Microbial life in ancient permafrost along a salinity gradient illuminated by metagenomics

Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface) and age (from ~ 10 kyr to 1.1 Myr) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and freshwater coastal permafrost (FCP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. Using 16S rRNA gene sequencing, we showed that the biodiversity decreased dramatically with permafrost age and separated the samples into three groups: FP and FCP together (10–100 kyr old), FP (> 900 kyr old), and MP (105–120 kyr old). Younger FP/FCP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes (MAGs) and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.