Tuesday, October 04, 2005

DNA in the mud

Last week's Science had a really suprising short letter showing an enormous amount of extracellular ("dead") DNA in the top few centimeters of ocean sediments. The amount of "extracellular" DNA greatly exceeds the amount contained within the living prokaryotes and viruses in this ecosystem.There is so much DNA in the ocean floor-- 0.45 gigatons!!-- that the phosphorous content of this molecule (about 10% by weight)is a major reservoir of phosphate for all the ocean.

The most interesting possibility would be that this DNA is intact enough to have biological activity. For example, plasmid or virioid DNA can be complexed with protiens in a way that would resist (chemical) degradation for a very long time. If even a fraction of this DNA were still encoding genes, it could be taken up by bacteria and contribute to their genomes as a huge extension to the horizontal gene (DNA) transfer process which already occurs between living organisms.

A second, more practical, consequence of large amounts of relatively intact DNA in the ocean sediments is on metagenomic surveys of this ecosystem. Metagenomics-- a fairly new method which uses special cloning and computational methods to survey the genomic capacity of a particular environment-- cannot by itself "see" if the DNA molecule being sequenced was obtained inside or outside of an organism. The specific concern is that one set of genes (for example, belonging to one class of microbe) would be overrepresented in the extracellular, nonliving pool.
Thus the metagenomic clone counting, which is used to estimate the relative abundances of "genes" in the environmental sample, would lose its presumed linkage to the biological activity of the sample. That is, DNA does not make a gene unless it's inside something alive, and the identical sequence obtained from extracellular DNA should not be scored as contributing to the genomic capacity of the ecosystem.

The issue of extracellar DNA should also be considered for large microbial concretions such as stromatolites, which, in fact, have also been analyzed by the metagenomic approach.

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