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1
Gilliam, Lucy. "Impact of anti-microbial GM plants on soil microbial populations". Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485401.
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The environmental risk assessment of GM plants is a fast moving area of science. Much research has focused on developing methods to evaluate potential effects on a range of organisms. Microorganisms play an essential role in many soil processes, with the rhizosphere as the prominent site of microbial activity. There is a general need for protocols to assess the effect of anthropogenic influences, the use of different crops and crop rotation an.d as well as GM plants, on the microbial community within the soil. The rhizosp~eres of three crop plants Brassica napus (Oilseed rape), Triticum aestivum (Wheat) and Solanum tuberosum (Potato) were compared using both genetic and functional diversity methods. The rhizospheres of four cultivars of potato were compared; GM potato (variety Kardal) modified with an anti-fungal transgene, GM potato (variety Kardal) with no transgene inserted (empty vector), parental .- line of potato (variety Kardal) and a different cultivar (variety Russet-Burbank). Genetic diversity of bacterial populations isolated from the rhizosphere were compared using PCR amplified DNA of 168 rRNA with denaturing gradient gel electrophoresis (DGGE) to obtain community fingerprints. Activity of the microbial populations was assessed using Biolog G.N MicroPlate™ community substrate utilisation and enzyme activity using a microplate method based on substrates linked to the fluorescent compounds methylumbelliferone (MUB) and 7-amino-4-methyl coumarin (AMC). By comparing the ~M plants to non-GM plants and other crops, observed differences are placed in context. This work shows that the GM line examined.appears to have little effect on soil microbial populations. Detected effects of1he GM potato line were minor compared with other sources of variation observed between plants cultivar or crop species, management practices and sampling time. To date, there has been little evidence that cultivation of GM plants leads to significant changes in microbial popUlations.
2
Driessen, Jennifer Petronella 1973. "Microbial populations as indicators of river 'health'". Monash University, Dept. of Chemistry, 2000. http://arrow.monash.edu.au/hdl/1959.1/8780.
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Logeswaran, Sayanthan. "Mapping quantitative trait loci in microbial populations". Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4881.
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Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual the extreme progeny may be selected by multiple generations of asexual reproduction and selection. In this thesis I will analyse this method of measuring phenotype in asexual cross progeny. The aim is to examine the behaviour of marker allele frequency due to selection over many generations, and also to identify statistically significant changes in frequency in the selected population. I will show that stochasticity in marker frequency in the selected population arises due the finite initial population size. For Mendelian traits, the initial population size should be at least in the low to mid hundreds to avoid spurious changes in marker frequency in the selected population. For quantitative traits the length of time selection is applied for, as well as the initial population size, will affect the stochasticity in marker frequency. The longer selection is applied for, the more chance of spurious changes in marker frequency. Also for quantitative traits, I will show that the presence of epistasis can hinder changes in marker frequency at selected loci, and consequently make identification of selected loci more difficult. I also show that it is possible to detect epistasis from the marker frequency by identifying reversals in the direction of marker frequency change. Finally, I develop a maximum likelihood based statistical model that aims to identify significant changes in marker frequency in the selected population. I will show that the power of this statistical model is high for detecting large changes in marker frequency, but very low for detecting small changes in frequency.
4
VanInsberghe, David(David Stephen). "The eco-evolutionary dynamics of microbial populations". Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122422.
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Thesis: Ph. D. in Microbiology Graduate Program, Massachusetts Institute of Technology, Department of Biology, 2019Cataloged from PDF version of thesis.
Includes bibliographical references.
Microbes have adapted to life in complex microbial communities in a large variety of ways, and they are continually evolving to better compete in their changing environments. But identifying the conditions that a particular microbe thrives under, and how they have become adapted to those condition can be exceedingly difficult. For instance, Clostridium difficile became widely known for being the world's leading cause of hospital associated diarrhea, but people can also have C. difficile in their gut without developing diarrhea. Although these asymptomatic carriers are now thought to be the largest source of infection, we know very little about how these people become colonized. In the first chapter of my thesis I use publicly available microbiome survey data and a mouse model of colonization to show that C. difficile colonizes people immediately after diarrheal illnesses, suggesting C. difficile is a disturbance adapted opportunist.
However, the differences between very recently diverged microbial populations that are adapted for growth in different conditions can be very difficult to detect. To address this limitation, I developed a method of identifying regions that have undergone recent selective sweeps in these populations as a means of distinguishing them, and specifically quantifying their abundance in complex environments. But part of what makes microbial evolution so difficult to interpret is the vast diversity of genes that are only shared by a fraction of all the members in a population. To better understand how these flexible regions are structured, I systematically extracted all contiguous flexible regions in nine marine Vibrio populations and compared their organization and evolutionary histories.
I found that horizontal gene transfer and social interactions have led to the evolution of modular gene clusters that mediate forms of social cooperation, metabolic tradeoffs, and make up a substantial portion of these flexible genomic regions. The observations made in these studies help us understand how microbes are organized into socially and ecologically cohesive groups, and how they have evolved to interact with complex and changing environments.
by David VanInsberghe.
Ph. D. in Microbiology Graduate Program
Ph.D.inMicrobiologyGraduateProgram Massachusetts Institute of Technology, Department of Biology
5
Huber, Julie A. "Phylogenetic and physiological diversity of subseafloor microbial communities at deep-sea seamounts /". Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/10991.
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McCartan, Cecilia. "The assessment of toxicity in environmental microbial populations". Thesis, Queen's University Belfast, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343059.
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Healey, David W. (David Wendell). "Phenotypic heterogeneity and evolutionary games in microbial populations". Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/98544.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 92-96).
One of the most interesting discoveries of the last decade is the surprising degree of phenotypic variability between individual cells in clonal microbial populations, even in identical environments. While some variation is an inevitable consequence of low numbers of regulatory molecules in cells, the magnitude of the variability is nevertheless an evolvable trait whose quantitative parameters can be "tuned" by the biochemical characteristics and architecture of the underlying gene network. This raises the question of what adaptive advantage might be conferred to cells that implement high variation in their decision-making. Currently, the predominant answer in the field is that stochastic gene expression allows cells to "hedge their bets" against unpredictable and potentially catastrophic environmental shifts. We proposed and experimentally demonstrated an alternative solution: that heterogeneity implements the evolutionarily stable mixed strategy (or mixed ESS), from the field of evolutionary game theory. In a mixed ESS, phenotypic heterogeneity is a result of competitive interactions between cells in the population rather than a response to uncertain environments, so unlike with bet-hedging, in a mixed ESS the evolutionary fitness of different phenotypes is frequency dependent. Each phenotype can invade the other when rare, and the resulting equilibrium-the stable mix of the two-is not necessarily the one that maximizes the population's fitness. We demonstrated these and other predictions of the mixed ESS using engineered "pure strategist" strains of the yeast GAL network. We demonstrated also that the wild type mixed strategist can invade both pure strategists and is uninvasible by either. Taken together, our results provide experimental evidence that evolutionary hawk-dove games between identical cells can explain the phenotypic heterogeneity found in clonal microbial populations.
by David W. Healey.
Ph. D.
8
Martin, F. Elizabeth. "Analyses of microbial populations associated with carious pulpitis". Connect to full text, 2002. http://hdl.handle.net/2123/4414.
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Thesis (Ph. D.)--Institute of Dental Research, Faculty of Dentistry, University of Sydney, 2002.Title from title screen (viewed Apr. 23, 2009) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the Faculty of Dentistry. Includes bibliography. Also available in print form.
9
Martinez, Robert J. "Multiscale analyses of microbial populations in extreme environments". Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24754.
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Thesis (Ph.D.)--Biology, Georgia Institute of Technology, 2008.Committee Chair: Patricia Sobecky; Committee Member: Ellery Ingall; Committee Member: Jim Spain; Committee Member: Martial Taillefert; Committee Member: Thomas DiChristina.
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Martin, Fjelda Elizabeth. "Analyses Of Microbial Populations Associated With Carious Pulpitis". Thesis, The University of Sydney, 2002. http://hdl.handle.net/2123/4860.
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Martin, Fjelda Elizabeth. "Analyses of microbial populations associated with carious pulpits". Thesis, The University of Sydney, 2002. http://hdl.handle.net/2123/4414.
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Dental caries continues to be a significant public health problem affecting mankind in many parts of the world. Microbial activities include the progressive localised destruction of teeth that without treatment, would eventually result in infection of the dental pulp and surrounding periapical tissues. Although the bacteria responsible for caries initiation and early caries progression have been extensively studied, the microbiology of dentine caries is reported to show considerable diversity and has not yet been fully identified. Few studies have analysed the microbiology of deep caries or examined the relationship between the microflora and the histopathy of chronic pulpits in symptomatic teeth. Matched carious dentine samples and dental pulps were obtained from teeth without evidence of periodontal disease but with coronal caries and symptoms of pulpits. Bacteria were cultured from the carious dentine samples under both anaerobic and microaerophilic conditions. Real-time polymerase chain reaction (PCR) technology was also used to identify and enumerate the bacteria. Development of the techniques for the efficient extraction of bacterial DNA from both Gram-negative and Gram-positive bacteria found in carious dentine was an essential prerequisite for molecular analysis. In addition, the dental pulps were processed and categorised into one of four groups on the basis of dominant pathology of the tissue (minimal inflammation, soft tissue degeneration, hard tissue degeneration, inflammatory degeneration). Analysis of the culture data indicated a predominance of Gram-positive bacteria, particularly lactobacilli, while Gram-negative bacteria were also present in significant numbers with Prevotella species the most numerous anaerobic group cultured. Real-time PCR indicated a greater anaerobic microbial load than that determined by colony counting. The total number of anaerobes detected by PCR was 41-fold greater, while Prevotella spp. and Fusobacterium ssp. were 82-fold and 2.4-fold greater respectively. PCR also identified the presence of Micromonas micros, Porphyromonas endodontalis and Porphyromonas gingivalis in 71%, 60% and 52% of carious dentine samples, respectively. Correlation matrices from the real-time PCR data revealed significant multiple associations involving Fusobacterium spp. in combination with P. endodontalis, M. micros and/or Prevotella in the tissue response categories of minimal inflammation, soft and hard disuse degeneration. A positive correlation was also observed between M. micros and P. endodontalis for the category of inflammatory degeneration of the dental pulp. These anaerobes have been strongly implicated in the endodontic infections that occur as sequelae to carious pulpitis. Accordingly, the data suggest that the presence of threshold levels of these bacteria in carious dentine may be indicative of irreversible pulpitis. Knowledge of the microbial predictors associated with irreversible pulpitis creates potential for the development of a diagnostic tool, and for restorative materials with antimicrobial properties.
12
Martin, Fjelda Elizabeth. "Analyses of microbial populations associated with carious pulpits". University of Sydney, 2002. http://hdl.handle.net/2123/4414.
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Doctor of PhilosophyDental caries continues to be a significant public health problem affecting mankind in many parts of the world. Microbial activities include the progressive localised destruction of teeth that without treatment, would eventually result in infection of the dental pulp and surrounding periapical tissues. Although the bacteria responsible for caries initiation and early caries progression have been extensively studied, the microbiology of dentine caries is reported to show considerable diversity and has not yet been fully identified. Few studies have analysed the microbiology of deep caries or examined the relationship between the microflora and the histopathy of chronic pulpits in symptomatic teeth. Matched carious dentine samples and dental pulps were obtained from teeth without evidence of periodontal disease but with coronal caries and symptoms of pulpits. Bacteria were cultured from the carious dentine samples under both anaerobic and microaerophilic conditions. Real-time polymerase chain reaction (PCR) technology was also used to identify and enumerate the bacteria. Development of the techniques for the efficient extraction of bacterial DNA from both Gram-negative and Gram-positive bacteria found in carious dentine was an essential prerequisite for molecular analysis. In addition, the dental pulps were processed and categorised into one of four groups on the basis of dominant pathology of the tissue (minimal inflammation, soft tissue degeneration, hard tissue degeneration, inflammatory degeneration). Analysis of the culture data indicated a predominance of Gram-positive bacteria, particularly lactobacilli, while Gram-negative bacteria were also present in significant numbers with Prevotella species the most numerous anaerobic group cultured. Real-time PCR indicated a greater anaerobic microbial load than that determined by colony counting. The total number of anaerobes detected by PCR was 41-fold greater, while Prevotella spp. and Fusobacterium ssp. were 82-fold and 2.4-fold greater respectively. PCR also identified the presence of Micromonas micros, Porphyromonas endodontalis and Porphyromonas gingivalis in 71%, 60% and 52% of carious dentine samples, respectively. Correlation matrices from the real-time PCR data revealed significant multiple associations involving Fusobacterium spp. in combination with P. endodontalis, M. micros and/or Prevotella in the tissue response categories of minimal inflammation, soft and hard disuse degeneration. A positive correlation was also observed between M. micros and P. endodontalis for the category of inflammatory degeneration of the dental pulp. These anaerobes have been strongly implicated in the endodontic infections that occur as sequelae to carious pulpitis. Accordingly, the data suggest that the presence of threshold levels of these bacteria in carious dentine may be indicative of irreversible pulpitis. Knowledge of the microbial predictors associated with irreversible pulpitis creates potential for the development of a diagnostic tool, and for restorative materials with antimicrobial properties.
13
Driscoll, William Wallace. "Social and Asocial Niche Construction in Microbial Populations". Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/228457.
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Cooperation presents a major challenge for evolutionary theory: how can competition favor a trait that imposes a cost on the individual expressing it while benefitting another? This challenge has been answered by theory that emphasizes the importance of assortment between individuals that tend to cooperate and those who tend to behave selfishly, or `cheat'. Microbial cooperation remains puzzling, given the generally high genetic and taxonomic diversity of most microbial communities. Many microbial populations rely on shared, beneficial extracellular products for an array of functions in nature. However, when these lineages are maintained in liquid cultures, many are invaded and outcompeted by spontaneous `cheater' mutants that forego investments in these products while benefitting from those produced by neighbors. The apparent evolutionary instability of microbial investments in extracellular products in well-mixed laboratory cultures finds a natural parallel in the phenomenon of toxic microalgal blooms. These extremely dense populations of often free-living microalgae destroy populations of competing microalgae and grazing zooplankton that normally control population densities. Bloom populations of planktonic microalgae are unstructured, and seem ill suited for the evolution of cooperation. In this thesis, I have established a new theoretical framework for understanding the evolution of microbial external goods. This framework highlights the importance of cell-level structure in the distribution of these external products, as well as genetic structuring in populations. This perspective informed an investigation into the social niche of a biofilm-dwelling regulatory mutant of the important biocontrol strain Pseudomonas chlororaphis. In the highly self-structured environment of a bacterial biofilm, a surprising mutualistic association between this mutant and the wild type emerged, underscoring the importance of microbial ecology in understanding the evolution of niche construction. Extending these lessons to the evolutionary problem of exotoxins in free-swimming microalgae yields the novel possibility that fluctuations in density of toxic strains shift a cell-level functioning exotoxin into a true public good that may be exploited by cheaters. I show that exotoxicity can serve cell-level functions in Prymnesium parvum. Despite these cell-level benefits, the existence of nontoxic lineages within toxic blooms hints at a complex interaction between rapid evolutionary and ecological changes in toxic blooms.
14
Mashaphu, Nthabiseng. "The microbial composition of a natural methanogenic consortium". Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&.
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Wetlands account for approximately 20% of annual global methane emissions. Many wetlands receive inputs of organic matter, nutrients, metals and various toxic compounds from adjacent agricultural and industrial areas. The present study aimed to investigate the microbial composition of a natural methanogenic consortium. A consortium-based molecular approach to study diversity of methanogenic microbial communities in a natural wetland at the primary inflow was used. Key microorganisms of a nethane producing consortium were identified. Extracted high molecular mss DNA ws analysed by PCR combined with denaturing gradient gel electrophoresis and subsequent sequencing of 16S rDNA. This study was also aimed to identify syntrophic microorganisms in the wetland system. The data obtained suggest a well established syntrophic relationship within the wetland.
15
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.
16
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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Di, Maiuta Nicola. "Characterisation of mixed microbial populations in white mineral dispersions". Thesis, University of Warwick, 2010. http://wrap.warwick.ac.uk/3388/.
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In recent years, the microbiology of white mineral dispersions and the application of microbiocides for their preservation have taken a central role for the producer and user with the aim of maintaining high quality requirements such as brightness, rheological parameters, and odour neutrality. Additionally, new applications of mineral dispersions set to open up markets in food, cosmetics and pharmaceutical applications have aroused the interest in the microbiology of white mineral dispersions. Due to the occurrence of biocide resistant bacteria, technical limitations in the usage of biocides, as well as the more rigorous regulatory situation created by the BPD, the demand for new biocide research to ensure continuing effective WMD preservation is increasing. Despite efforts to optimise the application of microbiocides for the storage and protection of mineral dispersions, costs for preservation and disinfection are escalating. These are reasons why the current preservation strategies have been revisited and new preservation strategies have been designed. The work described in this thesis demonstrates that the microbial diversity of white mineral dispersions is greater than previously assumed and gives detailed insight about the microbial diversity of mineral dispersions. The occurrence of microbial contamination in mineral dispersions is of a seasonal nature rather than manufacture site or product type specific. Furthermore, the incidence of biocideresistant bacteria in mineral slurries is increasing and the microbial degradation products of biocidal compounds are disadvantageous for dispersion stability (pH and viscosity). New strategies for the preservation of mineral dispersions have been developed and biocide performance against biocide-resistance bacteria has been enhanced by combining in-use biocides with a range of non-biocidal additives. The industrial application of these new findings contributes to a more efficient preservation of white mineral dispersions with respect to both environmental as well as financial resources and opens up a basis for alternative preservation strategies of white mineral dispersions.
18
Lindberg, Ellinor. "Detection and quantification of subsurface pesticide degrading microbial populations". Kgs. Lyngby : Institute of Environment & Resources, Technical University of Denmark, 2007. http://www.er.dtu.dk/publications/fulltext/2007/MR2007-043.pdf.
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Vanichpun, Apinya. "Microbial populations and foodborne pathogens control of Mung bean sprouts". Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/28979/.
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The two main objectives in this study were investigating the microbial quality and microbial communities of 'use-by date' Mung bean sprouts by using conventional culture and 16S/18S rDNA PCR-DGGE methods, and evaluating the efficacy of natural antimicrobial substances, chemical disinfectants, and thermal treatments in reducing and inhibiting the growth of the pathogens on mung bean seeds. Retail samples of pre-packed mung bean sprouts were obtained from three retailers in the local area. The microbial quality and communities were evaluated on the 'use-by date'. The highest counts of total aerobic counts (7.86 log10 CFU/g), yeasts and moulds (7.0 log10 CFU/g), total lactic acid bacteria (6.24 log10 CFU/g) and total coliforms (6.63 log10 CFU/g) were found in samples from one shop and the DGGE band sequences also identified major populations of LAB from the same samples, These indicated poor quality and spoilage of the samples from this location and could be related to improper storage at temperatures above 5°C. The combination of conventional culture methods with the PCR-DGGE technique revealed a larger diversity of bacterial communities than eukaryotic ones based on the relative number of amplimers present on most of the OGGE gels. Identification based on band analysis revealed that the Enterobacteriaceae (29.6%), soil bacteria (20.4%), lactic acid bacteria (18.5%). yeast (14.8%). Pseudomonas spp. (13%), and Flavobacterium (3.7%) constituted the major populations in bean sprout samples. Cluster analysis of the OGGE patterns of both 16S and 18S rDNA amplimers found no strong relationship between sample sources and batches indicating the variability of natural populations. The use of natural antimicrobial products, such as a mixture of lime juice and vinegar (1: 1, pH 2.83) and bacteriocin-like substances produced by Pediococcus acidilactici, failed to reduce and inhibit the growth of Listeria monocytogenes on mung bean seeds. The former solution had higher antimicrobial efficiency in reducing the pathogen on seeds (1.93 log10 CFU/g) compared to the Pediococcus broth culture (1.22 log10 CFU/g), but both solutions failed to inhibit the re-growth of the pathogen during the sprouting process and also reduced seed germination percentage by 13-18%. The evaluation of efficacy of sequential washing using a combination of chemical treatments (two-step dipping) against the pathogens on seeds showed that a two-step dipping treatment in a solution containing 2% sodium hypochlorite for to min followed by 5% lactic acid solution for 5 min was the most effective treatment. This treatment achieved the highest reductions of L. monocytogenes (2.91 log10 CFU/g) and Salmonella Typhimurium (3.20 l0g10 CFU/g) after treatment and continued to reduce the pathogen during the sprouting process. This may be due to the chemical residues on treated seeds which lowered both pathogens on sprouted seeds to below the limit of detection <50 CFU/g) by direct plating without significantly affecting seed viability. The use of thermal treatments based on a hot and cold water dipping was found to be more effective in reducing the normal flora on seeds and less affecting of seed germination compared to microwave heating. The use of a hot and cold water dipping treatment at 92°c for 1 min followed by ice-cold water at 5°C for 30 sec achieved the highest reduction of L. monocytogenes on seeds (>5 log10 CFU/g) but had the lowest germination percentage (89%) compared to other hot and cold water dipping treatments. Microwave heating at 1-4 kW showed a poorer efficiency in reducing nonnal flora on seeds and severely affected seed viability. Overall, a two-step washing with 2% sodium hypochlorite followed by 5% lactic acid seems to be the most successful treatment in reducing and inhibiting the recovery of the pathogen during the sprouting process. However, the chemical residues on treated seed may become a negative image to apply this treatment in the sprout industry.
20
Lowery, Nicholas Craig. "Evolutionary and therapeutic consequences of phenotypic heterogeneity in microbial populations". Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/22838.
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The historical notion of a microbial population has been of a clonal population of identical swimming planktonic cells in a laboratory flask. As the field has advanced, we have grown to appreciate the immense diversity in microbial behaviors, from their propensity to grow in dense surface-attached communities as a biofilm, to the consequences of social dilemmas between cells, to their ability to form spores able to survive nearly any environmental insult. However, the historically biased view of the clonal microbial population still persists – even when a rare phenotype is investigated, the focus simply shifts to that narrower focal population - and this bias can lead to some of the broader questions relating to the consequences of phenotypic diversity within populations to be overlooked. This work seeks to address this gap by investigating the evolutionary causes and consequences of phenotypic heterogeneity, with a focus on clinically relevant phenotypes. We first develop and experimentally validate a theoretical model describing the evolution of a microbial population faced with a trade-off between survival and fecundity phenotypes (e.g. biofilm and planktonic cells), which suggests that simultaneous investment in both types maximizes lineage fitness in heterogeneous environments. This model helps to inform the experimental studies in the following chapters. We find that biofilm-mediated phenotypic resistance to antibiotics is evolutionarily labile, and responsive to antibiotic dose and whether biofilm or planktonic cells are passaged. We also show that persistence in E. coli is age-independent, supporting the current hypothesis of stochastic metabolic fluctuations as the cause of this rare phenotype. Finally, we explore phenotypic variation across a library of natural isolates of P. aeruginosa, and find few organizing principles among key phenotypes related to virulence. Together these results suggest that phenotypic heterogeneity is a crucial component in the ecology and evolution of microbial populations, and directly affects pressing applied concerns such as the antibiotic resistance crisis.
21
Arevalo, Philip A. (Philip Alexander). "Horizontal gene transfer as a cohesive force in microbial populations". Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/113462.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2017Cataloged from PDF version of thesis.
Includes bibliographical references.
Populations are the central unit of evolution and ecology. In the context of evolution, populations are commonly defined as groups of organisms with a shared gene pool in which adaptive genes can spread freely through natural selection. Ecology takes a less abstract view of populations and conceives of them as members of a single species that occupy the same geographical area. Among sexual eukaryotes, gene pools are easily defined in terms of reproductive isolation and the geographical scales relevant for populations are well-matched to everyday human experience. Microbiologists, however, have faced a great challenge in applying these concepts to the microbial realm. Can closed gene pools form in the face of apparently rampant horizontal gene transfer? What exactly is a microbial species? And does the famous maxim that '"everything is everywhere" mean that the entire globe is to E. coli what Galapagos is to a finch? In this thesis, I hope to move closer to an answer to these large scale questions by asking two smaller ones. First, can ecologically cohesive microbial populations be identified using genomic information alone? Second, once such populations are identified, what are the relevant factors driving population-Ưlevel differentiation? Horizontal gene transfer plays a central role in answering both of these questions, acting both as a force that allows cohesive microbial populations to form and as a means by which new functions and capabilities are introduced into and spread within populations.
by Philip A. Arevalo.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
22
Stanley, Lynn. "A characterization of bacteria populations from two sites /". free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit?p9924929.
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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.
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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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Harrison, Adrian Briscoe. "Hydrocarbon pollution of soil : effects on microbial populations and biomediation methods". Thesis, University of York, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362025.
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Brown, James Robert. "A design framework for self-organised Turing patterns in microbial populations". Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607669.
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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.
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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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Sullivan, Madsen Paul. "Effects of and Influences on Microbial Populations of Missouri Maize Fields". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7706.
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The role of individual soil microorganisms changes over the course of a plant's life - microorganisms that have no discernable role at one developmental stage may affect the plant later in its growth. Traditional analysis of the soil microbiome, which has focused principally on the relative abundances (RA) of individual organisms, may be incomplete, as underlying differences in population size cannot be addressed. We conducted a metagenomic analysis of soil microorganisms from various maize (Zea mays L.) fields at two depths, accompanied by crop yield components, to provide insight into influences of edaphic microbes on maize productivity under commercial maize production systems in Missouri. This study assesses the influence of fungi and bacteria, not only in terms of RA, but also in their estimated absolute abundances (EAA), derived by combining the results of Illumina HiSeq sequencing data and phospholipid fatty acid abundance data. Significant interactions were identified between maize yield components and soil microbes at critical developmental states. Most interactions between fungi and yield components were negative, with notable exceptions. Bacterial interactions were more complex, with most interactions during early ear development identified as positive, and most interactions during tasseling identified as negative. In addition to the effects that microbial populations have on yield, plant populations reciprocally changed the microbial community. Plant developmental state was the greatest predictor of bacteria, with the microbial communities present during the active growing season being most similar to each other, whereas the preplant microbiome and post-reproductive microbiome being most similar to each other. Fungal communities were primarily dependent on location.
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Tayler, Sally. "Composition and activity of bacterial populations found on decaying stonework". Thesis, University of Portsmouth, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304908.
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Cadena, Cepeda Marleny Kloepper Joseph. "Assessing soil microbial populations and activity following the use of microbial inoculants effect on disease suppressiveness and soil health /". Auburn, Ala., 2006. http://repo.lib.auburn.edu/2006%20Fall/Theses/CADENA_MARLENY_3.pdf.
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Schmidt, Jill Lisa. "Spatial ecology of bacteria in surficial marine sediments /". Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/11058.
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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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Mancino, C. F., L. Salo, A. Hayes, I. Pepper i D. M. Kopec. "The Influence of Effluent Irrigation on Specific Soil Microbial Populations and Parameters". College of Agriculture, University of Arizona (Tucson, AZ), 1988. http://hdl.handle.net/10150/215852.
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Ike-Izundu, Nnenna Esther. "Interaction between arbuscular mycorrhizal fungi and soil microbial populations in the rhizosphere". Thesis, Rhodes University, 2008. http://hdl.handle.net/10962/d1004021.
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This study examined the rehabilitation potential of AM fungi with organic and inorganic fertilisers under pot and field trial conditions as well as their interaction with rhizospheric organisms and specific functional groups. In addition, the study highlighted the effects of land-use management on AM fungal populations in soil and the mycorrhizal status of some selected plants from one of the study sites. The study focussed on two sites that differ in operational activities and these included a mined area that was to be rehabilitated and a commercial farming site. A pot trial was conducted using an overburdened soil resulting from kaolin clay mining. Pots were seeded with Cynodon dactylon and treated with either Organic Tea or NPK (3:1:5) fertiliser, with or without AM fungal inoculum. The compatibility of these fertilisers with AM fungi was assessed by plant growth and percentage root colonisation. Maximum shoot height and plant biomass were observed at the 28th week with NPK (3:1:5) fertiliser supporting mycorrhizal colonisation by 80%. The result indicated the potential of AM fungi to be used in rehabilitation with minimal phosphate fertiliser. Similarly, a field trial was set-up using 17 x 17 m[superscript 2] plots in the mining site that were treated with the same organic and inorganic fertilisers as well as with AM fungal inoculum in different combinations. The interaction between AM fungi and soil microbial population was determined using culture dependent and culture independent techniques. The culture dependent technique involved the use of soil dilution and plating on general purpose and selective media. The result showed that there was no change in the total culturable bacterial number in the untreated and AM fungal treated plots, while a change in species composition was observed in the functional groups. Different functional groups identified included nitrogen fixing bacteria, pseudomonads, actinomycetes, phosphate solubilisers and the fungal counterparts. Gram-positive bacteria were observed as the predominant phenotypic type, while nitrogen fixers and actinomycetes were the predominant functional groups. Species identified from each functional group were Pseudomonas fulva, Bacillus megaterium, Streptomyces and actinomycetales bacteria. Meanwhile, fungi such as Ampelomyces, Fusarium, Penicillium, Aspergillus, Cephalosporium and Exserohilium were identified morphologically and molecularly. Furthermore, the mining site had a significantly higher bacterial number than the farming site thereby indicating the effects of land-use management on culturable bacterial numbers. The culture independent technique was carried out by cloning of the bacterial 16S rDNA and sequencing. Identified clones were Bradyrhizobium, Propionibacterium and Sporichthya. A cladogram constructed with the nucleotides sequences of identified functional species, clones and closely related nucleotide sequences from the Genbank indicated that nucleotide sequences differed in terms of the method used. The activity and establishment of the introduced AM fungal population was determined by spore enumeration, infectivity assay, percentage root colonisation and assessment of glomalin concentrations. The results indicated that the two land use types affected AM fungal populations. However, the establishment of AM fungi in the farming site was more successful than in the mining site as indicated by the higher infectivity pontential. Selected host plants, which were collected around the mine area, were observed to be mainly colonised by AM fungi and these were identified as Pentzia incana, Elytropappus rhinocerotis, Euphorbia meloformis, Selago corymbosa, Albuca canadensis and Helichrysum rosum. These plant species were able to thrive under harsh environmental conditions, thereby indicating their potential use as rehabilitation host plants. Generally, the findings of this study has provided an insight into the interaction between arbuscular mycorrhizal fungi and other soil microorganisms in two fields with differing land use management practices.
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BERTOLINI, MARTINA. "GROUNDWATER BIOREMEDIATION: MICROBIAL POPULATIONS INVOLVED IN CHLOROETHENES AND BTEX CONTAMINATED AQUIFER PROCESSING". Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/809422.
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Groundwater plays an important role in water supply around the world. 2 billion of people use aquifers as drinking water. Consequently, contamination of groundwater has a great social and economic impacts.
The use of organisms (microorganisms and plants) to remediate contaminated matrices, called bioremediation, is becoming more and more frequent. These techniques are cheaper than chemical and physical remediation techniques.
Chloroethenes, aromatic and aliphatic hydrocarbons are widely contaminant compounds because of their intensive use in industrial activity. It is possible to lower their concentration in the environment by means of microbial biodegradation in anaerobic and aerobic conditions.
In this study, an aquifer (located near Porto Marghera, Venice, Italy) contaminated by a leaching from a former landfill was analyzed. The contamination comprised chlorinated solvents, benzene, toluene, ethylbenzene and xylenes (BTEX) and aliphatic hydrocarbons. In 1995, an intervention with a pump and treat reactor was installed. Due to low efficiency and high maintenance costs of the physic-chemical treatment, the installation of a biological treatment, based on two permeable reactive biobarriers, was planned. After preliminary characterization of the microbial community at the site in order to evidence the presence of natural microbial populations involved in decontamination processes, in February 2016 a first biobarrier was installed to stimulate bacterial anaerobic organohalide respiration to dechlorinate chloroethenes. The injection of a reducing substrate was set up to create strong reducing conditions to improve the activity of anaerobic bacteria. A second biobarrier was meant to stimulate bacterial aerobic biodegradation of BTEX and aliphatic hydrocarbons. Urea, ammonium phosphate and O2 were planned to be injected in the aquifer. Moreover, this treatment was also forecasted to be used for complete vinyl chloride aerobic biodegradation.
In order to define the presence of organo-halide respiring bacteria at the aquifer, laboratory-based anaerobic microcosm study was set up. The effect of the biostimulation intervention (i.e., the addition of a reducing substrate) was also monitored in comparison with natural attenuation processes. Chlorinated ethenes were analyzed through gas-chromatography coupled to mass spectrophotometry (GC-MS). At microcosms scale, the natural organohalide respiration activity was influenced by the presence of reducing substrate, showing an increase of dechlorination of highly chlorinated ethenes, with a concomitant accumulation of vinyl chloride. Landfill active microbial community composition was determined through Illumina 16S rRNA sequencing of cDNA from RNA extracted from groundwater samples. Active organo-halide bacteria were quantified by quantitative Real Time PCR (q-PCR). Phylogenetic bacterial biomarkers for Dehalococcoides, Geobacteriaceae, and functional biomarkers tceA and vcrA, coding for chlorinated ethenes reductases, were applied. The ability of aerobic biodegradation of vinyl chloride, BTEX, aliphatic hydrocarbons and chlorobenzene was studied by the Most Probable Number (MPN) technique and q-PCR of etnC and tbmD genes, coding for alkene and toluene-benzene monooxygenases, respectively.
Once established the presence of bacterial natural attenuation activities for all the compounds, chemical and microbiological analyses were performed at field scale in order to monitor the efficacy of the bioremediation treatments. Moreover, the microbial community composition of anaerobic biobarrier was analyzed before and after 22 months of treatment, by 16S rRNA Illumina sequencing. Reducing substrate addition affected the microbial community composition at the site, causing an increase of fermentative bacteria, mainly belonging to Archaea domain, whereas typically recognized bacteria involved in organohalide respiration were not displayed. These data, along with a decrease in chlorinated solvents measured at the site, suggest a possible presence of a still unexplored biodiversity of OHR bacteria and further culturomics efforts will help to elucidate this. At the plume fringe in the aerobic part of aquifer, BTEX, chlorobenzene and aliphatic hydrocarbon degrading bacteria were characterized. Moreover, microbial consortia able to use vinyl chloride as sole carbon and energy form were selected, demonstrating the feasibility to remediate the site from the carcinogenic intermediate of organohalide respiration.
The microbiological work carried out during this Doctorate, along with hydrogeochemical data, demonstrated that a bioremediation intervention could successfully decontaminate this historical and naturalistically important site. Since the beginning of 2020, a full-scale biobarrier plant has been established and it is expected to run for 30 years in order to completely remediate the aquifer.
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Hoekstra, Dirk Tjalling. "Microbial population dynamics in indigenous olive wastewater biofilms". Thesis, Cape Peninsula University of Technology, 2007. http://hdl.handle.net/20.500.11838/829.
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Thesis (MTech (Food Technology))--Cape Peninsula University of Technology, 2007The olive industry in South Africa, although small compared to the rest of the world, is rapidly expanding and producing increased volumes of wastewater on an annual basis that could in future develop into a major environmental problem. Olive mill wastewater (OMWW) and table olive wastewater (TOWW) are characterised by high chemical oxygen demand (COD), biological oxygen demand (BOD) and phenolic content that are toxic to the environment. Due to the nature of olive wastewater (OWW), its irresponsible and unregulated environmental release will result in oxygen depletion, nutrient enrichment and accumulation of toxic compounds in receiving water bodies that ultimately disrupts aquatic and terrestrial ecosystems. An estimated 3500 - 4500 tons of olives are processed on an annual basis by 51 farmers .in the Western Cape. Economic forecasts predict a steady growth, i.e. increased production and processing of olives in the South African olive industry, in the future due to consumer demand. These production increases will consequently lead to increased volumes of wastewater production, which would, in tum, require an expansion of treatment capacity of the wastewater prior to release. Two South African olive factories were chosen for this study: Buffet Olives, situated in Dal Josefat (Paarl), that produces table olives and Vesuvio Estate on Sorento farm (Wellington) that produce extra-virgin olive oil. Preliminary COD determinations showed that indigenous OWW biofilms within a rotating biological contactor set-up reduced the COD from TOWW and OMWW by 47% and 32%, respectively, over a l0-day period. These preliminary results strongly suggested that biofilms indigenous to OWW have the potential to remediate the pollution problems of OWW. However, the overall aim of this study was to determine how sustainable the application of indigenous biofilms in the OWW are over two production seasons and whether it would be feasible to apply and develop these naturally occurring biofilms as an effective bioremediation tool to reduce the COD and polyphenol content of OWW.
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Alonso, Cecilia. "Identity and activity of marine microbial populations as revealed by single cell techniques". [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=979857090.
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Reis, Iolanda Maria da Silva. "Segregated modeling and selection of populations for polyhydroxyalkanoate production by mixed microbial cultures". Master's thesis, Faculdade de Ciências e Tecnologia, 2008. http://hdl.handle.net/10362/9664.
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Hiorns, William Dougall. "The design of 16S ribosomal RNA-targeted oligonucleotide probes of detection of natural populations of autotrophic ammonia-oxidising bacteria". Thesis, University of Liverpool, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333653.
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Friedland, Jolene M. "Effectiveness of treatment and diversity of microbial populations within a constructed wetland treating wastewater". Morgantown, W. Va. : [West Virginia University Libraries], 2004. https://etd.wvu.edu/etd/controller.jsp?moduleName=documentdata&jsp%5FetdId=3741.
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Thesis (M.S.)--West Virginia University, 2004.Title from document title page. Document formatted into pages; contains vii, 69 p. : ill. (some col.). Includes abstract. Includes bibliographical references.
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MacLean, Roderick Craig. "Adaptive radiation and the evolution of resource specialization in experimental populations of Pseudomonas fluorescens". Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85576.
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Understanding the origins of biological diversity is a fundamental goal of evolutionary biology. A large body of theory attributes ecological and genetic diversification to divergent natural selection for resource specialization. This thesis examines adaptive radiation in response to selection for resource specialization in microcosm populations of the asexual bacterium Pseudomonas fluorescens. The general protocol for these experiments is to introduce a clonal population of Pseudomonas into a novel environment and to allow evolution to occur through the spontaneous appearance of novel genotypes carrying beneficial mutations. Adaptation can then be quantified through direct comparisons between evolved populations and their clonal ancestors. These experiments show that resource heterogeneity generates divergent natural selection for specialization on alternative resources, irrespective of the spatial structure of the environment. Adaptive radiation is possible in sympatry because of genetic trade-offs in the ability to exploit different resources, but these trade-offs are often not the result of antagonistic pleiotropy among loci that determine fitness on alternative resources. The rate of phenotypic diversification declines during adaptive radiation, apparently because the ecological opportunities required to support specialist lineages disappear as a consequence of initial diversification. The ultimate outcome of repeated instances of adaptive radiation is the evolution of a community of ecologically equivalent specialists that share similar adaptive traits, despite differences in the underlying genetic basis of specialization in replicate radiations. Comparisons with the literature on experimental evolution in microbial populations illustrate the results of this thesis are well-supported by experiments in a wide range of microbial microcosms.
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Bertram, Janet. "Effects of cow urine and its constituents on soil microbial populations and nitrous oxide emissions". Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1334.
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New Zealand’s 5.3 million strong dairy herd returns approximately 106 million litres of urine to pasture soils daily. The urea in that urine is rapidly hydrolysed to ammonium (NH₄⁺), which is then nitrified, with denitrification of nitrate (NO₃⁻) ensuing. Nitrous oxide (N₂O), a potent greenhouse gas (GHG), is produced via nitrification and denitrification, which are enzyme-catalysed processes mediated by soil microbes. Thus microbes are linked intrinsically to urine patch chemistry. However, few previous studies have investigated microbial dynamics in urine patches. Therefore the objective of these four experiments was to investigate the effects on soil microbial communities of cow urine deposition. Methods used included phospholipid fatty acid (PLFA) analyses of microbial community structure and microbial stress, dehydrogenase activity (DHA) assays measuring microbial activity, and headspace gas sampling of N₂O, ammonia (NH₃) and carbon dioxide (CO₂) fluxes. Experiment 1, a laboratory study, examined the influence of soil moisture and urinary salt content on the microbial community. Both urine application and high soil moisture increased microbial stress, as evidenced by significant changes in PLFA trans/cis and iso/anteiso ratios. Total PLFAs and DHA showed a short-term (< 1 week) stimulatory effect on microbes after urine application. Mean cumulative N₂O-N fluxes were 2.75% and 0.05% of the nitrogen (N) applied, from the wet (70% WFPS) and dry (35% WFPS) soils, respectively. Experiment 2, a field trial, investigated nutrient dynamics and microbial stress with plants present. Concentrations of the micronutrients, copper, iron and molybdenum, increased up to 20-fold after urine application, while soil phosphorus (P) concentrations decreased from 0.87 mg kg ⁻¹ to 0.48 mg kg⁻¹. Plant P was also lower in urine patches, but total PLFAs were higher, suggesting that microbes had utilised the available nutrients. Microbial stress again resulted from urine application but, in contrast to experiment 1, the fungal biomass recovered after its initial inhibition. Studies published during the course of this thesis reported that hippuric acid (HA) and its hydrolysis product benzoic acid (BA) significantly reduced N₂O-N emissions from synthetic cow urine, thus experiment 3 investigated this effect using real cow urine. Cumulative N₂O-N fluxes were 16.8, 5.9 and 4.7% of N applied for urine (U) alone, U+HA and U+BA, respectively. Since NH₃-N volatilisation remained unchanged, net gaseous N emissions were reduced. Trends in total PLFAs and microbial stress were comparable to experiment 1 results. Experiment 4 studied HA effects at different temperatures and found no inhibition of N₂O-N fluxes from HA-amended urine. However, mean cumulative N₂O-N fluxes were reduced from 7.6% of N applied at 15–20°C to 0.2% at 5–10°C. Total cumulative N emissions (N₂O-N + NH₃-N) were highest at 20°C (17.5% of N applied) and lowest at 10°C (9.8% of N applied). Microbial activity, measured as potential DHA, increased with increasing temperature. This work has clearly shown that the stimulation and inhibition of the soil microbial community by urine application are closely linked to soil chemistry and have significant impacts not only on soil nutrient dynamics but also on N₂O-N emissions and their possible mitigation.
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Balzano, Sergio. "The role of microbial populations in the cycling of iron and manganese from marine aggregates". Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/168945/.
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Marine aggregates play an important role in the cycling of carbon, nutrients and trace metals. Within aggregates the oxygen depleted by aerobic microbial respiration may not be replaced rapidly, generating anoxic or suboxic microzones. Reduced compounds that are unstable in the oxygenated water column have been previously found associated with marine snow. Therefore, in the experiments described in this thesis, artificial aggregates were made in the laboratory from senescent phytoplankton material and incubated to investigate the role of the associated microbial populations to the biogeochemical redox cycling of iron and manganese and to the degradation of organic matter. The release of dissolved iron from artificial aggregates which did not contain any measurable (~10 μm) anoxic microzones, was demonstrated under dark conditions. The rate of release was controlled by the amount of reducible Fe(III) available, and appears to be limited by the competing oxidation of Fe(II). Moreover highly significant releases in reduced Mn were detected from aggregates incubated under a constant velocity shear, although the same aggregates did not affect the dissolution of iron. A possible reason is likely associated with the higher stability of Mn(II), compared to Fe(II) in aerobic environments. Molecular (16S rRNA gene) analyses showed the bacterial community associated with artificial aggregates to be similar to that found in natural aggregates and dominated by (predominantly uncultured) �- and �-Proteobacteria, Bacteroidetes, Planctomycetes and Cyanobacteria. It was possible to culture NO3 --, Fe(III)- and Mn(IV)-reducing bacteria from the artificial aggregates, and marine particles incubated with Fe(III) under anaerobic conditions contained a range of �- and �-Proteobacteria known to respire Fe(III) and in most cases Mn(IV). Moreover several microorganisms belonging to �-Proteobacteria were isolated from marine aggregates and strains affiliated to the genera Amphritea, Marinobacterium and Marinobacter, were demonstrated to grow through the reduction of Fe(III), with Marinobacter also capable of respiring Mn(IV). Whilst the precise mechanism of reduction is not clear, it is evident that marine aggregates can be a source of Fe(II) and dissolved Mn, in coastal waters and most probably other natural water systems. Fatty acid analyses revealed the prevalence of saturated over unsaturated fatty acids indicating that aggregates were already partially degraded when incubation started. Nonetheless, the lipids in the artificial aggregates were rapidly degraded further as indicated by a depletion in short chain (<20) saturated and monounsaturated fatty acids. In contrast, the concentrations of linear and branched, saturated long chain (>20) fatty acids fluctuated, suggesting that some of these lipids could have been produced in situ by marine microorganisms rather than deriving from II higher plant debris. In addition, a bacterial branched monounsaturated fatty acid (11- methyl-octadecenoic acid), which has not previously been found in marine particles was present in artificial aggregates. Roseobacter litoralis found among the aggregateattached bacteria contains 11-methyl-octadecenoic acid, and other bacteria present in artificial aggregates have the potential to produce long-chain saturated and polyunsaturated fatty acids. Thus, the fatty acid assemblage appears to reflect both organic matter degradation, including selective preservation, but also changes in the microbial assemblage. A range of future studies are suggested to elucidate the mechanisms for Fe(III) and Mn(IV) reduction in aggregates. These include microscale analyses of dissolved species and evaluation of the presence of metal binding ligands associated with aggregates. Moreover it is important to assess the activity of the Fe(III)- and Mn(IV)- reducing bacteria present in aggregates in situ and the production of long chain fatty acids in degrading aggregates.
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Misson, Benjamin Olivier. "Potentiel toxique et structure génétique de populations de Microcystis en lien avec les différentes phases de son cycle de vie". Thesis, Clermont-Ferrand 2, 2011. http://www.theses.fr/2011CLF22168/document.
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L‟eutrophisation croissante des écosystèmes aquatiques favorise le développement des cyanobactéries, parmi lesquelles Microcystis est la plus représentée dans les régions tempérées. La capacité de Microcystis à produire une puissante hépatotoxine, la microcystine, est à l‟origine de diverses perturbations écologiques, et de nombreuses nuisances sanitaires. La compréhension des facteurs déterminant la toxicité des efflorescences de Microcystis constitue, de fait, un enjeu majeur des recherches actuelles. Dans ce contexte, l‟objectif premier de ce travail de thèse était d‟étudier la variabilité temporelle et l‟implication potentielle de la toxicité de Microcystis à l‟échelle de son cycle de développement annuel. Pour cela, il était nécessaire de considérer, en particulier, les parties les moins connues du cycle de développement : la phase de survie benthique, et les transitions entre les phases benthique et planctonique, via les processus de recrutement et de sédimentation. Nous avons alors étudié le potentiel toxique des populations de Microcystis grâce à des approches complémentaires menées à différentes échelles spatio-temporelles, en considérant à la fois les gènes impliqués dans la synthèse de microcystines, leur transcription et les concentrations en microcystines. Cette étude s‟est appuyée, en parallèle, sur la caractérisation de la structure génétique des populations de Microcystis dans les compartiments benthique et planctonique. La prise en compte systématique de la phase de vie benthique a tout d‟abord permis d‟améliorer nos connaissances sur cette phase du cycle de développement de Microcystis. Ainsi, Microcystis peut survivre plusieurs années en profondeur dans les sédiments, sans que les populations ne perdent leur potentiel toxique, ou que leur structure génétique soit altérée. En revanche, en surface des sédiments, le potentiel toxique et la structure génétique des populations sont variables, de manière similaire à ce qui peut être observé dans la colonne d‟eau. Enfin, ces travaux ont également mis en évidence l‟influence des phases de transition entre l‟eau et les sédiments dans la variabilité du potentiel toxique et de la structure génétique des populations de Microcystis. Les processus de recrutement benthique et de sédimentation occasionnent, en effet, une sélection génétique, qui, bien que paraissant indépendante du potentiel toxique des génotypes, peut grandement affecter le potentiel toxique des sous-populations benthiques et planctoniques de MicrocystisThe increasing eutrophication of aquatic ecosystems promotes the development of cyanobacteria, among which Microcystis is the most widespread in temperate regions. The ability of this cyanobacterium to produce a potent hepatotoxin, called the microcystin, represent a serious threat for both natural life and human health. Thus, understanding the factors determining the toxicity of Microcystis blooms is a major challenge of actual research. In this context, the main goal of this work was to study the temporal variability and the potential implication of Microcystis toxicity, at the scale of its annual life cycle. For that, it was necessary to consider more particularly, the least known parts of the cycle : the benthic survival phase, and the transition between the benthic and the planktonic phases, through the benthic recruitment and the sedimentation processes. Then, we studied the toxic potential of Microcystis populations through complementary approaches conducted at different spatio-temporal scales, by considering the genes controlling the synthesis of the microcystin, their transcription and the concentrations of microcystin. In parallel, the genetic structure of Microcystis populations was characterized in both benthic and planktonic compartments. By considering systematically the benthic life stage, we were first able to improve our knowledge on this phase of Microcystis development cycle. Thus, Microcystis is able to survive several years in deep sediments, without the population‟s toxic potential or genetic structure being degraded. On the other hand, at the sediment surface, the toxic potential and the genetic structure of the populations vary, in a similar range to what observed in the water column. Furthermore, this work also shed the light on the influence of benthic-pelagic transitions in the variability of the genetic structure and the toxic potential of the populations of Microcystis. Indeed, a genetic selection occurs during the benthic recruitment and the sedimentation processes. Although such a selection does not seem to rely on the toxic potential of the genotypes, it can greatly modify the toxic potential of both benthic and planktonic sub-populations of Microcystis
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Dillard, Joshua Ryan. "Demographics and Transfer of Escherichia coli Within Bos taurus Populations". DigitalCommons@CalPoly, 2015. https://digitalcommons.calpoly.edu/theses/1484.
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In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. Bulls from the Cal Poly Bull Test were sampled every summer from May to September when around 200 bulls from ranches across California are housed together to be tested and eventually auctioned off. The impact of cattle origin (ranch, city) and habitation (pen) on E.coli isolate strain type were evaluated via pyroprinting . The cattle were studied to see if transfer was related to proximity of cohabitation. Since the complete population of intestinal E. coli could not be sampled, transfer could not be directly seen. The probability of sharing E. coli in each time point was used to infer transfer. There was an increase in the probability of sharing E. coli from the May sample date to the September date, indicating that some form of transfer was occurring. There was an even greater increase in the probability of sharing E. coli when the bulls were housed in close proximity. Lastly, ground squirrels cohabitating in the area were found to house some of the same strains as the cattle. This makes transfer between squirrels and cattle a possibility. Overall, this paper shows that the intestinal E. coli composition of bulls may be readily altered by the introduction of new bulls into a population.
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Masur, Deanne Christine. "Microbial and geochemical processes controlling the oxidation and reduction of arsenic in soils". Thesis, Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/masur/MasurD0507.pdf.
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Colles, Frances M. "Population structure and dynamics of Campylobacter populations carried by wild birds and chickens reared in a free-range woodland environment". Thesis, University of Oxford, 2006. http://ora.ox.ac.uk/objects/uuid:3dc7cdfb-29f6-4681-b8db-cb71129cd946.
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Ingestion of contaminated chicken meat is a major cause of Campylobacteriosis in Europe and the USA. The environment, including wild birds, is considered to be an important reservoir for chicken colonization. The aims of this study were to determine the population structure of Campylobacter amongst chicken and wild bird sources on a single farm, and to establish the extent to which genotypes flow between them and ultimately infect humans, using MLST and antigen sequence typing. A pilot study amongst farm animals and wild birds in Lancashire demonstrated that Campylobacter genotypes from human disease were common on the farm and could be isolated from more than one animal source. Between 30-50% of wild geese and Starlings were shedding Campylobacter, with a seasonal peak in shedding rate in Spring. Genotypes were divergent from those previously isolated from human disease, retail meat and farm animal sources, with the majority being restricted to the host source. The carriage rate of Campylobacter was between 70- 100% amongst 78 free-range poultry flocks tested at 56 days of age. Up to seven genotypes were found to co-exist within a flock, and genotypes varied throughout the year on a random basis. Some Campylobacter strains were isolated from one farm site only, but a small percentage of them had spread nationally and were stable over a period of a decade. A total of 23% of Campylobacter isolates from free-range chickens were indistinguishable to those from human disease, and 5% were indistinguishable from wild birds. A total of 6% of genotypes isolated from wild birds were indistinguishable from those isolated from human disease. Wild birds could not be completely disregarded as a potential reservoir of Campylobacter for both humans and poultry, but their role is likely to be limited.
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Olson, M. Brady. "On the population ecology of the toxigenic marine diatom genus, Pseudo-nitzschia : perspectives from the growth and mortality environments /". Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/10983.
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Weldon, Jennifer M. "Correlations between Arsenic in Maine Groundwater and Microbial Populations as Determined by Fluorescent In-Situ Hybridization". Fogler Library, University of Maine, 2005. http://www.library.umaine.edu/theses/pdf/WeldonJM2005.pdf.
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Högberg, Ann. "Cereal non-starch polysaccharides in pig diets : influence on digestion site, gut environment and microbial populations /". Uppsala : Dept. of Animal Nutrition and Management, Swedish Univ. of Agricultural Sciences, 2003. http://epsilon.slu.se/a413.pdf.
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Fuller, Robert A. "The interactions of toluic acid with indigenous microbial populations in a model Gravel Bed Hydroponic system". Thesis, University of Portsmouth, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310419.
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