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Yggdrasil and the tree of life’s new branches

In Norse mythology, Yggdrasil was the great world tree, central to the cosmos and connected to the Nine Worlds, which included Midgard (the home of humans) and Asgard (the home of the Gods).

The idea of a tree, connecting all forms of life on Earth, is also central to our understanding of biology, encoding both the way we classify living things and how we think they evolved.

Our view of that tree has changed radically in the last few decades, driven by the use of sequence data to measure relationships between organisms, rather than the descriptive methods of traditional taxonomy. One of the most radical changes was the re-organisation of the tree into three main branches. The prokaryotes (single-celled organisms without nuclei) were found to be divided into two major groups: the Bacteria and the Archaea. The third branch of the tree was the Eukarya (eukaryotes) – organisms that have cells with nuclei; including all plants, animals and fungi, and, at the end of one insignificant branch, us. It also became clear that the Eukarya were in fact a peculiar fusion of Archaea and Bacteria; their cells contain components that are descended from bacteria that were engulfed billions of years ago. Also, strikingly, most of the diversity of life was found in the single-celled microorganisms; the Bacteria and Archaea.

As more and more biological sequence data were accumulated on organisms, the structure of the tree continued to be refined. However, it’s now clear that our view of life was still limited by an important fact; we were only able to sequence the microorganisms that we could culture in the laboratory, and in fact these were the only microorganisms we could identify.

This all changed with the development of a new approach known as metagenomics. Rather than purifying the DNA of a single organism and sequencing it, in metagenomics you purify and sequence all the DNA from a sample in a random fashion. This was a new way of identifying all the organisms present in an environment – whether it was a hot spring or the human gut – and not just the ones that could be cultured. This has resulted in the addition of many new twigs to the tree of life. Recent work, however, has resulted in a more radical revision of the tree of life; not just twigs but major new branches have been discovered.

The tree shown below (from [1]) is a recent attempt to reconstruct a tree of life, including many organisms that have not been grown or isolated in the lab (shown by red dots). One of the most striking features of this tree are that a huge proportion of the diversity of life is represented by groups containing these novel organisms. The large purple area to the right is a group of the Bacteria known as the Candidate Phyla Radiation, which appears to represent organisms with a symbiotic lifestyle – about which nothing was known until the advent of metagenomics.

Another large group of new organisms are a superphylum of Archaea that seem to be closely related to the Eukaryotes: the intriguingly named Asgard Archaea [2]. The first members of this new group were identified by metagenomics of marine sediments near a hydrothermal vent known as Loki’s Castle, which was found between Greenland and Norway, and so were christened the Lokiarchaeota [3]. Subsequent discoveries of related phyla followed the scheme of names from Norse mythology: the Thorarchaeota, Odinarchaeota and Heimdallarchaeota; hence the collective name of Asgard Archaea [2]. Investigation of the genomes of these organisms has revealed a number of proteins previously only known from the eukaryotes, confirming the suspicion that they are closely related to their ancestors.

Metagenomics has revealed organisms whose existence was not only unknown but unsuspected. What other discoveries await us, in hot springs, the sea bed, or indeed, in the human body [4]?

A tree of life (from [1]). Red dots represent groups known only from metagenomic sequencing. The Eukarya are the green branches at the bottom right.

References

  1. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat. Microbiol. 2016;1:16048.
  2. Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 2017;541:353–8.
  3. Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015;521:173–9.
  4. Kowarsky MA, Camunas-Soler J, Kertesz M, Vlaminck I De, Koh LCW, Pan W, et al. Humans are colonized by many uncharacterized and highly divergent microbes. bioRxiv 2017;113746.