Revealing regional-scale differences in microbial community structure and metabolic strategies across different land use types and soil types and how these differences relate to soil carbon (C) cycling function is crucial for understanding the mechanisms of soil organic carbon (SOC) sequestration in agroecosystems. However, our understanding of these knowledge still remains unclear. Here, we employed metagenomic methods to explore differences in microbial community structure, functional potential, and ecological strategies in calcareous soil and red soil, as well as the relationships among these factors and SOC stocks. The results showed that the bacterial absolute abundance and diversity were higher and the fungal absolute abundance and diversity were lower in calcareous soil than in red soil. This may be attributed to stochastic processes dominated the assembly of bacterial and fungal communities in calcareous soil and red soil, respectively. This in turn was closely related to soil pH and Ca2 + content. Linear discriminant analysis showed that genes related to microbial growth and reproduction (e.g., amino acid biosynthesis, central carbon metabolism, and membrane transport) were enriched in calcareous soil. While genes related to stress tolerance (e.g., bacterial chemotaxis, DNA damage repair, biofilm formation) were enriched in red soil. The great difference in soil properties between calcareous soil and red soil may be the cause of this result. Compared with red soil, the higher soil pH, SOC, and calcium and magnesium content in calcareous soil increased the bacterial absolute abundance and diversity, thus increasing the SOC sequestration potential of microorganisms, but also increased the decomposition of organic carbon by fungi, thus increasing the SOC loss potential. However, the bacterial absolute abundance and diversity were much higher than that of fungi. Therefore, soil carbon sequestration potential was still greater than its loss potential in karst agroecosystems. Agricultural disturbance intensity may be the main factor affecting these relationships. Overall, these findings advance our understanding of how soil microbial metabolic processes are related to SOC sequestration.

Permafrost thaw represents one of Earth's largest climate feedback risks, potentially releasing vast carbon (C) stores as greenhouse gases (GHG). However, our ability to predict emissions remains limited by poor understanding of how changing organic matter (OM) composition affects microbial carbon processing. We test a metabolism-centered redox framework, which views microbial processes as coupled oxidative-reductive reactions, to mechanistically explain how organic matter metabolite quality controls greenhouse gas production in permafrost-affected peatland ecosystems. Rather than relying solely on geochemical redox measurements, our approach examines how microbes balance electron flow through metabolic pathways. Using active layer peat (9-19 cm) from contrasting environments (bog and fen), we employed multi-omics approaches, including metabolomics, metagenomics, and metatranscriptomics, to link OM chemistry to microbial function. Our results reveal distinct dissolved organic matter metabolite composition, with fen systems enriched in compounds with higher substrate quality (low molecular weight (MW) sugars with high H:C ratios and low aromaticity) and bog systems dominated by compounds with lower substrate quality (high MW phenols with lower H:C ratios and higher aromaticity). In fen samples, these sugar-like compounds correlated with higher oxidative metabolism and methanogenesis, supported by increased glycolysis gene expression. Initially, electrons from increased oxidative metabolism were balanced through nitrate and sulfate reduction, but as these electron acceptors were depleted, methanogenesis increased to maintain redox balance. Fen samples showed rapid degradation of both high- and low-substrate-quality compounds, suggesting sufficient energy for efficient C cycling. Conversely, bog samples exhibited more polyphenolic compounds, lower glycolysis activity, and higher stress-related gene expression, suggesting energy was diverted towards cell maintenance under acidic conditions rather than C processing. This approach suggests that predicting greenhouse gas emissions requires an understanding of how organic matter quality shapes microbial energy allocation strategies, providing a mechanistic framework for improving emission predictions from permafrost-affected peatlands and similar ecosystems.