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Title: Investigations of aquaculture methodologies to enhance success of Great Lakes lake sturgeon streamside facilities
Creator: Bauman, John Matthew
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Streamside rearing facilities (SRFs) have been widely advocated in the Great Lakes basin as the preferred method of culturing Lake Sturgeon in situations where restoration goals to enhance or repatriate populations can be met by stocking. However, over the past decade, targeted stocking goals have been difficult to achieve due in large part to low survival and low growth during early life periods. This study examined three specific early life periods encountered during streamside operation ...
Show moreStreamside rearing facilities (SRFs) have been widely advocated in the Great Lakes basin as the preferred method of culturing Lake Sturgeon in situations where restoration goals to enhance or repatriate populations can be met by stocking. However, over the past decade, targeted stocking goals have been difficult to achieve due in large part to low survival and low growth during early life periods. This study examined three specific early life periods encountered during streamside operation (egg, free-embryo, and larval) and aimed to quantify the effects of different methodologies on the body size and survival of lake sturgeon in a SRF. Information collected during the egg period provides insight regarding the use of different egg chemotherapeutants, de-adhesion and incubation procedures, as well as the documentation of microbial community composition on lake sturgeon egg surfaces. Among egg chemotherapeutants utilized in streamside hatcheries, hydrogen peroxide showed higher mean proportional survival compared to formalin and the control (although results were not statistically significant). Additionally, chemotherapeutants may have selected for microbial communities that have been determined in other studies to be pathogenic. The effects of de-adhesion and incubation on lake sturgeon eggs were quantified using egg survival, egg oxygen consumption rate, and body size as response variables. Results revealed that these variables, except egg survival, did not vary significantly among de-adhesion and incubation treatments. Microbial community composition data suggest de-adhesion and incubation techniques affect the bacterial community composition on the egg surface which may provide insight into mechanisms responsible for differences detected in survival. At the free-embryo period, the effects of rearing density and family on body size and survival in association with dissolved oxygen concentration were quantified to the time of emergence. A significant density and family effect on free-embryo body size at emergence was documented. Feeding regimes, as well as the effects of different weekly prophylactic chemotherapeutants were quantified during the larval period. Results from feeding regime studies revealed significant differences in body size as a function of feeding frequency in hatchery-produced larvae to 30 days post-exogenous feeding. In addition, using hatchery-produced as well as wild-caught larvae, significant differences in body size and survival as a function of alternate food types were documented. Results from the weekly prophylactic chemotherapeutant study revealed a significant treatment effect on the survival of young-of-year lake sturgeon at 49 days post-exogenous feeding. This investigation at multiple life periods highlights methods that improve survival and growth, as well as serves as a tool for the development of standard operating procedures for SRFs geared to enhance current production and recovery of the Great Lakes Lake Sturgeon.
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Title: A closed-loop biorefining system to convert organic residues into fuels
Creator: Chen, Rui
Date: 2015
Collection: Electronic Theses & Dissertations
Description: This project delivers an energy positive and water neutral, closed-loop biorefining system that converts organic wastes into renewable energy and reduces the overall impacts on the environment. The research consisted of three major stages: The first stage of this project was conducted in an anaerobic co-digestion system. Effects of the ratio of dairy manure-to-food waste as well as operating temperature were tested on the performance of the co-digestion system. Results illustrated an increase...
Show moreThis project delivers an energy positive and water neutral, closed-loop biorefining system that converts organic wastes into renewable energy and reduces the overall impacts on the environment. The research consisted of three major stages: The first stage of this project was conducted in an anaerobic co-digestion system. Effects of the ratio of dairy manure-to-food waste as well as operating temperature were tested on the performance of the co-digestion system. Results illustrated an increase in biogas productivity with the increase of supplemental food waste; fiber analysis revealed similar chemical composition (cellulose, hemicellulose and lignin) of final solid digestate regardless their different initial feedstock blends and digestion conditions. The molecular genetic analyses demonstrated that anaerobic methanogenic microorganisms were able to adjust their community assemblage to maximize biogas production and produce homogenized solid digestate. The second stage utilized electrocoagulation (EC) pretreated liquid digestate from previous stage to culture freshwater algae. Kinetics study showed a similar maximum growth rate (0.201-0.207 g TS day-1) in both 2× and 5× dilutions of EC solution; however, the algal growth was inhibited in original EC solution (1×), possibly due to the high ammonia-to-phosphate ratio. Algal community assemblage changed drastically in different dilutions of EC solution after a 9-day culture. The following semi-continuous culture in 2× and 5× EC media established steady biomass productivities and nitrogen removal rates; in addition, both conditions illustrated a phenomenon of phosphorus luxury uptake. Biomass composition analyses showed that algae cultured in medium containing higher nitrogen (2× EC medium) accumulated more protein but less carbohydrate and lipid than the 5× EC medium. The last stage involved hydrolyzing the algal biomass cultured in anaerobic digestion effluent and analyzing the effects of the neutralized algal hydrolysate on the performance of enzymatic hydrolysis of acid or alkali pretreated lignocelluosic substrates (poplar, corn stover, switchgrass, and solid fiber from anaerobic digestion). Results found that algal hydrolysate significantly improved the efficiency of enzymatic hydrolysis of lignin-rich, structurally recalcitrant biomass such as poplar and solid fiber from anaerobic digestion. This discovery broadened the potential application of algal biomass besides direct use for biofuel production.
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Title: Assessing the biodegradation of toluene, ethylbenzene and RDX and the identification of the microorganisms involved using stable isotope probing and high throughput amplicon sequencing
Creator: Jayamani, Indumathy
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Contamination of groundwater by organic pollutants is a worldwide environmental problem. Bioremediation is a viable option for cleaning and reclaiming sites contaminated with pollutants amenable to microbial transformation. However, our understanding of microorganisms playing key roles in bioremediation is still developing. In this study, specific aspects of biodegradation of three organic pollutants namely toluene, ethylbenzene and the nitramine explosive hexahydro-1,3,5-trinitro-1,3,5...
Show moreContamination of groundwater by organic pollutants is a worldwide environmental problem. Bioremediation is a viable option for cleaning and reclaiming sites contaminated with pollutants amenable to microbial transformation. However, our understanding of microorganisms playing key roles in bioremediation is still developing. In this study, specific aspects of biodegradation of three organic pollutants namely toluene, ethylbenzene and the nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) were investigated. The overall objectives of this research were to 1) assess the biodegradation potential of toluene, ethylbenzene and RDX using soils from various sources, 2) identify the major groups of microorganisms responsible for the degradation of ethylbenzene and RDX in these samples and 3) assess the effect of a potential co-contaminant, isobutanol, on toluene biodegradation.The first study examined the effect of isobutanol on the biodegradation of toluene under sulfate amended, nitrate amended or methanogenic conditions. The results indicated that toluene biodegradation was not greatly affected by isobutanol in five of the six experimental set-ups. However, toluene biodegradation was completely inhibited in one set of microcosms amended with sulfate and inocula from wastewater treatment plant activated sludge. This suggests that if co-contamination occurs, in some cases toluene degradation may be inhibited. In the second study, stable isotope probing (SIP) and high throughput sequencing were used with ethylbenzene degrading consortia to identify microorganisms benefiting from 13C label uptake from ethylbenzene (or metabolites). Several phylotypes were relatively more abundant in the heavy fractions from the labeled ethylbenzene amended soil microcosms compared to the controls indicating 13C label uptake. This included phylotypes within the families Oxalobacteraceae, Rhodospirillaceae, Xanthomonadaceae and Rhodocyclaceae (Proteobacteria) as well as the genus Gemmatimonas. This work indicates microorganisms not previously linked to ethylbenzene degradation could have significant roles in the carbon uptake from this pollutant.The third and fourth studies involved applying SIP and high throughput sequencing to investigate RDX degrading microbial communities. In the third study, microbial communities obtained from four soils previously unexposed to explosives were investigated. Sequences from the total DNA extracts of all soils illustrated an increase in abundance of Brevundimonas and/or unclassified Bacillaceae 1 compared to the microbial communities in the initial soil or no RDX treatments. The fourth study investigated a RDX degrading community obtained from a Navy Base previously contaminated with explosives with and without glucose. The microbial communities in the total DNA samples indicated phylotypes classing as Pseudomonadaceae and Acinetobacter was more abundant in the presence and absence of glucose respectively. The SIP study also found that unclassified Pseudomonadaceae were primarily responsible for label uptake in both treatments. When glucose was present, Comamonas also increased in abundance following RDX degradation and was enriched in the heavy fractions, suggesting, for the first time, that this phylotype is also important for RDX removal. Overall, these data suggest both novel RDX degraders and previously reported RDX degraders were associated with RDX removal in these soils.
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Title: Metagenomic insights into microbial diversity and resistance to antibiotics in wastewater treatment plants
Creator: Munir, Mariya
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Our water environment is greatly impacted by the presence of microbial contaminants which is a great concern it terms of public health exposure. Full-scale conventional and state-of-the-art wastewater utilities have been found to release pathogens and antibiotic resistant bacteria in the environment. Management and minimization of microbial pathogens and resistant bacteria in wastewater treatment plants is critical since the spread of pathogens and antibiotic resistant genes in the...
Show moreOur water environment is greatly impacted by the presence of microbial contaminants which is a great concern it terms of public health exposure. Full-scale conventional and state-of-the-art wastewater utilities have been found to release pathogens and antibiotic resistant bacteria in the environment. Management and minimization of microbial pathogens and resistant bacteria in wastewater treatment plants is critical since the spread of pathogens and antibiotic resistant genes in the environment poses a significant challenge to diverse aspects of our global community. The overall aim of this study is to provide metagenomic insights into bacterial, viral and phage diversity and resistance to antibiotics and metal compounds in wastewater utilities. Samples were collected from two different wastewater treatment systems, a conventional activated sludge utility and a membrane bioreactor (MBR), in Michigan. Metagenomic analyses were conducted on Illumina Miseq and Hiseq generated sequences using MGRAST and METAVIR analysis software. The findings suggest that there is a substantial shift in the phage community over the course of the activated sludge process. Phage populations are dynamic and phage DNA was associated with antibiotic resistant genes in wastewater. It was observed that there are differences in the abundance of functional genes related to resistance between bacterial, virus and phage communities. Genes coding for antibiotic resistance were identified in all bacterial, virus and phage communities, whereas genes coding for resistance to metals were mostly observed in bacterial and virus communities. The MBR utility samples showed slightly higher number of hits for all the functional categories compared to conventional wastewater treatment samples. Diverse viral and bacterial human pathogens were observed in treated wastewater samples. Diversity analysis does not provide quantitative data on pathogen loads or infectivity but it provides a list of potentially pathogenic viruses and bacteria that need to be considered during treatment management decisions. This study provided a bioinformatics approach for identifying microbial diversity in different wastewater treatment stages and technologies. The results of this work provide significant information that will contribute to sustainable wastewater management decisions.
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Title: The microbiome of acute bacterial gastroenteritis and the functional role of intestinal bacteriophages
Creator: Nohomovich, Brian
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Acute gastroenteritis has a major disease burden worldwide. There are 2.3 billion cases of acute gastroenteritis worldwide each year that accounts for 8% of all deaths in children under the age of 5. In the United States, there are an estimated 179 to 375 million cases annually. Gastroenteritis can have acute and chronic effects on human health. Pathogens often are not identified in cases of acute gastroenteritis due in part to the wide range of causative agents and the difficulties with...
Show more"Acute gastroenteritis has a major disease burden worldwide. There are 2.3 billion cases of acute gastroenteritis worldwide each year that accounts for 8% of all deaths in children under the age of 5. In the United States, there are an estimated 179 to 375 million cases annually. Gastroenteritis can have acute and chronic effects on human health. Pathogens often are not identified in cases of acute gastroenteritis due in part to the wide range of causative agents and the difficulties with standard culturing practices. The advent of next-generation sequencing has allowed the study of the intestinal microbiome to detect alterations in the composition as specific disease signatures. There have been few studies on the microbiome of gastroenteritis, but none have to date have studied both the virome and bacteriome together. Through this combined analysis, a deeper understanding of gastroenteritis can be generated.In this dissertation, the Microbiome (Virome and Bacteriome) of 79 cases and 125 member controls were examined. It was found that cases had lower diversity and richness in and increased abundances in Enterobacteriaceae. Additionally, associations with severe illness were made to a specific cluster of samples. Differential abundance analysis identified the involvement of both viruses and bacteria. Analysis of the same 79 cases in a recovery state (n = 63), identified the changes that occur during and after infection. These changes agree with the case and control analysis. The functional aspects were analyzed of the viral communities. Three novel bacteriophages were isolated from stool samples and characterized. Two of the bacteriophages were determined to be lysogenic and were found in 23 additional E. coli O157:H7 strains based on BLAST alignments. One of the lysogenic bacteriophages (PHG003), harbors an SbcC gene which is a predicted exonuclease but it's important to the host bacterium remains unknown. Additionally, a lytic bacteriophage (PHG001) was also isolated and exhibited a relatively broad host range and was incredibly virulent to E. coli O157:H7. Additionally, PHG001 exhibits a phage-antibiotic synergism with the use of ampicillin and mitomycin c. Either antibiotic with the bacteriophage exhibited a drastic reduction in bacteria growth. PHG001 also reduced shiga toxin expression compared to control levels."--Pages ii-iii.
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Title: Disturbance ecology of soil microbial communities in response to the Centralia, PA coal fire
Creator: Sorensen, Jackson Winther
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Microbial communities are ubiquitous in our world and play important roles in biogeochemical and ecosystems processes on Earth. The ability of these microbial communities to provide these different processes is frequently tied to their community structure, which can be thought of both in terms of membership (i.e. who is there) and the relative abundance of these members. Changes in environmental conditions often lead to changes in microbial community structure as well. Microbial communities...
Show moreMicrobial communities are ubiquitous in our world and play important roles in biogeochemical and ecosystems processes on Earth. The ability of these microbial communities to provide these different processes is frequently tied to their community structure, which can be thought of both in terms of membership (i.e. who is there) and the relative abundance of these members. Changes in environmental conditions often lead to changes in microbial community structure as well. Microbial communities are formed through the process of assembly, which in turn is driven by the four processes of 1) Selection 2) Dispersal 3) Drift and 4) Diversification. Understanding the relative importance of each of these processes in different systems is important for predicting how microbial communities will change in response to disturbances. This dissertation presents work that uses the coal fire in Centralia, PA as a model press disturbance for understanding soil microbial community responses to and recovery from disturbance. The experiments herein aim to shed light the relative roles of Selection, Dispersal, and Drift in governing these responses in soil microbial communities experience a temperature disturbance. An observation study of a chronosequence of fire disturbance in Centralia, PA is used to generate hypotheses as to the relative roles of Selection, Dispersal, and Drift in the assembly of soil microbial communities experiencing a temperature disturbance. Further, an in depth look at some of these communities using shotgun metagenomics is used to observe specific microbial traits and characteristics selected for by the temperature disturbance. Finally, a laboratory soil mesocosm warming experiment investigates the relative influence of Dispersal and dormancy in governing responses to and recovery from disturbance.
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Title: Deconstructing the correlated nature of ancient and emergent traits : an evolutionary investigation of metabolism, morphology, and mortality
Creator: Grant, Nkrumah Alions
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Phenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have...
Show morePhenotypic correlations are products of genetic and environmental interactions, yet the nature of these correlations is obscured by the multitude of genes organisms possess. My dissertation work focused on using 12 populations of Escherichia coli from Richard Lenski's long-term evolution experiment (LTEE) to understand how genetic correlations facilitate or impede an organism's evolution. In chapter 1, I describe how ancient correlations between aerobic and anaerobic metabolism have maintained - and even improved - the capacity of E. coli to grow in an anoxic environment despite 50,000 generations of relaxed selection for anaerobic growth. I present genomic evidence illustrating substantially more mutations have accumulated in anaerobic-specific genes and show parallel evolution at two genetic loci whose protein products regulate the aerobic-to-anaerobic metabolic switch. My findings reject the "if you don't use it, you lose it" notion underpinning relaxed selection and show modules with deep evolutionary roots can overlap more, hence making them harder to break. In chapter 2, I revisit previous work in the LTEE showing that the fitness increases measured for the 12 populations positively correlated with an increase in cell size. This finding was contrary to theory predicting smaller cells should have evolved. Sixty thousand generations have surpassed since that initial study, and new fitness data collected for the 12 populations show fitness has continued to increase over this period. Here, I asked whether cell size also continued to increase. To this end, I measured the size of cells for each of the 12 populations spanning 50,000 generations of evolution using a particle counter, microscopy, and machine learning. I show cell size has continued to increase and that it remains positively correlated with fitness. I also present several other observations including heterogeneity in cell shape and size, parallel mutations in cell-shape determining genes, and elevated cell death in the single LTEE population that evolved a novel metabolism - namely the ability to grow aerobically on citrate. This last observation formed the basis of my chapter 3 research where my collaborators and I fully examine the cell death finding and the associated genotypic and phenotypic consequences of the citrate metabolic innovation.
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Title: Developing novel biological processes to convert lignocellulose into lipid based biofuel
Creator: Ruan, Zhenhua
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Microbial lipids for biofuel production have recently attracted increasing attention because of their advantages over plant oils such as fast growth, year-round production, less demand on space, and easy scale-up. Particularly, microbes are able to utilize a variety of carbon sources (glucose, xylose, glycerol, starch, and lignocellulose) for the production of cell mass and lipids, which greatly improves the flexibility of microbial lipid based biofuel production. Among these carbon sources,...
Show moreMicrobial lipids for biofuel production have recently attracted increasing attention because of their advantages over plant oils such as fast growth, year-round production, less demand on space, and easy scale-up. Particularly, microbes are able to utilize a variety of carbon sources (glucose, xylose, glycerol, starch, and lignocellulose) for the production of cell mass and lipids, which greatly improves the flexibility of microbial lipid based biofuel production. Among these carbon sources, lignocellulose, the most abundant and renewable source in nature, is considered as an ideal raw material for microbial lipid production. Some oleaginous microbes (those can accumulate more than 20% of intracellular lipid), such as Mortierella isabellina, Rhodotorula glutinis, and Candida curvata etc., are able to uptake both glucose and xylose from lignocellulose and accumulate a relatively large amount of lipid in the cell. Despite their promise, the full potential of lignocellulose for microbial lipid fermentation has yet to be unlocked because of the challenges associated with its decomposition into fermentable sugars and low fermentation efficiency due to inhibitors generated from thermal/chemical pretreatment. In addition, liquid-solid separation, water usage, and low xylan utilization are other major issues impeding commercial microbial lignocellulose based lipid production. In response to addressing the aforementioned issues, the novel biological process of combined hydrolysis, which based on our co-hydrolysis process, was developed in the current study to efficiently release mono-sugars and acetate from lignocelluloses, and satisfy the need of fungal fermentation to accumulate lipids. Besides that, little is known about the effect of inhibitors from lignocellulose hydrolysis on oleaginous fungal cell growth and lipid production, so their individual and synergistic effects were studied as well. 13C isotope traced experiment was carried on to illustrate the carbon utilization regarding cell growth and lipid accumulation in the presence of inhibitors such as furfural and HMF. This study would play an important role in terms of microbial lipid fermentation from lignocellulose using oleaginous fungal fermentation platform.
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Title: Mortality and development of Aedes larvae exposed to potential natural pathogens Aspergillus niger, Fusarium oxysporum, and Pythium ultimum
Creator: Morningstar, Rebecca Jean
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Survival and development of Aedes triseriatus, the mosquito vector of La Crosse Encephalitis, were found to be inhibited in the presence of dried leaves of certain populations of the sugar maple Acer saccharum. It is suspected that these effects are due to fungal contaminants carried on the leaf surface. Pure cultures of Aspergillus niger and Fusarium oxysporum were isolated from experimental containers in which these effects...
Show moreSurvival and development of Aedes triseriatus, the mosquito vector of La Crosse Encephalitis, were found to be inhibited in the presence of dried leaves of certain populations of the sugar maple Acer saccharum. It is suspected that these effects are due to fungal contaminants carried on the leaf surface. Pure cultures of Aspergillus niger and Fusarium oxysporum were isolated from experimental containers in which these effects were observed. Pure cultures were used to challenge larvae of Ae. triseriatus and the invasive species Aedes japonicus japonicus. Results indicate that Aspergillus spores have a significant and repeatable lethal effect on larvae of the tested species, particularly those at the first and second instar. Results also indicate a significant inhibition of development in some experiments. Also implied is a possible competitive advantage of Ae. j. japonicus over Ae. triseriatus when exposed to spores of the fungus Aspergillus, as Ae. j. japonicus rates of survival were significantly higher than those of Ae. triseriatus when run concurrently.
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Title: Physiological and ecological investigations of Clostridium difficile
Creator: Robinson, Catherine D.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Disease caused by Clostridium difficile is currently the most prevalent nosocomial infection and leading cause of antibiotic-associated diarrhea. It is clear that the intestinal microbiota plays a role in preventing C. difficile infection in the absence of antibiotics; however, the mechanisms involved in this protective function are poorly understood. Since antibiotic administration is an inducing factor of C. difficile infection, treatment employing antibiotics often results in recurrent...
Show moreDisease caused by Clostridium difficile is currently the most prevalent nosocomial infection and leading cause of antibiotic-associated diarrhea. It is clear that the intestinal microbiota plays a role in preventing C. difficile infection in the absence of antibiotics; however, the mechanisms involved in this protective function are poorly understood. Since antibiotic administration is an inducing factor of C. difficile infection, treatment employing antibiotics often results in recurrent disease, yet it is still the primary line of treatment. Therefore, a central goal of research in this area is to better define the role of the intestinal microbiota in suppression of disease, and ultimately develop alternative ways to prevent and treat C. difficile infection. In this thesis, I present a novel in vitro model that was developed to study complex fecal communities. This in vitro model is a continuous-culture system that utilizes arrays of small-volume reactors; it is unique in its simple set-up and high replication. We adapted this model to operate as a C. difficile infection model, where in vivo C. difficile invasion dynamics are replicated in that the fecal communities established in the reactors are resistant to C. difficile growth unless disrupted by antibiotic administration. We then go on to use this model to show that newly emerged, epidemic strains of C. difficile have a competitive fitness advantage when competed against non-epidemic strains. We also show this competitive advantage in vivo, using a mouse infection model. This result is exciting, as it suggests that physiological attributes of these strains, aside from classical virulence factors, contribute to their epidemic phenotype. Finally, the metabolic potential of C. difficile in regards to carbon source utilization is explored, and reveals that epidemic strains are able to grow more efficiently on trehalose, a disaccharide sugar. Moreover, preliminary in vivo mouse studies suggest that trehalose utilization plays a role in colonization. Therefore, the growth advantage conferred by this increased ability to utilize trehalose may contribute to the ecological fitness of these strains in vivo. The in vitro model developed and presented in this thesis could be used to study many aspects of C. difficile-microbiota interactions and has the potential to elucidate mechanisms that are important for in vivo resistance to establishment of disease. In addition, the metabolic investigations described provide insight into understanding the physiology of not only C. difficile as a whole, but also physiological attributes unique to epidemic strains. Ultimately, these types of ecological and physiological investigations will bring us closer to finding better ways to treat and prevent disease caused by C. difficile.
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Title: Characterization of the development of the tonsillar microbiome in pigs
Creator: Peña Cortes, Luis Carlos
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Pig tonsils are identified as a potential reservoir for many bacterial and viral pathogens that can survive asymptomatically in this location and may have a high potential of being zoonotic. It has been suggested that the microbiome plays a significant/ substantial role in host colonization by pathogenic microorganisms and also exerts regulatory roles in the resistance to infection. Despite the important role that the tonsillar microbiome could play in the colonization and persistence of...
Show more"Pig tonsils are identified as a potential reservoir for many bacterial and viral pathogens that can survive asymptomatically in this location and may have a high potential of being zoonotic. It has been suggested that the microbiome plays a significant/ substantial role in host colonization by pathogenic microorganisms and also exerts regulatory roles in the resistance to infection. Despite the important role that the tonsillar microbiome could play in the colonization and persistence of pathogens in the host, there are no in-depth studies characterizing the development of tonsillar microbiome in pigs or how this microbiome is structured over time. Surprisingly a similar study is also absent in humans. There was a clear need to investigate the development of the tonsillar microbiome in pigs to lay the basis for future studies focused on more complex subjects such as the relationship between the normal tonsillar microbiome and pathogens in the tonsils. Understanding the development of the pig tonsillar microbiome over time and the role of the tonsillar microbiome in the acquisition and persistence of a pathogenic microorganism will lay the basis for the design of novel intervention strategies to control the presence of the pathogen and reduce the risk of transmission to other animals or humans. Moreover, these studies are expected to provide an animal model to test hypotheses generated by microbiome data that cannot be tested in humans. The goal of this study was to characterize tonsillar microbiome development in pigs, and how this microbiome is structured and how the structure changes through different times in the life of pigs. The chapters in this thesis will present pertinent data related with the composition of the pig tonsillar microbiome and how it alters through the life of pigs, possible maternal sources for some of the identified members of this microbiome, as well as the microbiome structure and progressive change through their life. Furthermore, the results will show that challenges associated with management procedures typically present in swine farms generate prominent changes in the microbiome composition and abundance of diverse bacterial families. Finally, the study will show the microscopic structure of the tonsillar epithelium and crypts and the presence of diverse bacterial communities on the surface of pig tonsils throughout different time points of their life. The final chapter will also describe the morphological changes of the tonsillar surface in pigs that are seen and are associated with changes in the microbial communities observed through different time points in their life. Taken together, the results presented here demonstrate that there is a temporal succession in the development of the pig tonsillar microbiome through the life of pigs."--Pages ii-iii.
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Title: Biological mechanisms of uranium transformation catalyzed by Geobacter bacteria
Creator: Cologgi, Dena L.
Date: 2012
Collection: Electronic Theses & Dissertations
Description: An insufficient knowledge of the biological mechanisms of contaminant transformation often limits the performance of in situ subsurface bioremediation and long-term stewardship strategies. The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of U(VI) from groundwater. However, the biological mechanism behind this reaction has remained elusive. Because Fe(III) oxide reduction requires the expression of conductive pili...
Show moreAn insufficient knowledge of the biological mechanisms of contaminant transformation often limits the performance of in situ subsurface bioremediation and long-term stewardship strategies. The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of U(VI) from groundwater. However, the biological mechanism behind this reaction has remained elusive. Because Fe(III) oxide reduction requires the expression of conductive pili in Geobacter, we also evaluated their contribution to uranium reduction. In chapter 2 of my dissertation I demonstrate a previously unrecognized role for Geobacter pili in the extracellular reduction of uranium and its essential function as a catalytic and protective cellular mechanism.The expression of pili by Geobacter also promotes cell aggregation and biofilm formation. Recent work has shown that Geobacter cells transition from planktonic to biofilm physiologies during the active phase of U reduction in the subsurface. Despite these findings, the contribution of Geobacter biofilms to uranium removal and reduction has not been investigated. In chapter 3 of my dissertation I demonstrate that multilayer biofilms are able to reduce and tolerate substantially more U than planktonic cells for prolonged periods of time, making them an attractive option for the development of permeable biobarriers for U bioremediation. I also demonstrate the role of pili as a primary U reductase in the biofilm.To gain further insight into how biofilms transform U, in chapter 4 of my dissertation I screened a library of transposon-insertion mutants and identified mutants with biofilm defects. This study confirmed the role of Geobacter pili in biofilm formation, and identified other genes encoding cell envelope and electron transport components that had not previously been implicated in biofilm development. These molecular markers can be used to predict and monitor the physiological state of Geobacter bacteria during the in situ bioremediation of U.Previous work, including the prior chapters of my dissertation, has highlighted the importance of the cell envelope and its components for the survival of Geobacter in the subsurface. However, little is known regarding the regulation of the cell envelope. Thus, I investigated the role of the Geobacter's ECF sigma factor, RpoE. In the last chapter of my dissertation, I show that RpoE is required for response to cell envelope stress, as well as the regulation of Geobacter's extracellular electron transfer pathways. This highlights the functional specialization that RpoE has undergone to control the adaptive responses that enable Geobacter bacteria to survive in the environment, and links my findings to the physiology of Geobacter in the subsurface.
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Title: Genomic versatility in the Burkholderia genus : from strains to species
Creator: Chain, Patrick S. G.
Date: 2011
Collection: Electronic Theses & Dissertations
Description: "The group of closely related organisms classified as Burkholderia encompass a very impressive array of phenotypic properties. Using a multitude of genomic and bioinformatic methods, this thesis explores the similarities and differences at various taxonomic levels among genomes sequenced from this genus, attempts to relate some of these discoveries to other species, and discusses the implications of these findings on broader scientific questions"--From abstract.

Title: Microbial communities and parasites associated with Diporeia spp. (Amphipoda, Gammaridae) and their potential impacts on diporeia spp. health in the laurentian Great Lakes basin
Creator: Winters, Andrew David
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Due to their unique position in the foodweb, Diporeia (Amphipoda, Gammaridae) are an important component in the Great Lakes ecosystem. Unfortunately, Diporeia abundances have been declining from the majority of their habitat throughout lakes Michigan, Huron, Erie, and Ontario. The hypothesis that pathogens are the probable disease agents behind Diporeia declines, whether due to the presence of invasive dreissenid mussels or not, was...
Show moreDue to their unique position in the foodweb, Diporeia (Amphipoda, Gammaridae) are an important component in the Great Lakes ecosystem. Unfortunately, Diporeia abundances have been declining from the majority of their habitat throughout lakes Michigan, Huron, Erie, and Ontario. The hypothesis that pathogens are the probable disease agents behind Diporeia declines, whether due to the presence of invasive dreissenid mussels or not, was investigated. This was investigated through examination of the bacterial communities associated with Diporeia through high throughput molecular techniques and gene sequencing, and identification of pathogens and their lesions through light and electron microscopical studies as well as phylogenetic studies. Analysis of 16S rRNA genes revealed that the bacterial communities associated with sediments were dominated by Actinobacteria and Acidobacteria while those associated with Diporeia were dominated by Flavobacterium spp. (Bacteroidetes) and Pseudomonas spp. (Gammproteobacteria). The presence of a bacterium belonging to Rickettsiales, an order of Bacteria containing known pathogens for freshwater amphipods, in Diporeia was confirmed. A significant temporal shift in bacterial community diversity was observed for Diporeia samples collected from one site in Lake Superior; however, the ecological significance of the shift remains to be determined. Microscopical examination of Diporeia collected from multiple sites in the southern basin of Lake Michigan between 1980 and 2007 revealed that Diporeia were host to a total of eight different groups of uni- and multicellular pathogens including, amoeba, microsporidia, haplosporida, filamentous fungi, yeast, ciliates, acanthocephala, and cestodes. Spatio-temporal variability in parasitic infections was observed with prevalences often fluctuating by depth, sampling site, and life stage of Diporeia. Additionally, the presence of the fish-pathogenic rhabdovirus viral hemorrhagic septicemia virus (VHSV) genotype IVb was confirmed in Diporeia samples collected from lakes Ontario, Huron, and Michigan, illustrating the role macroinvertebrates may play in VHSV ecology. Pathologies associated with pathogenic parasitic infections ranged from inflammation to destruction of tissues vital for the ecological performance of the amphipod. No significant positive correlations were observed between any group of parasites and dreissenid densities. My prevailing hypothesis is that parasite species belonging to Microsporidia and Haplosporidia are associated with detrimental effects that may have impacted Diporeia populations. Microscopical and phylogenetic investigations revealed the presence of two novel parasite species infecting Diporeia. The first parasite is a Haplsporidium sp. (Haplosporidia) that is similar to H. nelsoni, the causative agent of MSX disease in the eastern oyster (Crassostrea virginica). The second parasite is a Dictyocoela sp. (Microsporidia), a group of vertically transmitted parasites that infect both ovarian tissue and adjacent muscle of their amphipod hosts and are often associated with sex-ratio distortion in amphipod populations. Both novel parasites elicited a host immune response and were associated with destruction of muscle tissue in Diporeia. The findings of these studies shed light on pathogens as potential causes of Diporeia declines in the Laurentian Great Lakes.
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Title: Genetic diversity and virulence gene characterization of Group B Streptococcus
Creator: Springman, Amber Cody
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Group B Streptococcus (GBS, Streptococcus agalactiae) is a Gram-positive, beta-hemolytic bacterium that was first described as a causative agent in bovine mastitis. GBS has since become a leading cause of pneumonia, sepsis, and meningitis newborns and has also emerged as an opportunistic pathogen in the elderly and adults with underlying medical conditions. The accessibility to a collection of GBS strains from colonized women, newborns, adults, elderly, and bovines has provided an excellent...
Show moreGroup B Streptococcus (GBS, Streptococcus agalactiae) is a Gram-positive, beta-hemolytic bacterium that was first described as a causative agent in bovine mastitis. GBS has since become a leading cause of pneumonia, sepsis, and meningitis newborns and has also emerged as an opportunistic pathogen in the elderly and adults with underlying medical conditions. The accessibility to a collection of GBS strains from colonized women, newborns, adults, elderly, and bovines has provided an excellent basis for conducting molecular epidemiological studies. The use of molecular subtyping methods including multilocus sequence typing (MLST), PCR-based RFLP, and mulitiplex PCR has allowed for inferences into the phylogenetic relationships among strains and the identification of specific virulence determinants associated with different clonal lineages. During the first study of this dissertation, the extent of genetic diversity and allelic variation within key virulence genes were analyzed in a panel of 94 GBS strains from diverse sources (e.g. pregnant women, newborns, elderly adults, and bovines). In the second study, a more inclusive set of 295 human-derived and bovine-derived strains representing 73 sequence types were evaluated for the presence of and variation in horizontally acquired pilus islands (PIs). Extensive genetic analyses conducted in these studies revealed that recombination and horizontal gene transfer have played a major role in the diversification of GBS clonal lineages. Furthermore, evolutionary pressures have favored the selection of specific allelic determinants that has led to the emergence of highly specialized lineages that have become successful at causing disease in humans. Overall, this research has strong implications for vaccine development since many of the virulence genes examined herein have been proposed as vaccine candidates. The high degree of sequence variability observed in many of the potential vaccine targets underscores the difficulty of developing a broadly protective, universal vaccine against GBS. Continued efforts to assess the genetic diversity of GBS populations and the mechanisms involved in pathogenesis will prove critical for establishing new prevention measures to combat GBS-associated disease.
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Title: Development and application of a rapid, user-friendly and inexpensive method to detect and quantify Dehalococcoides mccartyi genes in groundwater samples
Creator: Kanitkar, Yogendra Hemant
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Tetrachloroethene (PCE) and trichloroethene (TCE) are the predominant contaminants at hazardous waste sites in the United States. The remediation of these chlorinated solvents at contaminated sites frequently involves bioremediation approaches such as biostimulation or bioaugmentation. Both approaches aim at increasing the population of Dehalococcoides cells in the subsurface. It has become common to quantify the population of these microorganisms both before and during the remediation...
Show moreTetrachloroethene (PCE) and trichloroethene (TCE) are the predominant contaminants at hazardous waste sites in the United States. The remediation of these chlorinated solvents at contaminated sites frequently involves bioremediation approaches such as biostimulation or bioaugmentation. Both approaches aim at increasing the population of Dehalococcoides cells in the subsurface. It has become common to quantify the population of these microorganisms both before and during the remediation process. TaqMan probe based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes, such as vcrA, bvcA, and tceA, is now a widely accepted molecular biological tool (MBT) for this task. To date, a wide range of qPCR protocols based on vcrA, bvcA, and tceA genes have been successful for monitoring the reductive dechlorination driven by Dehalococcoides cells. However, alternate molecular methods that are faster and cheaper may make quantification significantly easier. Loop mediated isothermal amplification (LAMP) assays were developed for the rapid and specific quantification of the RDase genes, vcrA, tceA, and bvcA in groundwater samples. As a first step, the developed LAMP assays were validated using DNA templates prepared from commercially available bioaugmenting cultures (SDC-9 and KB-1) and groundwater samples. To do this, the concentrations of Dehalococcoides mccartyi RDase genes with DNA templates obtained using LAMP were compared to concentrations obtained using qPCR on a real time thermal cycler. Additionally, the use of direct amplification was investigated. LAMP assays were then adapted for the development a field deployable kit. Here, an approach that requires only low cost laboratory equipment (a bench top centrifuge and a water bath) and significantly less time and resources compared to qPCR is described. The method involves the concentration of biomass from groundwater (without DNA extraction) and LAMP of the cell templates. The amplification products are detected by a simple visual color change (orange/green). Finally, the most probable number technique was incorporated into the altered visual detection LAMP method for the quantitative estimation of RDase gene concentrations in groundwater samples. Overall, quantification with LAMP on a real time thermal cycler was comparable to quantification with qPCR when DNA extracts prepared from SDC-9 and KB-1 or bioaugmented groundwater samples were used as templates for amplification. The LAMP assays to visually detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 X 105 gene copies per L for vcrA and 1.3 X 105 gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination. Quantification with the MPN-LAMP assay using cell templates underestimated the concentration of RDase genes in groundwater samples by an order of magnitude compared to quantification with DNA templates and qPCR assay. Based on these results, response factors to correlate the MPN-LAMP data to estimated concentrations of RDase genes in groundwater samples are suggested. Future work should include a technology transfer of MPN-LAMP protocols to remediation practitioners.
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Title: The application of molecular methods including stable isotope probing to identify the microorganisms involved in toluene and MTBE degradation in mixed microbial systems
Creator: Sun, Weimin (University and college faculty member)
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Sites containing leaking underground storage tanks (LUST sites) are a national problem, with over 443 568 releases confirmed as of 2003, resulting in BTEX (benzene, toluene, ethylbenzene, xylenes) or oxygenate (e.g. MTBE or TBA) contamination. These chemicals are a threat to drinking water supplies because of their human health effects and relatively high aqueous solubilities. Bioremediation can be a cost-effective method to remove such groundwater contaminants either through natural...
Show moreSites containing leaking underground storage tanks (LUST sites) are a national problem, with over 443 568 releases confirmed as of 2003, resulting in BTEX (benzene, toluene, ethylbenzene, xylenes) or oxygenate (e.g. MTBE or TBA) contamination. These chemicals are a threat to drinking water supplies because of their human health effects and relatively high aqueous solubilities. Bioremediation can be a cost-effective method to remove such groundwater contaminants either through natural attenuation or by advanced engineering methods. Understanding the microbial processes involved in the biodegradation of BTEX and MTBE has the potential to improve the efficiency of LUST site remediation. The overall aims of this project were to: 1) characterize the microorganisms able to degrade toluene under a range of redox conditions from a variety of soil and sediment sources using stable isotope probing (SIP); 2) investigate the diversity of the bssA and bamA genes in a wide range of anaerobic toluene-degrading consortia; and 3) identify the microorganisms able to transform MTBE anaerobically using SIP.The first study in this research involved using SIP to identify the active members in an aerobic toluene degrading consortium. Specifically, SIP was used with terminal restriction fragment length polymorphism (TRFLP) and the results indicated that a 313 bp terminal restriction fragment (T-RF) incorporated the majority of the 13C from 13C labeled toluene. Sequencing of 16S rRNA genes from these communities indicated the organism represented by this T-RF was a Polaromonas spp. Real-time PCR was also utilized to provide quantitative patterns in gradient fractions and document increases in Polaromonas populations as toluene was degraded. In the second study, SIP was applied to five toluene-degrading consortia under sulfate and nitrate amended conditions. In all, five different phylotypes were found to be responsible for toluene degradation and these included previously identified toluene degraders as well as novel toluene degrading microorganisms. In nitrate amended microcosms, inoculated from granular sludge, microorganisms classifying within the genus Thauera were the primary toluene degraders. Whereas in nitrate amended microcosms, inoculated from a different source (agricultural soil), microorganisms in the family Comamonadaceae (genus unclassified) were the key degraders. In one set of sulfate amended microcosms (agricultural soil), the primary degrader affiliated within the class Clostridia (genus Desulfosporosinus), while in other sulfate amended microcosms, the primary degraders affiliated with the class Deltaproteobacteria, classifying within the families Syntrophobacteraceae (digester sludge) or Desulfobulbaceae (contaminated soil) (genus unclassified for both). The third study involved an investigation into the diversity of anaerobic toluene-degrading functional genes (bssA and bamA genes) in a number of inocula sources. The results suggest that targeting the bamA and bssA genes in a quantitative or non-quantitative manner could be a productive approach for investigating toluene biodegradation potential over a range of samples and redox conditions. The final study involved using SIP to investigate the dominant degraders in an anaerobic MTBE degrading microcosms. These experiments indicated bacteria in the phyla Firmicutes (family Ruminococcaceae) and Alphaproteobacteria (genus Sphingopyxis) were the dominant MTBE degraders in a methanogenic MTBE-degrading consortium seeded from activated sludge.
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Title: Factors associated with concentrations of persistent enteric markers in water quality samples and sediment cores from the Lake St. Clair watershed
Creator: Brooks, Yolanda Marie
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Molecular methods to monitor water quality can address current and historical pollution. Molecular measurements of enteric markers from sediments can aid in the evaluation of historical water quality using a singular index and be used to analyze correlations to climate and human impact. However, the stability of the markers in defined storage conditions and durations is uncertain. The goals of this dissertation were to: 1) investigate how storage conditions and duration affected...
Show moreMolecular methods to monitor water quality can address current and historical pollution. Molecular measurements of enteric markers from sediments can aid in the evaluation of historical water quality using a singular index and be used to analyze correlations to climate and human impact. However, the stability of the markers in defined storage conditions and durations is uncertain. The goals of this dissertation were to: 1) investigate how storage conditions and duration affected concentrations of enteric molecular markers in water samples; and 2) evaluate the correlations of historical anthropogenic and climate variables with the deposition of persistent enteric markers in sediment cores from the Lake St. Clair watershed. Autoclaved water from the Red Cedar River was seeded with 10% (vol/vol) raw sewage and stored in liquid suspension (LS) or attached to a solid matrix (SM). Enterococci (ENT) 23S rDNA, Escherichia coli (EC) uidA, and Bacteroides thetataiotaomicon (BT) 1,6 alpha-mannanase were measured with quantitative polymerase chain reaction (qPCR) in order to evaluate their persistence for up to 28 and 366 days at 4o (long term and short term studies), and 27o and 37oC (short term study only). Five linear and non-linear best-fit models were fit to the indicator concentrations. Persistence of the indicators was enhanced on SM (p < 0.001), and decreased with time (p < 0.001). Persistence was also dependent on indicator species in the short term and long term studies (p < 0.001, and p = 0.001, respectively). The least to most persistent indicators were: BT < EC < ENT. The time needed for 90% decay of the indicators, T90, calculated with the best-fit models in the short term study (and long term study) ranged from 1 day for BT in LS at 37 ̊C to > 28 days for ENT and EC on SM at all temperatures (and 35.8 days for EC in LS to 164 days for ENT on SM at 4°C). At 4°C, the T90 values were greater in the long term study compared to the short term study. This study suggests that storage of water samples at 4°C attached to a solid matrix can increase the persistence of markers from fecal indicators.Surface sediments from Anchor Bay, northwestern Lake St. Clair (AB), and the mouth of the Clinton River (CR) were spiked with EC and Enterococcus faecium. qPCR measurements of ENT 23S rDNA and EC uidA extracted from 17 DNA extraction methods were compared. Within each location, Kruskal-Willis tests confirmed few significant differences between the concentrations of the indicators. The optimal method included a bead beating step with a DNA sorption blocker followed by centrifugation. This method evaluated the concentrations of ENT 23S rDNA and EC uidA in sediment cores from AB and CR, representing the years c.1757 - 2012, and c.1895 - 2012, respectively. EC concentrations in the AB and CR cores increased with year, and ranged from 1.42 x 106 to 16.9 x 106 cell equivalents (CE) per g-dry wt, and 1.81 x 106 to 8.46 x 106 CE per g-dry wt, respectively. ENT concentrations in the CR core increased with year, and ranged from 3 x 103 to 990 x 103 CE per g-dry wt. The ENT concentrations in the AB core experienced two steady states: ~1 x 104, and ~2 x 105 CE per g-dry wt during c.1757 – c.1878, and c.1902 – c.2010, respectively. ENT concentrations in both cores were correlated to river discharge (p = 0.046), while EC concentrations were correlated to air temperature (p = 0.018), and total nitrogen and total carbon concentrations (p = 0.038, and 0.029, respectively). Also, ENT and EC concentrations were significantly correlated to population in watershed (p = 0.003 and 0.023, respectively). This study offers a novel analysis of ≥ 100 years of the management of the Clinton River watershed.
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Title: The evolution of a key innovation in an experimental population of Escherichia coli : a tale of opportunity, contingency, and co-option
Creator: Blount, Zachary David
Date: 2011
Collection: Electronic Theses & Dissertations
Description: The importance of historical contingency in evolution has been extensively debated over the last few decades, but direct empirical tests have been rare. Twelve initially identical populations of E. coli were founded in 1988 to investigate this issue. They have since evolved for more than 50,000 generations in a glucose-limited medium that also contains a citrate. However, the inability to use citrate as a carbon source under oxic conditions is a species-defining trait of ...
Show moreThe importance of historical contingency in evolution has been extensively debated over the last few decades, but direct empirical tests have been rare. Twelve initially identical populations of E. coli were founded in 1988 to investigate this issue. They have since evolved for more than 50,000 generations in a glucose-limited medium that also contains a citrate. However, the inability to use citrate as a carbon source under oxic conditions is a species-defining trait of E. coli. A weakly Cit+ variant capable of aerobic citrate utilization finally evolved in one population just prior to 31,500 generations. Shortly after 33,000 generations, the population experienced a several-fold expansion as strongly Cit+ variants rose to numerical dominance (but not fixation). The Cit+ trait was therefore a key innovation that increased both population size and diversity by opening a previously unexploited ecological opportunity.The long-delayed and unique evolution of the Cit+ innovation might be explained by two possible hypotheses. First, evolution of the Cit+ function may have required an extremely rare mutation. Alternately, the evolution of Cit+ may have been contingent upon one or more earlier mutations that had accrued over the population's history. I tested these hypotheses in a series of experiments in which I "replayed" evolution from different points in the population's history. I observed no Cit+ mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, I observed a significantly greater tendency to evolve Cit+ among later clones. These results indicate that one or more earlier mutations potentiated the evolution of Cit+ by increasing the rate of mutation to Cit+ to an accessible, though still very low, level. The evolution of the Cit+ function was therefore contingent on the particular history of the population in which it occurred.I investigated the Cit+ innovation's history and genetic basis by sequencing the genomes of 29 clones isolated from the population at various time points. Analysis of these genomes revealed that at least 3 distinct clades coexisted for more than 10,000 generations prior to the innovation's evolution. The Cit+ trait originated in one clade by a tandem duplication that produced a new regulatory module in which a silent citrate transporter was placed under the control of an aerobically-expressed promoter. Subsequent increases in the copy number of this new regulatory module refined the initially weak Cit+ phenotype, leading to the population expansion. The 3 clades varied in their propensity to evolve the novel Cit+ function, though genotypes able to do so existed in all 3, implying that potentiation involved multiple mutations.My findings demonstrate that historical contingency can significantly impact evolution, even under the strictest of conditions. Moreover, they suggest that contingency plays an especially important role in the evolution of novel innovations that, like Cit+, require prior construction of a potentiating genetic background, and are thus not easily evolved by gradual, cumulative selection. Contingency may therefore have profoundly shaped life's evolution given the importance of evolutionary novelties in the history of life. Finally, the genetic basis of the Cit+ function illustrates the importance of promoter capture and altered gene regulation in mediation the exaptation events that often underlie evolutionary innovations.
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Title: Environmental processes controlling the fate and transport of aristolochic acid in agricultural soil and copper in contaminated lake sediment
Creator: Tangtong, Chaiyanun
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Fate and transport of toxic chemicals are important processes that describe how chemicals move and transform in the environment. Environmental processes such as adsorption, solubility, complexation, dissolution/precipitation, oxidation/reduction, plant uptake and biodegradation play major roles in controlling the fate and transport of chemicals. Understanding these processes is essential to assess the potential of human health risks, the exposure pathway or even the methods for prevention and...
Show moreFate and transport of toxic chemicals are important processes that describe how chemicals move and transform in the environment. Environmental processes such as adsorption, solubility, complexation, dissolution/precipitation, oxidation/reduction, plant uptake and biodegradation play major roles in controlling the fate and transport of chemicals. Understanding these processes is essential to assess the potential of human health risks, the exposure pathway or even the methods for prevention and remediation of these risks. Environmental problems can be caused by organic or inorganic chemicals and they have different fate and transport behavior in the environment. In this study, the fate and transport of Aristolochic acids (AAs) in soil and copper in sediment were used as examples to show the different behavior of organic and inorganic chemicals that induced problems in environment.AAs were believed to be causal agents that induced Balkan Endemic Nephropathy (BEN) by food contamination. They are active chemicals in Aristolochia species plants which are extensively found in the endemic villages. This study examined the essential environmental partitioning processes that control fate and transport of AAs. The results showed that the octanol-water partitioning coefficient (Kow) of AAs decreased when pH increased, which indicated the different hydrophobicity between neutral and anion forms. This trend was similar to the soil -water partitioning coefficient (Kd). Solubility (Sw) increased when pH increased. These suggested that AAs will be highly mobile in an alkaline environment. The Kow and Sw were increased when a calcium ion presented in solution. Even if AAs had a high sorption capacity to the soils, they had a high tendency to be desorbed too. The soil adsorption and desorption experiment indicated the cation bridging mechanism may play a major role in soil processes. Root exudates are not the main pathway that release AAs to the soil, but their seed decomposition can release a large amount of AAs, which can be degraded by microorganisms. The plant uptake showed AAs had high accumulation in the roots but less translocation to shoots. All evidence suggested the food contamination hypothesis is possible.Torch Lake, Houghton County, Michigan, which was impacted by copper mining waste, showed a persistent high level of copper in the top sediment. This copper can never be remediated by natural processes. I hypothesized that copper was released from mining waste by microbial mediate reactions and was sequestrated by organic matter and bacteria in the post sediment. To test this hypothesis, the fate and transport of copper were studied with the Phreeqc computer modelwhere the biogeochemical processes (e.g. complexation, precipitation, adsorption, reductive dissolution and biodegradation) were applied to the diffusion process. The results showed that oxidation/reduction conditions highly impact copper fate and transport in sediment. The TEAP process causes the sediment to enter the reducing condition and dissolve the copper waste to pore water. The bacteria in the top sediment adsorbed a large amount of copper but this sorption turned to more stable minerals as time proceeded. Due to the removal of copper by precipitation process, the copper which contributed the solid phases in the top sediment were expected from overlay water. This study showed that this modeling approach is an effective tool to describe the persistent high concentration of copper inTorch Lake sediment.
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