Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods such as metagenomic and 16S rRNA gene sequencing. However, these methods do not distinguish between active, dead, and dormant cells. This is of particular concern in ancient permafrost where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this we applied: (i) live/dead differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools and how they change over geologic time. We found clear evidence that cells capable of forming endospores are not necessarily dormant and that the propensity to form endospores differed among taxa. Specifically, Bacilli are more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of Clostridia, which are more likely to persist as vegetative cells over geologic timescales. We also found that exogenous DNA preserved within permafrost does not bias DNA sequencing results since its removal did not significantly alter the microbial community composition. These results extend the findings of a previous study that showed permafrost age and ice content largely control microbial community diversity and cell abundances.ImportanceThe study of permafrost transcends the study of climate change and exobiology. Permafrost soils store more than half earth’s soil carbon despite covering ∽15% of the land area (Tarnocai et al 2009). This permafrost carbon is rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling post thaw. Permafrost is also an analog for frozen extraterrestrial environments and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive permafrost we can focus efforts searching for evidence of life on cryogenic cosmic bodies. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains across geologic timescales.