Seasonal and experimental warming alter alpine soil microbiomes and in-situ CO2 and CH4 fluxes

Alpine ecosystems are highly vulnerable to climate change, yet the effects of warming on high-altitude soils remain largely unexplored. In particular, it is unclear how soil microbial communities will adapt to rising temperatures and how this will influence greenhouse gas (GHG) fluxes, including methane (CH₄) and carbon dioxide (CO₂). Understanding these microbial responses is crucial for predicting future carbon cycling in these fragile environments.

To address this knowledge gap, we first assessed the biodiversity across ten alpine permafrost affected sites. Results revealed large variations in compositional and functional profiles between sites that were largely driven by differences in vegetation cover (0.01 – 44.8 %), soil pH (3.7 - 7.4), and total organic carbon (0 -11.1 %).

Based on these results we selected four sites that differed distinctly in soil physicochemical parameters and microbial community composition to understand how climate warming affects alpine permafrost-affected soils. Here, we conducted a two-year in-situ study using open-top warming chambers (OTCs) that passively increase soil temperatures, allowing us to study microbial adaptation to warming under realistic field conditions.

Our results showed that GHG flux responses varied considerably between sites: barren soils exhibited minimal biological activity, whereas sparely vegetated soils released CO₂ and removed CH₄, suggesting active microbial methane oxidation. Seasonal and diurnal temperature variations strongly influenced GHG gas fluxes, highlighting the importance of long-term monitoring.

Bacterial community analysis revealed significant differences in composition between sites, and between natural and experimentally warmed soils. Building on this foundation, we are currently conducting metagenomic analyses to resolve the functional potential underpinning these microbial and biogeochemical patterns. This ongoing work aims to link taxonomic shifts to metabolic pathways involved in warming responses and carbon cycling.

Together, these findings deepen our understanding of how European alpine permafrost-affected soils respond to warming and highlight the central role of microbial communities in regulating GHG exchange. Such insights are essential for predicting the future contribution of alpine ecosystems to the global carbon cycle under a changing climate.