Dissertations / Theses: 'Environmental microbiology'

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Dumas, Eve-Marie. "Development of new imaging tools for environmental microbiology." Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=95020.

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Environmental microbiology is a field that has been explored for years using tools which are limited in their ability to adapt to the environment studied. The goal of this thesis is to develop new tools for in situ imaging of microorganisms. The first of these tools is a class of photoluminescent probes for fluorescence microscopy. Many microscopic dyes have been used with light microscopes to label microorganisms, but the protocol of each of these techniques limits either the type of organism targeted or the type of environment that can be studied. Most of these probes also only work for a short time due to photobleaching or degrade if stored. An emerging class of fluorophores in the field of cellular and microbiology is the quantum dot (QD), a semiconductor nanoparticle which has recently been made biocompatible. The use of QDs as bacterial probe I studied here, and characterized by studying the particles' interaction with and cytotoxicity to several test organisms, both Gram positive and Gram negative. We find that QDs are toxic to most bacteria due, among other things, to their production of reactive oxygen species. However, this affect varies from one strain to another, suggesting the existence of resistance mechanisms. Although QDs are more toxic to Gram negative strains, electron transfer and depolarisation does not seem to be the source of the toxicity. QDs have a promising future in microbiology as both labeling and anti-microbial agents. In the second part of the thesis, a new microscopic technology was explored for field use: live in-line holographic microscopy. A custom, laser-based holographic microscope was used in a Mars analogue site in order to determine whether it was capable of surviving the harsh conditions and of providing valid data. We experimented in automating the system by combining it with an amphibious robot which was shown to be able to pull the holographic microscope while the latter was recording. Overall, these findings
La microbiologie environnementale est une discipline qui a longtemps été explorée à l'aide d'outils qui sont limités par leur habileté à s'adapter à l'environnement. Le but de cette thèse est de développer de nouveaux outils pour l'imagerie de microorganismes in situ. Le premier de ces outils est une classe de sonde photolumineuse pour la microscopie fluorescente. Plusieurs teintures ont été utilisé avec des microscopes à lumière afin d'étiqueter des microorganismes, mais chacune de ces techniques est limitée par son protocole. Ces techniques peuvent soit seulement cibler certains types d'organismes, soit sont limitée au niveau de l'environnement étudié. De plus, La plupart de ces teintures sont blanchient par la lumière et ne peuvent être entreposée très longtemps. Les points quantiques (PQ), une nanoparticule semiconductrice qui est maintenant biocompatible, sont maintenant utilisés en microbiologie. J'ai explore ici, l'utilisation de PQs comme sonde bactérienne et les est caractérisée en étudiant leur interaction avec et la toxicité causée à plusieurs microorganismes. Nous avons démontré que la toxicité des PQs est causée, entre autre, par la libération d'espèces d'oxygène réactive. Cependant, l'effet observé varie selon la souche, suggérant l'existence d'un procédé de résistance aux PQs. Nous avons conclus que malgré le fait que les bactéries Gram négatives sont plus affectée par les particules que les Gram positives, le transfère d'électron et la dépolarisation ne sont pas en cause. Les PQs ont un futur prometteur en microbiologie entant que sonde et agent antimicrobien. Dans la seconde partie de cette thèse, l'utilisation d'une nouvelle technologie microscopique sur le terrain a été explorée. Un microscope holographique au laser modifié a été utilisé sur un site analogue à la planète Mars afin de s'assurer que l'instrument pouvait subir ces conditions extrêmes sans dommage et pouvait

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Jaber, Salah. "Canine faeces : the microbiology of an environmental health problem." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/3849/.

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The overall aim of the research work reported in this Thesis was to study a variety of aspects of dog faeces in relation to public health, their fertilizer potential and possibility that such faeces might be remediated using larvae, ultimately to provide a source of biodiesel. The results can be summarized as follows: 1) Dog faeces were shown to be source of pathogenic bacteria, notably Escherichia. coli and Salmonella. These bacteria were shown to be transferred to the soil of a local playing field by direct, in situ, transfer from dog faeces undergoing weathering. E. coli and Salmonella enterica were isolated from all four sites while no such isolates were obtained from the fifth location which was uncontaminated with dog faeces 2) It was shown here that “common or garden” slugs can transfer potentially pathogenic bacteria from dog faeces to lettuce. 3) The feeding of Black Soldier Fly Larvae on faeces led to a statistically significant increase in the number of bacteria inside the BSFL gut and the same trend was seen in relation to dog faeces fed Fruit Beetle Larvae. This trend of increasing bacterial numbers in larvae fed on dog faeces is particularly worrying in relation to the potential feeding of these larvae to animals- post exposure to faeces. 4) Dog faeces were shown to have potential inherent fertilizer content; the nutrients present being released over a time period mimicking the natural weathering of dog faeces in the environment. 5) As a generalization, the addition of both types of larvae to dog faeces significantly reduced the concentration of indigenous plant nutrients over the entire four week incubation period; exceptions to this were nitrate and phosphate concentrations in BSFL treated faeces, where significant increases were seen at week 4 and 3 respectively and in faeces treated with FBL, where ammonium concentrations were significantly increased at weeks 2-4, and phosphate at week 4. While the addition of both larvae therefore IV initially decreased levels of indigenous plant nutrients there was a trend in some of the nutrients to increase the longer the incubation went on. This suggests that perhaps a longer term exposure of dog faeces to the two larvae might have lead to increase in ammonium, nitrate, sulphate and phosphate concentrations. The addition of ammonium, elemental sulphur an insoluble phosphate to dog faeces which had been modified by the two larvae led to significant increases in nitrate, sulphate and plant-available phosphate, results which shows that that dog faeces contains the indigenous microflora required for the transformation of these amendments (which simulate fertilizer addition). The results suggest the possibility that larval modified dog faeces could be used as compost additive fertilizer, or perhaps even be used as an agricultural soil fertilizer. 6) The potential for using fly larvae for the bioremediation of dog faeces was investigated. Black Soldier Fly (BSFL) and Fruit Beetle (FBL) Fly larvae were shown to dramatically improve the physical nature of canine faeces, even after only a short exposure period, giving a bioremediated product which is markedly improved in terms of texture, reduced odour and overall reduced offensiveness. The bioremediated dog faeces product was also found to be suitable as potting compost when “diluted” with proprietary potting compost. 7) The haemolymph and total body extracts of BSFL and FBL were shown to be antibacterial. 8) The potential for using dog faeces and dog faeces which had been treated with BSFL and FB as a source of biodiesel was determined. It was shown that potential biodiesel precursors) (mainly fatty acids) were present both in the raw dog faeces and in faeces which were treated with the two different larvae. 9) The number of bacteria present in dog faeces disposed of in plastic bags dramatically increased over exposure to the UK summer, when temperatures were recorded between 10-270C.

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Iker, Brandon Charles. "Application of Advanced Molecular Techniques in Applied Environmental Microbiology." Diss., The University of Arizona, 2013. http://hdl.handle.net/10150/301699.

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Recent advancements in molecular biology such as next generation sequencing and more sensitive and rapid molecular detection methods like qPCR, have historically been developed for clinical applications in human genetics and for health care diagnostic purposes. The high demand for faster and more accurate molecular assays in the health care field has driven rapid development of inexpensive molecular techniques that when applied to the science of environmental microbiology, provides an unprecedented level of understanding of the microbial world around us. The goal of this dissertation is to begin to apply more advanced molecular technologies to problems in applied environmental microbiology. Appendix A is a brief literature review of next generation sequencing technologies for applications in environmental microbiology. Appendix B focuses on the development of a more robust virus nucleic extraction kit for the detection of viral genomes from environmental samples found to contain high concentrations of qPCR inhibitors, such as humic acids or heavy metals. Appendix C summarizes one of the largest virus surveys done in the US, using state of the art qPCR technologies in both wastewater influent and effluent from two wastewater treatment plants in the Southwest. Data suggests that traditional virus indicators may not be a viable tool to evaluate fecally impacted source water or virus removal during water treatment. The third study summarized in Appendix D, provides one of the first insights into the microbial ecology of biofilms utilized as biological treatment media using Roche 454 amplicon sequencing of the 16S rRNA gene.

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Amasah, Reda. "Studies on the environmental microbiology and biogeochemistry of desert surface soils." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2769/.

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Microorganisms play a key role in the functioning of the environment, particularly in relation to the biogeochemical cycles. Here, a study was made of the microbial activity of primitive desert surface soils in comparison with that exhibited by a fertile agricultural loam soil. The microbial transformations studied included nitrification, the hydrolysis of urea, the oxidation of elemental sulphur to sulphate and phosphate solubilisation; these processes were collectively used to study the biogeochemical activity of desert surface soils. Bacterial population densities in the desert surface soils, fertile loam soils and volcanic, cave rock samples were also determined. A variety of bacterial isolates from desert surface soils and cave rock samples have been identified using molecular identification techniques like DNA extraction, PCR amplification, determinations of 16S and 18S rRNA gene sequences. The isolation and characterization of extremophilic bacterial strains from a dormant volcano on the island of Reunion is reported, using molecular identification, morphological and physiological studies. As the area of the volcano, from which these bacteria were isolated, has not been recently active, it was considered of interest to determine if these bacteria grow, or merely survive, in a mesophilic environment. Nuclear magnetic resonance spectroscopy (NMR) was used to study the compatible solutes in these isolates when growing under high temperatures, low and high pH stresses and at various concentrations of NaCl. Finally, various environmental samples were tested in order to detect the presence of Mycoplasma using an EZ-PCR Mycoplasma Test Kit.

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Al-Mousa, Fawaz Ali F. "Neurotoxicity of environmental pollutants." Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/1461/.

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Brominated flame retardants (BFRs) and alkylphenols (APs) are pollutants commonly found within the environment and have human health concerns due to their endocrine disrupting and cytotoxic effects. BFRs are used to reduce the flammability of a variety of consumer products such as foam furnishings, whereas APs are found in plastic products used by the food industry. This study investigated the neurotoxicity of the most commonly used groups of BFRs and APs on SH-SY5Y human neuroblastoma cells. The results presented in this thesis showed (using cell viability assays) that these pollutants are toxic at low concentrations. Some compounds such as hexabromocyclododecane (HBCD) and 4-nonylphenol (4-NP) induce cell death (apoptosis) by caspases activation (Casp-8, Casp-9 and Casp-3) and cytochrome c release at low micromolar concentrations (IC50 ~ 4μM and 6μM, respectively). Consequently this study also showed that these compounds increased intracellular [Ca2+] levels and the production of reactive oxygen species (ROS) within SH-SY5Y cells by causing Ca2+-dependent depolarization of the mitochondria. In support of a Ca2+-mediated mechanism, the data presented here shows that some BFRs and APs inhibit Sarcoplasmic/ Endoplasmic Ca2+-ATPase (SERCA) and to corroborate this over-expressing SERCA1 improved cell viability especially in cells exposed to certain cytotoxic chemicals such as HBCD; this study is the first experiment of this type to be performed. This study also showed that some of these chemicals, at low concentrations had amyloidgenic effects causing the cleavage amyloid precursor protein (APP) into Beta-amyloid (Aβ) and could therefore be implicated in Alzheimer‟s disease (AD).

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Amos, Gregory C. A. "Environmental reservoirs of antibiotic resistance." Thesis, University of Warwick, 2013. http://wrap.warwick.ac.uk/58024/.

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Emerging antibiotic resistance mechanisms threatens the foundation of modern medicine. Growing evidence suggests anthropogenic inputs such as agriculture could form reservoirs of resistant bacteria which could directly or indirectly transfer to humans. Waste Water treatment plants (WWTPs) are an input which contains waste from several sources including that of human, animal and industry, providing a hot-spot for horizontal gene transfer to occur between bacteria from many origins. In this project we evaluated the role of WWTPs in creating environmental reservoirs of antibiotic resistance. An initial study investigated the impacts of WWTP effluent on the antibiotic resistant bacterial load in downstream rivers, particularly focusing on the class 1 integron as a marker for resistance. WWTP effluent was responsible for significantly higher levels of resistant bacteria in downstream river sediments compared to upstream, a result of the introduction and/ or selection for a diverse range of class 1 integrons. A second study investigated the effects of effluent on the clinically important antibiotic resistance gene blaCTX-M-15. Numerous examples of blaCTX-M-15 carried on new genetic contexts in association with new pathogenicity determinants were recovered, as was evidence for transfer of blaCTX-M-15 between diverse bacteria. The prevalence of blaCTX-M-15 as well as the diversity of its carriage were both increased greatly by WWTP effluent. The final study was on the Thames River basin in the UK, where we developed a model with the ability to predict antibiotic resistance load and exposure. This work suggests that WWTP effluent contributes to environmental reservoirs of resistant bacteria which could be of clinical importance. There is a danger that continued expansion of environmental reservoirs of antibiotic resistance will lead to increased therapeutic failure in the clinic and ultimately the end of the antibiotic era.

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McMullan, Geoffrey. "The biodegradation of organophosphonates by environmental bacteria." Thesis, Queen's University Belfast, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317516.

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Danczak, Robert E. "Dynamics in Microbial Ecology Across an Environmental Stability Gradient." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1530878203337741.

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Yuan, Heyang. "Bioelectrochemical Systems: Microbiology, Catalysts, Processes and Applications." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/79910.

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The treatment of water and wastewater is energy intensive, and there is an urgent need to develop new approaches to address the water-energy challenges. Bioelectrochemical systems (BES) are energy-efficient technologies that can treat wastewater and simultaneously achieve multiple functions such as energy generation, hydrogen production and/or desalination. The objectives of this dissertation are to understand the fundamental microbiology of BES, develop cost-effective cathode catalysts, optimize the process engineering and identify the application niches. It has been shown in Chapter 2 that electrochemically active bacteria can take advantage of shuttle-mediated EET and create optimal anode salinities for their dominance. A novel statistical model has been developed based on the taxonomic data to understand and predict functional dynamics and current production. In Chapter 3, 4 and 5, three cathode catalyst (i.e., N- and S- co-doped porous carbon nanosheets, N-doped bamboo-like CNTs and MoS2 coated on CNTs) have been synthesized and showed effective catalysis of oxygen reduction reaction or hydrogen evolution reaction in BES. Chapter 6, 7 and 8 have demonstrated how BES can be combined with forward osmosis to enhance desalination or achieve self-powered hydrogen production. Mathematical models have been developed to predict the performance of the integrated systems. In Chapter 9, BES have been used as a research platform to understand the fate and removal of antibiotic resistant genes under anaerobic conditions. The studies in this dissertation have collectively demonstrated that BES may hold great promise for energy-efficient water and wastewater treatment.
Ph. D.

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AhÌ£mad, MushtaÌ„q. "Physiological studies on environmental and hospital isolates of 'Enterococcus' spp." Thesis, University College London (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362430.

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Walter, Diana Joyce, and dianawalter@internode on net. "The Environmental Impact of Genetically Modified Crop Plants on the Microbiology of the Rhizosphere." Flinders University. Biotechnology, 2005. http://catalogue.flinders.edu.au./local/adt/public/adt-SFU20070301.161014.

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The effect of genetically modified crop plants on the microbiology of the rhizosphere was investigated using the single-gene Bt cotton as a case study. The project compared the rhizosphere microbiota of four Ingard® 1cotton plant varieties that were closely matched with their non-GM parental strains. The plants were grown in three different Australian soils, ie, a vertisol from a cotton-growing region, and two soils, a fine sandy loam and a red sand from South Australia that had not been exposed to cotton. At the time of the commencement of the project, the only commercially available genetically modified plants were cotton and carnations. The cotton industry in Australia is worth $1.5b annually, and care of the soil and the dynamics of its living microbial consortia needs to be understood for optimum management to enable agricultural sustainability. The general outline of the thesis incorporated four main sections: 1. Experimental setup and analysis of the soils and plants to be used, quantification of the Cry1A(c) plant-produced Bt protein, and its persistence in the soil environment. 2. Measurement of the selected microbial populations of bacteria, fungi, AMfungi, protozoans and nematodes, by counting and estimation by dilution and most-probable number methods. 3. Assessment of selected metabolic pathways to determine the effects on the soil microbial community by chemical and other biochemical methods 4. An overall analysis between different group ratios of expression of each of the variables tested, and the summary of the risk analysis and conclusion. The outcome of this work was the acquisition of scientific data to produce an environmental impact report. The findings of this study showed that generally the microbial populations and the products of major metabolic pathways correlated more closely within the non-GM and GM plant rhizospheres of the paired trials than those of separate trials, indicating that soil and plant cultivar had a stronger environmental effect. The results obtained from the paired trials did not show that there were consistent effects on the rhizosphere soil microbiota that could be attributed to the presence of the Cry1A(c) Bt plant protein on the selected strains of cotton plants. The results from the tests of the paired trials correlate highly with previously published work that the risk factors of genetically modified cotton plants on the microbiology of the rhizosphere soil were found be negligible and not consistent across trials. 1 ® Monsanto Co. St Louis, MO.

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Al-khzaiym, Tariq Mohammad Saleh. "Implication of the use of organic bismuth compounds on aspects of medical and environmental microbiology." Thesis, University of Sheffield, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414657.

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Kaplarevic, Mihailo. "Environmental genome informational utility system (EnGENIUS)." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 126 p, 2007. http://proquest.umi.com/pqdweb?did=1362531681&sid=19&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Haines, Sarah R. "Characterization of bioaerosols in dust collected on the International Space Station (ISS)." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1554869142685621.

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Komitopoulou, Evangelia. "Environmental sensing and stress resistance in Salmonella typhimurium." Thesis, University of Surrey, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252342.

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Wise, Ben. "Community Composition of Nitrite Reductase Genes in an Acid Mine Drainage Environment." Thesis, University of Colorado at Denver, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10607867.

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High elevation, mountainous regions have a high concentration of mining activities and resulting acid mine drainage (AMD) that is typically acidic and often contains elevated concentrations of metals. The impacts of AMD on denitrifying microbial communities is not well understood, despite these organisms’ central role in the nitrogen cycle, contribution to greenhouse gas production, and potential to provide ecosystem services through the mitigation of nitrogen pollution. This study examined denitrifying microbes across four regions within the Iron Springs Mining District (13 sites over four time-points) located in Southwest Colorado at high elevation that receive AMD or naturally-occurring acid rock drainage (ARD). Denitrification functional gene sequences ( nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.2, dissolved oxygen as low as 1.0 mg/L, and metals >10 mg/L (including aluminum, iron, manganese, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The total nirS community structure was correlated to iron, conductivity, sodium, and calcium, which may suggest that these factors play an important role in shaping the nirS community. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD and provide a foundation for future research to understand the rates and physiology of these denitrifying organisms.

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Sackett, Joshua David. "Comparative microbial ecology of sediment-associated microbial communities from anthropogenically and endogenously metal impacted systems." Thesis, University of Colorado at Denver, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=1598320.

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Microorganisms, particularly the Bacteria, are differentially impacted by metal toxicities, and will respond very quickly to changes in their environment, making them ideal bioindicators of environmental health. In this study, we evaluated the sediment-associated bacterial diversity of fifty-seven samples collected from twenty-four anthropogenically and endogenously metal impacted, geographically distinct sites in the Colorado Mineral Belt, and elucidated the factors that correlated with observed differences in the bacterial community structure. Overall, the geochemistry of all sites distinguished anthropogenic from endogenous sources of metal impact. Anthropogenic samples, on average, had higher concentrations of total recoverable and dissolved sodium and magnesium, and lower concentrations of aluminum and zinc, compared to the endogenous samples. Bacterial communities from both anthropogenically and endogenously metal impacted sites were characterized using Illumina high-throughput amplicon sequencing of the V4 region of the 16S rRNA gene. Overall, bacterial communities were remarkably diverse, with endogenously metal impacted sediments having higher diversity compared to anthropogenic sediments. The Actinobacteria and Betaproteobacteria dominated anthropogenic samples, and the Acidobacteria and Deltaproteobacteria dominated endogenous samples. Clustering of bacterial communities based on membership and structure (presence/absence and relative abundance of particular taxa, respectively) also distinguished samples based on their source of metal impact. Analysis of similarity (ANOSIM) tests indicated a significant difference between bacterial community structure based on source of metal impact (weighted UniFrac R_ANOSIM = 0.746, p = 0.001). Mantel tests indicated that total recoverable magnesium concentrations accounted for ∼54% of variance in community structure of all bacterial communities in the study. Dissolved aluminum concentrations accounted for ∼71% of the variation in all communities with an anthropogenic source of metal, and dissolved aluminum concentrations also accounted for ∼41% of the variation in bacterial communities with endogenous sources of metal impact.

This study provides one of the first direct comparisons between microbial community structures of sediments based on source of metal impact. This study is also one of the first comprehensive characterizations of bacterial communities from naturally occurring iron fen systems.

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Powell, David C. "Characterization of Iron-Bearing Solids Used by Naturally-Occurring Microbes in the Anaerobic Degradation of Hydrocarbons." W&M ScholarWorks, 2000. https://scholarworks.wm.edu/etd/1539617754.

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Heaton, Joanna Catherine. "The Environmental Microbiology of Salad Vegetables and Factors Affecting the Survival of Enteropathogens in the Phyllosphere." Thesis, Lancaster University, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518196.

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Lim, Chae-Hong. "The effect of environmental factors on the physiology of Aeromonas hydrophila in lake water." Thesis, University of Warwick, 1995. http://wrap.warwick.ac.uk/109022/.

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The survival and physiological responses of A. hydrophila were investigated in lake water microcosms under starvation and other stress conditions. Longer survival was shown in filtered- autoclaved water than in Whatman-filtered water than in untreated water. Longer survival also occurred at 4° than at 15° than at 25° than at 30° than at 37°C. The enhanced survival times over unamended controls suggesting that protozoa could be involved in regulating the size of the population of A. hydrophila. Nutrient amendments such as synthetic sewage, casein, ammonium sulphate, serine and glutamine also increased survival of A. hydrophila over that in unamended controls. Organic compounds released from Flavobacterium, Anacystis, and a number of algae also increased survival times of A. hydrophila in Filtered-autoclaved lake water microcosms. Cell size was reduced under starvation conditions and the numbers of cells capable of respiration also decreased but was always greater than their viable count especially if cells were starved at 37°C. This suggests that A. hydrophila is capable of entering a viable but non-culturable phase under starvation conditions. The effects of starvation on two enzymes, phosphatase and exoprotease, both important in the scavenging of nutrients were examined. The activity of alkaline phosphatase and exoprotease both increased under starvation stress with the largest increases being seen at higher starvation temperatures although the viable count often decreased below the limits of detection at the same time. Nutrient amendments, such as a variety of carbon and nitrogen sources, led to an increase in activity of both enzymes and also led to induction of alkaline phosphatase activity in cells grown in high phosphate medium to repress alkaline phopsphatase activity. This is an obvious indicator that derepression of alkaline phosphatase and synthesis of the enzyme could occur under these conditions in lake water microcosms. Exoprotease activity was also increased upon the addition of single nutrient source to the microcosms. Osmotic stress coupled with starvation stress also increased alkaline phosphatase activity and the addition of the osmoprotectant, betaine, also increased activity. In both cases activity increased although the viable count decreased, in some cases below the limits of dection. Exoprotease activity increased in osmotically shocked cells and increased further if betaine was added to the starvation medium. Plasmid transfer could still occur between A. hydrophila and Escherichia coli in unamended and lake water microcosms amended with carbon and some nitrogen sources. The transfer of the F group plasmid R1drd19 was temperature dependent with no detectable transfer occurring at temperatures below 15° C even in nutrient broth. Plasmid transfer was dependent upon the size of the donor and recipient populations with no detectable transfer occurring at low population densities but transfer at high densities shows that even under prevailing environmental conditions the transfer of F-plasmids was possible between E. coli and A. hydrophila. The changes in protein fingerprints of cell and periplasm extracts under starvation and other stresses were examined using two-dimensional gel electrophoresis. Several starvation specific proteins were identified on the gels and some proteins which were only transiently produced were noted. The N-terminal sequences of two stress proteins produced in response to starvation and ethanol and heat stress were obtained from the gels. Alkaline phosphatase one of the key proteins in the response to stress was also identified by colourimetric staining of two-dimensional gels. The survival of A. hydrophila under starvation and other stresses is dependent upon the sequential synthesis of many proteins, including alkaline phosphatase.

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Hoosain, Nisreen. "Phenotypic and molecular analysis of Helicobacter spp. and related micro-organisms identified in clinical & environmental specimens." Master's thesis, University of Cape Town, 2006. http://hdl.handle.net/11427/2709.

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Bai, Guiyun 1964. "Biosurfactant-enhanced nonaqueous phase liquid (NAPL) removal and bacterial transport in porous media." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282451.

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The well documented ineffectiveness of traditional pump-and-treat technology on the cleanup of non aqueous phase liquid (NAPL) contaminated sites has incurred an intensive research activities in improving the efficiency of NAPL removal from subsurface. Surfactant enhanced subsurface remediation has been proposed as one such option. In this dissertation, a series laboratory experiments were conducted to investigate the potential application of a microbially produced surfactant (biosurfactant) on NAPL removal and the effect on bacteria transport. Monorhamnolipid biosurfactant, produced by Pseudomonas aeruginosa ATCC 9027, was used in all the studies. Hexadecane was used as model NAPL to represent petroleum based products which are common NAPLs detected in contaminated sites. Results showed that rhamnolipid biosurfactant is effective in removing residual hexadecane from sandy soil. In the surfactant concentration tested in this study (40 to 1500 mg/L), mobilization of hexadecane is the main mechanism of the removal. In addition to displacement of hexadecane droplets from subsurface porous matrixes, dispersion or emulsification of hexadecane into surfactant solution also played an important role in hexadecane removal. The performance of this anionic rhamnolipid surfactant is greatly affected by the addition of electrolytes and the change of pH. Addition of Na⁺ and Mg²⁺ can significantly increase the solubilization capacity of rhamnolipid and reduce the interfacial tension between hexadecane and surfactant solution, while addition of Ca²⁺ has a competing effects of enhanced solubilization and Ca²⁺ induced rhamnolipid precipitation. Control of ionic strength and pH can be used to optimize surfactant systems to enhance the NAPL removal depending on the nature of NAPL (LNAPL or DNAPL). Addition of rhamnolipid can also enhance the transport of three bacterial cells with varying hydrophobicity, P. aeruginosa ATCC 9027, 27853, and 15442, by decreasing cell adsorption. This is because the adsorption of surfactant to the porous medium surface increases the surface negative charge density, hence the adsorption of bacteria to the surface is reduced. No significant influence of rhamnolipid on the bacteria surface properties is observed. The measured bacteria breakthrough curves were simulated by an advection-dispersion transport model incorporating two domain reversible sorption (instantaneous and rate-limited) and with two first order sink terms for irreversible sorption. Model simulation suggests that rhamnolipid mainly affects the irreversible sorption of cells.

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Sanchez, Luis R. "Removal of bacterial indicators and pathogens from dairy wastewater by a treatment system." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/284075.

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An integrated wastewater treatment facility at a dairy in Glendale, Arizona, consisting of an upper subsystem (solids separators, anaerobic lagoons, and aerobic ponds) and lower subsystem (wetland subsystems) has been proven to be successful in reducing indicator organisms and potential pathogens (bacteria, enteric viruses, and parasites). The collection sump of the new integrated system collects all dairy wastewater and pumps it to solid separators, which then flows by gravity to anaerobic lagoons and aerobic ponds. The upper subsystem achieved significant microbial reductions of >98 percent for total coliform, >91 percent for coliphage, >95 percent for enterococci, >91 percent for Listeria monocytogenes, and >99.9 percent for Cryptosporidium . Additional reductions although limited were observed in the outflow from the wetland cells.

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Sandrin, Susannah Kathleen. "The impact of microbial population dynamics on the transport and biodegradation of organic compounds." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/290445.

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The impact of microbial population dynamics on the biodegradation and transport of organic compounds was evaluated in this study. At the laboratory-scale, results from miscible-displacement studies demonstrated that transport and biodegradation behavior in systems with increasing biologic diversity and population density variation was considerably more variable. Biokinetic parameters associated with biodegradation of the target compound were found to be considerably different in batch versus flow-through systems. While growth rates were always higher in the flow-through systems, the impacts on microbial lag and cell yield were opposite in different soils. In homogeneous sand, microbial lag was longer and column cell yields were larger than values reported under batch conditions. However, in more heterogeneous soils, microbial lag was shorter and column yields were smaller in the flow-through systems. This was determined in part using a one-dimensional contaminant transport and biodegradation model that incorporates the effects of microbial lag, inhibition, bacterial transport and nonuniform distribution of microbes, which was developed as a part of this study. In the second part of this study, a contaminant transport and biodegradation model incorporating linear biodegradation was applied to recovery data from small input pulses of biotracers at the field scale. One field site was low in oxygen and fairly homogeneous. The other had been subjected to a surfactant flush that enhanced oxygen concentrations, and thus microbial population densities, near the injection wells. Application of this model allowed for quantitative determination of the spatial distribution of microbial activity at the field sites.

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25

Watts, Dexter Brown. "Mineralization in soils amended with manure as affected by environmental conditions." Auburn, Ala. :, 2007. http://repo.lib.auburn.edu/2007%20Spring%20Dissertations/WATTS_DEXTER_20.pdf.

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26

Friedrich, Max Nikolaus Donatus [Verfasser], and Andreas [Akademischer Betreuer] Kappler. "Combining Environmental Microbiology and Health Psychology to Promote Effective Handwashing / Max Nikolaus Donatus Friedrich ; Betreuer: Andreas Kappler." Tübingen : Universitätsbibliothek Tübingen, 2016. http://d-nb.info/1199615994/34.

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27

Maidment, Graeme G. "Optimisation of environmental conditions for unwrapped chilled foods on display." Thesis, London South Bank University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274293.

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28

Boczek, Laura Ann. "The widespread occurrence of the enterohemolysin gene ehly among environmental strains of Escherichia coli." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1132167846.

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29

Staffen, Dana Jean. "Environmental Factors Influence Nontypeable Haemophilus influenzae Biofilm Formation, Maturation and Gene Expression." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385497645.

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30

Salhi, Bachira. "Regulation of gene expression in Bacillus subtilis macrofiber by environmental physical stimuli." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185502.

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Extensive studies indicate that both genetic and epigenetic (physiological and biomechanical) factors play a role in the development of twist state which must correspond to the establishment of cell surface conformational state at the level of cell wall assembly. Therefore, in order to identify the unknown factors that control the macrofiber production, twist states and hand inversion, genetic studies concerning regulation of macrofiber production and macrofiber structural states seemed to be appropriate. Genetic studies were carried out by using an insertional mutagenesis method. Bank(s) of insertions were obtained that carry the Tn917 transposon at random locations in the genome. Selected isolates were characterized with respect to macrofiber production and twist, and helix hand inversion stimulated by various physiological factors. The bank(s) of insertional mutants were searched for those defective or impaired in response to ion-induced hand inversion. None were found to exhibit the desired phenotype. Clones with altered static state were not rare. Another approach was to take advantage of the transposon "lac system" and to use the bank of insertion mutants to study regulation of gene expression. The chromogenic substrate for β-galactosidase, X-gal, made possible the search for factors governing gene expression during macrofiber morphogenesis in a manner similar to the way in which developmental biologists study regulation of gene expression during embryogenesis. First, insertion strains were screened for lac-Z expression on TBAB (Tryptose Blood Agar Base) X-gal plates. Isolates were then characterized by growth in fluid media. One strain (3:1) was found that expressed the E. coli lac-Z structural gene when grown on solid media (TBAB X-gal), but not when grown in fluid media. These observations led us to an examination of the role the medium may play in the regulation of gene expression. Evidence was obtained indicating that a number of insertion strains respond to growth in viscous media by expression of lac-Z+ indicating that different host gene promoters can be regulated by a physical component of the environment. The degree of expression moreover was positively correlated with the degree of viscosity. Environmental physical forces applied to the "body" of a bacterial cell must therefore play a role in gene expression. In at least one strain, 5:7Oring, gene expression was found only in right-handed structures suggesting that either specific genes are involved in the twist state and hand determination or that helix hand itself may govern gene expression. Finally, the 5:7Oring strain shows also the presence of a probable intercellular signalling through a diffusible chemical that causes gene expression to occur only in certain cells found at specific locations within the population.

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31

Balasubrahmanyam, Sunil K. "Environmental dynamics of Benomyl and Thiabendazole." Thesis, Virginia Tech, 1986. http://hdl.handle.net/10919/50496.

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The comprehensive environmental dynamics of the heterocyclic Benzimidazole fungicides, Benomyl and Thiabendazole was investigated. This included examining their fate and distribution in the terrestrial and aquatic phases of a laboratory microcosm comprised of silty clay loam soil and plants. The soil component constituted a major relocation site, with approximately 45 and 75% of initial Benomyl (recovered as MBC) and Thiabendazole concentrations being recovered from the soil component of the microcosm, respectively, while 53 and 27% translocated into corn plants. The adsorption mechanism/s of these fungicides onto soil components were investigated using silty clay loam, silty loam and sandy soils as well as Ca-bentonite. These studies indicated that both fungicides were adsorbed to the highest degree on silty clay loam, followed by silty loam and sandy soils. Their adsorption on Ca-bentonite was found to be a function of the pH of the suspension, suggesting that in the presence of increasing ll *activity on the clay surfaces, Benomyl and Thiabendazole become protonated to form positively charged molecules. These may then react with the clay surfaces forming Fungicide-clay complexes. The effect of different CaCl, concentrations on the adsorption process demonstrated that an increase in the salt concentration, at a constant pH resulted in a decrease in the amounts of adsorbed fungicide. The transport of the fungicides (adsorbed onto soil particles) as a consequence of scdiment runoff into aquatic systems was also estimated. Results of the simulation of overland sediment runoff from sections of the Chowan river basin into the Meherrin river following a rainstorm, indicate that significant quantities of Benomyl and Thiabendazole could be transported into aquatic systems. Adsorption studies also indicated that the adsorption process is reversible. Thus, any significant increases in the pH of receiving bodies of water could result in the release of Benomyl and Thiabendazole from sediment causing a contamination of the aquatic system.
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32

Peele, Price Jason. "Control of RNA Structure by CspA Proteins in Rhizobia." Thesis, Washington State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10605605.

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Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins conserved throughout all domains of life. Here, the role of CspA family proteins in the symbiotic development of Sinorhizobium meliloti with Medicago sativa (alfalfa) is investigated. Expression and genetic deletion strain analysis revealed that CspA family proteins are differentially expressed in symbiosis and contribute to symbiotic effectiveness. RNAseq analysis of native co-immunoprecipitated RNAs identified a novel interaction between several CspA family proteins and the αR14 family of small non-coding RNA (sRNAs). Whole transcriptome analysis defined transcriptional defects associated with loss of CspA function. The development of a new in vitro RNA binding assay using broccoli, a Green Fluorescent Protein (GFP) RNA mimic, is described as well as its use in defining binding specificity of CspA family proteins with synthetic and native ?R14 family sRNA structures. This work concludes that CspA family proteins interact with and influence the stability of specific RNA structures and these interactions control RNA regulated processes important for symbiotic development.

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33

Trinh, Tan Frederick 1979. "The biodegradation of a synthetic co-polyester by hydrolase-producing microorganisms /." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=83938.

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The biological degradation of the synthetic aliphatic/aromatic co-polyester Ecoflex(TM) (BASF) by 30 strains of hydrolase-producing soil bacteria, fungi and yeasts was investigated at moderate environmental conditions. Previous studies had shown that these materials could be degraded. These studies were done uniquely in compost or by axenic compost isolates, and under thermophilic conditions, but it is likely that most of this material will be found in sites at more moderate conditions. Thus, a screening procedure was developed to assess the biodegradability of the co-polyester at ambient environmental conditions. The screening also allowed for the investigation of the mechanism of biodegradation in order to determine the fate of these xenobiotics and their degradation intermediates in the environment.
Results obtained from shake flask experiments showed that the aliphatic/aromatic co-polyester was readily degraded by most of the 30 microorganisms studied. However, less than 5% of the original Ecoflex(TM) film weight was lost after 21 days of exposure for all the microorganisms studied. Using GC-MS techniques, the degradation intermediates were identified to be the monomers of the co-polyester; namely, adipic acid and terephthalic acid. Finally, gel permeation chromatography (GPC) results suggest that an exo-enzyme type degradation, where only the ester bonds at the termini of the polymeric chains are hydrolyzed by the microbes.

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34

Juck, David F. "Examination of PCR parameters for the detection of low numbers of bacteria in potable water : development of a nested PCR protocol." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=22745.

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A simple and sensitive technique was developed for the detection of bacterial cells in a water sample using the nested Polymerase Chain Reaction (nested PCR). The test organism, Escherichia coli, was detectable at an absolute value of 1-5 cells/50 mL of spiked water using ethidium bromide staining and ultraviolet light visualization of PCR product formation on DNA agarose gels. Different parameters of the PCR were examined to determine which ones are the most critical in the design of a detection method for very low numbers of cells in potable water samples. The presence of the filters used for sample concentration in the PCR reaction tube was found to be the most inhibitory component of the procedure and the nested PCR protocol was used to circumvent this inhibitory effect.

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35

Li, Yueh-Fen. "An Integrated Study on Microbial Community in Anaerobic Digestion Systems." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385850266.

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36

Zhou, Xia 1953. "Inactivation of Escherichia coli and coliphage MS-2 by chloramine and copper." Thesis, The University of Arizona, 1991. http://hdl.handle.net/10150/277945.

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The efficacy of chloramine in the presence of copper chloride was evaluated for the inactivation of an indicator bacteria Escherichia coli and coliphage MS-2. Both microorganisms were exposed to chloramine with and without copper chloride. Results showed an increase in the inactivation rate of Escherichia coli and MS-2 phage with an increasing concentration of chloramine. To achieve a 99 percent reduction in the number of Escherichia coli, an exposure of 46, 21, 6, and 5 minutes was necessary for 1, 2.5, 5, and 10 mg chloramine/L, respectively. A 99 percent reduction of MS-2 phage occurred after 60 and 25 minutes of exposure to 5 and 10 mg chloramine/L. Chloramine in the presence of copper increased the inactivation rate of Escherichia coli and MS-2 phage. The time needed for 99 percent inactivation of E. coli and MS-2 phage was reduced. Copper increases the inactivation rate of bacteria and viruses by chloramine. (Abstract shortened with permission of author.)

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37

Bodour, Adria. "Approaches to assessing microbial communities in soil, two examples: Biosurfactant production and phenanthrene degradation." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/280136.

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This dissertation is concerned with studying aspects of the ecology of microorganisms from a functional perspective using different microbial populations in soils. In the first study, an investigation was done on the distribution of biosurfactant producing microorganisms. In the second study, temporal changes were observed in an indigenous phenanthrene degrading community following a long-term pulse of phenanthrene.

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38

Guerrero-Barajas, Claudia. "The role of redox mediators on the anaerobic degradation of chlorinated solvents." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280703.

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Chlorinated solvents are pollutants found frequently in the environment. Whereas lower chlorinated solvents are easily degraded under aerobic conditions, degradation of higher chlorinated solvents is favored under anaerobic conditions. It is known that some compounds can act as redox mediators assisting the electron exchange required for the anaerobic dechlorination reactions to occur. Redox mediators are compounds that can assist the anaerobic dechlorination reactions either abiotically or biologically by accelerating the degradation rates. The objective of this study is to evaluate the role of different redox mediators on the anaerobic degradation of higher chlorinated solvents such as chloroform (CF), carbon tetrachloride (CT) and perchloroethylene (PCE). The redox mediators studied are vitamin B12 (cyanocobalamin CNB12-hydroxocobalamin HOB12), riboflavin (RF) and a model of humic compound anthraquinone-2,6-disulfonate (AQDS). The study includes abiotic and biological redox mediated dechlorination. The biological studies involve two varieties of unadapted methanogenic sludge. The results obtained demonstrate that redox mediators greatly enhance the degradation rates of CF and CT when utilized at substoichiometric molar ratios. At the same time, the results also highlight the importance of the role of the microorganisms during the dechlorination process. Vitamin B12 and riboflavin presented larger impact than AQDS on the degradation rates of CF and CT. Since vitamin B12 had the highest positive impact on the biodegradation rates of CF and CT, an attempt was done to stimulate its biosynthesis by the methanogenic sludge during the CT dechlorination. The approach used to promote the biosynthesis of vitamin B12 involved different vitamin B12 precursors such as porphobilinogen, and some primary substrates such as methanol and 1,2-propanediol. The results obtained show that the formation of the corrin ring may be the limiting step during vitamin B12 biosynthesis. One carbon substrates such as methanol, combined with porphobilinogen had a positive impact on the biodegradation rates of CT. The study suggests that the combination of methanol and vitamin B12 precursors could be a good alternative to stimulate the vitamin B12 biosynthesis by methanogens and therefore, the enhancement of the biodegradation rates of chlorinated solvents. This study presents the lowest molar ratio of vitamins that enhanced the dechlorination rates reported so far for biodegradation of chlorinated solvents involving methanogens. Also, this is the first report on the use of riboflavin as a redox mediator during dechlorination processes.

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39

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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40

Law, Bibiana Felicity. "Assessment of the pathogenicity of Campylobacter jejuni from broiler chickens." Diss., The University of Arizona, 2005. http://hdl.handle.net/10150/282899.

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Sixty-three of 435 (14.5%) samples collected from broiler chickens were positive for C. jejuni. Twenty-two of 55 samples were from organic chickens (40%) and 41 of 380 samples were from conventional chickens (10.8%). Isolates were subjected to macrorestriction profiling using SmaI and analyzed for their ability to survive in macrophage cells and invade in epithelial cells. Antibiotic testing to cefaclor, ciprofloxacin, tetracycline, erythromycin, gentamicin, trimethroprim/sulfamethoxazole, and ampicillin were performed. Finally, 5 isolates of varying putative in vitro virulence traits were chosen for experimental inoculation of newborn piglets. Five piglets per isolate were tested and examined macroscopically and microscopically upon necropsy. Genotyping of isolates indicated 1 to 3 profiles per flock. Of the 22 organic isolates from chickens, only 3 (13.6%) were able to survive within macrophages. For the conventional isolates, 21 out of 41 (51.2%) were able to survive. However, the majority of isolates (90.5%) from both organic and conventional isolates were not capable of invading epithelial cells. No isolates exhibited resistance to ciprofloxacin or gentamicin. One isolate out of 63 (1.6%) was resistant to erythromycin, 52 (82.5%) to tetracycline, 28 (44.4%) to trimethroprim/sulfamethoxazole, and 6 (9.5%) to cefaclor. In terms of the piglet studies, regardless of the combination of in vitro invasion or survival results or type of flock, most piglets (16/25) in all groups exhibited hyperemia, edema, and hemorrhage in the small intestine or colon upon gross examination. Microscopic examination revealed congested mucosa and erosion of the epithelium in 10 of the 25 piglets from 4 of the 5 groups. In conclusion, this study suggests that C. jejuni isolated from broiler chickens are virulent in piglets and are probably capable of causing disease in humans. Furthermore, the results of the survival and invasion assays did not correlate with the results of the piglet studies and cannot be relied upon to predict degree of virulence. Therefore, another virulence factor is responsible for the pathogenesis, such as a toxin(s). As this is the first study to confirm putative in vitro virulence traits with an animal model, further research is recommended with the piglet model to assess pathogenicity.

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41

Karim, Mohammad Rezaul. "Survival of indicator microorganisms and enteric pathogens in wetlands." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/284066.

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Wetlands containing aquatic plants have been found to economically provide a mechanism for improving the microbial and other quality of wastewater. The purpose of this study was to elucidate the effect of vegetation and sedimentation on the survival of enteric microorganisms in constructed wetlands. The first part of this study was designed to determine the effect of vegetation on the survival of Escherichia coli, Salmonella typhimurium , bacteriophage MS-2 and poliovirus in wetlands. The organisms were added to the water from six wetland systems, containing different aquatic plants. The wetland systems received either fresh water or secondary sewage. The presence of aquatic plants significantly increased the die-off of E. coli, S. typhimurium, bacteriophage MS-2, and poliovirus in fresh water and secondary sewage. Additional work on the survival of E. coli in non-sterile, filter sterilized, and autoclaved wetland water indicated that one of the plausible mechanisms of bacterial die-off in constructed wetlands is through increased microbial competition or predation. The next phase of this study investigated the survival of indicator microorganisms in wetlands similar to field conditions. E. coli, bacteriophage MS-2, and PRD-1 were added to tanks which were unvegetated or contained different aquatic plants. E. coli die-off in unvegetated tanks was greater than the vegetated tanks. Temperature was found to be significantly correlated with the die-off of E. coli. Inactivation of bacteriophage MS-2 in unvegetated tanks was also higher than the vegetated tanks. In contrast, PRD-1 inactivation was greater in the vegetated tanks compared to the unvegetated tanks. Thus, a combination of unvegetated and vegetated wetland would probably result in the greatest reduction of microorganisms by the wetlands. The last phase of this study was to examine the relative occurrence and survival of indicator microorganisms and pathogens in the water column and sediments of two constructed surface flow wetlands. On a volume/wet weight basis the concentration of fecal coliforms and coliphage in the water column and sediment was similar. Giardia and Cryptosporidium concentration in the sediment were one to three logs higher in the sediment compared to the water column. The die-off rates of all the organisms were greater in the water, except for Giardia muris. Giardia die-off in the sediment was greater than in the water column. These results suggest that sedimentation may be the primary removal mechanism for the larger organisms in surface flow wetlands. Overall, these studies suggest that vegetation, microbial competition or predation, temperature/sunlight, and sedimentation play important roles in microbial reduction in constructed wetlands. The effect of vegetation on microbial survival appeared to be indirect, through increasing microbial competition. However, vegetation in constructed wetlands may offset the effect of temperature and sunlight, resulting in a longer survival of microorganisms. Thus a combination of non-vegetated and vegetated wetland would probably result in the greatest reduction of microorganisms from wetlands. Future experiments are needed to examine such combined wetlands.

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42

Roane, Timberly Michelle. "Bioaugmentation with metal-resistance microorganisms in the remediation of metal and organic contaminated soils." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/284515.

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Current thinking is that co-contaminated sites (i.e., sites with both organic and metallic pollutants) are difficult to bioremediate because the metal toxicity is such that organic degradation is inhibited. The objective of this research was to evaluate the potential of bioaugmentation with metal-detoxifying microbial populations as a viable remediative approach for such sites. Divided into three sections, this research found that metal-detoxifying microorganisms could facilitate the remediation of co-contaminated systems. The objective of the first study was to compare the microbial community response to cadmium exposure between metal-contaminated and uncontaminated soils. This study found that while cadmium adversely affected the numbers of culturable microorganisms in all soils, cadmium-resistant isolates were found in each soil, regardless of prior metal exposure. However, the metal-contaminated soil microbial communities were more resistant than the uncontaminated soil community. In one metal-stressed soil, resistance increased with increasing cadmium stress. A cadmium-resistant Pseudomonas spp. was found to increase in numbers with increasing cadmium, suggesting a different mechanism of cadmium resistance at high cadmium concentrations. The second study evaluated the diversity of cadmium-resistance/detoxification mechanisms in six cadmium-resistant isolates found in the first study. Genetic and microscopic analyses found several different approaches to cadmium resistance. Two mechanisms known to confer resistance were observed, including exopolymer and biosurfactant production. Two other isolates demonstrated intracellular cadmium accumulation via as yet unknown mechanisms. The mechanism of resistance for one isolate could not be identified. Four out of the six isolates detoxified cadmium as part of their resistance. Since metal detoxification is necessary to allow for organic degradation, these four isolates were included in 2,4-D degradation studies under co-contaminated conditions. The last study examined the use of cadmium-detoxifying microorganisms to enhance organic degradation under co-contaminated conditions. In pure culture and laboratory soil microcosms with cadmium and 2,4-dichlorophenoxyacetic acid (2,4-D) as model contaminants, four cadmium-detoxifying isolates supported the degradation of 2,4-D by the cadmium-sensitive 2,4-D degrader Alcaligenes eutrophus JMP134 in the presence of toxic levels of cadmium. Ina pilot field study, a cadmium-detoxifying Pseudomonas isolate enhanced 2,4-D degradation by A. eutrophus JMP 13 4 in the presence of cadmium.

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43

Catallo, W. James III. "Effects of selected nitrogen-containing aromatic compounds (NCACs) on physiological properties in Escherichia coli." W&M ScholarWorks, 1989. https://scholarworks.wm.edu/etd/1539616602.

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This research examined the effects of quinoline and 4-azafluorene on respiratory electron transport rate (ET), outer membrane permeability and topology, oxygen consumption, and viable cell density in Escherichia coli cell suspensions. ET was estimated spectrophotometrically using INT (2-(p-iodophenyl)-3-(p-nitrophenyl)-5-(phenyl)-2H-tetrazolium chloride, which is reduced in vivo to a red colored formazan (INTF). Both test compounds caused anomalous dose-response behavior in INT assays: in a defined window of doses, ET rates near or above the controls were observed. These doses showed altered INT reduction kinetics, decreased cellular oxygen demand, and decreased viable cell densities. Experiments with E. coli spheroplast preparations, gram(+) cells, and deep rough mutants suggested that the toxicants increased outer membrane permeability and inhibited normal respiratory function. Results of cell-free ET assays and transmission electron microscopy further indicated altered outer membrane structure and inhibition of respiratory ET via, (1) secondary topological effects on the periplasm and inner membrane, (2) redox cycling of electrons in the respiratory chain, or (3) both 1 and 2 together. Quantitative studies of INT chemical structure and aqueous electrochemistry at Hg, C, and Pt electrodes were conducted to address analytical shortcomings in the literature. Data include nuclear magnetic resonance spectra, results from normal and differential pulse polarography, cyclic voltammetry, ring disc electrode, and spectroelectrochemical experiments. The route of INT reduction involves a slow one electron reduction to a tetrazolinyl radical followed by a fast one electron reduction and addition of one proton to yield formazan. Results on C and Pt electrodes indicated interfering reactions involving adsorbed hydrogen species and the possibility of underpotential generation of hydrogen gas.

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44

Weber, Eva. "Ecological insights into unexplored Archaea through environmental ecophysiology, single-cell genomics and cultivation." Thesis, University of Aberdeen, 2017. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=231673.

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45

Jackwood, Ryan. "Predicting Fate and Transport of Fecal Bacteria through Soils Using an Advection-Dispersion Model." University of Toledo / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1384519085.

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46

Ding, Guannan. "Bacterial Movement in Soil During Winter Irrigation of Reclaimed Wastewater." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1409036088.

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47

Li, Li. "Modeling transport of contaminants influenced by complex microbial processes." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/279907.

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Many current models that describe biodegradation and transport of contaminants in porous media do not include provisions for nonideal (nonlinear, rate-limited) sorption, microbial lag, inhibition, microbial community heterogeneity, and cell transport. Therefore, a more complete model was developed that incorporates bacterial lag, inhibition effects, and cell transport/elution, as well as nonlinear, rate-limited sorption. The performance of the new model was evaluated by using the model to simulate the results of a series of miscible-displacement experiments conducted using a range of porewater velocities, substrate concentrations, and initial cell densities. The results show that the model can simulate the substrate breakthrough curves very well. The model was also able to predict the total biomass growth. The calibrated values obtained for the maximum specific growth-rate coefficient, the mean lag time, and lag-time variance were within the range of values obtained from batch experiments. These results suggest that the model performed well and that it successfully describes the system. The model was used to investigate the coupled interactions among sorption, biodegradation, and transport, and the results show that biodegradation can significantly influence the first, second, and third spatial moment when sorption is nonlinear or rate-limited depending on initial/boundary conditions, residence time, biomass growth dynamics, and time-dependent sorption/desorption processes. The influence of heterogeneous microbial communities on biodegradation and transport of contaminants was investigated in the last part of the study. A one-dimensional mathematical model was developed that incorporates multiple populations, each subject to its own set of growth-related coefficients. Breakthrough curves produced for different combinations of growth rates, half-saturation constants and initial biomass concentrations for multiple species exhibit oscillatory behavior under certain conditions, which is attributed to competition between different species. The results suggest that the existence of heterogeneous microbial communities can have a significant influence on biodegradation and transport. The results presented herein illustrate the significant impact that factors such as microbial lag, microbial community heterogeneity, and nonideal sorption/desorption can have on the transport of biodegradable contaminants in porous media. One product of this dissertation is the development and evaluation of a more comprehensive model that represents many important processes involved in transport of biodegradable contaminants. The use of this type of model should enhance our ability to investigate and hopefully understand the complex systems inherent to the subsurface wherein multiple coupled processes influence contaminant transport and fate.

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48

Dorn, Jonathan Graves. "Understanding bioremediation of contaminated groundwater: Application of a lux bioreporter to monitor in situ bacterial catabolism of naphthalene in saturated porous media." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280693.

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One attractive technology for restoration of hydrocarbon-contaminated groundwater is in situ bioremediation, a process where the degradative capacity of biological systems, usually bacteria, is harnessed to facilitate clean-up of environmental pollutants. However, the successful implementation of in situ bioremediation is contingent upon understanding how physicochemical and microbial factors affect the formation and dynamics of microbially active regions, known as bioactive zones (BAZs), in porous media. In this study, a novel, laboratory-scale fiber optic detection system was developed and employed to monitor real-time, in situ BAZ formation and dynamics during naphthalene transport in saturated porous media. Biological activity was measured non-destructively by detecting in situ bioluminescence from Pseudomonas putida RB1353, a naphthalene degrading, lux reporter organism. The first investigation focused on examining the impact of temperature, pH and initial cell number on P. putida RB1353's peak luminescence and V max during naphthalene catabolism. Statistical analyses based on general linear models indicated that temperature, pH, and initial substrate concentration accounted for 99.9% of the variability in luminescence during naphthalene catabolism. These results demonstrated that with careful characterization and standardization of measurement conditions, attainment of a reproducible luminescence response and an understanding of the response are feasible. The second investigation evaluated several potential limitations of the fiber optic detection system and the ability of the detection system to capture BAZ dynamics. The results indicated that the system is not adversely affected by biofilm formation on the optical fiber tips or by bioluminescence attenuation in the porous medium. Additionally, the utility of the detection system was demonstrated by effectively capturing the dynamics of in situ bacterial activity during naphthalene catabolism under changing physicochemical conditions. The third investigation employed the detection system to monitor real-time, in situ BAZ formation and dynamics during naphthalene transport in saturated porous media containing defined physicochemical and microbial heterogeneities. Despite successful transport of bacteria into sterile regions, BAZ formation was limited by local physicochemical conditions. Furthermore, bacterial transport against the advective flow enabled BAZ formation upgradient of inoculated regions. Ultimately, such investigations will improve the utility of in situ bioremediation by enhancing our understanding of BAZ dynamics in complex, heterogeneous systems.

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49

Tian, Susan Jane. "Varietal and environmental effects on the physicochemical properties of sweet potato starch." Thesis, University of Nottingham, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339597.

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Baceti, André Andrade. "Construção de biossensor para detecção de compostos BTEX baseado em fosfatase alcalina sob regulação xylR/Pu e avaliação de sua regulação metabólica." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-25102011-135001/.

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Abstract:

Este projeto teve como objetivo a construção de biosensores para a detecção de compostos monoaromáticos do grupo BTEX a partir dos componentes da via de degradação de compostos monoaromáticos codificada no plasmídeo TOL de Pseudomonas putida, mais precisamente: o promotor Pu e a proteína reguladora XylR, que ativa o promotor Pu após a ligação ao efetor monoaromático. Um objetivo secundário foi a verificação da existência de sequências reguladoras desconhecidas a montante do promotor Pu, construindo três variantes com fragmentos de Pu que se estendem por diferentes comprimentos a montante do promotor (Pu202 pb, Pu396 pb e Pu802 pb), cuja existência foi sugerida em trabalho anterior do laboratório. O promotor Pu foi ligado ao gene indicador para fosfatase alcalina isolado de E. coli. Todos os componentes das três variantes de biossensores foram clonados com sucesso. A construção de um dos plasmídeos de biossensoramento com a variante mais curta de Pu (Pu202) foi concluída.
Monoaromatic compounds are mainly responsible for the contamination of areas, this is because they are components of gas and the fuel stations most of accidents sites. Such compounds are highly toxic and, in between non-polar compounds, present high solubility and vapor pressure which assists them in dispersion at groundwaters and soil. This work aim to develop a biosensor based on alkaline phosphatase indicator gene under the regulation of the Pu promoter and its regulatory protein, XylR, that is activated by monoaromatic. Moreover, this work will continue a previous project of the research group that indicated a possible regulatory region not described for Pu, that hypothesis will be tested by producing different plasmids biosensors with varying sizes of Pu (202 bp, 396 bp and 802 bp). All biosensor fragments were purified and cloned on pGem T Easy and biosensor with Pu 202 pb was produced. Next goals are finishing others biosensors assemble and perform induction tests.

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Dissertations / Theses on the topic 'Environmental microbiology'

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