University of Notre Dame

File(s) under embargo







until file(s) become available

Using Experiments and Monitoring to Identify Controls on Ammonium Cycling, Nitrification, and Ecosystem Metabolism in Streams

posted on 2024-05-13, 22:10 authored by Anna Elizabeth Sleeter Vincent
Headwater streams receive nutrient and organic matter inputs from the surrounding landscape and are critical sites of biogeochemical cycling, particularly for nitrogen. The ecological integrity of headwater streams is threatened by disruptions to the balance of nitrogen inputs entering these systems, which can impact transformation rates and nitrogen export to downstream ecosystems. Headwater streams in agricultural landscapes receive excessive nitrogen inputs from the surrounding landscape and are engineered specifically to prevent flooding and promote drainage. These modifications exacerbate nutrient losses, particularly during critical high-flow periods. Compared to nitrate-N, which contributes to algal blooms and subsequent hypoxia in downstream ecosystems, the timing, magnitude, and drivers of ammonium-N losses are not well characterized in agricultural landscapes. However, these two forms of nitrogen are intrinsically linked via the process of nitrification. Using controlled experiments and field monitoring, I expand our understanding of the key drivers of ammonium-N removal and nitrification, and document the effects of land use, seasonal variation, and changing climatic conditions on stream metabolism in headwater streams impacted by agricultural activity. My first chapter explored controls on nitrification in streams receiving excess ammonium-N inputs. I used replicated bottle assays to estimate sediment nitrification in three agricultural watersheds between summer 2020 and spring 2021. Nitrification rates peaked in spring when water temperatures were highest and ammonium-N was in abundant supply. I compared nitrification rates to watershed-scale ammonium-N and nitrate-N export and found that 73-100% of ammonium-N has the potential to be nitrified, but nitrification contributed <1% to nitrate-N export. In my second chapter, I measured ammonium-N and nitrate-N removal in experimental streams under varying light availability, and during early/late biofilm colonization, to identify controls on ammonium-N and nitrate-N removal. Light, but not biofilm colonization, was a primary control on ammonium-N and nitrate-N removal, and I found that ammonium-N is preferentially removed compared to nitrate-N. In my third chapter, I compared ammonium-N and nitrate-N dynamics across spatial scales, and showed that conservation practices, such as the planting of winter cover crops, reduced ammonium-N and nitrate-N pools in agricultural soils. However, cover crops did not consistently reduce field-scale ammonium-N losses, likely due to variables that can decouple ammonium-N and nitrate-N losses such as flow, soil chemistry, and environmental variability. At the watershed scale, ammonium-N and nitrate-N yield correlated with runoff, but followed different patterns. While nitrate-N yield closely mirrored runoff, ammonium-N yields exhibited a step-function which points to the importance of storms as a driver of ammonium-N export. For my fourth chapter, I studied the impact of cover crops on watershed-scale export in a mixed agricultural landscape, expanding my analyses of nitrogen export to include soluble reactive phosphorus and pathogenic Escherichia coli bacteria. I demonstrated that the water quality signature of agricultural watersheds varied throughout the year, with winter and spring being critical for nutrient losses, but summer being a critical for E. coli export. Finally, for my fifth and final data chapter, I assessed the effects of floodplain restoration and land management (via cover crops) on stream metabolism, by quantifying rates of gross primary production (GPP) and ecosystem respiration (ER). I found that both floodplain restoration and winter cover crops increased stream GPP and ER, even during high flows, suggesting that conservation can mitigate the effects of land use on ecosystem function. Through this work, I demonstrate how biotic and abiotic drivers interact to influence ammonium-N losses across spatial scales, and furthermore, how patterns in nutrient and pathogen export can be influenced by restoration and management, while also improving ecosystem function of headwater streams draining agricultural lands.


Date Created


Date Modified


Defense Date


CIP Code

  • 26.0101

Research Director(s)

Jennifer L Tank

Committee Members

Gary Lamberti|Diogo Bolster|Todd Royer


  • Doctor of Philosophy

Degree Level

  • Doctoral Dissertation


  • English

Temporal Coverage

Midwest U.S.A., temperate headwater streams

Library Record


OCLC Number



University of Notre Dame

Program Name

  • Biological Sciences

Spatial Coverage

Midwest U.S.A., temperate headwater streams

Usage metrics



    No categories selected


    Ref. manager