I enjoyed this article in Science about looking for hidden types of life. There are, of course, plenty of microorganisms that can’t be cultured (this has been known for a long time). And there are plenty of odd DNA sequences that are pulled out of environmental samples, corresponding to undescribed bacteria and archaea.
But what about things that we’re not even seeing through those techniques?
Undiscovered life, if it exists, is either absent at the locations of existing environmental surveys or is missed by current approaches. There are reasons to believe that current approaches may indeed miss taxa, particularly if they are very different from those that have so far been characterized. The “universal” primers used to detect 16S rRNA genes from bacteria and archaea in environmental samples can miss major lineages because of primer mismatches (5). Similarly, the selection of specific single cells from environmental samples for genome sequencing has been based on rRNA gene identity, thus also relying on these universal primers. Organisms whose 16S rRNA genes are not recognized by the primers would not be detected using this approach. Past explorations of available metagenomic data sets have focused on the discovery of matches to the known genes and genomes—an analysis that is naturally biased against uncovering completely novel life. Finally, although we may soon have petabases of metagenomic sequence data, samples have been collected from only a minute fraction of Earth’s countless different environments.
Recognizing these limitations, it is reasonable to speculate that undiscovered and highly divergent branches of life may exist, possibly represented by domains whose marker genes differ extensively from those of the bacterial and archaeal branches on the tree of life.
The authors speculate that even the hypothetical “RNA world” organisms from the beginning of living systems might still be found in remote, protected environments (deep rocks, etc.) It’s just that our current methods of detection are likely to miss them, even if they’re present. I look forward to seeing where this goes, and what implications this work may have for chemical biology and synthetic biology. I also like the way that these studies may prove useful in identifying and confirming extraterrestrial organisms. The day when we have some of those to argue about is, I think, closer than many might think.