Biological Dark Matter and the Shadow Biosphere

ORIGINAL: The Beast, The Bard and The Bot

May 26, 2012

Dark matter. It’s mysterious. And the term has a nice ring to it. No surprise then, that the phrase is often co-opted in fields other than physics. Biology is no exception. The expression ‘biological dark matter’ is used mainly in two contexts:

• Large parts of the genome are so-called ‘junk DNA’, apparently not coding for proteins. And yet extensive RNA transcription (where an RNA strand complementary to the DNA sequence is produced) occurs in these regions. Why? What does it do? Mysterious, no? Hence, biological dark matter.
• But, what I’ll briefly look at here, is biological dark matter in the second context. With the advances in DNA sequencing technology, it has become possible to extract DNA directly from environmental samples, like a test tube of seawater, or a bit of soil (or, see video below, a nasal swab). This results in what is known as metagenomic data, which is basically comprised out of portions of sequences of all the organisms in the sample. And lo and behold, in this metagenomic data strange things appear. Pieces of DNA sequence that don’t seem to fit with known organism groups. Mysterious, no? So, once again, biological dark matter.

And now, I’ll let Dr. Nathan Wolfe do some of the talking.

Does this biological dark matter represent a strange new domain of life? That option is being explored, among others. For example, a recent study from 2011 investigates such metagenomic data and the mystery sequences in it. A few suggestions are offered in the article, such as

• artifacts from the experimental procedures,
• recombinants of some kind, 
• paralogs (shared DNA due to a duplication event) from ancient duplications, an unknown group of viruses, or, 
• a fourth domain of life.

Imagen: RRResearch

This last suggestion, a new form of life, ties in nicely with the recently developed idea of a shadow biosphere, or micro-organisms with a radically different molecular and biochemical make-up, which allowed them to escape detection thus far. Some ideas about these unknown life-forms include remnants of early RNA-based life and organisms that use alternative combinations of bases in DNA, or amino acids in proteins.

Crazy stuff, quoi? Intriguing as well. And not a priori impossible.

But, there are some things to keep in mind.

The division of life on earth isn’t always that easy. While the three domain idea is very influential, one can question whether using different criteria may yield a different division of life. If so, which criteria should be used?

And even if you accept the three domain system, there are still a lot of question about the three known domains. Perhaps this weird biological dark matter is just an unknown part of one of the existing domains?

Neither of these (very brief) considerations, of course, denies that the metagenomic data does indeed hints at some mystery. Whatever it is, it just begs for investigation. The authors of the shadow biosphere article conclude:

…a search for shadow microbes on Earth should be considered because finding an alternative form of life would be one of the greatest scientific discoveries of all time.

I’d like to add: Even if these tentative hints represent something else entirely, the hunt is sure to be interesting and likely to make worthwhile additions to our knowledge of life.

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Cleland, C., & Copley, S. (2006). The possibility of alternative microbial life on EarthInternational Journal of Astrobiology, 4 (3-4) DOI: 10.1017/S147355040500279X

Wu, D., Wu, M., Halpern, A., Rusch, D., Yooseph, S., Frazier, M., Venter, J., & Eisen, J. (2011). Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018011