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- Genre: Doctoral Dissertation
Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
Description
Hydrology and biogeochemistry are coupled in all systems. However, human decision-making regarding hydrology and biogeochemistry are often separate, even though decisions about hydrologic systems may have substantial impacts on biogeochemical patterns and processes. The overarching question of this dissertation was: How does hydrologic engineering interact with the effects of nutrient loading and climate to drive watershed nutrient yields? I conducted research in two study systems with contrasting spatial and temporal scales. Using a combination of data-mining and modeling approaches, I reconstructed nitrogen and phosphorus budgets for the northeastern US over the 20th century, including anthropogenic nutrient inputs and riverine fluxes, for ~200 watersheds at 5 year time intervals. Infrastructure systems, such as sewers, wastewater treatment plants, and reservoirs, strongly affected the spatial and temporal patterns of nutrient fluxes from northeastern watersheds. At a smaller scale, I investigated the effects of urban stormwater drainage infrastructure on water and nutrient delivery from urban watersheds in Phoenix, AZ. Using a combination of field monitoring and statistical modeling, I tested hypotheses about the importance of hydrologic and biogeochemical control of nutrient delivery. My research suggests that hydrology is the major driver of differences in nutrient fluxes from urban watersheds at the event scale, and that consideration of altered hydrologic networks is critical for understanding anthropogenic impacts on biogeochemical cycles. Overall, I found that human activities affect nutrient transport via multiple pathways. Anthropogenic nutrient additions increase the supply of nutrients available for transport, whereas hydrologic infrastructure controls the delivery of nutrients from watersheds. Incorporating the effects of hydrologic infrastructure is critical for understanding anthropogenic effects on biogeochemical fluxes across spatial and temporal scales.
ContributorsHale, Rebecca Leslie (Author) / Grimm, Nancy (Thesis advisor) / Childers, Daniel (Committee member) / Vivoni, Enrique (Committee member) / York, Abigail (Committee member) / Wu, Jianguo (Committee member) / Arizona State University (Publisher)
Created2013
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Characterization and Manipulation of Microbiomes From Arid Landfills for Improved Methane Production
Description
Environmentally harmful byproducts from solid waste’s decomposition, including methane (CH4) emissions, are managed through standardized landfill engineering and gas-capture mechanisms. Yet only a limited number of studies have analyzed the development and composition of Bacteria and Archaea involved in CH4 production from landfills. The objectives of this research were to compare microbiomes and bioactivity from CH4-producing communities in contrasting spatial areas of arid landfills and to tests a new technology to biostimulate CH4 production (methanogenesis) from solid waste under dynamic environmental conditions controlled in the laboratory. My hypothesis was that the diversity and abundance of methanogenic Archaea in municipal solid waste (MSW), or its leachate, play an important role on CH4 production partially attributed to the group’s wide hydrogen (H2) consumption capabilities. I tested this hypothesis by conducting complementary field observations and laboratory experiments. I describe niches of methanogenic Archaea in MSW leachate across defined areas within a single landfill, while demonstrating functional H2-dependent activity. To alleviate limited H2 bioavailability encountered in-situ, I present biostimulant feasibility and proof-of-concepts studies through the amendment of zero valent metals (ZVMs). My results demonstrate that older-aged MSW was minimally biostimulated for greater CH4 production relative to a control when exposed to iron (Fe0) or manganese (Mn0), due to highly discernable traits of soluble carbon, nitrogen, and unidentified fluorophores found in water extracts between young and old aged, starting MSW. Acetate and inhibitory H2 partial pressures accumulated in microcosms containing old-aged MSW. In a final experiment, repeated amendments of ZVMs to MSW in a 600 day mesocosm experiment mediated significantly higher CH4 concentrations and yields during the first of three ZVM injections. Fe0 and Mn0 experimental treatments at mesocosm-scale also highlighted accelerated development of seemingly important, but elusive Archaea including Methanobacteriaceae, a methane-producing family that is found in diverse environments. Also, prokaryotic classes including Candidatus Bathyarchaeota, an uncultured group commonly found in carbon-rich ecosystems, and Clostridia; All three taxa I identified as highly predictive in the time-dependent progression of MSW decomposition. Altogether, my experiments demonstrate the importance of H2 bioavailability on CH4 production and the consistent development of Methanobacteriaceae in productive MSW microbiomes.
ContributorsReynolds, Mark Christian (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Wang, Xuan (Committee member) / Kavazanjian, Edward (Committee member) / Arizona State University (Publisher)
Created2022
Description
The efficiency of the ocean’s biological carbon pump is mediated by fast-sinking particles that quickly settle out of the euphotic zone. These particles are conventionally associated with micro- (> 20 µm) sized diatoms and coccolithophorids, thought to efficiently transport carbon to depth owing to their dense mineral structures, while pico- (< 2 µm) and nanophytoplankton (2-20 µm) are considered to contribute negligibly due to their small size and low sinking speed. Despite burgeoning evidence of their export, the mechanisms behind it remain poorly understood. The objective of this dissertation is to acquire a mechanistic understanding of the contribution of pico- and nanophytoplankton to particle fluxes. I tested the hypotheses that pico- and nanophytoplankton may be exported via the following pathways: 1) physical aggregation due to the production of sticky Transparent Exopolymeric Particles (TEP), mediated by interactions with heterotrophic bacteria, 2) attachment to lithogenic minerals, and 3) repackaging by zooplankton. I found that despite the traditional view of being too small to sink, pico- and nanophytoplankton form aggregates rich in TEP, allowing cells to scavenge lithogenic minerals and thus increase their effective size and density. I discovered that interactions with heterotrophic bacteria were significant in mediating the process of aggregation by influencing the production and/or the composition of the phytoplankton-derived TEP. Bacteria differentially influenced aggregation and TEP production; some species enhanced aggregation without affecting TEP production, and vice-versa. Finally, by determining the microbial composition of sinking particles in an open-ocean site, I found pico- and nanophytoplankton significantly associated with particles sourced from crustaceous zooplankton, suggesting that their export is largely mediated by mesozooplankton.
Overall, I show that the hypothesized mechanisms of pico- and nanophytoplankton export are not mutually exclusive, but instead occur subsequently. Given the right conditions for their aggregation in the natural environment, such as interactions with aggregation-enhancing heterotrophic bacteria and/or the presence of lithogenic minerals, their cells and aggregates can escape remineralization within the euphotic zone, and thus be susceptible to grazing by mesozooplankton export within fecal pellets. The results of this dissertation provide a mechanistic framework for the contribution of pico- and nanophytoplankton to ocean particle fluxes.
ContributorsCruz, Bianca Nahir (Author) / Neuer, Susanne (Thesis advisor) / Lomas, Michael W (Committee member) / Passow, Uta (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2021
Description
Peatlands are significant global carbon sinks, where plant litter accumulation outpaces the rate of microbial degradation, which can result in significant emissions of methane and carbon dioxide. The Pastaza-Marañón foreland basin (PMFB) in the western Amazon contains the largest expanse of tropical peatlands in South America, characterized by a diversity of soil properties, including pH and mineral concentration. The PMFB is predicted to decrease in its carbon capture capacity along with a rise in greenhouse gas emissions as the climate changes. Therefore, it is imperative to understand the impact that soil properties have on the abundance of functions, microbial physiology, and interspecies interactions between microbial community members. Metagenomic sequencing of soil samples from three geochemically distinct peatlands revealed site-specific enrichment of functions related to carbon, nitrogen, phosphorus, and sulfur cycling. Additionally, 519 metagenome-assembled genomes (MAGs) were recovered, revealing variations in microbial populations responsible for organic matter degradation and nutrient (nitrogen and sulfur) cycling across sites. From these MAGs, a novel family within the Bathyarchaeia was identified, Candidatus Paludivitaceae. This family is putatively capable of carboxydotrophy, able to use CO for energy and biomass. Subsequently they could detoxify the environment of CO benefiting other community members and playing an indirect role in modulating carbon cycling. To experimentally investigate interactions of peatland microbes, co-culture experiments assessed the impact of carbon substrates (4-hydroxybenzoic acid, mannitol, and arginine) on microbial interactions from heterotrophs isolated from two geochemically distinct peatlands. Results indicate substrate and peatland type significantly influence nature and frequency of microbial interactions. The response of microbial genera to carbon substrate also varied showing the role of metabolic traits and substrate preferences in determining growth patterns of microbes. This research advances our understanding of microbial ecology in tropical peatlands and better informs predictions as the climate changes.
ContributorsPavia, Michael Joseph (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Bean, Heather (Committee member) / Bouskill, Nicholas (Committee member) / Penton, Christopher (Committee member) / Arizona State University (Publisher)
Created2024
Description
Phosphorus (P) is an essential resource for global food security, but global supplies are limited and demand is growing. Demand reductions are critical for achieving P sustainability, but recovery and re-use is also required. Wastewater treatment plants and livestock manures receive considerable attention for their P content, but municipal organic waste is another important source of P to address. Previous research identified the importance of diverting this waste stream from landfills for recovering P, but little has been done to identify the collection and processing mechanisms required, or address the existing economic barriers. In my research, I conducted a current state assessment of organic waste management by creating case studies in Phoenix, Arizona and New Delhi, India, and surveyed biomass energy facilities throughout the United States. With participation from waste management professionals I also envisioned an organic waste management system that contributes to sustainable P while improving environmental, social, and economic outcomes.
The results of my research indicated a number of important leverage points, including landfill fees, diversion mandates for organic waste, and renewable energy credits. Source separation of organic waste improves the range of uses, decreases processing costs, and facilitates P recovery, while creating jobs and contributing to a circular economy. Food is a significant component of the waste stream, and edible food is best diverted to food banks, while scraps are best given to livestock. Biomass energy systems produce multiple revenue streams, have high processing capacities, and concentrate P and other minerals to a greater extent than composting. Using recovered P in urban agriculture and native landscaping results in additional benefits to social-ecological systems by improving food security, reducing the urban heat island effect, sequestering carbon, and enhancing urban ecosystems.
The results of my research indicated a number of important leverage points, including landfill fees, diversion mandates for organic waste, and renewable energy credits. Source separation of organic waste improves the range of uses, decreases processing costs, and facilitates P recovery, while creating jobs and contributing to a circular economy. Food is a significant component of the waste stream, and edible food is best diverted to food banks, while scraps are best given to livestock. Biomass energy systems produce multiple revenue streams, have high processing capacities, and concentrate P and other minerals to a greater extent than composting. Using recovered P in urban agriculture and native landscaping results in additional benefits to social-ecological systems by improving food security, reducing the urban heat island effect, sequestering carbon, and enhancing urban ecosystems.
ContributorsStoltzfus, Jared Thomas Yoder (Author) / Childers, Daniel (Thesis advisor) / Basile, George (Committee member) / Abbott, Joshua (Committee member) / Arizona State University (Publisher)
Created2016
Description
Obesity is a worldwide epidemic accompanied by multiple comorbidities. Bariatric surgery is currently the most efficient treatment for morbid obesity and its comorbidities. The etiology of obesity is unknown, although genetic, environmental, and most recently, microbiome elements have been recognized as contributors to this rising epidemic. The role of the gut microbiome in weight-loss or weight-gain warrants investigation, and bariatric surgery provides a good model to study influences of the microbiome on host metabolism. The underlying goals of my research were to analyze (i) the factors that change the microbiome after bariatric surgery, (ii) the effects of different types of bariatric surgeries on the gut microbiome and metabolism, (iii) the role of the microbiome on the success of bariatric surgery, and (iv) temporal and spatial changes of the microbiome after bariatric surgery.
Roux-en-Y gastric bypass (RYGB) rearranges the gastrointestinal tract and reduces gastric acid secretions. Therefore, pH could be one of the factors that change microbiome after RYGB. Using mixed-cultures and co-cultures of species enriched after RYGB, I showed that as small as 0.5 units higher gut pH can aid in the survival of acid-sensitive microorganisms after RYGB and alter gut microbiome function towards the production of weight loss-associated metabolites. By comparing microbiome after two different bariatric surgeries, RYGB and laparoscopic adjustable gastric banding (LAGB), I revealed that gut microbiome structure and metabolism after RYGB are remarkably different than LAGB, and LAGB change microbiome minimally. Given the distinct RYGB alterations to the microbiome, I examined the contribution of the microbiome to weight loss. Analyses revealed that Fusobacterium might lessen the success of RYGB by producing putrescine, which may enhance weight-gain and could serve as biomarker for unsuccessful RYGB.
Finally, I showed that RYGB alters the luminal and the mucosal microbiome. Changes in gut microbial metabolic products occur in the short-term and persist over the long-term. Overall, the work in this dissertation provides insight into how the gut microbiome structure and function is altered after bariatric surgery, and how these changes potentially affect the host metabolism. These findings will be helpful in subsequent development of microbiome-based therapeutics to treat obesity.
Roux-en-Y gastric bypass (RYGB) rearranges the gastrointestinal tract and reduces gastric acid secretions. Therefore, pH could be one of the factors that change microbiome after RYGB. Using mixed-cultures and co-cultures of species enriched after RYGB, I showed that as small as 0.5 units higher gut pH can aid in the survival of acid-sensitive microorganisms after RYGB and alter gut microbiome function towards the production of weight loss-associated metabolites. By comparing microbiome after two different bariatric surgeries, RYGB and laparoscopic adjustable gastric banding (LAGB), I revealed that gut microbiome structure and metabolism after RYGB are remarkably different than LAGB, and LAGB change microbiome minimally. Given the distinct RYGB alterations to the microbiome, I examined the contribution of the microbiome to weight loss. Analyses revealed that Fusobacterium might lessen the success of RYGB by producing putrescine, which may enhance weight-gain and could serve as biomarker for unsuccessful RYGB.
Finally, I showed that RYGB alters the luminal and the mucosal microbiome. Changes in gut microbial metabolic products occur in the short-term and persist over the long-term. Overall, the work in this dissertation provides insight into how the gut microbiome structure and function is altered after bariatric surgery, and how these changes potentially affect the host metabolism. These findings will be helpful in subsequent development of microbiome-based therapeutics to treat obesity.
ContributorsIlhan, Zehra Esra (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / DiBaise, John K. (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Rittmann, Bruce E. (Committee member) / Arizona State University (Publisher)
Created2016
Description
This is a study of the plight of smallholder agriculture in Northwest Costa Rica. More specifically, this is the story of 689 rice farms, of an average size of 7.2 hectares and totaling just less than 5,300 hectares within the largest agricultural irrigation system in Central America. I was able to define the physical bounds of this study quite clearly, but one would be mistaken to think that this simplicity transfers to a search for rural development solutions in this case. Those solutions lie in the national and international politics that appear to have allowed a select few to pick winners and losers in Costa Rican agriculture in the face of global changes. In this research, I found that water scarcity among smallholder farms between 2006 and 2013 was the product of the adaptations of other, more powerful actors in 2002 to threats of Costa Rica's ratification of the Central American Free Trade Agreement. I demonstrate how the adaptations of these more powerful actors produced new risks for others, and how this ultimately prevented the rural development program from meeting its development goals. I reflect on my case study to draw conclusions about the different ways risks may emerge in rural development programs of this type. Then, I focus on the household level and show that determinants of successful adaptation to one type of global change risk may make farmers more vulnerable to other types, creating a "catch-22" among vulnerable farmers adapting to multiple global change risks. Finally, I define adaptation limits in smallholder rice farming in Northwest Costa Rica. I show that the abandonment of livelihood security and well-being, and of the unique "parcelaro" identities of rice farmers in this region define adaptation limits in this context.
ContributorsWarner, Benjamin (Author) / Childers, Daniel (Thesis advisor) / Eakin, Hallie (Committee member) / Abbott, Joshua (Committee member) / Wiek, Arnim (Committee member) / Arizona State University (Publisher)
Created2014
Description
Research shows that many water governance regimes are failing to guide social-ecological systems away from points, beyond which, damage to social and environmental well-being will be difficult to correct. This problem is apparent in regions that face water conflicts and climate threats. There remains a need to clarify what is it about governance that people need to change in water conflict prone regions, how to collectively go about doing that, and how research can actively support this. To address these needs, here I present a collaborative research project from the dry tropics of Guanacaste Province, Costa Rica. The project addressed the overarching questions: How can water be governed sustainably in water-contested and climate-threatened regions? And, how can people transition current water governance regimes toward more sustainable ones? In pursuit of these questions, a series of individual studies were performed with many partners and collaborators. These studies included: a participatory analysis and sustainability assessment of current water governance regimes; a case analysis and comparison of water conflicts; constructing alternative governance scenarios; and, developing governance transition strategies. Results highlight the need for water governance that addresses asymmetrical knowledge gaps especially concerning groundwater resources, reconciles disenfranchised groups, and supports local leaders. Yet, actions taken based on these initial results, despite some success influencing policy, found substantial challenges confronting them. In-depth conflict investigations, for example, found that deeply rooted issues such friction between opposing local-based and national institutions were key conflict drivers in the region. To begin addressing these issues, researchers and stakeholders then constructed a set of governing alternatives and devised governance transition strategies that could actively support people to achieve more sustainable alternatives and avoid less sustainable ones. These efforts yielded insight into the collective actions needed to implement more sustainable water governance regimes, including ways to overcoming barriers that drive harmful water conflicts. Actions based on these initial strategies yielded further opportunities, challenges, and lessons. Overall, the project addresses the research and policy gap between identifying what is sustainable water governance and understanding the strategies needed to implement it successfully in regions that experience water conflict and climate impacts.
ContributorsKuzdas, Christopher Paul (Author) / Wiek, Arnim (Thesis advisor) / Childers, Daniel (Thesis advisor) / Vignola, Raffaele (Committee member) / Eakin, Hallie (Committee member) / Basile, George (Committee member) / Arizona State University (Publisher)
Created2014