Bacteria trapped in permafrost breathe and repair their DNA for more than half a million years
Bacteria frozen in permafrost for hundreds of thousands of years slowly respirate and repair their DNA, according to a report in the Proceedings of the National Academy of Sciences this week. The strategy may explain how life persists over geologic time scales, the authors say. Other scientists have claimed to recover viable microbes that have been trapped in amber, salt or buried deep within the earth for tens to hundreds of millions of years, but how these ancient bacteria remained alive for so long under extreme conditions has remained a mystery. Researchers have postulated that they persist as dormant endospores in which metabolic activity has all but ceased. But those resting cells would still be buffeted by physical and chemical degradation, said Eske Willerslev of the University of Copenhagen in Denmark, who led the current effort. DNA, in particular, would become fragmented unless it could be repaired. “Many people, including myself, have been very skeptical about [those] results,” Willerslev told The Scientist. “There has not been a mechanism to explain how cells could survive for that long.” His team collected ice cores up to a million years old from the permafrost of Antarctica, Siberia and Canada’s Klondike, and placed them chambers chilled to -10 degrees C and filled with an atmosphere free of carbon dioxide. After waiting three months for CO2 trapped in air bubbles to dissipate, they collected gas emitted by the cores for another six months. Samples older than 600,000 years were inert, they found, but younger samples generated carbon dioxide – a sign of life. Previous work had shown that strands of DNA amplified from dead microbial fossils rarely exceed 500 base pairs, but the group targeted fragments 4,000 base pairs long. To estimate the integrity of the microbial DNA, they used an enzyme to break DNA strands at damaged regions. Even in samples pre-digested with the enzyme, the DNA was sufficiently well-preserved for the researchers to amplify 4,000 base-pair strands in the younger samples, evidence of active DNA repair. To make sure they were not amplifying DNA of modern bacteria contaminating the ancient samples, the researchers conducted all experiments in two labs. The paired findings agreed: Samples younger than 600,000 years old yielded long strands of DNA, while older ones yielded only shorter scraps. The team matched the amplified sequences to known groups of bacteria, and found that the variety of microbes diminished as the ice got older. “What I think we are seeing is a community that is slowly dying out,” Willerslev said. The oldest intact DNA they recovered mostly matched sequences for Actinobacteria, a phylum not known to form endospores, suggesting that slow metabolism and repair were key to longevity. Finding enough energy to continue a low level of activity shouldn’t be a problem, even in ice, said P. Buford Price of the University of California, Berkeley, who was not involved with the study. His past findings suggested that thin films of water, just a few molecules deep between the ice crystals, would be enough to transport nutrients from dust trapped in the permafrost, he told The Scientist. Price said he had “serious doubts” about earlier claims of ancient microbes, which could have been artifacts of contamination, but found the present study credible. “I believe it,” he said. “Willerslev argues forcefully that a better strategy for microbes to survive is not to go dormant, but to stay metabolically active and use that energy to repair DNA.” Such survival “seems plausible,” said Jeffrey Bada of the University of California, San Diego, who has developed probes for frozen Martian life for NASA. Bada, who was not a coauthor of the study, noted that cold temperatures slow chemical degradation, which would allow even sluggish repair to keep up. Willerslev said the findings may help study the possibility of life beyond Earth. Both Mars and Jupiter’s icy moon Europa are much colder than Earth’s permafrost, and may harbor torpid life.