Soil microbial community structure and function in permafrost regions: progress and perspectives

<sec><p indent="0mm">Permafrost regions contain 50% of the world’s soil carbon, and the stability of permafrost significantly influences the global carbon budget. Rising temperatures accelerate permafrost degradation and enhance microbial activity, leading to a self-reinforcing positive carbon-climate feedback loop through the mineralization of organic matter and the release of greenhouse gases. The assembly of microbial communities, their functional properties, and their response strategies are crucial for elucidating this process. However, current research lacks adequate inter-scale correlation, dynamic simulation, and functional gene network analysis. Therefore, there is an urgent need to systematically integrate multidisciplinary methods to reveal the community-and function-mediated carbon cycling processes. This paper systematically reviews the multi-scale response patterns of permafrost microbes based on metagenomics, stable isotope probing (SIP), and ecological network analysis. We quantified the roles of environmental selection and stochastic processes in community assembly using multivariate analyses (e.g., RDA, Mantel test) and null models. Additionally, interactions among the carbon, nitrogen, and phosphorus cycles were examined through functional gene annotation and metabolomics data. Long-term observations and simulation experiments were employed to uncover the dynamic changes in microbial communities and functions at elevated temperatures. </sec><sec> The primary findings are as follows: (1) character of Community Structure. Permafrost microbial communities exhibit significant vertical stratification and are region-specific, with bacteria (e.g., Proteobacteria, Actinobacteria) and fungi (e.g., Ascomycota) being the predominant taxa. (2) Mechanism of Community Assembly. Both environmental filtering (e.g., pH, nutrient availability) and stochastic processes (such as dispersal limitation and ecological drift) influence the formation of permafrost microbial communities. Notably, ecological drift predominates in community assembly within the active layer, while dispersal limitation plays a more critical role in the permafrost layer. (3) Metabolic Function and Element Cycling. Microbes possess a variety of functional modules associated with carbon degradation (e.g., cellulase genes) and the nitrogen cycle (e.g., nitrogen fixation genes), thereby contributing to a coupled C-N-P cycle in permafrost microbiomes. The metabolic activation of thawed permafrost results in an increase in methane emission flux by 2 to 3 orders of magnitude. Responses to climate warming reveal that freeze-thaw cycles regulate microbial succession through a process characterized by “physical screening, metabolic activation, and community reorganization”, resulting in a significant increase in functional gene diversity. The formation of thermokarst landforms further exacerbates carbon release, with microbial necromass carbon constituting the predominant portion of carbon loss. Additionally, permafrost microbes significantly influence the enhancement of global carbon-climate feedback by regulating biogeochemical cycles. Future research should address the technical challenges associated with deep sampling, integrate multi-omics and machine learning techniques, and develop a multi-level framework encompassing genes, communities, and ecosystems. Establishing long-term monitoring networks and conducting cross-regional joint experiments will provide essential data to quantify the contribution of microbes to carbon release, ultimately aiding in the formulation of pathways toward carbon neutrality. This paper provides theoretical evidence for the development of permafrost microbial ecologies and underscores the central role that microbes play in studies of global change. </sec>