Matching Items (15)
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Description
Methanogens are methane-producing archaea that play a major role in the global carbon cycle. However, despite their importance, the community dynamics of these organisms have not been thoroughly characterized or modeled. In the majority of methanogenesis models, the communities are approximated as a chemical reaction or divided into two populations

Methanogens are methane-producing archaea that play a major role in the global carbon cycle. However, despite their importance, the community dynamics of these organisms have not been thoroughly characterized or modeled. In the majority of methanogenesis models, the communities are approximated as a chemical reaction or divided into two populations based on the most common methanogenic pathways. These models provide reasonable estimate of methanogenesis rates but cannot predict community structure. In this work, a trait-based model for methanogenic communities in peatlands is developed. The model divides methanogens commonly found in wetlands into ten guilds, with divisions based on factors such as substrate affinity, pH tolerance, and phylogeny. The model uses steady-state, mixotrophic Monod kinetics to model growth and assumes peatlands operate as a semi-batch system. An extensive literature review was performed to parameterize the model. The acetoclastic module of the model was validated against experimental data. It was found that this portion of the model was able to reproduce the major result of an experiment that examined competition between Methanosaeta and Methanosarcina species under irregular feeding conditions. The model was analyzed as a whole using Monte Carlo simulation methods. It was found that equilibrium membership is negatively correlated with a guild's half-substrate constant, but independent of the guild's yield. These results match what is seen in simple pairwise competition models. In contrast, it was found that both the half-substrate constant and yield affected a guild's numerical dominance. Lower half-substrate constants and higher yields led to a guild accounting for a greater fraction of community biomass. This is not seen in simple pairwise competitions models where only yield affects final biomass. As a whole, the development of this model framework and the accompanying analyses have laid the groundwork for a new class of more detailed methanogen community models that go beyond the two compartment acetoclastic-hydrogenotrophic assumption. .
ContributorsLopez Jr, Jaime Gerardo (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Marcus, Andrew (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
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Description
While biodiesel production from photosynthesizing algae is a promising form of alternative energy, the process is water and nutrient intensive. I designed a mathematical model for a photobioreactor system that filters the reactor effluent and returns the permeate to the system so that unutilized nutrients are not wasted, addressing these

While biodiesel production from photosynthesizing algae is a promising form of alternative energy, the process is water and nutrient intensive. I designed a mathematical model for a photobioreactor system that filters the reactor effluent and returns the permeate to the system so that unutilized nutrients are not wasted, addressing these problems. The model tracks soluble and biomass components that govern the rates of the processes within the photobioreactor (PBR). It considers light attenuation and inhibition, nutrient limitation, preference for ammonia consumption over nitrate, production of soluble microbial products (SMP) and extracellular polymeric substance (EPS), and competition with heterotrophic bacteria that predominately consume SMP. I model a continuous photobioreactor + microfiltration system under nine unique operation conditions - three dilution rates and three recycling rates. I also evaluate the health of a PBR under different dilution rates for two values of qpred. I evaluate the success of each run by calculating values such as biomass productivity and specific biomass yield. The model shows that for low dilution rates (D = <0.2 d-1) and high recycling rates (>66%), nutrient limitation can lead to a PBR crash. In balancing biomass productivity with water conservation, the most favorable runs were those in which the dilution rate and the recycling rate were highest. In a second part of my thesis, I developed a model that describes the interactions of phototrophs and their predators. The model also shows that dilution rates corresponding to realistic PBR operation can washout predators from the system, but the simulation outputs depend heavily on the accuracy of parameters that are not well defined.
ContributorsWik, Benjamin Philip (Author) / Marcus, Andrew (Thesis director) / Rittmann, Bruce (Committee member) / School of Sustainability (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
The effect of ammonium on microbial fermentation was investigated to improve the efficiency of microbial electrochemical cells (MXC). Electron balances of anaerobic microbial cultures with varying ammonium concentrations (reported as g N-NH4+/L) were used to study the distribution of electrons from different fermentable substrates to acetate, propionate, and methane. Results

The effect of ammonium on microbial fermentation was investigated to improve the efficiency of microbial electrochemical cells (MXC). Electron balances of anaerobic microbial cultures with varying ammonium concentrations (reported as g N-NH4+/L) were used to study the distribution of electrons from different fermentable substrates to acetate, propionate, and methane. Results showed that with a high ammonium concentration (between 2.25 to 3g N-NH4+/L) fewer electrons routed to methane during the fermentation of 300 me-eq./L of electron donors .The majority of electrons (~ 60-80%) in the serum bottles experiments were routed to acetate and propionate for all fermentable substrates with high ammonium concentration. While methane cannot be utilized by anode respiring bacteria (ARBs) to produce current, both acetate and propionate can, which could lead to higher Coulombic efficiencies in MXCs. Experiments in microbial electrolysis cells (MECs) with glucose, lactate, and ethanol were performed. MEC experiments showed low percentage of electrons to current (between 10-30 %), potentially due to low anode surface area (~ 3cm2) used during these experiments. Nevertheless, the fermentation process observed in the MECs was similar to serum bottles results which showed significant diversion of electrons to acetate and propionate (~ 80%) for a control concentration of 0.5 g N-NH4+/L .
ContributorsLozada Guerra, Suyana Patricia (Co-author) / Joseph, Miceli (Co-author) / Krajmalnik-Brown, Rosa (Thesis director) / Torres, Cesar (Committee member) / Young, Michelle (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2013-05
Description
Computer simulations are gaining recognition as educational tools, but in general there is still a line dividing a simulation from a game. Yet as many recent and successful video games heavily involve simulations (SimCity comes to mind), there is not only the growing question of whether games can be used

Computer simulations are gaining recognition as educational tools, but in general there is still a line dividing a simulation from a game. Yet as many recent and successful video games heavily involve simulations (SimCity comes to mind), there is not only the growing question of whether games can be used for educational purposes, but also of how a game might qualify as educational. Endemic: The Agent is a project that tries to bridge the gap between educational simulations and educational games. This paper outlines the creation of the project and the characteristics that make it an educational tool, a simulation, and a game.
ContributorsFish, Derek Austin (Author) / Karr, Timothy (Thesis director) / Marcus, Andrew (Committee member) / Jones, Donald (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2013-05
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Description

The human gut microbiome is a complex community of microorganisms. These microbes play an important role in host health by contributing essential compounds and acting as a barrier against pathogens. However, these communities and associated functions can be impacted by factors like disease and diet. In particular, microbial fermentation of

The human gut microbiome is a complex community of microorganisms. These microbes play an important role in host health by contributing essential compounds and acting as a barrier against pathogens. However, these communities and associated functions can be impacted by factors like disease and diet. In particular, microbial fermentation of dietary components like polysaccharides, proteins, and fats that reach the gut are being examined to better understand how these biopolymers are utilized and affect community structure. Thus, evaluating the accuracy of methods used to quantify specific macromolecules is crucial to gaining a precise understanding of how gut microbes hydrolyze those substrates. This study presents findings on the accuracy of the Megazyme RS kit (Rapid) modified for high performance liquid chromatography (HPLC) readings and the DC Protein Assay when performed on samples from complex gut media with potato starch treatments and bovine serum albumin (BSA) treatments. Overall, our data indicates that the megazyme RS kit needs further modification to detect expected starch content with the HPLC and that the DC Protein Assay is not suitable for specific protein analysis.

ContributorsKlein, Rachel Marie (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Marcus, Andrew (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

The objective of this work is to perform LCAs three wastewater treatement alternatives at battalion-sized (500 soldier) FOBs. Three systems will be explored: traditional wastewater treatment of combined blackwater and graywater streams using activated sludge and anaerobic digestion (the status quo); MXC treatment of blackwater to produce H2O2 for disinfection

The objective of this work is to perform LCAs three wastewater treatement alternatives at battalion-sized (500 soldier) FOBs. Three systems will be explored: traditional wastewater treatment of combined blackwater and graywater streams using activated sludge and anaerobic digestion (the status quo); MXC treatment of blackwater to produce H2O2 for disinfection of blackwater and graywater; a hybrid system of blackwater treatments with MXCs to produce electricity with graywater disinfection using H2O2 produced offsite. Environmental impacts are assessed using Impact 2002+ midpoint and endpoint categories, primarily reported for human health and environmental impacts. Uncertainity analysis is performed using two techniques. First, a pedigree matrix is developed to identify the highest areas of uncertainties in data. Second, a sensitivity analysis is used to explore the effects on endpoint categories from varying transportation distance, the percentage of wastewater that is reused as nonpotable water, and coagulant doses.

Created2014-06-13
Description

Microbial peroxide producing cells (MPPCs) are a type of microbial electrochemical cells that are used to produce hydrogen peroxide (H2O2). Different catholytes were evaluated in biotic and abiotic reactors to determine their impacts on reactor performance. The abiotic reactor produced cathode efficiencies of less than 1%, leading us to investigate

Microbial peroxide producing cells (MPPCs) are a type of microbial electrochemical cells that are used to produce hydrogen peroxide (H2O2). Different catholytes were evaluated in biotic and abiotic reactors to determine their impacts on reactor performance. The abiotic reactor produced cathode efficiencies of less than 1%, leading us to investigate the potential causes of the low efficiency. An acid wash of the reactor parts was observed to significantly decrease the degradation rate of peroxide in the reactor, indicating that metal impurities in the catholyte solution was the driving cause of the low peroxide yields in the reactor. Diffusion testing confirmed that peroxide diffused across the anion exchange membrane (AEM) at a rate of 13.3 mg/L/hr, but had no significant impact on the overall peroxide produced in the reactor. We also confirmed that auto-decay of H2O2 was not responsible for the low observed yields.

ContributorsGreenfield, Aaron (Author) / Torres, Cesar (Thesis director) / Young, Michelle (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2023-05
Description

This outlines a mathematical model created in MATLAB for the purposes of predicting nitrous oxide emissions from wastewater treatment plants with updated an updated understanding of AOB metabolic pathway.

ContributorsOverbey, Jorja (Author) / Hart, Steven (Thesis director) / Young, Michelle (Committee member) / Wirkus, Stephen (Committee member) / Barrett, The Honors College (Contributor) / School of Music, Dance and Theatre (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2023-05
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Description
pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or

pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut.
Created2017-05-03
Description

The Combined Activated Sludge-Anaerobic Digestion Model (CASADM) quantifies the effects of recycling anaerobic-digester (AD) sludge on the performance of a hybrid activated sludge (AS)-AD system. The model includes nitrification, denitrification, hydrolysis, fermentation, methanogenesis, and production/utilization of soluble microbial products and extracellular polymeric substances (EPS). A CASADM example shows that, while

The Combined Activated Sludge-Anaerobic Digestion Model (CASADM) quantifies the effects of recycling anaerobic-digester (AD) sludge on the performance of a hybrid activated sludge (AS)-AD system. The model includes nitrification, denitrification, hydrolysis, fermentation, methanogenesis, and production/utilization of soluble microbial products and extracellular polymeric substances (EPS). A CASADM example shows that, while effluent COD and N are not changed much by hybrid operation, the hybrid system gives increased methane production in the AD and decreased sludge wasting, both caused mainly by a negative actual solids retention time in the hybrid AD. Increased retention of biomass and EPS allows for more hydrolysis and conversion to methane in the hybrid AD. However, fermenters and methanogens survive in the AS, allowing significant methane production in the settler and thickener of both systems, and AD sludge recycle makes methane formation greater in the hybrid system.

ContributorsYoung, Michelle (Author) / Marcus, Andrew (Author) / Rittmann, Bruce (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor)
Created2013-08-13