Tuesday, August 14, 2007

Ancient Microbes Revived from Antarctic Ice May Be Spreading Their Genes

After being encased in Antarctic ice for 8 million years, ancient microbes thawed by a team of researchers revved up their metabolic engines again and began making proteins and replicating. These are the oldest organisms ever brought back to life after a deep freeze.

The research team, a group primarily from Rutgers, looked at the microbial population in some of the oldest ice known on earth, obtained from Antarctica’s Beacon Valley. Using microscopy, the researchers could see that these samples had a variety of bacteria encased inside. But microscopy can only tell you so much; to learn more, the research team turned to DNA sequencing.

The standard way of identifying what you have in a mixed population of bacteria is to sequence the 16S ribosomal DNA - a gene encoding an important component of the protein-synthesizing machinery. This gene is plays such an important functional role that it changes very slowly over evolutionary time, thus allowing scientists to easily compare DNA sequences among organisms that have diverged from each other for hundreds of millions of years. The 16S rDNA sequences from these ice samples revealed nearly a dozen different types of bacteria in the 8 million-year-old ice; that’s not much compared to a fresh, modern sample of seawater, but that's great for very old ice.

Some of these ancient bacteria were alive. When the researchers melted the ice (but keeping it still cold and dark - these are sensitive bacteria), they found that at least some of the bacteria were able start up their metabolism, which was measured using radioactive metabolites that the bacteria could ingest and incorporate into their protein or DNA.

16S rDNA can tell you what kinds of bacteria you have, but another intriguing question is what genes do these bacteria have? Are most of their genes similar to those of today’s known bacteria? After sequencing as much of the bacterial genomes as they could, the researchers found that a substantial 46% of the genome sequence did not match any known genes. This is not actually so surprising - in spite of all of the DNA sequence from thousands of organisms stored in GenBank, we know that we have sampled only a fraction of the different types of genomes on earth. The genomes of multicellular organisms are relatively similar to each other, but that bacterial world represents a vast, poorly explored genetic resource. We know most of the genes on our planet are in fact missing from our databases; we best understand the biology of that small subset of bacterial and archaebacterial genes that was present in the ancestors of all eukaryotic organisms.

While scientists may not know much about most bacterial genes, evolution is not blind to them. Bacteria are remarkably generous with their genes; they pass them on not only to their descendants, but to their neighbors as well. This phenomenon of lateral gene transfer, or LGT, makes the evolutionary analysis of bacteria fiendishly difficult. The authors of the ice microbes paper raise another fascinating (or depressing, if you study bacterial evolution) possibility: that ancient ice is a “gene popsicle,” facilitating gene transfer not only across species, but also across time. With the onset of an ice age, microbes, harboring a given set of genes, get preserved for thousands or millions of years, until the ice melts. That’s when these ancient bacteria return to the local ecosystem, where they can pass on their ancient genes via LGT to modern bacterial species. These modern species then, with luck, use these recently revived genes to better adapt to their environment. As the authors of the paper put it:

“Our analysis suggests that melting of polar ice in the geological past may have provided a conduit for large-scale... LGT, potentially scrambling microbial phylogenies and accelerating the tempo of microbial evolution.”

This is a mind-boggling prediction, which will be difficult to test without a lot more bacterial genome sequencing. However, the idea again demonstrates the tremendous resources evolution has to work with. As the biologist Leslie Orgel reportedly once said, “Evolution is cleverer than you are.”

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