Permafrost thaw with warming reduces microbial metabolic capacities in sub-surface soils.

Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (P = 0.011) within the deep organic layer (15 -25 cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0 - 5 cm, 5 - 15 cm, and 45 - 55 cm). Warming treatment altered fungal community composition and microbial functional structure (P < 0.050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulfate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in sub-surface soils below 15 cm, despite a 25.2% higher (P < 0.05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in sub-surface soils are reduced, likely arising from enhanced thaw by warming.