Tantalising deep sea diversity...

I don't think I'd ever be able to work on a large-scale environmental genomics project -- the mere idea of having nothing but a GenBANK accession number with a fragment of ribosomal DNA for an organism really REALLY bugs me. Don't get me wrong: it's valuable data suggesting how much unseen diversity there may actually be, but this is exactly what bugs me about it -- It's simply tantalising. It's there, we can see it, but you may never encounter these mysterious organisms again. All we have for them is a tiny fragment of a sequence, and based on that, a prediction of what the organism may be related to. It's captivating and irritating at the same time.

In the latest PNAS issue, we've got one such case for a group of organisms that is particularly intriguing: deep sea protists. While drooling over those awesome diagrams of freakish deep sea fishes and reading about the metabolic madness of resident prokaryotes, one can't help but wonder just how freakish the protists must be as well, considering they're crazy enough at 1atm. Trees like this must leave one speechless; note all the numbers indicating organisms of which we just know a tiny fragment of DNA, and nothing else:

Note entire clades containing nothing but undescribed organisms. Red long-dashed lines indicate 'orphaned' organisms devoid of close relatives in GenBANK (at an arbitrary threshold). Near Perkinsus we've got a whole sea of basal alveolates. Arrow indicates position of Euglenozoa (removed due to excessively long branches). (Scheckenbach et al. 2009 PNAS)

(Some of the branchings seem kinda fishy though... ciliates branching with choanos and parts of Hacrobia? Rest of Alveolates+Haptos branching with Excavates prior to Heterokonts? Meh. This is apparently an SSU rDNA tree, and Alveolates are almost always monophyletic in SSU trees. However, considering the swaths of utterly unknown phyla there, perhaps it's not too surprising that the tree may be messed up. But then again, that's not really the point of this particular tree...)

They note a large diversity in predominantly parasitic clades, although whether these mystery organisms themselves are parasites remains a question. The stuff near Perkinsus is really interesting -- perhaps some may come in handy for understanding dinoflagellate and "proto-alveolate" (pardon my paraphyly) evolution. Now to take a look at the Euglenozoan clade:

Euglenozoan part of the tree. (Scheckenbach et al. 2009 PNAS)

Remember Diplonemids? An enigmatic apparently 'species-poor' group sister to Kinetoplastids? Judging from the tree above, we must be seriously missing something! I am perplexed by the lack of Euglenids, although perhaps they just didn't bother with Euglenid-specific primers, or maybe deep sea Euglenids are actually that rare. They do seem to be more of a freshwater group, though there are marine representatives as well. Interesting...

Hopefully at least some of these mysterious organisms will resurface again someday, and be properly described, classified and perhaps even brought into culture! One cannot help but imagine how beneath some of these GenBANK accession numbers may lurk landmark findings shedding light on some mysteries of evolutionary and developmental biology. After all, there is more to an organism than a fragment of rDNA!

Scheckenbach, F., Hausmann, K., Wylezich, C., Weitere, M., & Arndt, H. (2009). Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor Proceedings of the National Academy of Sciences, 107 (1), 115-120 DOI: 10.1073/pnas.0908816106