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.

An understanding of the formation of spatial heterogeneity is important because spatial heterogeneity leads to functional consequences at the ecosystem scale; however, such an understanding is still limited. Particularly, research simultaneously considering both external variables and internal feedbacks (self-organization) is rare, partly because these two drivers are addressed under different methodological frameworks. In this dissertation, I show the prevalence of internal feedbacks and their interaction with heterogeneity in the preexisting template to form spatial pattern. I use a variety of techniques to account for both the top-down template effect and bottom-up self-organization. Spatial patterns of nutrients in stream surface water are influenced by the self-organized patch configuration originating from the internal feedbacks between nutrient concentration, biological patchiness, and the geomorphic template. Clumps of in-stream macrophyte are shaped by the spatial gradient of water permanence and local self-organization. Additionally, significant biological interactions among plant species also influence macrophyte distribution. The relative contributions of these drivers change in time, responding to the larger external environments or internal processes of ecosystem development. Hydrologic regime alters the effect of geomorphic template and self-organization on in-stream macrophyte distribution. The relative importance of niche vs. neutral processes in shaping biodiversity pattern is a function of hydrology: neutral processes are more important in either very high or very low discharge periods. For the spatial pattern of nutrients, as the ecosystem moves toward late succession and nitrogen becomes more limiting, the effect of self-organization intensifies. Changes in relative importance of different drivers directly affect ecosystem macroscopic properties, such as ecosystem resilience. Stronger internal feedbacks in average to wetter years are shown to increase ecosystem resistance to elevated external stress, and make the backward shifts (vegetation loss) much more gradual. But it causes increases in ecosystem hysteresis effect. Finally, I address the question whether functional consequences of spatial heterogeneity feed back to influence the processes from which spatial heterogeneity emerged through a conceptual review. Such feedbacks are not likely. Self-organized spatial patterning is a result of regular biological processes of organisms. Individual organisms do not benefit from such order. It is order for free, and for nothing.

Climate change is causing hydrologic intensification globally by increasing both the frequency and magnitude of floods and droughts. While environmental variation is a key regulator at all levels of ecological organization, such changes to the hydrological cycle that are beyond the normal range of variability can have strong impacts on stream and riparian ecosystems within sensitive landscapes, such as the American Southwest. The main objective of this study was to investigate how anomalous hydrologic variability influences macroinvertebrate communities in desert streams. I studied seasonal changes in aquatic macroinvertebrate abundances in eleven streams that encompass a hydrologic gradient across Arizona’s Sonoran Desert. This analysis was coupled with the quantification and assessment of stochastic hydrology to determine influences of flow regimes and discrete events on invertebrate community composition. I found high community variability within sites, illustrated by seasonal measures of beta diversity and nonmetric multidimensional scaling (NMDS) plots. I observed notable patterns of NMDS data points when invertebrate abundances were summarized by summer versus winter surveys. These results suggest that there is a difference within the communities between summer and winter seasons, irrespective of differences in site hydroclimate. Estimates of beta diversity were the best metric for summarizing and comparing diversity among sites, compared to richness difference and replacement. Seasonal measures of beta diversity either increased, decreased, or stayed constant across the study period, further demonstrating the high variation within and among study sites. Regime shifts, summarized by regime shift frequency (RSF) and mean net annual anomaly (NAA), and anomalous events, summarized by the power of blue noise (Maximum Blue Noise), were the best predictors of macroinvertebrate diversity, and thus should be more widely applied to ecological data. These results suggest that future studies of community composition in freshwater systems should focus on understanding the cause of variation in biodiversity gradients. This study highlights the importance of considering both flow regimes and discrete anomalous events when studying spatial and temporal variation in stream communities.