Saturday, May 14, 2011

"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.


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

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