Permafrost thaw due to anthropogenic climate change results in increased microbial metabolic activity and subsequent emissions of greenhouse gases (GHGs) to the atmosphere from ancient carbon stores. As the permafrost thaws, the microbial community changes in terms of diversity and functional potential in response to warmer temperatures and increased carbon/water availability. Frozen permafrost carbon stores are mostly inaccessible to microbial metabolism, however, with permafrost thaw they become available for microbial decomposition which releases greenhouse gases (CO2, CH4, and N2O) to the atmosphere. Understanding the extent of ancient carbon degradation and resulting GHG emissions is challenging due to heterogeneity of permafrost environments (e.g. vegetation cover, latitude, soil chemistry, precipitation, types of organic carbon stored, and permafrost depth). Anticipating how microbial population shifts will affect further GHG emissions and whole ecosystem function across cryospheric landscapes will help identify habitats at high risk of ecosystem collapse and contribute to better models of climate change prediction. This can be achieved through a combination of high-resolution monitoring of the changing microbial in the collapsing terrestrial cryosphere and rigorous integration of microbial sequence data with landscape geography and chemistry to predict population level shifts and their downstream ecosystem impacts.