Friday, January 05, 2007

The Incredible Shrinking Bacterium

How's this for an ecosystem niche: 30-50C (84-122F), pH -0.5 to 1.5. micromolar arsenic & copper and nearly molar iron. That's the witches brew found in an abandoned mine in California. Last week's Science (alas, subscription will be required to read) contains a paper describing one of the archeans that lives in a biofilm in the midst of that awful solution. The bug was identified initially as a novel 16S rRNA sequence in a metagenomics sequencing project. Further sequencing pieced together 4Kb from this bug and another 13K from a related species.

The 16S sequences contain some significant mismatches from commonly used 'universal' rRNA primers, which shows a big advantage of metagenomics for discovering novel organisms: it is unbiased.

Things get really interesting when in situ hybridization was used to localize the bugs -- they are the tiniest well documented organisms yet, roughly 244nM x 175 nM -- a volume of <6nM^3 -- vs. about 20nM^3 for the previous record holder. As they comment, if half the cell is occupied by ribosomes it works out to about 350 ribosomes -- and not leaving much room for anything else.

It is interesting that the paper studiously avoids mentioning nanobacteria or nanobodies. Nanobacteria are microscopic structures which have been claimed to be self-replicating and putatively linked to various biomineralization processes and diseases, but their existence is controversial. Nanobodies are even smaller structures claimed to be biological in character.

I had been thinking about nanobacteria recently in the context of looking at some internet lists of controversial ideas that have become accepted. Nanobacteria struck me as one of the shakier contenders, and a quick Entrez Search (try this) appeared to confirm the concern. In particular, there is a paucity, particularly in recent times, of papers in well known journals. This doesn't mean the hypothesis is wrong, just that calling it accepted is a stretch.

Nanobacteria had a huge spotlight thrown on them when it was claimed that structures in a Mars-derived meteorite resembled nanobacterial fossils. Given the shaky nature of nanobacteria, I wouldn't have wanted to hang my revolutionary theory on it, but NASA went ahead.

What is particularly striking about the nanobacterial story is the lack of confirmed DNA data from such a beast. My Entrez search didn't seem to find any, and the Wikipedia entry states that the only claimed nanobacterial sequence is too close to a common contaminant to be believed, especially since no reagent-only PCR control was run.

If nanobacteria are anything like conventional lifeforms, they should have nucleic acids in them. A metagenomics run through a nanobacterial preparation should find something; in the absence of getting a novel sequence (and confirming that sequence's location in the nanobacteria by in situ), one would be forced to invoke non-nucleic acid life-like forms ala prions -- or honorably admit defeat. In other words, do exactly what this new paper in Science did. Perhaps nanobacterial hunting should be proposed the next time someone is giving away next generation sequencing runs, though I think I know one even better I'll write up here at some unspecified time in the future.

No comments: