on.

So the next time you see a newspaper article reporting new research, do keep an eye out - drop a comment here if you see something noteworthy that shows how caution is necessary.

Fungus attacking Afghan opium

Opium, like any other crop, is prone to pests and diseases, and a fungal disease is making a big dent in this year's production. One wonders how well studied the fungal diseases affecting drug crops like opium and cannabis are. Farmers, of course, blame NATO and its anti-drug operations, saying that it looks like a white powder sprayed from the air, while officials deny any responsibility for the outbreak.

Fungus-Derived Genes Make Aphids Red

Carotenoids are pigments produced by many organisms, among them bacteria, plants, algae, and fungi. They're what gives carrots, red leaves, and some flowers their reddish/orange color. However, no animal has been known to produce them or to have the metabolic pathways required for carotenoid biosynthesis, until now.

In Science, Nancy Moran and Tyler Jarvik report the discovery of carotenoid biosynthesis genes in the genome of the pea aphid, Acyrthosiphon pisum, which has a body color polymorphism (some individuals are red, others are green). It was formerly thought that they got their pigmentation from their diet, or from their bacterial gut symbionts. Suspicions were raised, however, when no trace of a carotenoid pathway could be found in the primary bacterial symbiont of aphids, Buchnera, which is among the best-studied of bacterial symbioses, and in two other symbiont bacteria. Because the genome of the pea aphid was recently released, they searched for, and found, carotenoid synthesis genes, which are most closely related to similar genes in the fungi. This led them to conclude that aphids have gained the carotenoid biosynthesis pathway by lateral gene transfer from fungi.

Lateral gene transfer (also horizontal gene transfer) was long thought to be a rare or exceptional phenomenon, but this adds one more example to a growing list of transfer events which have been uncovered by new genomic methods.

References:
Moran & Jarvik, Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids, Science 328, 624-627 (30 Apr 2010). (DOI: 10.1126/science.1187113)
Takema Fukatsu, Perspectives: A Fungal Past to Insect Color, Science 328, 574-575 (30 Apr 2010).

Giant fungus

The Devonian fossil Prototaxites, long a puzzle thought to be a vascular tree species, may actually be a fungus.... C. Kevin Boyce of the University of Chicago and co-workers used isotopic ratios to show that it was more likely to be a heterotroph than an autotroph, and based on its anatomy it was most likely to have been a fungus.

Journal reference: Geology, May 2007; v. 35; no. 5; p. 399–402; doi: 10.1130/G23384A.1

Fungal Endophytes

Is a leaf all that it seems to be -- just a leaf? It turns out that fungal endophytes - fungi that live inside plants without harming them - are common and to be found in almost all leaves of tropical forest plants. It seems that the more we learn about organisms and their interactions, the more the idea of the 'free living organism' turns out to be a big lie! Not only are all organisms dependent upon others in obvious ways such as for food and nutrient cycling, but virtually all macroscopic creatures seem to have microscopic organisms living in them too (and frequently even the microscopic ones are hosts to yet smaller ones.)

We commonly understand fungi to adopt a saprobiontic lifestyle, acting as decomposers in the soil, in wood, in leaf litter, or perhaps as pathogens and parasites such as rusts and smuts. But the diversity of these lifestyles may be matched by the diversity of fungal endophytes, which live in the leaf tissues of plants without showing any symptoms or substantially impairing host productivity. They offer benefits to their hosts' fitness, such as preventing pathogenic infection, and possibly making leaves less palatable to herbivores. At the same time the leaves offer a substrate for the fungi to grow upon and provide food substances for their growth and reproduction. Most of these endophytes are transmitted horizontally rather than vertically, though the most well-studied case, that of grass endophytic fungi, are vertically transmitted.

Check out the webpage of Betsy Arnold from the University of Arizona. Her lab does a lot of work on fungal endophyte diversity and interactions with their host plants. Their diversity is still barely understood, especially in the tropics, and culture methods are relatively simple. This could be a pretty cool project for those of you living in places where the leaves aren't all falling off the trees!

Cure for amphibian chytridiomycosis?

"Frog killer fungus 'breakthrough,'" by Kim Griggs. BBC News, 30 Oct 2007.

New Zealand scientists have claimed that the common antibiotic chloramphenicol can be used to cure amphibians infected with chytridiomycosis, the fungal disease which is causing widespread worldwide decline of amphibian populations and is pushing many endangered frog species to the edge of extinction.

Update: Poster from the team which did the research