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Beecroft, Nelli. "Development of a microbial fuel cell (MFC) and analysis of microbial community dynamics." Thesis, University of Surrey, 2010. http://epubs.surrey.ac.uk/770152/.
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The basis of this work was to understand how the performance of Microbial Fuel Cells (MFCs) can be understood and improved by analysing the behaviour of the microbial communities in the anodic chamber. It was hypothesized that specific types of species generally become more abundant in MFCs over time leading to enhanced power production. An acclimatised microbial consortium obtained from a tubular MFC was used as the inoculum for the MFC described in this study: It was found to lead to a different bacterial composition, but similar power density, to those observed in an MFC inoculated with the unacclimatised community (anaerobic sludge). Using anaerobic sludge as inoculum in four replicate MFCs, both the anodic biofilm and the suspended communities evolved differently. The spatial and temporal dynamics of microbial communities were studied in the tubular MFCs. Although the removal of organic compounds was spatially different, the dynamics of the dominant bacteria showed spatial similarity, probably attributed to the versatile metabolic capabilities of species. No specific species were found the relative abundance of which would have clearly enhanced and correlated with the power production. Using similar substrate feeds and inocula, the communities consisted of metabolically different species in the two reactor types studied. Functional redundancy was observed in the anodic communities of both reactor designs. These findings suggest that the exoelectrogenic ability could be present among a range of bacteria wider than generally thought. 2 The results of this study suggest that the development of the microbial communities in MFCs with a given inoculum and substrate are determined by the reactor design and the operational conditions. Secondly, the adaptation of bacterial communities to produce electricity may not require specific changes in community composition but instead be based on the ability of bacteria to adapt generating electricity and enhance their exoelectrogenic capacity over time.
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Jones, Katy June. "Bioinformatic analysis of biotechnologically important microbial communities." Thesis, University of Exeter, 2018. http://hdl.handle.net/10871/34543.
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Difficulties associated with the study of microbial communities, such as low proportions of cultivable species, have been addressed in recent years with the advent of a range of sequencing technologies and bioinformatic tools. This is enabling previously unexplored communities to be characterised and utilised in a range of biotechnology applications. In this thesis bioinformatic methods were applied to two datasets of biotechnological interest: microbial communities found living with the oil-producing alga Botryococcus braunii and microbial communities in acid mine drainage (AMD). B. braunii is of high interest to the biofuel industry due to its ability to produce high amounts of oils, in the form of hydrocarbons. However, a number of factors, including low growth rates, have prevented its cultivation on an industrial scale. Studies show B. braunii lives in a consortium with numerous bacteria which may influence its growth. This thesis reports both whole genome analysis and 16S rRNA gene sequence analysis to gain a greater understanding of the B. braunii bacterial consortium. Bacteria have been identified, some of which had not previously been documented as living with B. braunii, and evidence is presented for ways in which they may influence growth of the alga, including B-vitamin synthesis and secretion systems. AMD is a worldwide problem, polluting the environment and negatively impacting on human health. This by-product of the mining industry is a problem in the South West of England, where disused metalliferous mines are now a source of AMD. Bioremediation of AMD is an active area of research; sulphur-reducing bacteria and other bacteria which can remove toxic metals from AMD can be utilised for this purpose. Identifying bacteria and archaea that are able to thrive in AMD and which also have these bioremediation properties is therefore of great importance. Metagenomic sequencing has been carried out on the microbial community living in AMD sediment at the Wheal Maid tailings lagoon near Penryn in Cornwall. From these data have been identified a diverse range of bacteria and archaea present at both the sediment surface level and at depth, including microorganisms closely related to taxa reported from metalliferous mines on other continents. Evidence has been found of sulphur-reducing bacteria and of pathways for various other bioremediation-linked processes.
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Perez, Sarah Isa Esther. "Exploring microbial community structure and resilience through visualization and analysis of microbial co-occurrence networks." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/53928.
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Cultivation independent microbial ecology research relies on high throughput sequencing technologies and analytical methods to resolve the infinite diversity of microbial life on Earth. Microorganisms live in communities driven by genetic and metabolic processes as well as symbiotic relationships. Interconnected communities of microorganisms provide essential functions in natural and human engineered ecosystems. Modelling the community as an inter-connected system can give insight into the community's functional characteristics related to the biogeochemical processes it performs. Network science resolves associations between elements of structure to notions of function in a system and has been successfully applied to the study of microbial communities and other complex biological systems. Microbial co-occurrence networks are inferred from community composition data to resolve structural patterns related to ecological properties such as community resilience to disturbance and keystone species. However, the interpretation of global and local network properties from an ecological standpoint remains difficult due to the complexity of these systems creating a need for quantitative analytical methods and visualization techniques for co-occurrence networks. This thesis tackles the visualization and analytical challenges of modelling microbial community structure from a network science approach. First, Hive Panel Explorer, an interactive visualization tool, is developed to permit data driven exploration of topological and data association patterns in complex systems. The effectiveness of Hive Panel Explorer is validated by resolving known and novel patterns in a model biological network, the C. elegans connectome. Second, network structural robustness analysis methods are applied to study microbial communities from timber harvested forest soils from a North American longterm soil productivity study. Analyzing these geographically dispersed soils reveals biogeographic patterns of diversity and enables the discovery of conserved organizing principles shaping microbial community structure. The capacity of robustness analysis to identify key microbial community members as well as model shifts in community structure due to environmental change is demonstrated. Finally, this work provides insight into the relationship between microbes and their ecosystem, and characterizing this relationship can help us understand the organization of microbial communities, survey microbial diversity and harness its potential.Science, Faculty of
Graduate
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Jutras, Eileen Maura 1958. "Field-scale biofiltration: Performance evaluation and microbial analysis." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282533.
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Biofiltration has been shown to be an effective method for the remediation of volatile organic compounds (VOC's), particularly petroleum vapors extracted from the vadose zone. Many bacteria have the enzymatic pathways necessary for aerobic mineralization of VOC's to form cell biomass, carbon dioxide and water. Molecular methods such as nucleic acid hybridizations and the polymerase chain reaction (PCR), are methods that can be applied to environmental samples to characterize bacterial community structure and function. The research presented here reports the use of a field-scale biofilter for the remediation of unleaded gasoline vapors extracted from the vadose zone. An evaluation of contaminant removal efficiency over a five month period showed that the biofilter removed 90% of total petroleum hydrocarbons and greater than 90% of the EPA priority pollutants benzene, toluene, ethylbenzene, and xylene. The bacterial consortium in the biofilter medium readily adapted to increased loading rates, and variations in temperature and moisture. A combination of conventional cultural and molecular methods was used to track the bacterial populations over the course of the experiment. Polymerase chain reaction amplification of the small ribosomal subunit DNA sequence was used for identification of bacterial isolates and the design of DNA hybridization probes. Hybridization of these probes to community DNA samples taken from the biofilter over time revealed changes in specific bacterial populations as bioremediation occurred. Specifically, bacteria that could use gasoline, toluene, ethylbenzene or xylene were prevalent throughout the biofilter. Bacterial populations that could degrade xylene gradually increased over time, while overall total population size was the similar in the background sample and at the end of the study.
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Muhamad, Ali Howbeer. "Metabolomics investigation of microbial cell factories." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/metabolomics-investigation-of-microbial-cell-factories(2e2f5f58-d38a-4c77-966b-56ce92aec619).html.
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The stream of new technological advancements and their integration into the field of microbiology have contributed significantly towards our understanding of life in the micro-scale world, making the fields of microbiology and biotechnology shine like never before. Since 1980, the recombinant protein-based therapeutics industry has become one of the fastest growing sectors in the biopharmaceutical market. Nearly 30% of commercially available recombinant proteins are produced in Escherichia coli, making this species one of the most commonly used bacterial expression systems for the production of recombinant biotherapeutics. However, when it comes to the production of enzymes and bioactive secondary metabolites (antibiotic, antifungal, antiviral and immunosuppressant), Streptomyces species remain the major producer within this sector. Meeting the high demand for such products requires a clear and in-depth understanding of the bioprocesses involved to achieve high yield and quality products, whilst keeping the process industrially attractive. It is generally accepted that the metabolome, as a down-stream process to the genome and proteome, may provide a clearer picture of a biological system. Thus, in this thesis a series of metabolomics approaches were adopted to obtain a deeper insight into the metabolic effects of recombinant protein production in E. coli and Streptomyces lividans. Furthermore, a Geobacter-based biomagnetite nanoparticle production system which displayed a prolonged lag phase upon scale-up was investigated by employing metabolic profiling and fingerprinting approaches combined with multivariate analysis strategies, to identify growth-limiting metabolites. The results of this analysis identified nicotinamide as the growth limiting metabolite. Nicotinamide-feeding experiments confirmed the above findings, leading to improved biomass yield whilst restoring the lag phase to bench-scale level. Raman and Fourier transform infrared spectroscopies combined with stable isotopic probing strategies were also employed to demonstrate the application of metabolic fingerprinting in providing detailed biochemical information for quantitative characterisation and differentiation of E. coli cells at community and single-cell levels. The single-cell approach proved promising, offering detailed biochemical information and perhaps accompanying other cultivation-free approaches such as metagenomics for further future investigations. It is hoped that the advances made in these studies have proved the potential applications of metabolomics strategies to aid the optimisation of microbially-driven bioprocesses.
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Thomason, Michael John. "The microbial chiral inversion of drug molecules." Thesis, University of Brighton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284046.
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Sztyler, Magdalena K. "Molecular analysis of microbial communities from oil industry environments." Thesis, University of Portsmouth, 2014. https://researchportal.port.ac.uk/portal/en/theses/molecular-analysis-of-microbial-communities-from-oil-industry-environments(efa3e316-9da0-48ef-b9d9-cfd42a61fbc0).html.
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The effects of microbiologically influenced corrosion (MIC) can be very expensive to correct, dangerous to workers and its mechanisms are poorly understood. Understanding these processes is important so that they can be monitored and mitigated (Koch et al., 2001). It is now accepted that for the assessment of biocorrosion risks, the most powerful approach is to detect functional genes encoding the enzymes that play an important part in material deterioration (Schadt et al., 2004). The main aim of this study was to identify the microbial community present in corroded and non-corroded systems, and to detect genes that might be implicated in corrosion processes, particularly iron corrosion, so that a biochip could be designed for risk assessment of oil environments. In this thesis the microbial populations and their actives were assessed using sequencing and hybridisation techniques for three oil field sites, generating information that can help identify MIC risk. The final section of the thesis describes the development and design of functional gene probes, identified from hybridisation studies that might be included in a biochip for risk assessment in oil field environments. Microbial groups known to be involved in MIC, such as sulphate-reducing procaryota, iron-reducing bacteria, nitrate-reducing bacteria, hydrocarbon-degrading bacteria were detected, according to their 16S rRNA gene sequence, in the water injection system and production pipelines. In addition to these expected groups, sequences for Firmicutes, acetogens and methanogens were detected. Firmicutes, primarily Clostridium species, and Synergistetes sequences pre-dominated the corroded systems. Functional genes involved in biocorrosion, many of which belonged to the groups named above, were detected using the GeoChip, and a list of marker genes that can be utilised for biocorrosion monitoring has been proposed. Oligonucleotide probes for biochip development were either designed or selected from published sources. A quick and inexpensive method for probe evaluation during microarray development is described. A total of 16 probes, representing 15 genes were tested; all the probes exhibited similar hybridisation behaviour under standard conditions. The results presented in this thesis were part of an extensive EU project, BIOCOR, involving academic and industrial partners, on fundamental and applied aspects of microbial corrosion in oil field environments, which was funded to generate the knowledge needed to develop monitoring techniques for corrosion. The results presented in this thesis are the final report to the European Commission.
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Kioroglou, Dimitrios. "Analysis of microbial populations in wines through NGS methodologies." Doctoral thesis, Universitat Rovira i Virgili, 2020. http://hdl.handle.net/10803/670208.
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La vinificación es un proceso complejo que involucra varias etapas hasta el embotellado y comercialización del vino.
Durante este proceso, la cantidad limitada de nutrientes provoca la competencia microbiana, que resulta en la
producción de metabolitos que modulan el producto final del vino. Esta actividad microbiana puede conferir
características organolépticas beneficiosas o indeseables a la calidad del vino. En los últimos años, el enfoque
principal se ha centrado en la detección y el seguimiento de microorganismos determinados, que supuestamente
estropean el vino, y la aplicación de metodologías empíricas para la prevención del crecimiento microbiano
indeseable. Sin embargo, los hallazgos de las investigaciones han mostrado una base multifactorial del deterioro del
vino, y han subrayado la necesidad de una estrategia innovadora que permita el estudio de la diversidad microbiana
en su totalidad. La secuenciación de última generación parece un enfoque adecuado y prometedor para este
propósito, ya que parece capaz de superar las limitaciones de las metodologías convencionalesevaluación de los resultados derivados en función de su alineación con hallazgos anteriores y su capacidad para proporcionar nuevos conocimientos. En general, el trabajo actual ha logrado corroborar estudios previos, sugerir mejoras sobre las implementaciones relacionadas con la bioinformática y la estadística y ampliar nuestro conocimiento sobre varios factores que influyen en la vinificación. Winemaking is a intricate process, involving various stages until the wine bottling and commercialization. During this process, the limited amount of nutrients leads to microbial competition, which in turn results in the production of metabolites that modulate the final wine product. This microbial activity may confer beneficial or undesirable organoleptic characteristics to the wine quality. The past years, the main focus has been given to the detection and monitoring of specific putative wine-spoiling microorganisms and the application of empirical methodologies for the prevention of unwanted microbial growth. Nevertheless, research findings have shown a multifactorial basis of the wine spoilage and underlined the need for an innovative strategy that will allow the study of the microbial diversity in its entirety. Next-generation-sequencing appears a suitable and promising approach for this purpose, as it seems able to overcome the limitations of conventional methodologies. In this work, various aspects associated to the NGS-based metataxonomic analysis have been studied, in relation to the performance of the NGS technology against conventional applications, and the establishment of a bioinformatic and statistical framework for the analysis of metataxonomic data.
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Faulwetter, Jennifer Lynn. "Analysis of microbial biofilm community composition within constructed wetlands." Diss., Montana State University, 2010. http://etd.lib.montana.edu/etd/2010/faulwetter/FaulwetterJ1210.pdf.
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Constructed wetlands (CWs) are ecologically-based water treatment systems that provide cost-effective amelioration of waterborne pollutants. Fundamental understanding of removal mechanisms, especially microbial processes, limits greater usage of constructed wetlands as a wastewater treatment system. The influence of plant species selection, season, and organic load rate on pollutant removal was previously linked to the redox condition of the sub-surface wetland environment. The goal of this research was to determine which of these environmental variables (including spatial location within the CW) influenced the dominant microbial populations and/or the activity of various sub-populations. Once identified, a constructed wetland might be optimized for growth of microorganisms involved in removal of a specific pollutant. To assess environmental factors, microbial population samples were taken in six locations (effluent, 3 root and 2 gravel areas) within replicate unplanted microcosms and wetland microcosms planted with Deschampsia cespitosa or Leymus cinereus during the summer (24°C) and winter (4°C) seasons. Microcosms were fed a synthetic domestic wastewater in 20-day batches for at least 12 months prior to sampling. The most recent techniques in molecular biology including denaturing gradient gel electrophoresis (DGGE) and quantitative PCR were utilized and included treatment with and without propidium monoazide (PMA) to distinguish between "live" and "dead" microbial communities. Primer sets targeted the entire bacterial community (16S rDNA) and two functional groups, nitrifying bacteria (amoA gene) and sulfate reducing bacteria (dsrB gene). Results indicated that overall microbial community structure (16S rDNA) was affected by general location within the microcosm (effluent, root, gravel) as well the plant species present. Specific microbial groups appeared to be affected differently with relative gene quantities of sulfate reducing bacteria and nitrifying bacteria being influenced by a combined effect of plant species and season. For dsrB, D. cespitosa had the lowest relative gene quantities overall. Both genes were more abundant in the summer season, indicating seasonal importance. Location within the microcosms was also important, with anoxic environments (column bottom) being more important for dsrB presence and a diverse population of cultivated sulfate reducers. The roots were an important location for both microbial diversity and activity for all genes investigated.
'Co-authored by Vincent Gagnon, Carina Sundberg, Florent Chazarenc, Mark D. Burr, Jacques Brisson, Anne K. Camper, Otto R. Stein, Albert E. Parker, Alfred B. Cunningham, and Frank M. Stewart.'
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Nebe-v, Caron Gerhard. "Analysis of naturally occurring microbial populations from diverse environments." Thesis, Coventry University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323034.
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Quedeville, Vincent. "Mathematical analysis, modelling and simulation of microbial population dynamics." Thesis, Toulouse, INPT, 2020. http://www.theses.fr/2020INPT0033.
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La physiologie d’organismes unicellulaires est la conséquence d’un métabolisme central dont le bilan entrée-sortie témoigne à la fois de la richesse du milieu de culture des cellules et de leur état propre. Lorsque des bactéries sont cultivées dans un fermenteur biologique alimenté en un point, transportées dans un écoulement turbulent, elles doivent composer avec des gradients de concentration tout au long de leur séjour dans le réacteur. Simuler cette physique dans une démarche de modélisation multi-échelle nécessite de prendre en compte les lois, bien connues, de l’hydrodynamique, mais aussi de la biochimie des cellules, laquelle est encore assez mal comprise à l’heure actuelle. De plus, le coût prohibitif des expériences numériques impose de réduire les modèles afin de limiter la durée des calculs à quelques semaines. Dans ce contexte, l’attention a été portée sur la phase biologique. La dynamique de la population bactérienne est donnée par une équation intégro-différentielle de transport-rupture dans l’espace des propriétés internes des particules. Le choix des variables les plus à-propos est d’une importance capitale pour rendre compte au mieux de l’évolution temporelle de l’état des cellules au cours de leur trajectoire dans le fermenteur, laquelle est assimilable à un processus markovien. La longueur des micro-organismes rend compte de leur morphologie et leur progression dans le cycle cellulaire, et la vitesse d’assimilation du substrat environnant du transfert de matière avec la phase liquide. La résultante en est le calcul des flux d’entrée dans le métabolisme central des organismes dont les sorties sont les vitesses apparentes d’allongement et, en cas de sur-assimilation, mobilisation de réactions périphériques de combustion de l’excès de matière organique. Outre leur histoire propre, les rendus métaboliques des individus peuvent être impactés par la disponibilité du substrat à leur voisinage, laquelle résulte de l’alimentation et de l’état de mélange du réacteur. Les variables d’état sont à support compact, ce qui soulève la question du caractère bien posé du problème mathématique, de même que résoudre une EDP sur un borné est traditionnellement plus difficile que dans ℝ^n, n∈ℕ. Il est montré que la solution de Malthus de l’équation de transport-rupture est de classe C¹ dès que la fragmentation l’emporte sur la croissance des cellules près du bord droit du support de la distribution en taille. Dans l’ensemble, la solution est continue à chaque instant dans l’espace des états. Ces résultats autorisent la mise en place d’algorithmes de résolution (dans ce travail, par méthodes de Monte- Carlo, Volumes Finis et Quadrature de MOMents) du problème bien posé, lesquels sont exploités pour simuler cinq expériences de génie biochimique dont les conclusions sont détaillées dans la littératureThe physiology of unicellular organisms results from a central metabolism which input-output balance accounts for both the cells’ state and their culture medium’s abundance. When bacteria are cultivated in a locally fed fermenter and transported in a turbulent flow, they have to deal with concentration gradients throughout their trajectory in the reactor. Simulating this physics in a multiscale modelling approach requires taking into account not only the well-known laws of hydrodynamics, but also the cells’ biochemistry which is still ill-understood to date. Moreover, the prohibitive cost of the numerics forces to reduce the models to constrain the duration of the experiments to a few weeks. In this context, special consideration has been given to the biological phase. The bacteria population dynamics is given by an integro-differential transport-rupture equation in the space of the particles’ inner coordinates. Picking the most appropriate variables is of paramount importance to best report the time evolution of the cells’ state throughout their history in the fermenter, the latter being comparable to a markovian process. The microorganisms’ length testifies to their morphology and their progress in the cell cycle, whereas the uptake rate of the surrounding resources leads to an evaluation of the material transfer between the liquid and biotic phases. The result is the estimation of the source term in the organisms’ central metabolism which outputs are the apparent rate of anabolism and, if over-uptake, activation of peripheral reactions to combust the surplus in organic compounds. Beyond their own history, the individuals’ metabolic yields can be impacted by the substrate availability at their neighbourhood, which stems from the feeding and the level of mixing in the reactor. The state variables have a compact support, what raises the question of the mathematical problem’s wellposedness, similarly as solving a PDE over a bounded set is traditionally more difficult than over ℝ^n, n∈ℕ. It is shown that the Malthus eigenfunction associated with the transport-rupture equation is C¹ as soon as fragmentation trumps cell growth near the right-hand edge of the size-distribution’s support. All in all, the solution is continuous at each time in the state space. These results allow the implementation of numerical codes to solve (in this work, by Monte-Carlo, Finite Volume, or Quadrature of MOMents methods) the well-posed problem, the algorithms being exploited to simulate five biochemical engineering experiments which conclusions are detailed in the literature
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Trexler, Ryan Vincent. "Lipid Analysis and Microbial Community Characterization of Subsurface Shale." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480679153855158.
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Capouya, Rachel Danielle Capouya. "Analysis of microbial communities in three diverse commodity systems." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543510790291037.
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Jaenicke, Sebastian [Verfasser]. "The MGX framework for microbial community analysis / Sebastian Jaenicke." Bielefeld : Universitätsbibliothek Bielefeld, 2020. http://d-nb.info/1204561842/34.
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Kretszchmar, McCluskey Vanessa Kirsten Curtis Patricia A. "Microbial analysis of shelled eggs and chemical and functional analysis of liquid eggs." Auburn, Ala., 2007. http://hdl.handle.net/10415/121.
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Jacobsen, Forsberg Ida-Renée. "Biogas from Livestock Manure : Microbial Community Analysis of Biogas Reactors." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for bioteknologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-19391.
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The aim of this experiment was to monitor the microbial communities in two biogas reactors and evaluate the efficiency of denaturing gradient gel electrophoresis (DGGE) as a technique for visualizing shifts in the microbial compositions. The reactors were followed from September 2011 to May 2012. The first reactor is a pilot scale upflow anaerobic sludge blanket (UASB) reactor situated at Foss farm outside of Porsgrunn, running on cow manure. The second reactor is lab scale and situated at Telemark University College, running on pig manure. Samples were taken from the reactors at regular intervals. DNA was extracted from the samples and amplified by polymerase chain reaction (PCR). The primers were 338f and 518r, targeting the 16S rDNA sequence. Changes in the microbial diversity were detected by DGGE in both reactors. Some bands appeared and other disappeared during the period. These changes could not be correlated to changes in operating conditions. This was probably because DGGE reflects cell amounts and not microbe activity levels. DGGE is a highly reproducible and consistently performing fingerprinting technique. It is capable of reflecting long term shifts in the microbial communities and several samples can be compared in one gel. This makes DGGE an effective method for monitoring reactors over time. Several DGGE bands were excised and sequenced, but the results were either negative, or of too poor quality, for further analysis. The probable cause was insufficient separation of bands leading to multiple sequences in the extracted DNA. This may be overcome by using a more specific primer set to reduce the amount of bands.
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Rogers, Michael. "PCR-SSCP analysis of microbial communities in a model system." Thesis, University of Kent, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270818.
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Vet, Stefan. "Dynamical analysis of nutrient-explicit models for small microbial communties." Doctoral thesis, Universite Libre de Bruxelles, 2020. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/308887.
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Microbes form complex communities on Earth. They are crucial for global nutrient recycling in soil and oceans. Inside our body, our intestinal microbiome contributes to our metabolism and protects us against diseases. The dynamics of these microbial communities and their response to environmental changes depend on intra- and inter-species interactions. Computational models are useful to simulate the behavior of such systems and to predict their response to prebiotics or to antibiotics for example. However, due to the multiple, nutrient-dependent interactions, modeling the behavior of such communities remains a real challenge. Mathematical modeling allows for an understanding of the general principles underlying the nonlinear dynamics of microbial communities. Population-based models are based on the abundances of each species but typically do not incorporate the interaction mechanism. Interactions can be mediated by the metabolism of microbes. Therefore, explicit modeling of nutrients is required for a mechanistic understanding of the dynamical behavior of interacting communities. In this thesis we developed and analyzed models accounting for the nutrient-mediated microbial interactions, focusing on competition and mutualistic cross-feeding. In the first part of the thesis, we constructed a nutrient-explicit model that reproduced experimental time series of a small synthetic microbial community, consisting of three species that interact via cross-feeding and competition. The comparison of mono-culture and co-culture dynamics reveals emergent behaviors in co-cultures and highlights the influence of key factors on the population dynamics. In the second part of the thesis, we showed how nutrient-explicit models for mutualistic cross-feeding are related to population-based models, such as the Lotka-Volterra equations. This allows to predict the occurrence of bistability and the presence of a survival threshold. Finally, we extended these results by considering the spatial dimension, and studied how diffusion and advection influence the survival of the community. Our results demonstrate that nutrient-explicit models are able to reproduce experimental time series of microbial communities and to predict the factors determining survival or extinction. By providing a mechanistic understanding of the nonlinear behavior related to microbial interactions, we take a step forward towards the development of predictive models of microbial communities.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Huang, Wen-hsin. "Application of comparative molecular field analysis for predicting microbial sulfoxidation /." Digital version accessible at:, 2000. http://wwwlib.umi.com/cr/utexas/main.
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Kocurek, Klaudia Izabela. "Development of liquid extraction surface analysis mass spectrometry for protein analysis in microbial colonies." Thesis, University of Birmingham, 2019. http://etheses.bham.ac.uk//id/eprint/8848/.
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Liquid extraction surface analysis (LESA) is an ambient mass spectrometry (MS) technique applied for the analysis of proteins from a range of biological substrates. The work described in this thesis focuses on the development of LESA MS-based approaches for the analysis of proteins from microbial biofilms directly on solid nutrient media. Both microbiological research applications as well as clinical applications for the identification of pathogens were considered during development. The reproducibility of LESA sampling on model surfaces and bacterial colonies was investigated. Complementary imaging methods were used to characterise the effects of LESA sampling on the surface of colonies. Sampling protocols were optimised to access proteins from Gram-positive bacteria. Identification of over 40 proteins by LESA MS was subsequently demonstrated for Gram-positive and Gram-negative clinical isolates; de novo sequencing of a novel protein from an unknown strain was also achieved. Characteristic protein masses were used to differentiate closely related species of streptococci. The capabilities of LESA MS for protein identification and characterisation were expanded by the coupling of high-field asymmetric waveform ion mobility spectrometry (FAIMS) into the workflow, overcoming several limitations encountered in the earlier stages of the project. The final challenge involved the sampling of yeast colonies, not ordinarily amenable to lysis by solvents compatible with LESA due to the presence of a thick cell wall. A device was constructed to allow the lysis of yeast colonies directly on agar plates by application of high voltage electric pulses to the colonies prior to LESA sampling. The extraction and identification of proteins in three yeast species was subsequently demonstrated.
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Feng, Xinmei. "Microbial dynamics during barley tempeh fermentation /." Uppsala : Dept. of Microbiology, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200659.pdf.
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Chan, Yu-ki, and 陳裕琪. "Environmental genomic analysis of refuge habitats in hyper-arid deserts." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46917366.
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Kenny, Stephen. "In situ surface analysis of novel marine foul-release coatings." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/42564/.
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Exposure of artificial surfaces such as ship hulls to a marine environment leads to the attachment of assorted biomolecules, single celled organisms and marine invertebrates such as barnacles or mussels. Together, they form a structure known as a biofilm. These films lead to higher fuel consumption and add considerable expense to the operation of ships used by industrial and naval organisations. The work presented in this thesis describes the surface analysis of a novel poly(dimethylsiloxane) (PDMS) based foul-release coating. The coating also contains poly(ethylene glycol) groups (PEG). The differing chemical properties between these two domains led to an observed surface modification effect in water, whereby contact angle measurements decreased from ~110o to ~65 o over a period of five minutes. This effect was rapidly reversible on drying. Time of Flight-Secondary Ion Mass Spectrometry cryogenic depth profiling experiments confirmed this change in surface chemistry where the frozen surface of the coating was shown to have a higher intensity of ions associated with PEG groups at the surface compared to that in the bulk. Water immersion also led to a swelling of the surface seen by a change in the surface topography by Atomic Force Microscopy investigations. When applied to glass surfaces the coatings were flat and generally defect free regardless of the application method used. On exposure to Pseudomonas aeruginosa the coatings were found to be ten times more effective at preventing bacterial adhesion in the first instance than a PDMS standard. The mechanism of action was shown to be non-toxic by live/dead staining and did not appear to affect the way in which bacteria move on a surface. A flow adhesion assay demonstrated that a flow rate of almost two orders of magnitude lower was required to remove fifty percent of bacteria from a coated surface than on a glass standard, demonstrating the foul-release ability of the switching coating. Sea trials in a French coastal region highlighted the importance of exposing candidate coatings to a true marine environment for a suitable duration in order to determine their potential for use. Ultimately we show that the coating presented is a candidate for use as an effective coating for preventing marine biofouling and surface analysis was deemed to be an appropriate methodology to analyse coatings that have changing properties on exposure to water.
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Friedline, Christopher J. "Phylometagenomics: a new framework for uncovering microbial community diversity." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/499.
Full textAbstract:
Microbial communities are recognized as major drivers of global biogeochemical processes. However, the genetic diversity and composition, as well as processes leading to the origin and diversification of these communities in space and time, are poorly understood. Character- ization of microbial communities using high-throughput sequencing of 16S tags shows that Operational Taxonomic Unit (OTU) abundances can be approximated by a gamma distribu- tion, which suggests structuring around small numbers of highly abundant OTUs and a large proportion of rare OTUs. The current methods used to characterize how communities are structured rely on multivariate statistics, which operate on pair-wise distance matrices. My analyses demonstrate that use of these methods, by reducing a highly-dimensional data set (tens of samples, thousands of OTUs), results in a significant loss of information. I demon- strate that, in some cases, up to 80% of the least abundant OTUs may be removed while still recovering the same community relationships; this indicates these metrics are biased toward the highly abundant OTUs. I also demonstrate that the observed patterns of OTU abundance detected from microbial communities can be robustly modeled using techniques similar to those used to model the presence and absence of genes in genome evolution. Using simulation studies, I show that general Markov models in a Bayesian inference framework out- perform traditional, multivariate ecological methods in recovering true community structure. Applying this new methodology to Atlantic Ocean communities uncovered a distance-decay effect which was not revealed by the traditional methods; applying to communities discov- ered on Hog Island point toward mechanisms of thicket establishment. Although the ocean data set operated on a much larger, continental scale, characterization of the sequence data generated from the nutrient-poor soil on Hog Island, a barrier island off the Virginia coast, allows for a better characterization of the processes affecting these communities on a much smaller scale. Finally, using 16S data from the Human Vaginal Microbiome Project, gener- ated here at VCU under the umbrella of the overall NIH HMP initiative, I give examples of the quality control, analysis and visualization pipeline that I developed to support the efforts of this project. In conclusion, my analyses of the metagenomic sequence data from bacterial communities sampled from different environments demonstrate that the proper identification of the biological processes influencing these communities requires the development and im- plementation of new statistical and computational methodologies that take advantage of the extensive amount of information generated in next-generation, high-throughput sequencing projects.
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Cerro, Gálvez Elena. "Analysis of the impact of organic pollutants on marine microbial communities." Doctoral thesis, Universitat Politècnica de Catalunya, 2019. http://hdl.handle.net/10803/668421.
Full textAbstract:
Increasing amounts of organic synthetic chemicals are currently emitted to the environment by human activities. The more recalcitrant fraction of this pollutant mixture reaches marine ecosystems mainly through rivers, continental run-off, and diffuse atmospheric inputs. Once in seawater, it represents the anthropogenic fraction of the dissolved organic carbon (ADOC) pool. However, the total amount of ADOC is unknown, while its effects to ecosystems and detailed composition is largely unknown. Over the past decades, the scientific research effort has focused on the effects of organic pollutants (OPs) in marine biota, especially in oil spills events or under toxicological testing in laboratories, neglecting the importance of the chronic pollution perturbation of the biosphere composition caused by diffusive inputs of large number of pollutants at low concentrations. Our aim was to combine functional genomic tools with quantitative biogeochemical approaches under manipulated conditions to determine the bidirectional interaction between marine microbial community structure and function and the ADOC present in coastal seawater. Additionally, it was also intended to perform similar experiments in areas with diverse environmental conditions to elucidate the role of the trophic conditions and levels of pollutants in the response.
In order to fulfil the proposed objectives, several OP amendment experiments were performed with different OP additions and contrasted seawater from the North-Western Mediterranean, the Arctic and the Antarctic. On the one hand, the effect caused by 4 families of pollutants individually (alkanes, polycyclic aromatic hydrocarbons, organophosphate esters and perfluoroalkyl substances (PFAS)) was tested in 5 marine bacterial communities of the NW Mediterranean, and the specific effect of perfluorooctanesulfonate (PFOS) and perfluorooctanoate acids (corresponding to the family of PFAS) in communities from Deception Island (Antarctica). On the other hand, experiments were conducted to observe the effect of an operationally defined ADOC, which consisted of the non-polar extract of seawater, to bacterial communities from coastal waters with very different starting environmental conditions (Livingston Island (Antarctica), Svalbard (Arctic), Barcelona and Blanes (Mediterranean)).
The results suggest that the baseline ADOC pollution ubiquitously present in the oceans, two orders of magnitude lower than DOC, is modifying bacterial communities and its functionality. ADOC induced the growth of rare taxa, most of them known as pollutants degraders, but also modified the activity of some metabolic pathways from certain taxonomical groups, such as those related to hydrocarbon breakdown and PFOS desulfurization. Consequently, this work provided evidences that ADOC might be changing the dynamics of ocean biogeochemical cycles. The relevance of this perturbation will need to be constrained with future research. At the same time, marine microorganisms are adapted to modulate the concentration and state of incoming pollutants, as an example, we have observed a PFOS decrease in incubations with bacteria from Antarctic waters. However, the bidirectional interaction between ADOC and marine bacteria is closely related with environmental variables and conditions (nutrients availability, water temperature, etc.), as well previous exposure to pollutants probably facilitating an adaptation of the communities. In terms of the pool of ADOC, the same ADOC perturbation did not result in the same response for marine communities in the Mediterranean, Arctic and Antarctica. The suite of microbial responses are thus taxa and compound specific and besides the growth of the rare biosphere, range from degradation of pollutants, changes in the enzymatic activities, modification of the composition of the cell membranes and surface properties, compound specific stress responses, among others.En la actualidad, se emiten cantidades cada vez mayores de productos químicos sintéticos orgánicos al medio ambiente. La fracción más recalcitrante de esta mezcla llega a los ecosistemas marinos principalmente a través de ríos, escorrentía continental y por la entrada difusiva atmosférica. Una vez en el agua de mar, ésta representa la fracción antropogénica de la reserva de carbono orgánico disuelto (ADOC). Sin embargo, la cantidad total de ADOC, su composición específica y sus efectos en los ecosistemas son en gran parte desconocidos. En las últimas décadas, el esfuerzo de investigación científica se ha centrado en los efectos de los contaminantes orgánicos (CO) en la biota marina, especialmente en eventos de derrames de petróleo o mediante pruebas toxicológicas en laboratorio, descuidando la importancia de la contaminación crónica y ubicua causada por la entrada atmosférica. Nuestro objetivo era determinar la interacción bidireccional entre la estructura y función de la comunidad microbiana marina y el ADOC presente en el agua de mar. A su vez, también se quería dilucidar el papel de las condiciones tróficas y los niveles de contaminantes iniciales en la posterior respuesta. Para cumplir con los objetivos, se realizaron varios experimentos de adición de CO a diferente concentración y composición, así como en varias aguas de mar del Mediterráneo, Ártico y Antártida. Por un lado, se probó el efecto causado por 4 familias de contaminantes de manera individual (alcanos, hidrocarburos aromáticos policíclicos, ésteres de organofosfato y sustancias perfluoroalquílicas) en 5 comunidades del Mediterráneo. També se examinó el efecto específico de los ácidos perfluorooctanosulfonato (PFOS) y perfluorooctanoato en la Isla Decepción (Antártida). Por otro lado, se realizaron experimentos para observar el efecto del ADOC, que consistía en el extracto no-polar de agua de mar, en las comunidades bacterianas con condiciones ambientales iniciales muy diferentes (Isla Livingston (Antártida), Svalbard (Ártico), Barcelona y Blanes (Mediterráneo). Los resultados sugieren que la contaminación de ADOC, presente de manera ubicua en los océanos y dos órdenes de magnitud más baja que el DOC (Dissolved Organic Carbon), está modificando las comunidades bacterianas y su funcionalidad. En los experimentos realizados, el ADOC indujo el crecimiento de especies microbianas raras, la mayoría de ellas conocidas como degradadoras de contaminantes, pero también modificó la actividad de rutas metabólicas de ciertos grupos taxonómicos, como los relacionados con la degradación de hidrocarburos y la desulfuración de PFOS. En consecuencia, este trabajo ha proporcionado evidencias sólidas de que el ADOC debe de estar cambiando la dinámica de los ciclos biogeoquímicos oceánicos. Al mismo tiempo, los microorganismos marinos están adaptados para modular la concentración y el estado de los contaminantes entrantes. Como ejemplo, hemos observado una disminución a lo largo del tiempo de la concentración de PFOS en las incubaciones con bacterias marinas antárticas. Sin embargo, la interacción bidireccional entre ADOC y microorganimos está estrechamente relacionada con las variables y condiciones ambientales (disponibilidad de nutrientes, temperatura del agua, etc.), así como la exposición previa a los contaminantes, probablemente facilitando una mejor adaptación de las comunidades. En términos del ADOC, la misma perturbación con ADOC no resultó en la misma respuesta para las comunidades marinas en el Mediterráneo, el Ártico y la Antártida. El conjunto de respuestas microbianas es, por lo tanto, específico de cada taxón y CO. Dicha respuesta puede verse reflejada en el crecimiento de la biosfera rara, la biodegradación de los contaminantes, los cambios en las actividades enzimáticas, la modificación de la composición de las membranas celulares y sus propiedades de superficie, o una respuesta de estrés específica al compuertso, entre otras (...)
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Christie, Graham. "Application of novel particle analysis instrumentation for monitoring microbial fermentation processes." Thesis, University of Warwick, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322688.
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Devine, Carol A. "16S ribosomal DNA analysis of microbial populations associated with hydrocarbon reservoirs." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312360.
Full textAbstract:
The sulphate-reducing bacteria (SRB) are a diverse group of organisms which use sulphate as a terminal electron acceptor and produce the highly toxic gas, hydrogen sulphide. The deleterious effects of this include hydrocarbon reservoir souring, formation damage and microbial corrosion. The SRB are of major economic importance to the oil industry. However, knowledge of the microbial ecology of the deep subsurface remains limited. The aim of this project was to investigate whether organisms are indigenous to the hydrocarbon formation and/or are introduced during drilling operations. A range of molecular techniques such as 16S rDNA sequence analysis, probing with labelled oligonucleotides, and denaturing gradient gel electrophoresis (DGGE) were employed to investigate the microbial diversity in oil field samples. A wide range of bacterial 16S rDNA sequences were identified using these molecular methods. An analysis of drilling mud samples revealed a diverse range of bacterial 16S rDNA sequences confirming that bacteria, including SRB, can be introduced to the reservoir during drilling operations. A number of bacterial 16S rDNA sequences were recovered from a geological core sample taken from a depth of 9,770 feet. The microbial diversity was remarkable in such a high temperature, high pressure environment. This lends credence to the theory that certain bacteria may be indigenous to the subsurface environment. Scanning electron micrographs of core which had been incubated in growth medium indicated the presence of 'nannobacteria'. These tiny coccoids, with a diameter of only 0.1 μm are far smaller than the generally accepted minimum size for cellular life forms. The nannobacteria grew in regular colony shaped structures and were seen only in sections taken from inside the rock. This study indicates that hydrocarbon reservoirs provide an environment in which bacteria, if introduced during drill operations, may become established. However, the subsurface also contains complex indigenous microbial populations that demonstrate considerable species diversity and may include unrecognised life forms.
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Wayne, Jonathan Mark. "The development of molecular techniques for microbial population analysis in landfills." Thesis, Open University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367222.
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TemÃteo, Guilherme de Alencar. "Analysis of microbial contamination of device acrylic manufactured in dental laboratories." Universidade Federal do CearÃ, 2014. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=12052.
Full textAbstract:
Universidade Federal do CearÃA possÃvel presenÃa de microorganismos potencialmente patogÃnicos em prÃteses dentÃrias recÃm-chegadas dos laboratÃrios protÃticos deve ser considerada. Este estudo avaliou o nÃvel de contaminaÃÃo bacteriana e fÃngica de espÃcimes de resina acrÃlica confeccionados em 14 laboratÃrios de prÃtese dentÃria, inscritos no Conselho Regional de Odontologia do CearÃ, na cidade de Fortaleza. Cada laboratÃrio foi solicitado a confeccionar 10 espÃcimes de resina acrÃlica, a partir de modelos padronizados de silicona de adiÃÃo estÃreis, desconhecendo os objetivos da pesquisa. Os espÃcimes recebidos dos laboratÃrios foram colocados em tubos individuais contendo BHI caldo e incubados a 37ÂC por 48 horas e, em seguida, removidos, lavados, colocados em soluÃÃo salina estÃril e agitados para desprendimento microbiano. A suspensÃo obtida foi diluÃda em 1:100, 1:1000 e semeada em placas com Ãgar Sangue, Sabouraud Dextrose Ãgar e HICrome UTI ÃgarÂ, para incubaÃÃo por 48 horas a 37ÂC. Foi obtido o nÃmero de unidades formadoras de colÃnias (UFC) bacterianas e fÃngicas viÃveis, alÃm da identificaÃÃo e quantificaÃÃo de algumas espÃcies de bactÃrias, comparando-se os laboratÃrios por meio dos testes de Kruskall-Wallis e Dunn (α=0.05). Houve contaminaÃÃo advinda de todos os laboratÃrios analizados, com uma contagem de UFC mÃdia de 101438 de bactÃrias e 71047 de fungos. Pseudomonas spp foi o microorganismo a mais prevalente identificado (p<0,05). Foi concluido que existe risco de contaminaÃÃo por bactÃrias potencialmente patogÃnicas e fungos em dispositivos protÃticos recÃm chegados dos laboratÃrios.
The possible presence of potentially pathogenic microorganisms in denture newly arrived from prosthetic laboratories should be considered. This study evaluated the level of bacterial and fungal contamination of specimens of acrylic resin made in 14 dental laboratories registered with the Regional Council of Dentistry of CearÃ, Fortaleza. Each laboratory was asked to fabricate 10 specimens of acrylic resin, from standard models of sterile silicone addition, unaware of the research objectives. Specimens received from laboratories were placed in individual tubes containing BHI broth, incubated at 37ÂC for 48 hours and then removed, washed and placed in sterile saline and stirred for microbial detachment. The suspension obtained was diluted (1:100, 1:1000) and plated on blood agar plates, and Sabouraud Dextrose Agar and Agar HiCrome ICU by incubation for 48 hours at 37ÂC. The number of colony forming units (CFU) bacterial and fungal viable was obtained, besides the identification and quantification of some species of bacteria, comparing the laboratory by means of the Kruskal-Wallis and Dunn (α = 0.05) tests. There was contamination originating from all laboratories analyzed, with a mean CFU counts of 101438 bacteria and 71047 fungi. Pseudomonas spp was the most prevalent microorganism identified (p < 0.05). It was concluded that there is a risk of contamination with potentially pathogenic bacteria and fungi in prosthetic devices newly arrived from dental laboratories.
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McNeil, Betina C. "Mutational Analysis and Characterization of Microbial Pesticides Isolated from Bacillus Thuringiensis." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1316527600.
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Ciotola, Richard J. "Sustainability Analysis and Microbial Community Dynamics in Ambient Temperature Anaerobic Digesters." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1349892050.
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Orschler, Laura. "Developing a Framework for microbial Community Analysis for Wastewater Treatment Systems." Phd thesis, Verein zur Förderung des Instituts IWAR der TU Darmstadt e.V, 2021. https://tuprints.ulb.tu-darmstadt.de/14151/1/Orschler_Tuprints_2020.pdf.
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PCR-based methods have caused a surge in the integration of eco-physiological approaches into research on partial nitritation anammox (PNA). PNA systems have been characterized as fine-tuned biological nitrogen removal (BNR) process with a very complex ecosystem. Therefore, molecular methods, which offer a wide range of approaches comparable to a workman’s toolbox, have been intensively used to understand these PNA systems and achieve a stable process. On the one hand, quantitative PCR (qPCR) became the most com-mon method to quantify target microorganisms in engineered systems such as PNA and oth-er ecological studies and is therefore the so-called gold standard for a fast and reliable quantification. On the other hand, next-generation sequencing (NGS) as a new and ad-vanced approach enabled in-depth analysis, provided new genomes in public databases, and resulted in a more conscious look on the PNA microbiome.
All research work combined in this study revealed a framework to overcome challenges for better integration of the molecular methods in wastewater microbiome studies - which is mainly about understanding the current biases in molecular methods, standardization, and selection of the right combination of molecular methods. In general, data consistency and accuracy strongly depend on the primer selection and data interpretation. The reevaluation of existing primers and the design of a more specific primer will improve the respective mo-lecular studies and support our understanding, which then leads to an improved assessment of nitrification-denitrification (N-DN) and PNA systems.
The combination of traditional microbiology and the modern molecular biological methods has received only marginal attention in this work but will be the non-plus ultra-method for further insights into complex microbiomes.
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Sims, Gary Patrick. "Identification and phylogenetic analysis of morphologically similar naked amoebae using the ssrRNA." Thesis, University of Glasgow, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360123.
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Keay, Lisa Jane Optometry & Vision Science Faculty of Science UNSW. "Public health impact of contact lens related microbial keratitis." Awarded by:University of New South Wales. School of Optometry and Vision Science, 2006. http://handle.unsw.edu.au/1959.4/26307.
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This thesis describes the impact of contact lens-related microbial keratitis in terms of incidence and severity. Disease outcome is defined by visual outcome, costs to the healthcare system, costs to the individual and duration of disease. A successful 12-month surveillance study was conducted of the populations of Australia and New Zealand to detect all cases of contact lens-related microbial keratitis. A random telephone survey of 32,000 households in Australia and 7,500 in New Zealand accurately determined the level of use of various contact lenses in the community. The impact of new contact lens types: silicone hydrogels and daily disposables were investigated. Increased risk persisted in overnight wear with silicone hydrogel materials. Microbial keratitis associated with silicone hydrogel materials had slightly shorter disease duration however other factors had a stronger influence on severity. Rigid gas permeable and frequent replacement soft lenses when used for daily wear constitute the lowest risk. Cost analysis was developed in a hospital case series of microbial keratitis. This analysis was applied in the surveillance study including cases managed in the private health care sector. Disease duration and associated costs are novel indices of severity for contact lens-related disease. The most dramatic effects on disease severity were seen with the type of organism involved. Keratitis attributed to environmental organisms (Gram-negative bacteria, Acanthamoeba, fungi and Nocardia species) were 10x more likely to cause loss of visual acuity, had longer duration of symptoms and incurred higher costs. Importantly, delays in receiving treatment increased disease duration and associated costs. Greater awareness of the need for specialist healthcare is indicated amongst health care providers and contact lens wearers. The hypothesis that overnight wear in silicone hydrogel lenses would not increase the risk of infection has been disproven. This information is of value to practitioners who are responsible for informing contact lens wearers about the risk of contact lens-related infections and should be weighed against the benefits of continuous wear. The identification of factors which contribute to the outcomes of disease will be used in education campaigns amongst health care providers and contact lens wearers to minimise the impact of disease.
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Yadav, Pooja. "Quantitative Analysis of Microbial Species in a Metagenome Based onTheir Signature Sequences." Bowling Green State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1499250693514184.
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Si, Weiduo. "The effect of plant residue decomposition on microbial community composition in soil." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324866.
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Lam, Zamas. "Investigation of mass spectrometric techniques for the structural determination and the sequencing of some bacterial capsular polysaccharides from the family Enterobacteriaceae: Klebsiella and Escherichia coli." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/26429.
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The structural elucidation of bacterial capsular polysaccharides is traditionally performed by using "wet chemical procedures" but instrumental methods such as nuclear magnetic resonance spectroscopy and novel mass spectrometric techniques are coming into prominence.
In this thesis three different mass spectrometric techniques were investigated to establish their applicability for the sequencing of bacterial capsular polysaccharides. These techniques included fast atom bombardment (FAB), desorption chemical ionisation (DCI) and laser desorption ionisation Fourier transform ion cyclotron resonance spectroscopy (LDI-FTICR). The soft ionisation produced by these methods allows sequential loss of individual sugar residues without excess thermal decomposition of the ring. Thus sequencing of oligosaccharides could be achieved.
The most common of all these three techniques is FAB which is already considered to be a well established form of soft ionisation, although the exact mechanism of ionisation is unknown. The utilisation of DCI has not been thoroughly exploited in carbohydrate research, due to the non-volatility of oligosaccharides and the possible thermal decomposition of the sample in the source. LDI-FTICR due to the general unavailability of the instrument has only been used for model studies of "shelf carbohydrates".
In the course of this work it was found that FAB MS and DCIMS complement each other. The sequence of linear oligosaccharides of up to five sugar units can be deduced from either the native or permethylated sample. If the oligosaccharides investigated were generated by phage-borne enzyme, the total sequence of the native polysaccharide can be established. This was illustrated by the use of FABMS on Klebsiella K44 de-O-acetylated oligosaccharide and the reduced oligosaccharide. The sequence of the polysaccharide was shown to be:
[Formula Omitted]
The structural elucidation of bacterial capsular polysaccharides is traditionally performed by using "wet chemical procedures" but instrumental methods such as nuclear magnetic resonance spectroscopy and novel mass spectrometric techniques are coming into prominence.
In this thesis three different mass spectrometric techniques were investigated to establish their applicability for the sequencing of bacterial capsular polysaccharides. These techniques included fast atom bombardment (FAB), desorption chemical ionisation (DCI) and laser desorption ionisation Fourier transform ion cyclotron resonance spectroscopy (LDI-FTICR). The soft ionisation produced by these methods allows sequential loss of individual sugar residues without excess thermal decomposition of the ring. Thus sequencing of oligosaccharides could be achieved.
The most common of all these three techniques is FAB which is already considered to be a well established form of soft ionisation, although the exact mechanism of ionisation is unknown. The utilisation of DCI has not been thoroughly exploited in carbohydrate research, due to the non-volatility of oligosaccharides and the possible thermal decomposition of the sample in the source. LDI-FTICR due to the general unavailability of the instrument has only been used for model studies of "shelf carbohydrates".
In the course of this work it was found that FAB MS and DCIMS complement each other. The sequence of linear oligosaccharides of up to five sugar units can be deduced from either the native or permethylated sample. If the oligosaccharides investigated were generated by phage-borne enzyme, the total sequence of the native polysaccharide can be established. This was illustrated by the use of FABMS on Klebsiella K44 de-O-acetylated oligosaccharide and the reduced oligosaccharide. The sequence of the polysaccharide was shown to be:
[Formula Omitted]
The location of acid-labile pyruvic acid acetal group, like base-labile acetate group, is also difficult to establish chemically.
The fragment ions arising from permethylated oligosaccharides were mostly non-reducing end residues. This is due to the stability of oxonium ion formation. However, when an amino sugar was investigated, oxonium ions were not observed. Instead the cleavage took place between the glycosidic oxygen and the reducing end residue. This fragmentation route is in sharp contrast to previously reported spectral data. This may be due to the fact that amino sugars strengthen the glycosidic bond between the oxygen and the carbon-1.
LDI-FTICR was investigated for its applicability to a "real" sample. The sequence of the linear Klebsiella K44 de-O-acetylated, phage degraded oligosaccharide was determined from the spectrum. Furthermore, a few positions of linkage were also deduced from ring cleavage fragments. Although linkage positions can be obtained from methylation analysis data, some sugar residues such as deoxyhexoses are more labile than others, thus positions of linkage obtained from LDI-FTICR can be used for confirmation.Science, Faculty of
Chemistry, Department of
Graduate
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Pardelha, Filipa Alexandra Guerreiro. "Constraint-based modelling of mixed microbial populations: Application to polyhydroxyalkanoates production." Doctoral thesis, Faculdade de Ciências e Tecnologia, 2013. http://hdl.handle.net/10362/13111.
Full textAbstract:
Dissertação para obtenção do Grau de Doutor em
Engenharia Química e BioquímicaThe combined use of mixed microbial cultures (MMC) and fermented feedstock as substrate may significantly decrease polyhydroxyalkanoates (PHA) production costs and make them more competitive in relation to conventional petroleum-based polymers. However, there still exists a lack of knowledge at metabolic level that limits the development of strategies to make this process more effective. In this thesis, system biology computational tools were developed and applied to PHA production by MMC from fermented sugar cane molasses, rich in volatile fatty acids (VFA). Firstly, a metabolic network able to describe the uptake of complex mixtures of VFA and PHA production was defined. This metabolic network was applied to metabolic flux analysis (MFA) to describe substrate uptake and PHA production fluxes over the enrichment time of a culture submitted to the feast and famine regimen. Then, the minimization of the tricarboxylic acid cycle (TCA) fluxes was identified as the key metabolic objective of a MMC subjected to this regimen by flux balance analysis (FBA). This model enabled to predict, with an acceptable accuracy, the PHA fluxes and biopolymer composition. Subsequently, data gathered from microautoradiography-fluorescence in situ hybridization (MAR-FISH) was used to develop a segregated FBA model able to predict the flux distribution for the three populations identified in the enriched culture. These results were slightly better than those obtained by the non-segregated FBA and were consistent with MFA results. Finally, a dynamic metabolic model was proposed based on the previous models and on a regulatory factor for VFA uptake and PHA production. This model allowed to identify the dynamics of the process and regulatory factor as well as to validate the previous results. Globally, this thesis enabled to demonstrate the potential of using computational tools to understand and optimize PHA production by MMC.
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Malosso, Elaine. "Effects of plant amendment on microbial community structure and fungal biomass in Antarctic soils." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289240.
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Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.
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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host.
The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population.
With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.
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Ibáñez-Peral, Raquel. "Analysis of microbial diversity in an extreme environment: White Island, New Zealand." Australia : Macquarie University, 2009. http://hdl.handle.net/1959.14/44764.
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"June, 2008".Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences, 2009.
Bibliography: p. 227-259.
Literature review -- Materials and methods -- Sampling sites and sampling material -- Enrichment cultures and molecular analyses -- Optical and binding characterisation of the QDs -- Applications of the QDs -- Concluding remarks.
White island, the most active volcano in New Zealand, is a poorly studied environment that represents an ideal site for the investigation of acidophilic thermophiles. The microorganisms present on here are continually exposed to extreme environmental conditions as they are surrounded by steamy sulphurous fumaroles and acidic streams. The sediment temperature ranges from 38°C to 104°C whilst maintaining pH values below 3. A survey of the volcanic hydrothermal system of White Island was undertaken in order to gain insights onto the microbial diversity using culture-dependant techniques and molecular and phylogenetic analyses. A novel liquid medium based on "soil-extract" was designed which supported growth of bacterial and archaeal mixed cultures. Molecular analyses revealed that the dominant culturable bacterial species belong to the Bacteroidetes, Firmicutes and α-Proteobacteria groups. Several previously uncultured archaeal species were also present in the mixed cultures. The knowledge gained from these studies was intended to help in the development of a novel microbial detection technique suitable for community analysis. -- Conventional molecular techniques used to study microbial biodiversity in environmental samples are both time-consuming and expensive. A novel bead-based assay employing Quantum dots (QDs) was considered to have many advantages over standard molecular techniques. These include high detection speeds, sensitivity, specificity, flexibility and the capability for multiplexed analysis. QDs are inorganic semiconductor nanoparticles made up of crystals about the size of proteins. It has been claimed that the physical and chemical properties of the QDs have significant advantages compared to organic dyes, including brighter fluorescence and resistance to photo-bleaching. Their optical properties facilitate the simultaneous imaging of multiple colours due to their flexible excitation and narrow band emission. Functionalised QDs are able to bind to different biological targets such as DNA, allowing high-throughput analysis for rapid detection and quantification of genes and cells. -- The optical and physical characteristics of the QDs as well their interaction with biomolecules are shown to be suitable for the development of a novel bead-based technique able to target the key microbial species and identify them by flow cytometric measurements (FCM). The broad absorption and narrow emission spectra of the QDs, as well as their fluorescence intensity and specify to target biomolecules, was compared to other organic fluorophores. The potential advantages and limitations of QDs as a fluorophores for biological applications are discussed. -- The data acquired during this study provides a broad overview of the microbial diversity and ecology of the volcanically-active hydrothermal systems of White Island and constitutes the baseline for the development of a novel bead-based technique based on QDs.
Mode of access: World Wide Web.
xvii, 259 p. ill. (some col.)
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Vaithanomsat, Pilanee. "Isolation and analysis of recombinant EPSP synthases from microbial pathogens and cyanobacteria." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325387.
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Koltai, Mihály [Verfasser], and Victor [Akademischer Betreuer] Sourjik. "Quantitative analysis of microbial sensing and motility / Mihaly Koltai ; Betreuer: Victor Sourjik." Heidelberg : Universitätsbibliothek Heidelberg, 2016. http://d-nb.info/118061500X/34.
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Koga, shinji. "Screening and enzymological studies of novel microbial enzymes useful for clinical analysis." Kyoto University, 2001. http://hdl.handle.net/2433/150353.
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Iguchi, Hiroyuki. "Functional analysis of interaction mechanism in C1-microbial consortia stimulating methane oxidation." Kyoto University, 2012. http://hdl.handle.net/2433/157680.
Full textAbstract:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第16889号
農博第1905号
新制||農||996(附属図書館)
学位論文||H24||N4650(農学部図書室)
29564
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 阪井 康能, 教授 矢﨑 一史, 教授 小川 順
学位規則第4条第1項該当
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Drees, Kevin Paul. "Quantitative analysis of soil microbial diversity in the hyperarid Atacama Desert, Chile." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/284318.
Full textAbstract:
The Atacama Desert of northern Chile is one of the most arid regions on Earth. The central plateau, between the coastal escarpment and the Andes, is devoid of vegetation and receives only millimeters of rain every few years. Though plants are absent in the soils of this desert, perhaps bacteria can survive, and even thrive, in these hyperarid conditions. This dissertation represents the first comprehensive study of bacterial diversity in the driest central latitudes (approximately 24°S) of the Atacama Desert. Study 1 covers the development of a soil DNA extraction method for the study of soil bacterial populations. This method was field tested in an ecology study in the Santa Catalina Mountains of southern Arizona. In Study 2, Atacama soils were sampled in two transects at approximately 24°S and 25°S. The first transect runs across the absolute (plantless) desert and through several narrow bands of sparse vegetation at high altitudes in the Andes. The second transect is within the well-developed fog zone near Paposo on the Pacific coastal escarpment, where an endemic plant community called lomas is established. Analysis of DGGE profiles of bacterial !6S rRNA genes extracted from these soils with Kruskal's Isotonic Multidimensional Scaling indicates that the bacterial populations cluster into several groups, including the low diversity populations of the core absolute desert, and the higher diversity high elevation Andean populations influenced by the vegetation of Andean biomes. Only one group clustered in the lomas; the rest of the profiles were unique, demonstrating the high diversity of bacterial populations within this diverse vegetation community. Soil 3107, which is within the absolute desert, clustered with the Andean bacterial populations. This soil lies within the transition zone between the low precipitation of the absolute desert (approximately 2.4 mm per year) and the higher precipitation of the high elevation Andes (approximately 47.1 mm per year). This Andean bacterial population may extend further into the absolute desert than the Andean vascular plants due to superior aridity tolerance. Alternatively, this bacterial population may be a relic from when the Andean vegetation advanced through this elevation in a wet period 3000 years ago.
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Haller, Carolyn A. "Dissimilatory FE(III) reduction by Shewanella putrefaciens : biochemical and genetic analysis." Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/25616.
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Hall, Susan. "The role of the soil microbial community in decomposition in a raised mire system." Thesis, University of Stirling, 2001. http://hdl.handle.net/1893/1923.
Full textAbstract:
Peatlands make up 3% of the earth's land surface and contain about one third of the C contained in soils globally. The role of peatlands in the C cycle is as a net sink. Organic matter accumulates in these areas because the rate of net primary productivity (NPP) exceeds the rate of decay. Peatlands are often harsh environments, characterized by cold, wet and anoxic conditions, therefore it is not accelerated NPP which exerts the main control over the accumulation of peat, but the slow rate of decomposition. During the decomposition process, nearly all organic matter passes through the soil microbial pool, and so the soil microbial community is an important factor in the decomposition process. Despite the obvious importance of the soil microbial community in decomposition in peatlands, our knowledge of their role in peatland C cycling is still largely limited. This thesis addresses some aspects of the soil microbial community and investigates their role in decomposition in a raised mire. The soils in a raised mire system may be categorized according to their nutrient input into nutrient rich, mineral soils and soils of the lagg fen, and nutrient poor, soils of the mire expanse. The soil microbial community in the three soils was characterized in terms of size, activity and composition. The size of the soil microbial community in the soils of the mire expanse was small in comparison with that of the mineral soils and soils of the lagg fen, however it was very active. The hypothesis that nutrients restrict the size of the soil microbial community in the soils of the mire expanse was tested. The data showed that nutrients did not significantly effect the size of the soil microbial community. Litterbags were used to investigate the decomposition of a range of plant species found on the different soils and mass loss and C02 production were used as indicators of decomposition. C02 production was a more sensitive and reliable measure of decomposition than mass loss. The size of the soil microbial community was an important factor in decomposition rate. Litter quality of the above ground biomass was not related to decomposition rate. The relationship between the size of the microbial community in contact with decaying plant material and decomposition was investigated. In this study, microbial colonization of decaying litter was not correlated with the measure of litter quality used. This work has provided baseline information the environmental factors that influence decomposition and future work should focus on investigating the changes in the soil microbial community during the decomposition process.
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Porter, Aaron. "MICROBIAL COMMUNITY FUNCTION IN FRESHWATER WETLAND SOILS: USING EXTRACELLULAR ENZYME ANALYSIS TO STUDY THE EFFECT OF MOISTURE AND VEGETATION." VCU Scholars Compass, 2011. http://scholarscompass.vcu.edu/etd/2526.
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Differences in microbial function via extracellular enzyme activity (EEA) were investigated to determine the potential effects of hydrology and plant-soil-microbe interactions in a young non-tidal freshwater riparian wetland. To study these relationships, three plots were established along a moisture gradient (Wet, Intermediate, Dry) within VCU Rice Center Within each main plot, five subplots were left undisturbed while another five were cleared of all above-ground plant biomass. Homogenized soil cores (top 10 cm) were analyzed for pH, redox, C:N, soil organic matter (SOM) content, saturation, and temperature. Microbial function was assessed using extracellular enzyme analysis. For most enzymes, a site difference was observed due to soil moisture content, which had an effect on soil pH, redox potential, and plant community composition. For most extracellular enzymes the presence of vegetation was associated with higher activity. It is important to note that reestablishing native hydrologic and vegetated conditions are paramount in achieving previous functionality.
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Wagley, Pravin Kumar. "Molecular analysis of microbial community structure in open ponds for algal biodiesel production." Thesis, Wichita State University, 2012. http://hdl.handle.net/10057/5980.
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Algal farming in open ponds can be done with simple technology and low capital expenditures. However, in relatively uncontrolled ponds the likelihood that microbial contamination that could affect algal yield is high. We are interested in understanding natural contamination as an ecological process to better control the trajectory of microbial community assembly. Nannochloropsis salina was grown in small outdoor open ponds (100 L; 10 cm deep) through three cycles of batch culture using a simplified brackish growth medium. Time-course samples were monitored via pigment analyses, and direct microscopic counts. Extracted metagenomic DNA was subjected to touchdown PCR for amplification of 16S rRNA genes with universal bacterial primers and 18S rRNA genes with algae-specific primers, both using GC-clamps. PCR products of similar lengths were separated by melting characteristics using denaturing gradient gel electrophoresis (DGGE). Contamination of the open ponds by algae was not observed over three two-week batch culture cycles, however, contamination by bacteria was observed. Salinity and pH were likely major factors behind limited algal contamination. DGGE bands from bacterial 16S rRNA gene amplifications were excised, eluted, reamplified, and sequenced, revealing a diverse consortium of bacteria including Aeromonas, Loktanella, Marinobacter, and Pseudomonas. Most of the bands were seen on third and fourth day of the batch culture. As the culture progressed, the number of bands seen with DGGE decreased. Band migration was measured and relative front values were calculated. A 2% overall window was used to analyze how closely one band is associated with another. Overall there were 22 individual bands designated as novel based on relative front values. A dendrogram of relatedness was created to compare time-course samples from triplicate ponds, supporting the conclusion that community assembly was more of stochastic than deterministic in nature.Thesis (M.S.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Biological Sciences