BackgroundGlobal warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze-thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found.ResultsWe observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming.ConclusionsOur study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.

Global climate change has altered soil freeze-thaw (FT) patterns but less is known about the responses of soil microbial diversity, soil multifunctionality, and their relationship to FT events. Daxing'an Mountains in China, located in high-latitude permafrost ecosystems, are one of the most sensitive areas to climate change and FT patterns. Here, simulated FT conditions were used to determine the impact of FT events on soil microbial diversity and multifunctionality as well as to elucidate the relationships between bacterial and fungal diversity and multifunctionality. Community composition, alpha-diversity index, and co-occurrence network complexity of fungi significantly changed during FT events, whereas the same parameters did not exhibit significant alterations for bacteria. Soil fungal communities were more sensitive to FT events than soil bacterial communities. FT events significantly affected soil multifunctionality. A random forest analysis showed that the fungal diversity index was the main predictor of soil multifunctionality. Moreover, changes in soil abiotic factors also affected the relationship between soil microbial diversity and multifunctionality. Soil multifunctionality was also constrained by fungal community network complexity. Structural equation model showed that the FT amplitude and FT cycles exerted different impact paths on soil multifunctionality. The effect of FT cycles on soil multifunctionality (0.289) was greater than that of FT amplitude (0.080). As global climate change is expected to accelerate in the future, extension of the FT period in high-altitude and high-latitude regions may have a severe impact on soil function compared to extreme low temperatures caused by the presence of thin snow cover.