Dissertation
Oxygenic denitrification and anaerobic digestion: microbial processes addressing agricultural pollution
University of Iowa
Doctor of Philosophy (PhD), University of Iowa
Spring 2024
DOI: 10.25820/etd.007519
Abstract
The Midwestern United States is a leading worldwide producer of corn and soybeans, directly linked to hog and cattle production. The resulting intensive agricultural production contributes to NO3 - pollution through nutrient runoff and climate change via N2O and CH4 emissions, negatively impacting human and environmental health. Promising technologies and strategies leveraging microbial processes are increasingly implemented to sustainably address Midwest agricultural pollution. However, these biotechnologies have limitations that hinder their successful implementation and usefulness. Therefore, this work aims to fill knowledge gaps in applicable microbial processes to inform better strategies and technologies addressing nutrient runoff and greenhouse gas emissions from Midwest agriculture.
This work facilitates identifying and potentially stimulating oxygenic denitrification, a unique nitrogen cycling process currently overlooked in agricultural settings, to inform its use in NO3 - and N2O mitigation strategies. The diversity, distribution, and abundance of the nitric oxide dismutase (nod) gene, a biomarker distinguishing oxygenic denitrification, was investigated in freshwater sediments and agricultural soils in Iowa. DNA analysis revealed greater diversity and abundance of nod sequences from agricultural soils than freshwater sediments. Our phylogenetic analysis of 88 recovered nod sequences improved understanding of nod gene diversity and distribution in the environment, showcased the importance of using nod as a biomarker for identifying oxygenic denitrification compared to other biomarkers, and demonstrated that this process was occurring in agricultural soils for potential stimulation and use. Finally, we demonstrated a more than ten-fold increase in relative nod abundance and an almost nine-fold increase in relative Methylomirabilota (a known phylum including oxygenic denitrifying bacteria) abundance in fully saturated soils compared to variably saturated soils. This finding improves our limited understanding of environmental factors affecting oxygenic denitrifying bacteria and, subsequently, the potential to stimulate them as a denitrification strategy. Overall, this work positively contributes to the understanding of nod genes, and thus oxygenic denitrification, in agricultural settings, advancing the use of this unique microbial process for sustainable NO3 - and N2O mitigation at agricultural sites.
Anaerobic digestion of cattle manure is a currently underutilized microbial-driven technology that turns waste into beneficial products while minimizing emissions of NO3 - , N2O, and CH4. Therefore, this work aims to expand the use and potential benefits of on-farm AD by broadening the range of viable waste feedstocks and improving our understanding of how microbiomes influence digester operation. The chemical and microbial responses to changes in the carbon-to-nitrogen ratio (C:N) and organic loading rate (OLR) during anaerobic co-digestion of cattle manure digestate mixed with industrial organics were characterized. C:Ns of 25 and 35 with OLRs ≤ 4 gVS L-1 d-1 maintained stable methane production between 0.33 and 0.39 gVS L-1 d-1. Using 16S rRNA high-throughput sequencing coupled with PICRUSt2, taxonomy and mapped predicted gene abundances were associated with the major anaerobic digestion stages. C:N (25, 35) and OLR (2, 4 gVS L-1 d-1) had minimal impacts on community structure and function, with a slight but notable increase in acetoclastic methanogens and alpha/beta diversity (Shannon and Bray-Curtis) at C:N 35. Digestion was unsustainable at C:N 35 and OLR 6.5 gVS L-1 d-1, revealed by low methane production and souring. Souring correlated with increased hydrolysis and acidogenesis driven by Prevotellaceae. The microbial data indicated the potential of souring before the chemical data. Overall, our comprehensive investigation informs critically needed strategies for high methane production and efficient anaerobic digester operation, as this waste-to-energy technology is increasingly implemented to address agricultural pollution and climate change.
Details
- Title: Subtitle
- Oxygenic denitrification and anaerobic digestion: microbial processes addressing agricultural pollution
- Creators
- Emily V Schmitz
- Contributors
- Craig Just (Advisor)Timothy Mattes (Advisor)Greg LeFevre (Committee Member)Hunter Schroer (Committee Member)
- Resource Type
- Dissertation
- Degree Awarded
- Doctor of Philosophy (PhD), University of Iowa
- Degree in
- Civil and Environmental Engineering
- Date degree season
- Spring 2024
- Publisher
- University of Iowa
- DOI
- 10.25820/etd.007519
- Number of pages
- xvi, 143 pages
- Copyright
- Copyright 2023 Emily V Schmitz
- Grant note
- We thank the Johnson County Historic Poor Farm for allowing us to collect samples. This study was funded by Environmental Protection Agency Agreement 00D888019 and National Science Foundation Award 1802583. (32)
- Language
- English
- Date submitted
- 12/27/2023
- Description illustrations
- Illustrations, tables, graphs, charts
- Description bibliographic
- Includes bibliographical references.
- Public Abstract (ETD)
The intensive agricultural production in the Midwest contributes to pollution through nutrient runoff and climate change via greenhouse gas emissions, negatively impacting both human and environmental health. The main pollutant from nutrient runoff is nitrate. The main greenhouse gases of concern are nitrous oxide and methane. Leveraging microbial processes can be an effective and sustainable way to address agricultural pollution.
This work facilitates finding and potentially stimulating oxygenic denitrification, a unique nitrogen cycling process currently overlooked in agricultural settings, to better inform its use in nitrate, nitrous oxide, and methane mitigation strategies. This work demonstrated that Iowa agricultural soils harbored more diverse and abundant nod genes, biomarkers for oxygenic denitrification, than freshwater sediments. Elevated nod abundance due to increased soil saturation in the environment and due to ample nitrogen and methane in laboratory experiments was also demonstrated.
Anaerobic digestion is another underutilized microbial-driven technology that addresses agricultural pollution by turning waste into valuable resources through the production and capturing of methane. We expanded the potential waste sources that can be input into this system by demonstrating the feasibility of co-digesting industrial organics with cattle manure digestate. Furthermore, by characterizing the function and identity of the microbes performing this process, we enabled more targeted and informed decision-making for more efficient digestion. Overall, this thesis positively contributes to knowledge about microbial processes that can be leveraged to inform agriculture mitigation strategies and technologies.
- Academic Unit
- Civil and Environmental Engineering
- Record Identifier
- 9984647356902771
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