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The moldy kingdom gets a new neighbor

A diagrammatic tree depicting the organisation of most eukaryotes into six major groups. The relationships amongst most of the major groups and the position of the ‘root’ of the tree are shown as unresolved (note however, the grouping of Opisthokonta and Amoebozoa). The arrow shows a possible precise placement of the root, based on gene fusion data. (Simpson and Roger 2004)

Depending on your view of phylogenetics, a recent publication in Nature reporting the discovery of a new kingdom-level branch on the tree of life, basal to Kingdom Fungi, is either a major revision of our current view of taxonomy or completely unsurprising and expected. While we mostly refer to the four kingdoms within Domain Eukarya as Protista, Plantae, Fungi, and Animalia, it’s understood by the scientific community that Protista is essentially a catch-all category, not a true clade, for eukaryotes that don’t quite fit into the other three groups. While this is convenient for organization, it fails to adequately express the diversity of protists. Four kingdoms is a useful system, but there’s no reason why diversity at the kingdom level couldn’t be much higher. A strict cladist could  create hundreds, if not thousands of kingdoms from Protista alone.

It’s not only splitters that get in on the action either. Some taxonomists have argued that Fungi and Animalia are part of a single kingdom, Opisthokonta, based on several shared characteristics found nowhere else in Eukarya. Even in a recent paper that attempted to resolve some eukaryote phylogeny into a succinct 6 kingdom system, there are still a few lonely branches, that don’t quite fit anywhere else.

This is all leading up to the fact that high level taxonomy is messy. It is a system we’ve developed to understand evolutionary relationships among organisms, but it is an imperfect view of reality. So we shouldn’t be surprised when new groups appear whose classification may be ambiguous.

Cryptomycota – the new group described by Jones et al. (2011) – is exceptional. Now, to be fair, it’s not going to turn our conventional view of taxonomy on its head. Cryptomycota is an addition to the tree of life, not a deletion or revision. What is truly exciting is that an entire new group of organisms, potentially as diverse and broadly distributed as Kingdom Fungi, has only recently been discovered. Most of the time, when major changes to the tree of life are made, it is because of new data, new analysis tools, or the discovery of a few new species that fill in some missing bits. When the now-defunct Monera became Archaebacteria and Eubacteria, it wasn’t because we had never seen an Archaen until the study, we just didn’t quite understand what Archeans were.

Cryptomycota are entirely new.

To start, Jones and her team extracted environmental DNA from a host of diverse ecosystems using targeted primers to identify basal members of the fungal tree of life. What they discovered was that an entirely new group, only identified from molecular analyses existed at the phylogenetic tree’s base. This group was discovered in many different ecosystems, including deep-ocean sediments, freshwater lakes, rhizospheres, aquifers, and even chlorinated drinking water.

There are thousands of microbes that are known only from molecular studies and have never been seen. They comprise an invisible biosphere and may have major ecosystem functions, but without any ecologic data, it is almost impossible to assess the importance of these microbes. Using their molecular data, Jones et al. design florescent probes that bind to DNA and cause the target organism to fluoresce under specific lighting conditions. With these probes, they were able to visually identify Cryptomycota in environmental samples and begin to infer characteristics of their biology.

Putative cryptomycota skeleton life cycle (Jones et al. 2011)

Three life-stages have been so far identified in Cryptomycota. They have a cyst stage, common to many fungal groups, a free-swimming zoospore stage, and an attachment stage, where they are found attached to a host organism, often diatoms. There may, and probably are, many other possible life stages, and with a group this diverse, there may be several different development strategies.

Curiously, so far all observed Cryptomycota lack a chitinous cell wall, a trait diagnostic of Kingdom Fungi. The next big debate over this group is whether or not they actually are fungi. Because Cryptomycota lack this characteristic, and because the group is as diverse as Kingdom Fungi, it is likely that this group has the potential to be classified as its own kingdom.

Simpson A, & Roger A (2004). The real ‘kingdoms’ of eukaryotes Current Biology, 14 (17), 693-696

Jones, M., Forn, I., Gadelha, C., Egan, M., Bass, D., Massana, R., & Richards, T. (2011). Discovery of novel intermediate forms redefines the fungal tree of life Nature DOI: 10.1038/nature09984

Marine science and conservation. Deep-sea ecology. Population genetics. Underwater robots. Open-source instrumentation. The deep sea is Earth's last great wilderness.

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