When a research team started analysing the genetics of microorganisms from their university pond, they might have expected to find a couple of new species. Instead, they discovered a group of fungi that could double the size of that biological kingdom1.
Thomas Richards, an evolutionary geneticist at the University of Exeter, UK, and his colleagues have called the fungi the cryptomycota, or 'hidden fungi', because they have remained undiscovered until now, despite being present in common environments. Mycologists usually study fungi that can be grown in the lab, and Richards says that this has given them a biased understanding of fungal diversity. By looking at environmental samples, his team has rewritten the fungal evolutionary tree. The results are published today in Nature.
Richards and his colleagues isolated DNA from microbes growing in an Exeter pond, and compared the genetic sequences with some from known fungi. They then built a phylogenetic tree — a diagram that uses genetic similarity to show where organisms branched away from one another during evolution — and found that the microbial DNA contained a group of sequences that diverged from those of known fungi.
The researchers repeated the analysis in reverse, comparing the genetic signature of the cryptomycota with sequences from DNA databases of samples from other freshwater environments, soils and marine sediments. They discovered the cryptomycota almost everywhere they looked, and found that they were roughly as genetically diverse as all the known fungi put together.
"This group might be large and diverse enough to be a new phylum," says David Hawksworth, a mycologist at the Complutense University of Madrid. A phylum is just one taxonomic step down from a kingdom. There are currently seven phyla in the kingdom Fungi; by comparison, there are 40 in the kingdom Animalia, which incorporates all animals.
To find out what the microbes looked like, Richards and his team filtered them out of fresh and marine water and mixed in fluorescently labelled small DNA molecules that bound to the cryptomycota DNA sequences. Under fluorescence microscopes, they could see that the cryptomycota cells were ovoid shaped and 3–5 micrometres across.
But what sets the cryptomycota apart from the rest of the fungi is their lack of a cell wall made from chitin, the chemical from which insect exoskeletons are built. Development of a chitin-rich wall was one of the most important developments in fungal evolution, driving their success and diversification by allowing them to control how minerals and nutrients flowed into and out of their cells. The cryptomycota "must be a really ancient group of organisms that diverged from the rest of the fungi by the loss of chitinous walls", says Hawksworth.
The lack of such a wall might be a clue to how the cryptomycota live. Richards and his team also saw some cryptomycota attached to other cells in the water or soil samples, such as algae. "These fungi could be phagotrophic parasites that feed by attaching to or living inside other cells," says Tim James, a fungal geneticist from the University of Michigan in Ann Arbor. According to James, the lack of a chitin cell wall could let the cryptomycota feed by phagotrophy – engulfing food and digesting it internally, as opposed to osmotrophy – taking in nutrients from outside the cell, which is what most known fungi do.
The only previously known fungus that the team found to fall within the new group is the genus Rozella — long thought to be an oddity because of its lack of a chitinous cell wall — which diverged from the rest of the fungi very early on. "We thought that the Rozella branch of fungus was just a twig that had hung on over the course of evolution," says James, "but this paper shows us it's part of a whole evolutionary bush."
This is important, because it is an example of extensive diversity in the evolutionary tree stemming from more than one main branch point. The fungi make up the biological kingdom most closely related to animals, and "better understanding the genomic innovations that led to fungal diversity might help us understand the genomic innovations that led to animal diversity", says Richards.
The diversity of the cryptomycota shows they have been evolutionarily successful. The next step is to find out what special features have allowed them to do so well, says James. "Whatever job they do, they've probably been doing it for almost a billion years, so it's likely to be useful."