Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems.

The global transport and deposition of anthropogenic nitrogen (N) to downwind ecosystems are significant and continue to increase. Indeed, atmospheric deposition can be a significant source of N to many watersheds, including those in remote, unpopulated areas. Bacterial denitrification in lake sediments may ameliorate the effects of N loading by converting nitrate (NO3-) to N2 gas. Denitrification also produces nitrous oxide (N2O), a potent greenhouse gas. The ecological effects of atmospheric N inputs in terrestrial ecosystems and the pelagic zone of lakes have been well documented; however, similar research in lake sediments is lacking. This project investigates the effects N of deposition on denitrification and N2O production in lakes. Atmospheric N inputs might alter the availability of NO3- and other key resources to denitrifiers. Such altered resources could influence denitrification, N2O production, and the abundance of denitrifying bacteria in sediments. The research contrasts these responses in lakes at the ends of gradients of N deposition in Colorado and Norway. Rates of denitrification and N2O production were elevated in the sediments of lakes subject to anthropogenic N inputs. There was no evidence, however, that N deposition has altered sediment resources or the abundance of denitrifiers. Further investigation into the dynamics of nitric oxide, N2O, and N2 during denitrification found no difference between deposition regions. Regardless of atmospheric N inputs, sediments from lakes in both Norway and Colorado possess considerable capacity to remove NO3- by denitrification. Catchment-specific properties may influence the denitrifying community more strongly than the rate of atmospheric N loading. In this regard, sediments appear to be insulated from the effects of N deposition compared to the water column. Lastly, surface water N2O concentrations were greater in high-deposition lakes compared to low-deposition lakes. To understand the potential magnitude of deposition-induced N2O production, the greenhouse gas inventory methodology of Intergovernmental Panel on Climate Change was applied to available datasets. Estimated emissions from lakes are 7-371 Gg N y-1, suggesting that lakes could be an important source of N2O.