Effect of varying temperature increases on the microbial community of Pleistocene and Holocene permafrost

The total area covered by permafrost has been continually decreasing over the past decades. This study investigates the effect of various temperature increases on the microbiome of permafrost sampled at the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel site in Fox, Alaska, USA, corresponding to the Holocene (around 8000 years before present (ybp)) and Pleistocene (around 36,000 ybp), respectively. The soil was subjected to two thawing time courses, with temperature increasing from −4 °C to either +4 °C or +25 °C, and total nucleic acid was extracted at each time point. Consistent with previous 16S rRNA amplicon sequencing studies on the Permafrost Tunnel, the Pleistocene was dominated by Clostridia, while the Holocene was mainly composed of Clostridia, Bacteroidia and Alphaproteobacteria at −4 °C. Thawing at +25 °C resulted in divergent microbial profiles for permafrost of both ages, with the Pleistocene becoming more similar to the active layer, while the Holocene was relatively less impacted. Prediction of metabolic function revealed that bacteria from the Holocene permafrost activated degradation pathways upon thawing at +25 °C, while bacteria from the Pleistocene were more involved in amino-acid biosynthesis pathways, suggesting different mechanisms of adaptation.