Ancient bacteria show evidence of DNA repair

Abstract

Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.

Fig. 1.

Sequence diversity (average percentage of nonmatching nucleotides for sequence pairs within samples) as a function of permafrost age.

Fig. 2.

UNG treatment leads to strand breaks in damaged DNA during the PCR denaturation step.

Fig. 3.

Proportion of clones before and after UNG treatment (see Fig. 2). Low-GC Gram-positive bacteria (yellow) such as the endospore-former Clostridia exhibited DNA damage. Gram-negative bacteria (white) and high-GC Gram-positive bacteria (green) such as Actinobacteria have no known capacity for dormancy.

Fig. 4.

Respiration in micrograms of CO₂-C per gram of dry soil per day as a function of permafrost age; the range depicted represents the minimum detectable difference by this method.