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Title: Exploring the nodule microbiome community structure of Trifolium species
Creator: Shetty, Prateek
Date: 2016
Collection: Electronic Theses & Dissertations
Description: "Plant associated microbes have been shown to increase plant growth and production drastically, yet we are just beginning to understand the parameters that impact these interactions. Rhizobia are primary bacterial symbionts of legumes and infect root hairs to form nodules, within which, the symbiotic rhizobia fix atmospheric nitrogen into biologically available forms in exchange for carbon from the host. The aim of this project is to understand the community structure and diversity of the...
Show more"Plant associated microbes have been shown to increase plant growth and production drastically, yet we are just beginning to understand the parameters that impact these interactions. Rhizobia are primary bacterial symbionts of legumes and infect root hairs to form nodules, within which, the symbiotic rhizobia fix atmospheric nitrogen into biologically available forms in exchange for carbon from the host. The aim of this project is to understand the community structure and diversity of the nodule microbiome, with emphasis on the less abundant members, among coexisting clover species. North American clover Trifolium-Rhizobium communities are a good system to study host interactions with microbiomes given the high local species diversity. We analyzed the nodule microbiome of six congeneric clover plants when they were grown in soils conditioned by members of their own species and in soils conditioned by congener species by sequencing the 16s rRNA gene. The visualized microbiomes are similar, with 96% of all reads belonging to the order Rhizobiales. The rest of the OTUs belong to rarer groups of microbes. Further, the structure of the microbiome is impacted by both the host plant species and the soil in which the host is grown in, with soil explaining a larger degree of variation. There also is a strong interaction between soil and host in structuring the microbiome. The results are similar when the microbiome is analyzed with and without its most dominant order (Rhizobiales)."--Page ii.
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Title: Biotic and abiotic factors influence formation and ontogenic dynamics of molecularly defined gastro-intestinal microbial communities in lake sturgeon (Acipenser fulvescens) and channel catfish (Ictalurus punctatus
Creator: Shairah Abdul Razak
Date: 2017
Collection: Electronic Theses & Dissertations
Description: ABSTRACTBIOTIC AND ABIOTIC FACTORS INFLUENCE FORMATION AND ONTOGENIC DYNAMICS OF MOLECULARLY DEFINED GASTRO-INTESTINAL MICROBIAL COMMUNITIES IN LAKE STURGEON (Acipenser fulvescens) AND CHANNEL CATFISH (Ictalurus punctatus).ByShairah Abdul RazakGastrointestinal (GI, gut) microbial communities (microbiota/ microbiomes) play essential roles in host development and physiology. During early life stages, fish gut microbiome composition is shaped by complex interactions of factors including...
Show moreABSTRACTBIOTIC AND ABIOTIC FACTORS INFLUENCE FORMATION AND ONTOGENIC DYNAMICS OF MOLECULARLY DEFINED GASTRO-INTESTINAL MICROBIAL COMMUNITIES IN LAKE STURGEON (Acipenser fulvescens) AND CHANNEL CATFISH (Ictalurus punctatus).ByShairah Abdul RazakGastrointestinal (GI, gut) microbial communities (microbiota/ microbiomes) play essential roles in host development and physiology. During early life stages, fish gut microbiome composition is shaped by complex interactions of factors including dispersal of bacteria from the surrounding water, age-dependent changes in the gut ecosystem, and changes in dietary regimes. To investigate ecological processes that generate and maintain compositional patterns of gut microbiome diversity, I integrated molecular methods with experimental gut microbiome research and community ecology theory in two important fish species, lake sturgeon (Acipenser fulvescens) and channel catfish (Ictalurus punctatus) during early larval stages. Sequence reads of 16S rRNA gene were analyzed using multivariate ordination methods based on Bray-Curtis distance matrices followed by hypothesis testing using permutational multivariate analysis of variance (PERMANOVA). In the first chapter, sturgeon larvae were raised in four rearing hatchery treatments representing a combination of two factors: water source (stream vs ground water) and diet (Artemia vs Artemia supplemented with detritus). As fish grew, microbiota shifted from dominance by phyla Proteobacteria to Firmicutes. Water possibly served as the primary bacterial inoculant during early (pre-feeding) stages of development. Neutrality tests indicated that neutral processes were not strongly structuring community composition. Sturgeon gut microenvironment appears to have selected for microbial taxa, regardless of differences in treatments. The second chapter focused on alteration of gut microbiota modulated by diet and nutrient availability. Sturgeon gut microbiota differed among fish raised on different dietary regimes (control vs transition). Gut microbiota of fish exposed to a dietary transition from Artemia to frozen Chironomids were dominated by the genus Aeromonas (phylum Proteobacteria) while fish from the control group were dominated by genus Clostridium_sensu_stricto (phylum Firmicutes) at the end of experiment. Screening for cultured bacteria with extracellular protease activity revealed that fish fed with Chironomids harbored protease-positive taxa from phylogenetically distinct and more diverse clades. Next, I documented the impact of prophylactic treatments (Chloromine-T, NaCl followed by hydrogen peroxide; and hydrogen peroxide) on lake sturgeon larvae gut microbiota compared to ambient environmental conditions (control) using hatchery-produced and wild-origin fish. Gut microbiome responses to prophylactic treatments were found to be inconsistent across fish genotypes. The last chapter documented variability in channel catfish larval gut microbiome composition among families and nursery ponds characterized by different rearing water in a pond aquaculture setting. I documented a strong influence of rearing environment (pond water) on gut microbiome colonization. Gut microbiome composition was dominated by different phyla before (Proteobacteria) vs after pond stocking (Firmicutes). Different predominant genera were also detected over time. Results from my research inform community ecology theory concerning effects of stochastic and deterministic forces affecting microbial community establishment and stability. This research is also relevant for downstream applications incorporating microbial-based management strategies in commercial and conservation aquaculture.
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Title: Use of nucleic acid based methods to study the bacterial community of the cricket hindgut
Creator: Santo Domingo, Jorge W.
Date: 1994
Collection: Electronic Theses & Dissertations

Title: Factors influencing the competitive advantage of Pseudomonas sp. strain KC for subsequent remediation of a carbon tetrachloride impacted aquifer
Creator: Knoll, Wilfred Hans
Date: 1994
Collection: Electronic Theses & Dissertations

Title: Response of model microbial communities to increased productivity
Creator: Bohannan, Brendan James Marc
Date: 1997
Collection: Electronic Theses & Dissertations

Title: The effect of 2,4-dichlorophenoxyacetate selection on microbial communities in microcosm and field studies and the impact on ecosystem function
Creator: Asuming-Brempong, Stella
Date: 1999
Collection: Electronic Theses & Dissertations

Title: Microbial community analysis assessed by pyrosequencing of rRNA gene : community comparisons, organism identification, and its enhancement
Creator: Sul, Woo Jun
Date: 2009
Collection: Electronic Theses & Dissertations

Title: The relationship of chromium and selected heavy metals on the microbial community structure in sediments
Creator: Thatcher, Hilary
Date: 2001
Collection: Electronic Theses & Dissertations

Title: Ecological effects on the evolution of cooperative behaviors
Creator: Connelly, Brian Dale
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Cooperative behaviors abound in nature and can be observed across the spectrum of life, from humans and primates to bacteria and other microorganisms. A deeper understanding of the forces that shape cooperation can offer key insights into how groups of organisms form and co-exist, how life transitioned to multicellularity, and account for the vast diversity present in ecosystems. This knowledge lends itself to a number of applications, such as understanding animal behavior and engineering...
Show moreCooperative behaviors abound in nature and can be observed across the spectrum of life, from humans and primates to bacteria and other microorganisms. A deeper understanding of the forces that shape cooperation can offer key insights into how groups of organisms form and co-exist, how life transitioned to multicellularity, and account for the vast diversity present in ecosystems. This knowledge lends itself to a number of applications, such as understanding animal behavior and engineering cooperative multi-agent systems, and may further help provide a fundamental basis for new industrial and medical treatments targeting communities of cooperating microorganisms.Although these behaviors are common, how evolution selected for and maintained them remains a difficult question for which several theories have been introduced. These theories, such as inclusive fitness and group selection, generally focus on the fitness costs and benefits of the behavior in question, and are often invoked to examine whether a trait with some predetermined costs and benefits could be maintained as an evolutionarily-stable strategy. Populations, however, do not exist and evolve in a vacuum. The environment in which they find themselves can play a critical role in shaping the types of adaptations that organisms accumulate, since one behavior may be highly beneficial in one environment, yet a hindrance in another. Ever-changing environments further complicate this picture, as maintaining a repertoire of behaviors for surviving in different environments is often costly. In addition to these environmental forces, the number and composition of other organisms with which individuals interact impose additional constraints. The combination of these factors results in significantly more complex dynamics.Using computational models and microbial populations, this dissertation examines several ways in which ecological factors can affect the evolution of cooperative behaviors. First, environmental disturbance is examined, in which a cooperative act enables organisms and their surrounding neighbors to survive a periodic kill event (population bottleneck) of varying severity. Resource availability is then studied, where populations must determine how much resource to allocate to cooperation. Finally, the effect that social structure, which define the patterns of interactions among the individuals in a population, is investigated.
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Title: Bacteria, microbial communities and engineering : studies on the microbial ecology of selected engineered systems
Creator: Yang, Fan
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Environmental contaminants, such as soluble metal ions and agricultural wastes pose great risks for both human health and ecosystems. To reduce these risks, environmental engineers have developed remediation approaches that take the advantage of microbial communities and populations. Understanding these microbial resources is instrumental to manage and apply them in various engineered systems. In this dissertation, I study microbial communities and populations from three different approaches...
Show moreEnvironmental contaminants, such as soluble metal ions and agricultural wastes pose great risks for both human health and ecosystems. To reduce these risks, environmental engineers have developed remediation approaches that take the advantage of microbial communities and populations. Understanding these microbial resources is instrumental to manage and apply them in various engineered systems. In this dissertation, I study microbial communities and populations from three different approaches and demonstrate how basic microbial information can assist us in optimizing engineered systems. The first part of my dissertation focuses on understanding the genomic advantages of Ralstonia pickettii strains, which allows them to adapt to high copper environments. We have previously shown that these two strains were able to sequester a large amount of copper. Hence, these two bacterial strains have a great potential in for application to industrial wastewater treatment. Understanding the genomic evolution and adaptation behind the copper binding phenomenon could unveil the industrial potential of these bacterial strains. The second part of this dissertation focuses on understanding the role of anaerobic bacterial populations and communities in uranium immobilization. A large amount of research has been conducted on identifying the bacterial communities involved in in situ uranium immobilization. However, the extant of soil microbial diversity made it difficult to identify the most important specific populations. We employed enrichment culture methods to increase the abundance of potential important bacterial populations and to link the community functions. Finally, I present a study on microbial communities in methane producing agricultural waste co-bioreactors. Methane production has been reported as a highly cooperative reaction between bacteria and archaea. Linking bacterial populations to specific functions would help optimize agricultural waste degradation as well as alternative energy production. I chose these three topics to emphasize the importance of microbial populations in engineered systems. By understanding the roles of individual bacteria populations as well as their interactions with each other in a community, I hope to manage and utilize these microbial resources to improve our living environment.
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Title: Microbial communities associated with the zebra mussel (Dreissena polymorpha) in the Laurentian Great Lakes basin (USA)
Creator: Winters, Andrew D.
Date: 2008
Collection: Electronic Theses & Dissertations

Title: Genomic insights into ecologically important questions for soil bacteria
Creator: Konstantinidis, Konstantinos T.
Date: 2004
Collection: Electronic Theses & Dissertations

Title: Influence of soil age and vegetative cover on microbial community composition : a ribosomal DNA analysis of Hawaiian soils
Creator: Nüsslein, Klaus R. L.
Date: 1998
Collection: Electronic Theses & Dissertations

Title: Vertical and horizontal distribution of denitrifier communities in Pacific Northwest and Arctic marine sediments
Creator: Grüntzig, Verónica
Date: 2007
Collection: Electronic Theses & Dissertations

Title: Analysis of microbial communities in a contaminated aquifer undergoing uranium bioremediation
Creator: Cardenas Poire, Erick
Date: 2009
Collection: Electronic Theses & Dissertations

Title: A chemical analysis of the role of molecular and conformational structure in the adaptation of microorganisms to extreme environments
Creator: Lee, Jeongrim
Date: 1997
Collection: Electronic Theses & Dissertations

Title: The influence of general and inducible hypermutation on adaptation during experimental evolution
Creator: Weigand, Michael R.
Date: 2011
Collection: Electronic Theses & Dissertations
Description: Hypermutator (or mutator) strains of bacteria have been observed in a variety of clinical, environmental, and laboratory populations with up to 1000-fold increases in spontaneous mutation rates. Defects in DNA repair machinery responsible for general hypermutation most commonly include the inactivation of methyl-directed mismatch repair that result in constitutive increases in mutation rate. Alternatively, mutagenic DNA repair only transiently raises mutation rates through the activation of...
Show moreHypermutator (or mutator) strains of bacteria have been observed in a variety of clinical, environmental, and laboratory populations with up to 1000-fold increases in spontaneous mutation rates. Defects in DNA repair machinery responsible for general hypermutation most commonly include the inactivation of methyl-directed mismatch repair that result in constitutive increases in mutation rate. Alternatively, mutagenic DNA repair only transiently raises mutation rates through the activation of low-fidelity polymerases in response to DNA-damaging stress conditions. The widespread existence of both general and inducible mutator genotypes suggests that evolutionary strategies of bacteria include mechanisms for increasing mutability. This work investigates the influence of hypermutation on adaptation through experimental evolution with the contextually relevant model organisms Pseudomonas cichorii 302959 and P. aeruginosa PAO1. Following ~500 generations of growth, both model organisms exhibited comparable improvements in fitness, independent of mutator status, suggesting that hypermutation does not impede adaptation through mutation accumulation. Both general and inducible hypermutation facilitated genotypic diversification that was not observed in non-mutator lineages. The mechanistic differences underlying general and inducible hypermutation were reflected in unique spectra of nucleotide substitutions but did not restrict access to parallel adaptive traits despite considerable variation in gene expression profiles. The diversity in colony morphologies and gene expression traits observed in mutator lineages may represent a broad exploration of sequence space that is no doubt a favorable strategy for adaptation.
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Title: Comparative ecological analysis of ribosomal RNA gene copy number in heterotrophic soil bacteria
Creator: Klappenbach, Joel Albert
Date: 2001
Collection: Electronic Theses & Dissertations

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