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.

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

“…These results also generally agree with the community composition reported from other polar soils (Kobabe et al (2004); Liebner et al (2008); Wagner et al (2009);Yergeau et al (2007Yergeau et al ( , 2009b). Non-spore forming Actinobacteria were reported to dominate ancient permafrost potentially because of their metabolic activity at low temperature and the presence of DNA-repair mechanisms (Johnson et al, 2007). Their abundance in the samples assessed here seems to confirm that Compared with other publicly available metagenomic data sets (downloaded from MG-RAST) or to other surface soils from the same region (Yergeau et al, 2009a), the active layer soil and the 2-m permafrost had highly similar functional and phylogenetic community compositions.…”

Bacterial genome replication at subzero temperatures in permafrost

“…This may be the result of the use of 13 C-acetate to discern activity. Alternatively, because spore-forming bacteria may remain in a dormant, non-metabolically active state in subzero environments (Bakermans and Nealson, 2004;Johnson et al, 2007), it is not surprising that Gram þ bacteria would not be detected by the clonal libraries derived from the 13 C-DNA.…”

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

“…Only specific microorganisms subsist at these elevated temperatures and high salinity due to modifications in proteins, DNA, and cell membrane composition as well as intracellular accumulation of low molecular compounds (Aerts et al 1985;Kempf and Bremer 1998;Kumar and Nussinov 2001;Roberts 2005). Moreover, some microorganisms are able to get into a dormancy stage by forming spores, cysts or other types of resting cells and survive starvation, exposure to extreme temperatures, and elevated background radiation (Burke and Wiley 1937;Amy 1997;Suzina et al 2004;Johnson et al 2007). The exploitation of sedimentary geologic formations in the North German Basin (NGB) has provided suitable conditions for temporary aquifer heat and cold storage (ATES aquifer thermal energy storage) (Schmidt et al 2004).…”