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Drainage leads to trade-offs between crop production efficiency and wetland conservation, with complex impacts on ecosystem services. In North America’s Prairie Pothole Region, wetland drainage is widespread, often to increase the available land for cultivation, prevent crop loss due to flooding, and manage soil salinity. Wetlands are known for providing key ecosystem services such as improved water quality, flood mitigation, and carbon storage. There is limited research on how changes to soil hydrology and soil redistribution through wetland drainage can impact soil carbon storage and persistence in this region. This research evaluates factors that contribute to soil carbon storage in drained prairie pothole wetland based on 33 drained wetlands in Saskatchewan, Canada. These analyses showed regional differences in the response of soil carbon storage to drainage that are driven by environmental factors such as annual precipitation, temperature, and wetland permanence. We observed increasing soil carbon storage from the Dark Brown to Black soil zones, as well as with longer wetland pond permanence. The sampling depth used for calculating soil carbon storage was especially important when comparing geographically across the soil zones as the Black soil zone had greater soil carbon stored at depth. Soil carbon was also intensively monitored over 2 years following installation of surface drainage across a wetland complex (8 drained wetlands) where water was partially directed to a consolidation wetland. We further assessed changes in soil carbon dynamics and protection from microbial decomposition based on three soil organic matter fractions, ATR-FTIR for organic matter functional groups, and phospholipid fatty acid analysis to understand the microbial community abundance and structure. After 2 years following drainage, ephemeral wetlands with short pond permanence were found to be most sensitive to drainage and the only wetland class with decreases in soil carbon. The temporary and seasonal wetland classes showed no significant differences in soil carbon content but there were changes in the organic matter with depth due to soil redistribution during drainage implementation. Jointly, this research provides region-specific estimates of soil carbon storage in drained prairie pothole wetlands that can be used to inform wetland soil carbon management in cultivated fields.

Evidence-based decisions governing sustainable agricultural land management practices require a mechanistic understanding of soil organic matter (SOM) transformations and stabilization of carbon in soil. Large amounts of carbon from organic fertilizers, root exudates, and crop residues are input into agricultural soils. Microbes then catalyze soil biogeochemical processes including carbon extracellular transformation, mineralization, and assimilation of resources that are later returned to the soil as metabolites and necromass. A systems biology approach for a holistic study of the transformation of carbon inputs into stable SOM requires the use of soil “omics” platforms (metagenomics, metatranscriptomics, metaproteomics, and metabolomics). Linking the data derived from these various platforms will enhance our knowledge of structure and function of the microbial communities involved in soil carbon cycling and stabilization. In this review, we discuss the application, potential, and suitability of different “omics” approaches (independently and in combination) for elucidating processes involved in the transformation of stable carbon in soil. We highlight biases associated with these approaches including limitations of the methods, experimental design, and soil sampling, as well as those associated with data analysis and interpretation.