Freshwater ecosystems are dominated by small, shallow lakes, and these systems have among the highest rates of carbon burial in the world. Understanding the mechanisms that influence the way shallow lakes process and accumulate carbon is important given the rising effort to mitigate anthropogenic carbon emissions. In aquatic ecosystems, the amount of carbon available for permanent burial is affected by the balance between primary production and respiration (i.e. net ecosystem production), the amount of carbon exported from the system as a gas or through groundwater fluxes, and the quality of the organic matter deposited in the sediments and the environment in which it is deposited. The Prairie Pothole Region (PPR) of North America is a noteworthy region to evaluate carbon cycling in small freshwater ecosystems because it contains approximately 207,000 km2 of prairie lakes. Lakes in this region also typically exist in two alternative regimes: a clear water regime dominated by submerged macrophytes and/or macroalgae, and a turbid water regime dominated by phytoplankton. Based on the physiological and ecological differences of the dominating primary producers of these regimes, it is likely that one regime may accumulate carbon at a faster rate than the other.
In order to understand the mechanisms that influence carbon burial, I sampled nine shallow lakes located within the PPR over the course of three years to determine whether lake regime influenced net ecosystem production rates and exchange of carbon dioxide between the lakes and the atmosphere. I also determined the decomposition rate of macrophyte and algal material under aerobic and anaerobic conditions. Over the course of three growing seasons, the lake regime (clear or turbid) did not predict whether the lakes had a positive or negative net ecosystem production rate (autotrophic or heterotrophic, respectively), or whether the lakes were a carbon sink or source to the atmosphere. Because the variability in metabolism and CO2 exchange with the atmosphere was not strongly influenced by the biological differences between the regimes, the metabolism and CO2 exchange was more likely influenced by complex interactions driven by climate (i.e. temperature, wind turbulence, watershed input) that I was unable to distinguish. Annual production rates of these lakes were as high as 1345 g C m-2 yr-1, and over the course of three years, net ecosystem production was essentially neutral, as gross primary production (GPP) rates were approximately equal to ecosystem respiration (R). This balance implies that more carbon was retained in these shallow lakes in comparison to many other lake ecosystems where R exceeds GPP via the mineralization of terrestrial carbon. Although these lakes were metabolically neutral, the balance between gross primary production and respiration did not strongly influence the exchange of CO2 with the atmosphere, because of the hard-water nature of these particular lakes. On average these lakes were a net carbon source, emitting approximately 114 mg C m-2 d-1, and changes in pH strongly influenced the exchange of CO2 between the lake and the atmosphere. Due to greater carbonate precipitation in the clear regimes, the lakes in the turbid regime had a larger buffering capacity and therefore a diminished metabolic influence on pH and therefore CO2 exchange. Finally, the most carbon retained during the one-year decomposition experiment were the primary producers of the clear-water regime (Charophyte, Potamogeton pectinatus, Myriophyllum sibiricum) under anaerobic conditions (26% carbon retention). The phytoplankton of the turbid regime only retained 1% of its original carbon content under aerobic conditions. When these decay rates were applied to GPP estimates of each regime, it was estimated that almost five times as much carbon should remain in the clear water lakes in comparison to the lakes of the turbid regime. Consequently, the clear-water, macrophyte/macroalgae dominated lakes should accumulate carbon at a faster rate than the lakes in the turbid water regime. Accordingly, shallow lakes may be managed for the clear water state not only to improve habitat, but also to sequester carbon.