Biotic controls on soil carbon dynamics in boreal forest ecosystems of Alaska must be fully understood as these soils store 17% of terrestrial soil carbon and are undergoing rapid climate change. An important biotic mechanism controlling carbon cycling is the abundance of microbial functional groups in soil that regulate important processes such as decomposition and methanogenesis within the ecosystem. Soil fungi are key regulators of the decomposition of soil carbon in upland ecosystems, and methanogens and methanotrophs are important regulators of the carbon cycle in boreal wetlands. We hypothesized that the abundance of these microbial functional groups directly affects carbon cycling process rates in soil. Using quantitative PCR techniques, we quantified the abundance of soil fungi in upland forests in burn/no burn and permafrost/no permafrost comparisons. Burning significantly reduced the abundance of soil fungi, while the presence of permafrost (which impedes soil drainage and increases soil moisture), had little effect. The abundance of soil fungi was directly related to the production of ligninase enzymes and the decomposition rates of ¹³C-labelled lignin. In a boreal wetland moisture gradient, we used quantitative PCR to measure the abundances of methanogens and methanotrophs at two depths in soil. Concurrently we measured net methane and CO₂ production from soils. We will discuss our results in the context of the value of utilizing quantitative versus diversity estimates of soil microbial communities when making linkages to soil function.