We’ve known for a while that there are three great divisions in the tree of life: the Eukaryotes (organisms with “true” cells having a membrane-enclosed nucleus, organelles, and a cell membrane); Eubacteria (“true” bacteria); and Archaea (prokaryotes like Eubacteria, but with genes and biochemistry more closely related to those of Eukaryotes than to Eubacteria). Archaea were discovered as “extremophiles”: organisms living in bizarre and difficult habitats like high-temperature springs or vents, and habitats with high concentrations of toxic substances like salt or sulfur; but now we know of many Archaea living in “normal” habitats.

There’s a bit of doubt about the relationship between these three great groups, but most data point to the Archaea being more closely related to Eukaryotes (which include us) than to Eubacteria. That is, we’re more closely related to this:

Than the species above is to this:

That seems weird, but what happened is that one-celled creatures like primitive bacteria diverged into two groups early in the history of life, and then one of those groups subsequently evolved into the modern Archaea and modern Eukaryotes. In other words, the one-celled ancestor of all complex organisms was also the ancestor of modern Archaea. (The one-celled ancestor was probably similar to living Archaea). That’s not hard to grasp.

A new paper in Nature Microbiology by Laura Hug et al. (reference and free link below) went further, though. Beyond confirming the relationships of the three great branches of life, they showed that the Eubacteria themselves are divided into two great groups that diverged long ago, one of which they call the Candidate Phyla Radiation, or CPR. (Articles on the Hug et al. paper were also written by Carl Zimmer in the April 11 New York Times and by Ed Yong in The Atlantic.)

Further, many of the Archaea and Eubacteria in the Hug et al. paper were not discovered by taking a known organism and determining its DNA sequence. Instead, they were identified by simply isolating DNA fragments from different environments, like salt pans, and sequencing those fragments over and over again until the researchers were satisified that each genome represents a different species. Such organisms can be identified, and in principle reconstructed in the laboratory, but since most of these can’t be cultured in a laboratory environment, we can’t actually see the species. That opens up a whole new way to find species, despite the fact that we can’t see them and may know little about their nature.

The findings also raise the possibility that there are millions of “species” of Eubacteria and Archaea—the species concept becomes a bit fuzzy in these largely asexual groups—that we’ll find in the future. Already, though, it’s clear that Archaea and Eubacteria are the dominant groups on Earth. That’s no surprise since they’ve had the longest time to radiate, and their niches can be everywhere.

The results can be stated briefly. Hug et al. constructed their tree by using the known DNA sequences of 2072 species, and then sequenced the genomes of 1011 new species recovered by sampling DNA from the environment. Total: 3083 species in their trees. The choice of environments for the new species is funny:

This study includes 1,011 organisms from lineages for which genomes were not previously available. The organisms were present in samples collected from a shallow aquifer system, a deep subsurface research site in Japan, a salt crust in the Atacama Desert, grassland meadow soil in northern California, a CO₂-rich geyser system, and two dolphin mouths.

Dolphin mouths! But imagine the number of new species they’d get if they’d sampled even more weird environments, like the deep-sea bottom, or even the mouths of llamas. It goes to show how little we know about the diversity of one-celled life.

To construct the phylogenetic tree, the authors used the genomic DNA that codes for ancient proteins present in all three groups: ribosomal proteins. These are the proteins that make up the ribosomes—the little granules in the cell on which proteins are synthesized using as a template the messenger RNA transcribed from the cell’s own DNA.

And here are the trees (you can see the details in the paper, which is available for free):

In the tree above you see the three great divisions, with the huge radiation of bacteria at the top (including the purple group at upper right, the recently discovered Candidate Phyla Radiation), the Archaea at lower left, more closely related to “true” celled species than to bacteria, and the Eukaryotes, a relatively smallish group in green at lower right. Eukaryotes comprise most of the species we find interesting, but see how small that group  is relative to bacteria-like species. That’s because the ancestors of modern bacteria first appeared about 3.8 billion years ago, but eukaryotes only 1.5 billion years ago. The former have had much more time to radiate.

The groups with red dots are those that lack “isolated” representatives: species that are singleton, distant relatives within the group. I’m not quite sure why they were interested in that, though I am sure a reader will inform me.

Anyway, I give below Hug et al.’s tree based on evolutionary distance (sequence divergence), which gives you a clearer idea of the relationships of the groups. You can see that the Eukaryotes are in fact a small group within the Archaea, so that, at least for these proteins, some Archaea are more closely related to living eukaryotes than to other Archaea. In other words, Archaea is a “paraphyletic” group—one that does not include all the descendants of a common ancestor (some of those descendants are Eukaryotes).

One last point. Many of the species in the newly-found CPR must be symbiotic (living in association with other species), because they lack the genes necessary for independent life. As Hug et al. note (my emphasis):

Of particular note is the Candidate Phyla Radiation (CPR), highlighted in purple in Fig. 1 [the first figure above]. Based on information available from hundreds of genomes from genome-resolved metagenomics and single-cell genomics methods to date, all members have relatively small genomes and most have somewhat (if not highly) restricted metabolic capacities. Many are inferred (and some have been shown) to be symbionts. Thus far, all cells lack complete citric acid cycles and respiratory chains and most have limited or no ability to synthesize nucleotides and amino acids. It remains unclear whether these reduced metabolisms are a consequence of superphylum-wide loss of capacities or if these are inherited characteristics that hint at an early metabolic platform for life. If inherited, then adoption of symbiotic lifestyles may have been a later innovation by these organisms once more complex organisms appeared.

The authors call these species “symbiotic,” implying that they get their essential amino acids and nucleotides from other species, but those symbionts can be either mutualistic (both species benefit), commensalistic (the CPR species benefits, there’s no cost to the other one) or parasitic (the CPR species benefits at the expense of its partner[s]). This rely-on-others simplicity, like the CPR radiation itself, was pretty much a surprise. That, along with the vast diversity of species found only by sequencing DNA from the environment, are the two big results of this study.

Sadly, although in principle it’s possible to reconstruct these cryptic bacteria from their genomes—we can synthesize CPR genomes and then inject them into living bacteria whose own DNA has been removed—we’ll never really see them because we can’t culture most of these in the lab. For the time being, and until we develop better culture techniques, we’ll be living in a world full of species whose existence we can discern, but whose characteristics we’ll never see.

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Hug, L. A. et al. 2016. A new view of the tree of life. Nature Microbiol.  doi:10.1038/nmicrobiol.2016.48