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Rooks, Michelle Gabrielle. "Microbiome-Targeted Interventions for Colitis-Associated Bacteria." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493456.
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Complex interactions between mammalian hosts and their gut microbes have evolved over many millennia and have established a sophisticated communication system that is essential for symbiosis and mutualism. Perturbations to host-microbiota homeostasis in the context of a genetically susceptible host are central to the development of inflammatory bowel disease (IBD). In-depth understanding of the underlying mechanisms that control homeostasis and dysbiosis are essential for determining how to reliably modulate the host-microbiota continuum to prevent and treat disease. However, deciphering whether alterations in the microbiota are a cause or consequence of IBD remains a considerable challenge, as is defining the role of specific microbes in the pathogenesis of disease. This thesis explores the gut microbiome in mouse models of experimental colitis and evaluates the contribution of specific microbial clades and pathways in potentiating mucosal inflammation with the goal of identifying novel microbiome-targeted interventions for disease management.
To improve our understanding of microbial dysbiosis and dysfunction in IBD, we use the TRUC (T-bet-/-RAG2-/- ulcerative colitis) mouse model to profile the gut microbiome in active disease versus treatment-induced remission. 16S ribosomal RNA gene surveys of stool from mice treated with antibiotics, immunodulatory therapies, or a fermented-milk dietary intervention reveal microbial features modified among health and disease states. Discriminatory biomarkers of active disease included increased Enterobacteriaceae and shifts from carbohydrate and energy metabolism to pathways favoring bacterial pathogenesis, specifically cell motility and two-component systems. An unexpected observation is a significant enrichment in genes for microbial benzoate degradation in active colitis. Intermediates of benzoate metabolism – catechols – share the same backbone as host catecholamines, which can signal through two-component systems to promote virulence in pathogenic Enterobacteriaceae. Based on expansions in Enterobacteriaceae and increased gene abundances for benzoate degradation, two-component systems, and bacterial motility proteins, we identify a potential signaling axis linking host adrenergic stress with enhanced bacterial virulence in a preclinical model of colitis.
Enterobacteriaceae sense and respond to microbiota-generated signals and host-derived catecholamines through the QseBC two-component quorum sensing system. QseC is a membrane-bound sensor kinase that surveys the external milieu and, upon signal detection, activates its cognate response regulator, QseB, to induce expression of virulence genes. To investigate whether blocking QseC signaling could reduce disease severity, we test the effects of a QseC inhibitor (LED209) in the TRUC, Il-10-/-, and dextran sodium-sulfate models of experimental colitis. LED209 attenuates disease across all three models, with the most striking protective effect in TRUC and dextran sodium sulfate-treated mice. LED209 also prevents the expansion of Enterobacteriaceae in Il-10-/-and dextran sodium-sulfate-exposed mice, but not in TRUC mice, indicating a potential difference in microbiota responses based on genetic context. Moreover, measuring catecholamines in cecal content and stool show that LED209 does not significantly affect the luminal catecholamine pool and thus, may not disrupt host or microbial catecholamine metabolism. Collectively, these data show that QseC inhibition can ameliorate disease in distinct models of experimental colitis and suggest a role for QseC-mediated bacterial virulence in the pathogenesis of IBD.
Although a single pathogen has not been identified as a causative agent, several bacteria continue to be implicated in the initiation and progression of IBD, including adherent-invasive Escherichia coli (AIEC). As a proof-of-principle, we genetically inactivate qseC in the Crohn’s disease-associated AIEC strain LF82. We show that absence of qseC leads to downregulated virulence gene expression and defects in flagellar assembly and motility in vitro and reduced colonization efficiency in vivo. Overall, these studies provide evidence that QseC may be an upstream virulence node utilized by colitogenic bacteria to survey their host and potentiate disease and may be a useful target for microbiota-directed therapies in IBD.Biological Sciences in Public Health
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Savio, Claudia. "Symbiotic and associated bacteria in Tephritid flies." Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3427445.
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The Tephritidae family, commonly known as “fruit flies”, is a large Dipteran family. It includes many notorious agricultural pests, as the olive fly (Bactrocera oleae), the cherry fruit fly (Rhagoletis cerasi) and the walnut husk fly (R. completa).
The importance of bacteria in the life history of fruit flies is well-known. In the beginning of last century Petri (1909) was the first to report the presence of symbiotic bacteria within the olive fruit fly (Bactrocera oleae); recently it was designated as “Candidatus Erwinia dacicola”. In Tephritids flies, the bacteria are housed in the midgut and in a specialized intestinal diverticulum, located in the fly head, called oesophageal bulb.
In this thesis, some aspects of the relationship between the above mentioned Tephritid flies and bacteria has been investigated, such as the microflora composition, the symbiont genetic variability and the bacterial transmission.
The thesis is composed of five studies.
The first study analyzes in details the genetic variability of Ca. E. dacicola in various Italian olive fly populations, studying the 16S rRNA gene. The presence of only two symbiont lineages, not coexisting in the same fly individual, was clearly noticed. Interestingly, the olive fly populations of the two main Italian islands, Sicily and Sardinia, are exclusively represented by one of the two lineages, which could suggest a non-random distribution. On the other hand, the peninsular populations show both bacterial haplotypes, in different proportions. No significant correlation was found between the two symbiont haplotypes and the observed host fly haplotypes, providing evidences for a mixed model of vertical and horizontal transmission of the symbiont during the fly life cycle.
The second study extends the previous study to a wider range. The presence of only two symbiont haplotypes was still confirmed for the Mediterranean and African populations. Surprisingly the symbiont haplotypes seem to be more related to the territory than the numerous host haplotypes.
The third study deals with the identification of the microflora composition of R. completa and R. cerasi. All the life stages of the cherry fruit fly and the adult stage in R. completa have been taken into account, using both culture dependent and independent methods. Bacteria detected within the oesophageal bulbs of both species are affiliated to Enterobacteriaceae family. The results on the bacterial transmission show a different mechanisms respect to the olive fly and the subfamily Tephritinae symbionts.
In the fourth study, the Klebsiella spp. strains isolated from the oesophageal bulb of R. completa and Ceratitis capitata were examined for their ability to incorporate the gene encoding green fluorescent protein (GFP). These bacteria were successfully labelled by conjugation with the gfp gene and the gfp gene was stably maintained in the transgenic strains. Moreover, the colonizing ability of gfp-tagged bacteria in the original host was tested. Here a non-invasive technique to monitor the bacterial fate during the fly life stages was used. Gfp-tagged bacteria were successfully ingested by walnut husk flies where they established a stable population in the fly gut over time and throughout developmental stages. This is the first report in Tephritid flies of native engineered bacteria re-introduced in its original host and the shuttle system used in this study could be a useful tool to expand and strengthen the possibility of biological control of the insect pest.
The last study is part of Isabel Martinez-Sañudo PhD thesis, for which I contributed to experimental works. The main goal of this study was to analyse the phylogenetic relationships between flies of the Tephritinae subfamily and their symbiotic bacteria. Some species of this subfamily are in effect known to host specific non-culturable symbiont bacteria (‘‘Candidatus Stammerula spp.”) in their midgut. The cophylogenetic analysis reveals the presence of congruence, even if imperfect, between hosts and symbionts. This non-strict congruence is probably due to events such as losses, duplications and hosts switching, which are likely to arise during the biological cycle of the fly in consideration of the extracellular status of these symbionts.I Tefritidi, noti anche come “fruit fly”, rappresentano una vasta famiglia di Ditteri comprendenti specie dannose per l’agricoltura quali la mosca dell’olivo (Bactrocera oleae), la mosca del ciliegio (Rhagoletis cerasi), la mosca del noce (R. completa) e la mosca mediterranea della frutta (Ceratitis capitata). L’importanza delle associazioni batteriche nella famiglia dei Tefritidi è nota sin da quando Petri, all’inizio del secolo scorso, riportò la presenza di un battere simbionte, in seguito designato “Candidatus Erwinia dacicola”, in un diverticolo del capo della mosca dell’olivo chiamato bulbo esofageo. I successivi studi hanno evidenziato, sia con metodi tradizionali, sia con un approccio di tipo molecolare, lo stretto legame esistente tra batteri e tefritidi, siano essi simbionti ereditari e coevoluti e non coltivabili o semplici batteri associati. Nel presente lavoro sono stati analizzati in dettaglio alcuni aspetti delle relazioni batteriche in alcune specie di tefritidi, quali la variabilità genetica dei simbionti, la composizione della microflora batterica e la presenza di trasmissione attraverso i diversi stadi di sviluppo dell’ospite. La tesi si articola in cinque capitoli. Il primo lavoro analizza la variabilità genetica nel battere simbionte di B. oleae “Ca. Erwinia dacicola” in diverse popolazioni italiane della mosca dell’olivo, usando il gene ribosomale 16S come marcatore. Lo studio ha evidenziato la presenza di soli due aplotipi del simbionte, evidenziando anche che la loro presenza contemporanea all’interno di uno stesso ospite sembra in base a tutti i reperti non essere non essere probabile. La distribuzione di queste due linee batteriche nelle popolazioni di B. oleae sembra inoltre non essere casuale, poiché le popolazioni delle due maggiori isole italiane (Sardegna e Sicilia) ospitano uno o l’altro dei due aplotipi. Al contrario, le popolazioni della penisola ospitano, in proporzioni significativamente diverse, entrambi gli aplotipi del simbionte. Non è emersa una correlazione tra gli aplotipi di “Ca. E. dacicola” e gli aplotipi mitocondriali del loro ospite. Tale risultato potrebbe essere spiegato ammettendo l’esistenza, oltre alla prevalente trasmissione verticale, di accidentali passaggi orizzontali del simbionte. Nel secondo lavoro l’indagine è stata estesa a un areale più ampio circummediterraneo della mosca dell’olivo. I due aplotipi di “Ca Erwinia dacicola” rinvenuti in Italia sono stati riscontrati con frequenze diverse anche in Africa. Inaspettatamente gli aplotipi del simbionte risultano essere più correlati al territorio di quanto non lo siano i numerosi aplotipi mitocondriali dell’ospite. Nel terzo lavoro è stata indagata la composizione della microflora di R. completa e R. cerasi prelevate in natura, analizzandone i diversi stadi di sviluppo sia con approccio tradizionale coltura-dipendente che con approccio molecolare coltura-indipendente. Dal lavoro è emerso che le entità batteriche predominanti presenti nel bulbo esofageo appartengono alla famiglia delle Enterobacteriaceae. I risultati ottenuti evidenziano un meccanismo di trasmissione dei batteri diverso da quello evidenziato per i simbionti della mosca dell’olivo e della sottofamiglia Tephritinae. Nel quarto lavoro è stata studiata l’abilità di ceppi di Klebsiella isolati originariamente dal bulbo esofageo di R. completa e C. capitata di incorporare il gene per l’espressione di una proteina fluorescente (GFP) e quindi la capacità del battere cosi modificato di ri-colonizzare l’ospite originario. Questa tecnica non distruttiva ha consentito il monitoraggio del destino dei batteri nel corso degli stadi di sviluppo dell’insetto. I batteri modificati sono stai ingeriti con successo dalle mosche del noce e ne hanno colonizzato in modo stabile l’intestino medio allo stadio di larva e quindi nella pupa. Si tratta del primo caso in cui un battere tipico della microflora di un tefritide è stato ingegnerizzato con successo e quindi introdotto nell’ospite nativo. La tecnica utilizzata in questo studio potrebbe costituire un valido strumento per espandere questo tipo di ricerca anche al controllo biologico di altre specie dannose in agricoltura. L’ultimo lavoro fa parte parzialmente della tesi di dottorato della Dott.ssa Isabel Martinez-Sañudo, per il quale ho contribuito nella parte sperimentale. L’obbiettivo principale di questo studio è stato quello di indagare le relazioni filogenetiche tra le mosche della sottofamiglia delle Tefritine e i loro batteri simbionti. Alcune specie di questa sottofamiglia sono infatti note per ospitare un simbionte specifico ereditario e non coltivabile (‘‘Candidatus Stammerula spp.”) nell’intestino medio. Tali batteri simbionti sono presenti solo in due delle cinque tribù della sottofamiglia studiate. L’analisi della cofilogenesi ha rivelato la presenza di una congruenza, seppure imperfetta, tra ospiti e simbionti.
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Alvarez, Julia D. "Studies on Venezuelan fish and shrimp associated bacteria." Thesis, Heriot-Watt University, 1998. http://hdl.handle.net/10399/619.
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Slabbert, Róan Stephanus. "Evaluation of acid resistance in food-associated bacteria." Thesis, Bloemfontein : Central University of Technology, Free State, 2011. http://hdl.handle.net/11462/147.
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Thesis (M. Tech. Environmental health) -- Central University of technology, Free State, 2011Although the application of low pH is common practice in food preservation, the emergence of acid tolerance has been reported world-wide amidst a growing concern that preservation with weak acids, such as organic acids may be influenced as a result of food-borne bacteria becoming acid tolerant or acid resistant. The present study was conducted to assess the acid tolerance of a wide range of bacterial species and consequently the sustainable application of organic acids as food preservatives in particularly acidic foodstuffs. Acid tolerance was determined in 19 bacterial strains predominantly associated with food spoilage and food poisoning. After exposure to hydrochloric acid 16% of the isolates were found to be intrinsically tolerant to low pH and included amongst others the enteric bacteria Escherichia coli and Salmonella spp. The latter organisms are known causative agents in food spoilage and poisoning, and the results highlight the predicaments related to their ability to survive in acidic foodstuffs as well as the human gastric environment. Bacterial strains were further exposed to increasing concentrations of various acidic foodstuffs in order to determine the development of acid tolerance by gradual decrease in pH, as opposed to exposure to acid shock. After induction, the protein profiles of resulting acid tolerant isolates were compared with those of the original un-induced strains. Exposure to acidic foodstuffs resulted in various survival profiles, where not only pH but also the type of acidulant (foodstuff or inorganic acid) were found to be contributing factors in acid tolerance development. Bacterial protein composition after exposure to acidic foodstuffs showed considerable variation which may be indicative of acid tolerance development whereas the mechanisms involved may be the result of multiple modifications in bacterial composition. After the induction of acid tolerance, susceptibility of induced strains to various organic acids were determined at various pH values. This was done to investigate whether acid tolerance would influence the inhibitory activity of organic acids as antimicrobial agents in acidic food. Decreased susceptibility was not significantly demonstrated with the exception of only selected isolates, the latter including E. coli and S. typhimurium. Organic acid activity was found to be much more effective at lower pH values and it would be necessary to elucidate whether this inhibition is the result of a lower pH or more specifically the activity of the organic acids. The effect of exposure to an acidic environment on phenotypic characteristics of Gram-negative bacteria, and more specifically psychrotrophic organisms was evaluated in order to show the combined effect of organic acids and low temperature preservation. The characteristic yellow pigment of various Chryseobacterium species was found to be not as apparent after acid exposure while in some cases the colonies were observed as white. In Pseudomonas aeruginosa the characteristic green pigment was much more prominent after acid exposure. These morphological alterations may be important factors that should be considered in identification procedures employed in food safety laboratories. Finally, the influence of acidic exposure via acidic foodstuffs and also organic acids on the protein composition and outer membrane protein structure of various bacterial cells was investigated. No specific relationships with the MICs (Minimum Inhibitory Concentrations) of organic acids after induction with the selected acidic foodstuffs could be established, although various differences were found in protein expression. From the results, it may be suggested that the outer membrane of various pathogenic bacteria is involved in acid tolerance development and this supports the reports on the importance of membrane integrity in the protection against low pH. In conclusion, the study endeavoured to add to the body of knowledge with regard to alternative food preservation regimes utilising organic acids, either solely or in combination with selected extrinsic and intrinsic parameters.
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Tyler, Heather Lee. "Plant-associated bacteria biological, genomic, and metagenomic studies /." [Gainesville, Fla.] : University of Florida, 2009. http://purl.fcla.edu/fcla/etd/UFE0041068.
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Bharadwaj, Dharam Parkash. "The plant - arbuscular mycorrhizal fungi - bacteria - pathogen system : multifunctional role of AMF spore-associated bacteria /." Uppsala : Dept, of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200790.pdf.
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Cuschieri, Katie Sarah. "Species diversity of aggregate-associated marine ammonia-oxidising bacteria." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602054.
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Two broad communities can be distinguished in marine systems, those attached to amorphous aggregate material dispersed throughout the water column and those that are freely suspended in the water column (planktonic). It has been suggested that two distinct microbial populations are associated with each habitat due to phenotypic adaptation to the different conditions in aggregates and the surrounding water. The aim of this study was to investigate the diversity of aggregate-associated and planktonic marine ammonia oxidisers (AOBs - the organisms responsible for the rate limiting step in nitrification) in both natural environments and laboratory-reared systems and to determine whether aggregate material selected for particular groups of AOBs. Detection of AOBs relied heavily on the use of molecular analysis of extracted DNA. Thus, a preliminary study was performed to assess whether preferential lysis occurred when representatives of both genera within the B-subgroup AOBs {Nitrosospira multiformis and Nitrosomonas europaea) were exposed to lysis procedures commonly applied to marine samples. Minimal bias existed, with Nitrosomonas europaea proving to be less susceptible to lysis only when the lytic agents (sodium dodecyl sulphate and lysozyme) were absent or at concentrations 100-fold less than those applied in routine environmental extraction. Environmental populations of aggregate-associated and planktonic AOBs in the NW Mediterranean Sea were assessed in summer and winter at stations both within and beyond regions of fresh water inflow (the plume). Molecular analysis involved amplification, by the polymerase chain reaction, of 16S rRNA genes from extracted DNA using AOB-specific primers. Analysis of 16S rDNA sequences coupled with DGGE and specific probing revealed temporal and spatial effects in community structure of AOBs. In the summer, genus level selection of AOBs was observed with Nitrosospira dominating in the aggregate population and Nitrosomonas dominating in the planktonic phase. This was found in the surface waters of geographically distant sites within and outside the plume. Between-site differences were evident in the deeper waters with Nitrosospira-like sequences more abundant in plume diluted waters and Nitrosomonas like sequences more abundant outside this zone, while genus level selection between aggregate-associated and planktonic communities was not detected. In winter, a uniform pattern of AOB distribution emerged with an even distribution of two Nitrosospira sequences at each site on all aggregate and planktonic samples. The AOB community structure of sediment samples was not wholly resolved by application of direct molecular techniques and the culturable diversity was later examined by an enrichment-based approach. A laboratory-reared aggregate system was developed to assess the distribution and selection of inoculated pure and enrichment cultures of AOBs and to assess the effect of sampling technique on the observed community structure. Enclosed vessels containing North Sea water were rotated until aggregation of autochthonous particulate material formed discrete aggregates. No genus level selection of AOBs was observed in aggregate-associated and planktonic communities in North Sea water yet differences in the distribution of closely related sequences within cluster 1 Nitrosospira were observed between the two communities. Observed aggregate and planktonic community structure was affected by the method used to separate the two fractions. Active bacterial production was not necessary for aggregate formation if a pooled suspension of aggregates was sterilised and added to a medium of cell-free filtered sea water. Thus, the successful inoculation and retrieval of an N. multiformis culture within the cell free system suggested that it was appropriate for investigation of the colonisation dynamics of inoculated AOBs.
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Ridsdale, Carmen Jane. "Interactions of arbuscular mycorrhizal fungi and spore-associated bacteria." Thesis, Rhodes University, 2013. http://hdl.handle.net/10962/d1018269.
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Arbuscular mycorrhizal (AM) fungi are naturally occurring in roots of terrestrial plants. AM fungi are capable of benefiting the host plant through various mechanisms such as enhanced nutrient supply, alleviation of environmental stress and inhibition of plant fungal pathogens. AM fungal spore-associated bacteria have been previously isolated and shown to have plant growthpromoting (PGP) abilities by several authors. Some bacterial isolates are able to promote AM fungal colonisation of host plants and are known to be mycorrhizal helper bacteria (MHB). This study focused on the isolation of AM fungal spore-associated bacteria, characterization of the isolates according to plant growth promoting abilities and evaluation of their potential to enhance plant growth and mycorrhizal colonisation. AM fungi were extracted from soils sampled from natural indigenous forest sources, raspberry (Rubus idaeus cv. Heritage) and strawberry (Fragaria ananassa) farms in South Africa and from a raspberry (Rubus idaeus cv. Autumn Bliss) plantation in Argentina. A total of 52 sporeassociated bacteria were isolated from the external and internal surfaces of AM fungal spore morphotypes from the two countries. The bacterial isolates were evaluated for their PGP abilities such as phosphate solubilisation, indole-3-acetic acid production, ammonia production and inhibition of the fungal pathogens Fusarium oxysporum and Phythophthora nicotianae through mechanisms such as siderophore and/ or hydrolytic enzyme production. A total of 23 bacterial isolates from both South Africa and Argentina showing the most potential to be PGP, were identified molecularly as belonging to the genera Acinetobacter, Alcaligenes, Bacillus, Microbacterium, Micrococcus, Serratia and Staphylococcus. The ability of ten selected bacterial isolates showing multiple PGP capacity were evaluated for their plant growth promotion and mycorrhizal colonisation enhancement ability on raspberry (Rubus idaeus cv. Meeker). Significant differences in increased shoot and root dry weights were shown by the treatments compared to the uninoculated control. The highest increase in shoot and root dry weights were shown by South African (Bacillus mycoides) and Argentinean (Alcaligenes faecalis) isolates. AM fungal colonisation was significantly enhanced by the South African (Bacillus mycoides) and Argentinean (Micrococcus luteus) isolates compared to the AM fungal singly inoculated control.
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Fandino, Laura B. "Molecular ecology of bacteria associated with marine phytoplankton blooms /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3064445.
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Ye, Jingxiao. "Intestinal bacteria associated with colitis and inflammatory bowel disease." Diss., [Riverside, Calif.] : University of California, Riverside, 2009. http://proquest.umi.com/pqdweb?index=0&did=1957340931&SrchMode=2&sid=2&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1269024239&clientId=48051.
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Thesis (Ph. D.)--University of California, Riverside, 2009.Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 20, 2010). Includes bibliographical references. Also issued in print.
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Erwin, Patrick M. "Characterization, community structure and ecological importance of sponge-associated bacteria." Birmingham, Ala. : University of Alabama at Birmingham, 2007. https://www.mhsl.uab.edu/dt/2008r/erwin.pdf.
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Thesis (Ph. D.)--University of Alabama at Birmingham, 2007.Additional advisors: Asim K. Bej, James B. McClintock, Julie B. Olson, Marc Slattery. Description based on contents viewed June 11, 2008; title from title screen. Includes bibliographical references.
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Liu, Oscar H. "RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-9937.
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Helicobacter pylori infects more than half of the world's population, and is known to be involved in several diseases including gastric cancer. Its close interactions with the stomach and host immune system serves as a good model to study the co-adaptation and co-evolution of the organisms in the stomach micro-environment. In this project, we utilized RNA-seq and data analysis tools to investigate differentially expressed genes by H. pylori in patients at different stages of early gastric cancer development. We also investigated the abundance and diversity of bacterial genera other than H. pylori, and looked for correlations with H. pylori presence and number. For differential gene expression of H. pylori, one gene was differentially expressed between samples of corpus atrophy without metaplasia vs. samples of antrum gastritis, and eight genes were found to be differentially expressed between samples of corpus atrophy with metaplasia vs. samples with pan-gastritis. When samples were clustered into different groups based on the expression data, 52 genes (shared or unique to the specific comparison groups) were found to be differentially expressed, but no apparent patterns were observed that could be explained by medical or sample collection data. For bacterial diversity and abundances, we found several genera colonizing the stomach, of which some have been previously identified. While most of these bacteria colonize regardless of the presence of H. pylori, the abundance of three genera, Wolinella, Campylobacter, and Veillonella, seem to be correlated with the presence of H. pylori.
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Kömerik, Nurgül. "Susceptibility of mucositis-associated Gram-negative bacteria to photodynamic action." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.401728.
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Axelsson, Karolin. "Chemical signals in interactions between Hylobius abietis and associated bacteria." Doctoral thesis, KTH, Organisk kemi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-187817.
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The pine weevil (Hylobius abietis L.) is one of the two topmost economically important insect pests in Swedish conifer forests. The damage increase in areas were the silvicultural practice is to use clear cuttings were the insects gather and breed. During egglaying the female protects her offspring by creating a cave in roots and stumps were she puts her egg and covers it with frass, a mixture of weevil feces and chewed bark. Adult pine weevils have been observed to feed on the other side of the egg laying site and antifeedant substance has been discovered in the feces of the pine weevil. We think it is possible that microorganisms present in the frass contribute with antifeedant/repellent substances. Little is known about the pine weevils associated bacteria community and their symbiotic functions. In this thesis the bacterial community is characterized in gut and frass both from pine weevils in different populations across Europe as well as after a 28 day long diet regime on Scots pine, silver birch or bilberry. Volatile substances produced by isolated bacteria as well as from a consortium of microorganisms were collected with solid phase micro extraction (SPME) and analyzed with GC-MS. The main volatiles were tested against pine weevils using a two-choice test. Wolbachia, Rahnella aquatilis, Serratia and Pseudomonas syringae was commonly associated with the pine weevil. 2-Methoxyphenol, 2-phenylethanol, 3-methyl-1-butanol were found in the headspace from Rahnella aquatilis when grown in substrate containing pine bark. 2-Methoxyphenol and 3-methyl-1-butanol, phenol and methyl salicylate were found in pine feces. Birch and bilberry feces emitted mainly linalool oxides and bilberry emitted also small amounts of 2-phenylethanol. A second part of the thesis discusses the role of fungi in forest insect interactions and the production of oxygenated monoterpenes as possible antifeedants. Spruce bark beetles (Ips typhographus L.) aggregate with the help of pheromones and with collected forces they kill weakened adult trees as a result of associated fungi growth and larval development. A fungi associated with the bark beetle, Grosmannia europhoides, was shown to produce de novo 2-methyl-3-buten-2-ol, the major component of the spruce bark beetle aggregation pheromone. Chemical defense responses against Endoconidiophora polonica and Heterobasidion parviporum were investigated using four clones of Norway spruce with different susceptibility to Heterobasidion sp. Clone specific differences were found in induced mono-, sesqui and diterpenes. A number of oxygenated monoterpenes which are known antifeedants for the pine weevil were produced in the infested areas.QC 20160601
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Altabtbaei, Khaled. "METAGENOMIC ANALYSIS OF PERIODONTAL BACTERIA ASSOCIATED WITH GENERALIZED AGGRESSIVE PERIODONTITIS." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1466590877.
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Bae, Sung Sook School of Chemical Engineering & Industrial Chemistry UNSW. "Investigation of bacteria associated with Australian wine grapes using cultural and molecular methods." Awarded by:University of New South Wales. School of Chemical Engineering and Industrial Chemistry, 2005. http://handle.unsw.edu.au/1959.4/23348.
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This thesis presents a systematic investigation of bacterial species associated with wine grapes cultivated in Australian vineyards during 2001-2004. Grapes, sampled throughout cultivation, were analysed for bacterial species using a combination of cultural and molecular methods. Red (Shiraz, Cabernet Sauvignon, Merlot) and white (Chardonnay, Semillon, Sauvignon Blanc) grape varieties were examined. Factors affecting the bacterial ecology of grapes were considered. The bacterial populations of mature undamaged grapes at harvest were consistently low at 102-103 CFU/g. Higher populations (103-106 CFU/g) were found on grapes at earlier stages of maturity and correlated with application of Bacillus thuringiensis as a biological pesticide. B. thuringiensis was the most prevalent bacterial species on wine grapes throughout cultivation, as determined by plate culture, enrichment culture and PCR-DGGE. B. thuringiensis carried over into wine processing but did not grow in juice or wine and did not adversely affect the growth of Saccharomyces cerevisiae or Oenococcus oeni in liquid culture. B. thuringiensis inhibited the growth of several spoilage and mycotoxigenic fungi found on grapes. Curtobacterium flaccumfaciens was the second most prevalent species detected on wine grapes. Its populations rarely exceeded 103-104 CFU/g. Other bacteria (Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, Sphingomonas) were sporadically found on grapes. Lactic acid bacteria and acetic acid bacteria were rarely detected on undamaged grapes by culture and PCR-DGGE methods. A greater incidence of lactic acid bacteria was detected by specific enrichment procedures, especially on damaged grape berries. Species found were Lactobacillus plantarum, Lactobacillus mali, Lactobacillus lindneri and Lactobacillus kunkeei. The malolactic organism, O. oeni, was never isolated from any grape sample, raising questions about its enological origin. Enrichment cultures also revealed the presence of other bacteria (e.g. Sporolactobacillus inulinus, Asaia siamensis) not previously found on wine grapes. Atypical, hot and dry conditions during cultivation may account for the low populations of bacteria found on wine grapes. This factor combined with the overwhelming presence of B. thuringiensis prevented meaningful comparisons of data to determine influences of vineyard location, grape variety, grape maturity, climate and viticultural practices on the bacterial ecology of grapes. More systematic and controlled studies of these variables are required.
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Pieterse, Reneé. "Control of bacterial pathogens associated with mastitis in dairy cows with natural antimicrobial peptides produced by lactic acid bacteria /." Link to the online version, 2008. http://hdl.handle.net/10019/891.
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Roselló, Prados Gemma. "Characterization and improvement of plant-associated Lactobacillus plantarum. Novel biocontrol agent for fire blight disease." Doctoral thesis, Universitat de Girona, 2016. http://hdl.handle.net/10803/403404.
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Fire blight is a disease caused by Erwinia amylovora. For the limited effectiveness of copper products and the new regulations for the sustainable use of pesticides, biological control is considered a good alternative for the control of fire blight. Therefore, this thesis focuses on the research of lactic acid bacteria strains as biocontrol agents of fire blight. Three out of one hundred strains, which were identified as Lactobacillus plantarum TC54, TC92 and PM411, were selected by their ability to inhibit E. amylovora infections in different performed assays. A multivariate statistical analysis, combining different phenotypic and genotypic properties, determined that strains TC92 and PM411 were good candidates as biocontrol agents. Finally, the combination of lactic acid and strains TC92 and PM411 was used to increase the biocontrol efficacy and reliability in the biocontrol of fire blightEl foc bacterià és una malaltia causada pel bacteri Erwinia amylovora. L’eficàcia limitada dels productes cúprics i les noves normatives d’ús sostenible dels productes fitosanitaris, fan que el control biològic es consideri una bona alternativa en el control d’aquesta malaltia. Aquesta tesi es centra en la recerca de soques de bacteris de l’àcid làctic com a agents de biocontrol del foc bacterià. Tenint en compte la seva eficàcia en el control de les infeccions causades per E. amylovora en diferents assajos realitzats es van seleccionar 3 soques de 100 inicials, identificades com a Lactobacillus plantarum TC54, TC92 i PM411. Un anàlisi estadístic multivariant, combinant diferents propietats genotípiques i fenotípiques, va confirmar que les soques TC92 i PM411 eren bones candidates a agents de biocontrol. Finalment, per incrementar la seva eficàcia i fiabilitat en el control del foc bacterià, es va utilitzar la combinació d’àcid làctic i les dues soques seleccionades
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Kumar, Purnima. "Molecular analysis of bacteria associated with chronic periodontitis and periodontal health." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1124221576.
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Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains x, 104 p.; also includes graphics (some col.). Includes bibliographical references (p. 92-104). Available online via OhioLINK's ETD Center
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Bacchetti, de Gregoris Tristano. "Studies on the acorn barnacle Balanus amphitrite and its associated bacteria." Thesis, University of Newcastle Upon Tyne, 2011. http://hdl.handle.net/10443/1238.
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Despite being a model organism to study settlement in marine invertebrates, little is known about the genetics of the barnacle Balanus amphitrite. To fill this gap, cDNA libraries representative of different developmental stages were generated and sequenced. Nearly 14,000 genes were annotated, which may represent 2/3 of the species’ total protein coding regions. The database that was created to allow public access to this genetic information will profoundly benefit future research aiming to understand the molecular regulation of development and settlement in this species. Furthermore, a quantitative real-time PCR assay to study gene expression in B. amphitrite was designed and validated. Eleven genes were studied for their ability to normalize qRT-PCR data. Total RNA extracted from seven developmental stages was reverse transcribed and the expression stability of the selected genes was compared. It was found that transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, and their use to normalize gene expression data is recommended. Conflicting evidence exists on the role of bacteria in B. amphitrite settlement. However, there is a paucity of information on the microbial community naturally associated with this barnacle. In order to reveal the existence of stable associations, a 16S rRNA-based, taxon-specific qPCR assay was developed to monitor the preponderance of 5 bacterial phyla and classes. Furthermore, attempts to profile these qPCR products by DGGE were made. This new method was applied to characterise the bacterial communities associated with different B. amphitrite developmental stages and body parts. It was found that the structure of these communities changed throughout the barnacle life cycle in a highly reproducible manner. Furthermore, bacteria isolated from the barnacle shell were capable of inducing settlement of conspecific larvae. The analysis of these communities at a lower taxonomic level should confirm if any of these ecologically important bacteria are vertically transmitted.
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Xiujie, Luan. "Study of the bacteria associated with exacerbation of late-onset asthma." Thesis, University of Derby, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323640.
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Barke, Joerg. "Antifungals of acromyrmex, allomerus, and tetraponera ant- and cultivar-associated bacteria." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/47859/.
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The central purpose of this thesis is to test the utility of ant-microbe associations for discovering antifungal compounds with novel molecular (sub-) structures. Novel antifungals displaying reduced adverse side-effects, increased water-solubilities, and/or strong fungicidal properties would be helpful in medical science for responding to the rising prevalence of human mycoses and for solving problems with adverse side-effects in currently used antifungal drugs. Host-symbiont systems may represent a source of bacterial species that, due to their co-evolved association with hosts, have evolved antifungals differing in their molecular structures from antifungals of well-explored environmentalsources. To test the suitability of ant-microbe symbioses for discovering novel antifungals, I characterise ectosymbiotic bacteria and antifungal metabolites in three ant-associated niches: Acromyrmex octospinosus worker ants, fungal cultivars of Allomerus decemarticulatus and A. octoarticulatus, and Tetraponera penzigi worker ants and their putative fungal cultivar. I find that the A. octospinosus and T. penzigi niches hosted multiple bioactive actinobacteria including Streptomyces, Pseudonocardia, Nocardiopsis, and Saccharopolyspora. A Streptomyces strain from the Acromyrmex octospinosus niche was shown to produce the structurally unmodified antifungals candicidin and antimycin, which is suggestive of bacterial recruitment from environmental sources. Antimycin consisted of two sets of six molecules varying in number of attached CH2 groups. Both sets differ in polarity and fragmentation pattern. Only one set of antimycins inhibited the growth of Candida albicans, and this set revealed tandem-LCMS analogies with an antimycin A1-A4 standard. A Pseudonocardia strain from the same A. octospinosus niche was found to produce a partially novel (to science) and potentially water-soluble nystatinlike antifungal, which is suggestive of host-symbiont coevolution. These findings indicate that the host ant is able to use multiple-drug therapy in the form of antifungal �cocktails� to tackle resistance evolution in fungal pathogens. Overall, this research demonstrates that ant-microbe associations provide new opportunities for finding abundant bioactive bacteria and novel antibiotics.
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Mechan, Llontop Marco Enrique. "Identification, Characterization, and Use of Precipitation-borne and Plant-associated Bacteria." Diss., Virginia Tech, 2020. http://hdl.handle.net/10919/96402.
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Bacteria are ubiquitously present in every ecosystem on earth. While bacterial communities that reside in specific habitats, called the microbiota, have characteristic compositions, their constituents are exchanged between habitats. To understand the assembly processes and function of a microbial community in an ecosystem, it is thus important to identify its putative sources and sinks.
The sources and sinks of the plant leaf microbiome, also called the phyllosphere microbiome, are still under debate. Here, I hypothesized that precipitation is a so far neglected source of the phyllosphere microbiome. Using 16S rRNA amplicon and metagenomic sequencing, I identified the genera Massilia, Sphingomonas, Methylobacterium, Pseudomonas, Acidiphilium, and Pantoea as members of the core rain microbiome in Blacksburg, VA. Further, I used rainwater as a bacterial inoculum to treat tomato plants. I showed that rain-borne bacteria of the genera Chryseobacterium, Enterobacter, Pantoea, Paenibacillus, Duganella, Streptomyces, Massilia, Shinella, Janthinobacterium, Erwinia, and Hyphomicrobium were significantly more abundant in the tomato phyllosphere 7 days post-inoculation, suggesting that these rain-borne bacteria successfully colonized the tomato phyllosphere and had a direct impact on the composition of its microbiome. These results were confirmed by comparing the phyllosphere microbiota of tomato plants grown under greenhouse conditions, and thus never exposed to rain, compared to plants grown outside under environmental conditions, including precipitation.
Since a large diversity of bacteria is associated with rain, I also hypothesized that rain-borne bacteria are well adapted to environmental stresses, similar to the stressors microbial biopesticides are exposed to in the field. I thus explored rain as a source of resilient biopesticides to control fire blight, caused by the bacterial pathogen Erwinia amylovora, on apple. In an in-vitro dual culture assay, I identified rain-borne isolates displaying broad-range inhibition against E. amylovora and several other plant pathogens. Two rain-borne isolates, identified as Pantoea agglomerans and P. ananatis, showed the strongest inhibition of E. amylovora. Further experiments showed that these two Pantoea isolates survive under environmental conditions and have a strong protective effect against E. amylovora. However, protection from disease in an orchard was inconsistent, suggesting that the timing of application and formulations must be improved for field applications. Using a UV-mutagenesis screen and whole-genome sequencing, I found that a phenazine antibiotic produced by the P. agglomerans isolate was the likely active molecule that inhibited E. amylovora.
Bacterial communities are constantly released as aerosols into the atmosphere from plant, soil, and aquatic sources. When in the atmosphere, bacteria may play crucial roles in geochemical processes, including the formation of precipitation. To understand the potential role of decaying vegetation as a source of atmospheric Ice Nucleation Particles (INPs), I analyzed a historic leaf litter sample collected in 1970 that had maintained Ice Nucleation Activity (INA) for 48 years. A culture-dependent analysis identified the bacterial species Pantoea ananatis and the fungal species Mortierella alpina to have INA and to be present in the leaf litter sample. Further, I determined that both P. ananatis and M. alpina produced heat-sensitive sub-micron INPs that may contribute to atmospheric INPs.
The development of new sequencing technologies has facilitated our understanding of microbial community composition, assembly, and function. Most research in bacterial community composition is based on the sequencing of a single region of the 16S rRNA gene. Here, I tested the potential of culture-independent 16S rRNA sequencing of the phyllosphere microbiome for disease diagnosis. I compared the community composition of the microbiome of the aerial parts of cheddar pinks (Dianthus gratianopolitanus) that showed disease symptoms with the microbiome of healthy plants to identify the causative agent. However, I found that the pathogen is probably ubiquitous on cheddar pinks since it was present at similar abundance levels in symptomatic as well as healthy plants. Moreover, the low-resolution of 16S rRNA sequencing did not allow to identify the pathogen at the species or strain level.
In summary, in this thesis, I found support for the hypothesis that rain is one of the sources of the phyllosphere microbiome, that rain is a promising source of biopesticides to control plant diseases in the field, that leaf litter is a source of atmospheric INPs, and that 16S rRNA sequencing is not well suited for pathogen identification in support of plant disease diagnosis. Finally, in additional research to which I contributed but that is not included in this thesis, I found that metagenomic sequencing can identify pathogens at the species and strain level and can overcome the limitations of 16S rRNA sequencing.Doctor of Philosophy
Bacteria are present in nearly every ecosystem on earth. Bacterial communities that reside in a specific habitat are known as microbiota and have characteristic compositions and functions that directly impact the health of ecosystems. Microbiota associated with plants, the so-called plant microbiota, play a crucial role in plant fitness. Thus, it is important to study the assembly and diversity of plant microbiota and their impact on the ecosystem. The sources of leaf microbiota remain to be elucidated. Here, I have studied the contribution of rainfall to the bacteria that live on and in plant leaves. First, using DNA sequencing, I identified the bacteria present in rainfall in Blacksburg, VA. Then, using rain as bacterial inoculum, I found that some rain-borne bacteria, including members of the genera Pantoea, Massilia, Janthinobacterium, and Enterobacter, are efficient colonizers of tomato leaves. Either absence or low abundance of rain-borne bacteria from tomato leaves never exposed to rainfall confirmed further that bacteria in rain contribute to the assembly of plant leaf microbiota. The identification of all putative sources and sinks of leaf microbiota is important when trying to manipulate them to improve plant health and crop yield. Since I found that rainfall contains many different bacteria, I also studied the potential application of rain-borne bacteria in agriculture. The main limitations of commercial bio-pesticides are their poor survival and limited efficacy in the field. Here, I speculated that rain-borne bacteria are well adapted to environmental stressors and could represent efficient bio-pesticides under field conditions. In fact, I isolated two rain-borne bacteria from the genus Pantoea that strongly inhibited Erwinia amylovora, the causal agent of the fire blight disease of apple, in the laboratory under controlled conditions. However, I observed inconsistent results in a 2-year field trial in an orchard. Using mutagenesis and DNA sequencing, I found the active molecule that likely inhibited E. amylovora, in one of the rain-borne isolates. Finally, the access to newer and cheaper sequencing technologies has recently facilitated the study of bacteria at large scale. Most research of microbiota is based on the sequencing of a single region of one gene, the 16S rRNA gene. Here, I tested the potential of 16S rRNA sequencing of leaf microbiota for disease diagnosis. However, I identified the pathogen in healthy and diseased plants, suggesting its ubiquitous presence. Further, due to the low-resolution of 16S rRNA sequencing, it was impossible to identify the pathogen at the species level. In summary, I found that rain is a source that contributes to leaf microbiota, that rain is a promising source of bio-pesticides to control plant diseases, and that 16S rRNA sequencing is not recommended as a tool to diagnose plant diseases.
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Witzig, Stephen B. "Signals affecting the urease status of plant-associated bacteria, Methylobacterium spp." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/5049.
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Thesis (M.S.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on May 12, 2009) Includes bibliographical references.
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WAGER, JORJ ANNE. "BACTERIA ASSOCIATED WITH THE CACTOPHILIC SPECIES DROSOPHILA ARIZONAE AND DROSOPHILA ALDRICHI." Thesis, The University of Arizona, 2008. http://hdl.handle.net/10150/192247.
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Parks, Georgia. "Microbial Analysis of Surfactant-Associated Bacteria in the Sea Surface Microlayer and Remote Sensing of Associated Slicks." Thesis, NSUWorks, 2019. https://nsuworks.nova.edu/occ_stuetd/515.
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The sea-surface microlayer (SML) is the boundary layer at the air-sea interface where many biogeochemical processes occur. Many organisms (e.g., bacteria) produce surface active agents (surfactants) for life processes, which accumulate in the SML and dampen short gravity-capillary waves, resulting in sea surface slicks. Synthetic aperture radar (SAR) is capable of remotely sensing these features on the sea surface by measuring reflected backscatter from the ocean surface in microwaves. This study coordinates SAR overpasses with in situ SML and subsurface (SSW) microbial sample collection to guide subsequent analysis after 16s rRNA sequencing on the Illumina MiSeq. In April 2017, 138 SML and SSW samples were collected near a targeted oil-seep where the Taylor Platform was knocked down in the Gulf of Mexico, both in and out of visually-observed oil slicks. In July and August 2018, 220 SML and SSW samples were collected near the Looe Key coral reef and a coastal seagrass area. Analysis of microbial abundance and diversity between the two experiments shows that within oil slicks, surfactant- and oil-associated bacteria prefer to reside within the SSW rather than in the SML. In natural slicks in the coastal seagrass area, these bacteria are more abundant in the SML. Outside of these slicks, surfactant-associated bacteria are more abundant within the SML than the SSW. This suggests that the presence of oil reduces the habitability of the SML, whereas natural slicks created by foam and other surfactants creates a more habitable environment in the SML. With lower wind speed, abundance of these bacteria are greater, as increased wind speed results in a harsher environment. The diurnal cycle had an effect on the relative abundance of surfactant-associated bacteria in the SML and SSW. Our results demonstrate the usefulness of synthetic aperture radar to remotely sense sea surface slicks in coordination with in situ surfactant-associated bacteria data collection of the sea surface slicks.
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Pieterse, Renee. "Control of bacterial pathogens associated with mastitis in dairy cows with natural antimicrobial peptides produced by lactic acid bacteria." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/2323.
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Thesis (MSc (Microbiology))--Stellenbosch University, 2008.Mastitis is considered to be the most costly disease affecting the dairy industry. Management strategies involve the extensive use of antibiotics to treat and prevent this disease. Prophylactic dosages of antibiotics used in mastitis control programmes could select for strains with resistance to antibiotics. In addition, a strong drive towards reducing antibiotic residues in animal food products has lead to research in finding alternative antimicrobial agents. Streptococcus macedonicus ST91KM, isolated from bulgarian goat yoghurt, produces the bacteriocin macedocin ST91KM with a narrow spectrum of activity against Grampositive bacteria. These include mastitis pathogens Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Staphylococcus aureus and Staphylococcus epidermidis as well as Lactobacillus sakei and Micrococcus varians. Macedocin ST91KM is, according to tricine-SDS PAGE, between 2.0 and 2.5 kDa in size. The activity of macedocin ST91KM remained unchanged after 2 h of incubation at pH 2.0 to 10.0 and 100 min at 100 °C. The peptide was inactivated after 20 min at 121 °C and when treated with pronase, pepsin and trypsin. Treatment with α-amylase had no effect on activity, suggesting that the mode of action does not depend on glycosylation. Precipitation with 60 % saturated ammonium sulphate, followed by Sep-Pak C18 separation recovered 43 % of macedocin ST91KM. Amplification of the genome of strain ST91KM with primers designed from the sequence of the macedocin prescursor gene (mcdA) produced two fragments (approximately 375 and 220 bp) instead of one fragment of 150 bp recorded for macedocin produced by S. macedonicus ACA-DC 198. Strain ACA-DC 198 was not available. However, the DNA fragment amplified from strain LMG 18488 (ACA-DC 206), genetically closely related to strain ACADC 198, revealed 99 % homology to the mcdA of S. macedonicus ACA-DC 198 (accession number DQ835394). Macedocin ST91KM may thus be a related bacteriocin described for S. macedonicus. The peptide adsorbed equally well (66 %) to L. sakei LMG13558 and insensitive cells, e.g. Enterococcus faecalis BFE 1071 and FAIR E92, and Streptococcus caprinus ATCC 700066. Optimal adsorption of macedocin ST91KM was recorded at 37 °C and 45 °C and at pH of 8 - 10. Addition of solvents decreased adsorption by 50%, suggesting that the receptors to which the bacteriocin binds have lipid moieties. The addition of MgCl2, KI and Na2CO3 completely prevented adsorption of macedocin ST91KM to the target cells, possibly due to competitive ion adsorption on the bacterial cell surface. The peptide has a bacteriocidal mode of action, resulting in lysis and the release of DNA and β-galactosidase. Atomic force microscopy of sensitive cells treated with macedocin ST91KM have shown deformation of the cell structure and developing of irregular surface areas. Antimicrobial susceptibility patterns were evaluated against eighteen mastitis pathogens. All isolates tested were resistant to methicillin and oxacillin, but had minimum inhibitory concentrations (MICs) falling in the intermediate and susceptible range against erythromycin. S. agalactiae and S. epidermidis had the highest sensitivity to macedocin ST91KM. A teat seal preparation containing macedocin ST91KM effectively released bacteriocin inhibiting the growth of the bacterial pathogen. Macedocin ST91KM could form the basis for an alternative dry cow therapy to prevent mastitis infections in dairy cows, as it is effective against pathogens that display resistance to conventional antibiotic therapy.
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Grewal, Parwinder Singh. "Studies on saprobic rhabditid nematodes and their associated bacteria affecting mushroom culture." Thesis, Imperial College London, 1990. http://hdl.handle.net/10044/1/46322.
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Reardon, Catherine Leona. "Molecular Analysis of Diversity, Gene Expression and Activity of Mineral-Associated Bacteria." Thesis, Montana State University, 2005. http://etd.lib.montana.edu/etd/2005/reardon/ReardonC1205.pdf.
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This dissertation investigated the diversity and hydrogenase activity and gene expression of mineral-associated microorganisms. Surface-associated microbes have been shown to dominate diversity and activity in the environment, however molecular analysis of sediment-associated communities is hindered by both inaccessibility to the subsurface and co-extraction of inhibitory compounds. In order to analyze microbial communities in which the environmental conditions previously had precluded the use of traditional sediment extraction techniques, biofilm coupons (metal, mesh cylinders containing surrogate substrata) were used to recover microorganisms able to attach and compete in a biofilm. The community recovered from the contaminated site using hematite as a surrogate substratum was dominated by microbes most closely related to Alcaligenes sp. (metal-tolerant), Frateuria sp. (acidophilic), and Methylobacterium radiotolerans (radionuclide-tolerant) which together reflect the acidic, metal-, and radionuclide-contaminated environment. Hematite, as compared to other substrata, was shown to recover communities most closely representative of sediment communities inhabiting the saturated zone. Surface-associated cells have been shown to express greater activity than suspended populations and mineral-associated sulfate-reducing bacteria (SRB) mediate the formation of different secondary minerals as compared to suspended cells. In order to investigate the affect of surface-association on enzyme activity, hydrogenase enzyme activity was compared in hematite-associated and suspended populations of the SRB Desulfovibrio desulfuricans Essex 6. Hydrogenase activity of surface-associated populations was higher than that displayed by suspended cells. Hydrogenase likely affects the pH and pE of the conditions immediately surrounding the cell. The greater rate of activity may be one factor which contributes to the formation of a mineral phase not observed in the presence of suspended populations of this bacterium. In order to determine the portion of cells expressing hydrogenase in the surface-associated populations, in situ reverse-transcription PCR was applied to the hematite-associated cells and all cells were expressing the [NiFe] hydrogenase gene. This thesis demonstrates that environmental conditions of contaminated subsurface environments select for microorganisms able to tolerate or utilize the contaminants. Also, the hydrogenase activity of surface-associated populations is not representative of the suspended cells thus indicating the importance of studying attached populations where enzyme activity likely influences the conditions at the mineral-microbe interface.
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Lindh, Jenny. "Identification of bacteria associated with malaria mosquitoes - Their characterisation and potential use." Doctoral thesis, Stockholm : Department of Genetics, Microbiology and Toxicology, Stockholm University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-6685.
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Chaisiri, K. "Molecular ecology of chigger mites (Acari: Trombiculidae) and associated bacteria in Thailand." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3004727/.
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Chiggers are the tiny six-legged larval stage of mites in the family Trombiculidae. These mites, particularly the genus Leptotrombidium, act as important vectors of Orientia tsutsugamushi, the causative agent of scrub typhus disease in the Asia-Pacific region (including Thailand). Although the medical impact of these mites has been recognized in the country due to the increasing incidence of the disease in humans, knowledge of the ecology and epidemiological role of these mites is still very limited to date. A systematic review of mite-associated bacteria was conducted from 193 publications (1964 - January 2015) providing a reference database of bacteria found in mites of agricultural, veterinary and medical importance. Approximately 150 bacterial species were reported from 143 mite species with Cardinium, Wolbachia and Orientia as the dominant genera. Nationwide field sampling of small mammals from 13 locations in Thailand revealed a high diversity of chigger mites. From approximately 16,000 mites isolated from 18 host species examined (1,574 individual animals), 38 chigger species were found including three species new to science (i.e., Trombiculindus kosapani n. sp., Helenicula naresuani n. sp. and Walchia chavali n. sp.) and 10 new records for the first time in the country. Brief taxonomic information for the morphological identification of chiggers is provided. A combination of autofluorescent and brightfield microscopy was demonstrated to be a novel approach to study both the morphology and DNA profile of the same individual chigger. Most chigger species showed low host specificity. The diversity of chiggers on hosts was influenced by host intrinsic (i.e., host phylogeny and maturity) and extrinsic factors (i.e., habitat and geographical location). Chigger species richness and host-chigger network connectance were found to be interrelated variables explaining human scrub typhus incidence in Thailand. Chigger-associated bacteria were investigated for the first time using an Illumina MiSeq 16S rRNA amplicon sequencing approach. DNA of O. tsutsugamushi was detected in the chigger population as expected. In addition to O. tsutsugamushi, Borrelia and Mycobacterium were identified aspotential pathogens of human and animals. Potential symbiotic bacteria of arthropods; e.g., Candidatus Cardinium, Pseudonocardia, Rickettsiella and Wolbachia were also discovered for the first time in chiggers. An important technical limitation was that chigger DNA starting quantity (individual specimens versus pooled mites) was found to have a significant impact on the apparent microbiome profile. These outcomes from the studies of chigger taxonomy and the ecology of host-chigger interactions, as well as the composition of the microbiome in chiggers, are of key importance to the chigger research field, providing essential information for disease epidemiology with vector control implications.
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Wu, Chenxi. "Indicative Bacteria in Stored Biosolids and Wastewater Associated Pharmaceuticals in the Environment." University of Toledo / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1278966096.
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Shaffer, Justin Park, and Justin Park Shaffer. "Endohyphal Bacteria of Tropical Plant-Associated Fungi: Diversity, Evolutionary Relationships, and Ecology." Diss., The University of Arizona, 2017. http://hdl.handle.net/10150/625601.
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A growing understanding of complex biotic interactions clarified the importance of symbioses with respect to the ecology and evolution of life. In particular, knowledge of symbioses between eukaryotes and microorganisms such as bacteria and fungi has revolutionized the fields of medicine and agriculture, and made clear the roles of microbes in fostering human and environmental sustainability. For example, diverse fungi associate with the seeds of plants following dispersal. These fungi can influence seed survival and germination in a host-specific and spatially explicit manner, thus influencing plant community dynamics in agricultural and natural systems. In species-rich tropical forests, seed-fungus interactions are emerging as one of the most important aspects of plant demography and community ecology. However, even closely related fungi can have opposing effects on seeds of particular plants, such that mechanisms influencing host-specific effects require further attention. Such mechanisms can include genomic traits of fungi and hosts, and the environmental context of interactions. However, studies have shown that many fungi also harbor endosymbionts than can influence their functional traits. In particular, fungi often harbor endohyphal bacteria that influence fungal phenotypes. This suggested the potential for similar, co-occurring microbes to influence the ecology of seed-associated fungi. Here, I explore the diversity, evolutionary relationships, and influence on fungal phenotypes of endohyphal bacteria inhabiting seed- and leaf-associated fungi with a focus that begins in tropical forest ecology and expands to include gene expression in an emerging model system from the temperate zone.
To determine the occurrence, abundance, taxonomic diversity, and phylogenetic diversity of endohyphal bacteria among tropical seed-associated fungi, my coauthors and I used PCR and fluorescence microscopy to screen members of two common orders of seed-associated fungi, comparing their communities to those in closely related foliar endophytic fungi. We revealed a high frequency and diversity of endohyphal bacteria among both groups of fungi. We then used phylogenetic and community ecological analyses to show a lack of congruence between phylogenies of bacteria and fungi. Although seed-associated and foliar endophytic fungi share evolutionary histories, they harbor distinct endohyphal bacterial communities.
To explore the influence of endohyphal bacteria on fungal phenotypes important for interactions with seeds, my coauthors and I examined a single fungus-bacterium pair consisting of a member of a well-known group of pathogenic fungi found to harbor an endohyphal bacterium closely related to those with known chitinolytic activity. We created fungal clones that were free of endohyphal bacteria, and carried out a phenotypic microarray assay comparing use of 95 unique carbon sources by cured and uncured clones. Across the majority of substrates, the fungal clones harboring endohyphal bacteria grew more rapidly and to a greater extent than the cured clones. Thus the endohyphal bacterium was associated with broader substrate use and more effective use of a variety of substrates relevant to plant biology, including seed germination.
To assess the influence of endohyphal bacteria with respect to the outcomes of seed-fungus interactions, my coauthors and I examined six fungus-bacterium pairs and their interactions with the seeds of five tropical pioneer tree species. We showed that although endohyphal bacteria have little impact on colonization of seeds by fungi, they significantly altered the survival and germination of infected seeds. In most cases, endohyphal bacteria reduced the negative impacts of fungi on seeds: strains harboring them responded more similarly to uninoculated controls, whereas strains cured of them exhibited significantly reduced survival and germination. Seeds infected by fungi of the same genotype that differ with respect to the identity of their endohyphal bacteria exhibited differences, but so did seeds infected by strains of those isolates not harboring bacteria, suggesting that factors in addition to the presence of endohyphal bacteria can drive variation in the outcomes of seed-fungus interactions. Together these analyses suggest intricate interactions between fungi and bacteria that result in context-dependent outcomes. This turned our focus to gene expression as a means to understand mechanisms of interactions between endohyphal bacteria and their fungal hosts.
Last, my coauthors and I describe methods we developed to co-culture fungi and their endohyphal bacteria for downstream analysis of differences in gene expression among a fungus-bacterium pair and axenic cultures of each symbiont. We focused on an emerging model system: a foliar endophytic strain of Pestalotiopsis aff. neglecta (Ascomycota) known to harbor an endohyphal bacterium in the genus Luteibacter (Xanthomonadaceae). The focal bacterium is in part reliant on its host fungus for acquisition of certain sulfur-containing compounds such as sulfate. We showed that inoculating a low-methionine growth medium with bacteria recovered in exponential phase from a high-methionine medium supports growth suitable for comparing axenic growth with that in co-culture with its host fungus. Although bacterial cell density in co-cultures was significantly greater than that in axenic cultures, the opposite was true for the host fungus. We expect results from transcriptomics analyses to reflect partial reliance on– and antagonism of Pestalotiopsis by Luteibacter, and here present the first pipeline of methods for examining gene expression for a facultatively symbiotic endohyphal bacterium and its host, a member of the most species-rich and economically important fungal phylum.
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Dung, Nguyen Quang. "Hysterangium mats and associated bacteria under eucalyptus gomphocephala in south-western Australia." Thesis, Dung, Nguyen Quang (2012) Hysterangium mats and associated bacteria under eucalyptus gomphocephala in south-western Australia. Masters by Research thesis, Murdoch University, 2012. https://researchrepository.murdoch.edu.au/id/eprint/12513/.
Full textAbstract:
Eucalyptus gomphocephala (tuart) is an ecologically and culturally important woodland and forest tree native to south-western Australia. Unfortunately, tuart has been markedly declining in recent decades, and the mortality rate is as high as 90% in some populations. The cause of tuart decline is still poorly understood and we know nothing about how the decline changes populations of organisms such as ectomycorrhizal (ECM) fungi and beneficial bacteria. Therefore, this study investigated aspects of mycorrhizal fungal mats under healthy tuart, including effects on forest soil properties, and presence of beneficial bacteria.
A common mat morphotype (grey, hydrophobic) was chosen for this research and the ECM fungus was identified as a Hysterangium sp. based on fungal morphology, ECM structure and ITS gene region analysis. The effect of the ECM mats on soil moisture, nutrients, microbial biomass (ninhydrin-reactive N) and microbial community (Biolog Ecoplate) was investigated. Potential PGPR with ability to solubilize phosphate (hydroxylapatite-Ca5HO13P3), produce IAA and use ACC acid as the sole carbon source were screened. Hysterangium mats significantly improved soil moisture, soil pH, nutrient level and microbial biomass compared to non-mat soils, however, there was no evidence of any difference in microbial diversity and activity between mat and non-mat soils. Twenty eight IAA producing bacterial isolates, 7 phosphate solubilizing isolates and 2 ACC deaminase producing isolates were screened from mat and non-mat soils.
Interactions among beneficial bacteria, ECM fungi and eucalypt seedlings were then investigated. ECM synthesis was also conducted between Hysterangium MURU6276 and E. gomphocephala seedlings in vitro. The plant growth promoting ability of bacteria to eucalypt seedlings was assessed through a bioassay using petri dishes containing MMN medium overlaid with cellophane. Half plate petri dishes were used to screen for mycorrhiza helper bacteria. ECM association between Hysterangium MURU6275 and E. gomphocephala seedlings was confirmed in vitro. Most bacterial isolates from under tuart had stimulating or inhibiting effects on the root growth of E. gomphocephala and/or E. grandis. The best 6 growth promoting isolates were T1M3, T1N2, T2N7, T3N4, T4N4 and T4N6. However, there was no evidence of the presence of mycorrhiza helper bacteria amongst the isolated bacteria.
These findings provide the basis for further detailed research on biochemical processes and the diversity and functions of bacterial populations under Hysterangium mats associated with tuart. Areas for further study are suggested.
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RIVA, VALENTINA. "PLANT ASSOCIATED BACTERIA: A SUSTAINABLE RESOURCE TO MINIMIZE WATER FOOTPRINT IN AGRICULTURE." Doctoral thesis, Università degli Studi di Milano, 2019. http://hdl.handle.net/2434/691225.
Full textAbstract:
Water scarcity is one of the major worldwide problems affecting in particular agriculture, an intensive water consumer activity. In the frame of the EU H2020 MADFORWATER project, aimed to develop integrated technological and management solutions to reduce water footprint in agriculture, this PhD thesis focused on plant-associated bacteria to improve the productivity of crops growing under drought conditions and wastewater phytodepuration efficiency to allow water reuse for irrigation purposes. A large collection of 681 bacterial strains was isolated from the root apparatus of six plants species adapted to dry soils or other unconventional environmental conditions. The isolates have been taxonomically identified and functionally characterized in order to select the most promising strains exploitable in in vivo experimentations. The isolate collection was compared with a literature-derived dataset of bacterial families identified in the plant microbiome by molecular methods. The comparison demonstrated that we were able to bring into culture members of 20% of the bacterial families detected by culture-independent approaches, partially confirming on the plant biome recent concepts emerged on others environmental microbiota. Moreover, the collection included ubiquitous and potentially beneficial core members of the plant microbiota and satellite taxa, which could have a role in sustaining plant growth under peculiar environmental conditions. The bacterial community associated to Argania spinosa, a drought tolerant tree relevant for the ecology and economy of Morocco, was described for the first time, by culture dependent and independent approaches. The Plant Growth Promoting (PGP) potential of isolates obtained from the root and soil environment of Argan revealed a particular abundance of PGP related traits in strains isolated from the residuesphere fraction, providing a putative explanation to the tradition of local farmers of using argan litter as soil amendment. A selection of strains was tested in in vivo experiments aimed to evaluate their potential to improve plant growth, water use efficiency and fruit productivity. Five PGP bacteria were applied on tomato plants, cultivated in greenhouse under optimal and deficit irrigation and plant physiology, biomass and fruit yield were compared with control, not bacterized plants. All the bacterial inocula showed at different extent to have the potential capacity to alleviate plant water stress, improving different plant and soil parameters, but no statistically significant effect was reported on plant productivity. Further experiments are needed to confirm the results, nevertheless it was demonstrated the importance of performing long-term experiments to obtain reliable and applicable data about the real efficacy of PGP crop application. A second selection of PGP strains significantly showed in microcosm constructed wetlands the ability to tolerate metal contaminated wastewaters and to enhance the azo-dye phytodepuration capacity of Juncus acutus plants. These bacteria have thus the potential to improve the quality of water treated in low cost systems, and will be selected in the project for experimentation at higher pilot scale. This work demonstrated the relevance of the plant microbiota in sustaining plant growth, and provided a collection of strains which need to be further evaluated but could potentially be exploited to mitigate water shortage effects in agriculture.
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Haslett, Norman G. "Factors influencing the production and nature of surface-associated Pseudomonas fragi extracellular polymeric substances (EPS)." Thesis, Queen's University Belfast, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295391.
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Rodriguez, Rodolfo Enrique del Rio. "Aerobic bacterial flora associated with tropical ornamental fish imported into Scotland : their significance and control." Thesis, University of Stirling, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341256.
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Negandhi, Karita L. "Microbial Communities with Emphasis on Coral Disease-Associated Bacteria within Florida Reef Sponges." NSUWorks, 2009. http://nsuworks.nova.edu/occ_stuetd/109.
Full textAbstract:
Previous studies have shown that bacteria associated with coral diseases are not found in the surrounding water column at detectable levels, yet at the same time, coral diseases are becoming more prominent. Sponges are coral reef residents, which expel filtered seawater that is practically sterile of microbes. Therefore sponges harbor very diverse and abundant microbial communities. This leads to the possibility that coral disease associated bacteria (CDAB) may be present within reef sponge microcosms. In order to identify internal microbes, nonculturable techniques including fluorescent in situ hybridization (FISH), electron microscopy (EM) and 16S small subunit (SSU) rRNA gene cloning and sequencing were applied to local Florida reef sponges Agelas tubulata, Amphimedon compressa and Aplysina fistularis. This study targeted potential coral bacterial pathogens with FISH including Aurantimonas coralicida, Cytophaga sp., Desulfvibrio spp., Firmicutes, Serrattia marcescans, and Vibrio shiloni AK-1. All of the targeted coral disease associated bacteria were found within A. compressa and A. tubulata with FISH, but not in every individual. Differences in the spatial arrangement of targeted microbes were also seen within these sponge hosts. For instance, the two anaerobic bacteria Desulfovibrio spp. and S. marcescans were found in aggragates. In addition, electron microscopy revealed a higher abundance of bacteria in Applysina fistularis choanosome compared to the ectosome.
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Whalley, Peter. "The proteolytic and saccharolytic activity of some natural waters and their associated bacteria." Thesis, University of Warwick, 1987. http://wrap.warwick.ac.uk/99338/.
Full textAbstract:
This study is concerned with the relationship between two hydrolytic enzyme activities, saccharase and protease and other limnological factors, including bacterial flora, in natural waters of varying degrees of organic pollution. Published methodologies for measuring proteolytic and saccharolytic activities were employed to yield data whose statistical distribution was found to be modelled by a log-normal distribution. Natural activities were correlated with biochemical oxygen demand, suspended solids, viable bacteria, combined nitrogen, dissolved solids, flow and temperature. Regression equations are formulated with biochemical oxygen demand and bacterial numbers either singly or combined explaining most of the variation in enzyme activity. Other contributory factors were suspended solids, flow and temperature. These equations could predict enzyme activity at other sites with acceptable levels of confidence. The best predictive equations for enzyme activities were: log Saccharase = 0.2 log BOD + 0.1 log Suspended solids + 0.8 log Viable count + 0.9 Protease = -469 Temperature + 56708 Flow + 443 BOD - 1.54 Viable count + 6853 Aquatic bacteria producing enzyme activity were isolated from watercourses and identified as belonging to the genera Pseudomonas. Flavobacterium and Flexibacter. When grown in defined media, enzyme production was stimulated by the addition of sucrose or casein to the medium. In the case of one organism casein could act as sole source of carbon and nitrogen. Extracts of cell suspension were shown to have enzyme activities. When investigated these activities had maximum values dependent on pH and temperature. This pH and temperature profile of activity was also demonstrated in samples of river water. Enzyme extracts followed Mlchaelis-Menten reaction kinetics with Michaelis' constants similar to those reported in comparable extracts.
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Sjöberg, Veronika, Olof Sandström, Maria Hedberg, Sten Hammarström, Olle Hernell, and Marie-Louise Hammarström. "Intestinal T-cell responses in celiac disease : impact of celiac disease associated bacteria." Umeå universitet, Immunologi/immunkemi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-64525.
Full textAbstract:
A hallmark of active celiac disease (CD), an inflammatory small-bowel enteropathy caused by permanent intolerance to gluten, is cytokine production by intestinal T lymphocytes. Prerequisites for contracting CD are that the individual carries the MHC class II alleles HLA-DQ2 and/or HLA-DQ8 and is exposed to gluten in the diet. Dysbiosis in the resident microbiota has been suggested to be another risk factor for CD. In fact, rod shaped bacteria adhering to the small intestinal mucosa were frequently seen in patients with CD during the "Swedish CD epidemic" and bacterial candidates could later be isolated from patients born during the epidemic suggesting long-lasting changes in the gut microbiota. Interleukin-17A (IL-17A) plays a role in both inflammation and anti-bacterial responses. In active CD IL-17A was produced by both CD8(+) T cells (Tc17) and CD4(+) T cells (Th17), with intraepithelial Tc17 cells being the dominant producers. Gluten peptides as well as CD associated bacteria induced IL-17A responses in ex vivo challenged biopsies from patients with inactive CD. The IL-17A response was suppressed in patients born during the epidemic when a mixture of CD associated bacteria was added to gluten, while the reverse was the case in patients born after the epidemic. Under these conditions Th17 cells were the dominant producers. Thus Tc17 and Th17 responses to gluten and bacteria seem to pave the way for the chronic disease with interferon-γ-production by intraepithelial Tc1 cells and lamina propria Th1 cells. The CD associated bacteria and the dysbiosis they might cause in the resident microbiota may be a risk factor for CD either by directly influencing the immune responses in the mucosa or by enhancing inflammatory responses to gluten.
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El, Semary Nermin Adel Hussein. "Anabaena and associated bacteria : molecular approaches to studying microbial community structure and taxonomy." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420889.
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Al-Own, Fada'a. "Population structure of insect pathogenic bacteria in UK soil and their associated nematodes." Thesis, University of Bath, 2013. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.606941.
Full textAbstract:
Surveys for entomopathogenic bacteria and their associated nematode hosts were conducted locally (University of Bath campus) and across southern England. Sampling involved trialing a novel Android app. (Epicollect) to manage sample collection data. Galleria larvae were used to bait UK soil samples. Insects which became infected were placed on White traps to collect any emerging nematodes, from which bacteria were isolated. Bacteria were also isolated from the haemolymph of any infected larvae. Bacterial isolates were classified on the basis of 16s rDNA and recA gene sequences. Serratia proteamaculans-like strains dominated the samples, and Multilocus sequence analysis (MLSA) was developed for the characterization of these Serratia isolates. We determined the sequences of (350-450-bp) fragments from five housekeeping genes of 84 isolates of Serratia proteamaculans. MLSA was shown to be effective for distinguishing closely related strains found in the insects’ haemolymph and from different nematodes. goeBURST was used to visualize the relationships between the STs, and the data showed a high level of discrimination, resolving 69 STs from the 84 isolates. In addition, the data derived from this study were represented in a phylogenetic network using the Splits Tree-network methods, to show the rate of recombination within and between the genes. From a total of 256 infected Galleria 23.04% were nematode positive. The nematodes were identified based on 18S rDNA 19 isolates were close relatives of the species Pristionchus entomophaga and Diplogasteriodes magnus (Diplogastridae). A further 16 isolates were more closely related to Steinernema glaseri (Steinernematidae). All three nematode types were isolated from diverse habitats and soil types, but were isolated more frequently in cold seasonal conditions. The bacterial sequence data suggest that the nematode- associated strains of bacteria belong to specific clades, distinct from the free living infective strains, which hints at ecological diversity within the S. proteamaculans population. Two of the Serratia proteamaculans-like strains had been chromosomally labeled with GFP to confirm the specifics of their association with the nematode hosts. The associated S. proteamaculans-like isolates isolated from Bath and Chepstow soils were examined further for their pathogenicity to Galleria mellonella and Manduca sexta larvae. Serratia Bath isolates, isolated from Pristionchus were more virulent toward both insect hosts than the Serratia from the Chepstow isolates associated with Steinernema nematodes. This suggests that host specificity may play important role in the virulence of the strain.
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Dimude, Juachi Uzochukwu. "CTX-M β-lactamases and associated integrons : their dissemination in Gram-negative bacteria." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/11729.
Full textAbstract:
Gram-negative bacteria are able to cause many infections including blood stream infections (BSI).These bacteria may become resistant to antibiotics, often by acquiring genes in the presence of antibiotic selection pressure. Multi drug resistant Gram-negative bacteria have become an increasing problem worldwide. A study of antibiotic resistance in Gram-negative bacteria isolated from blood cultures from patients in the New Royal Infirmary of Edinburgh (NRIE) was performed. In addition, a study was performed on isolates from patients in an intensive care unit in Egypt. All isolates were investigated for susceptibility to an extensive range of antibiotics. Gram-negative bacteria from Edinburgh found to be resistant to either cefotaxime or ceftazidime were investigated further. Among the cefotaxime/ceftazidime resistant isolates, Polymerase Chain Reaction (PCR) analysis revealed the presence of CTX-M- β-lactamases. Seven E.coli isolates were found to have CTX-M-15 β-lactamases while the CTX-M-14 β-lactamase was detected in six Enterobacter cloacae. The insertion sequence ISEcp1 was detected upstream of the blaCTX-M-15 gene in some isolates while IS26 was found truncating the ISEcp1 in other isolates. Conjugation experiments found the blaCTX-M-15 gene was transferable to E. coli J62-2. All the isolates had detectable plasmids, a plasmid ~260kb carried the blaCTX-M-15 gene. Analysis of the -containing isolates by PFGE shows that those carrying the CTX-M-14 β-lactamase were identical indicating cross infection within the hospital. The CTX-M- 15 β-lactamase-containing isolates showed four isolates had ≥85% similarity but the others were diverse. Class 1 integrons were found in eight of the CTX-M β-lactamase containing isolates with the associated gene cassette and sul1 gene. The isolates from Egypt were found to be resistant to carbapenem, which is the final mainstream antibiotic option in the treatment of multidrug resistant Gram-negative bacteria. Further analysis revealed all carried the CTX-M-14 β-lactamase and two additionally carried the VIM-4 metallo β-lactamase, which accounted for the resistance to the carbapenems. Furthermore, the insertion sequence ISEcp1 was found upstream of the blaCTX-M-14 gene in two of the isolates. The blaVIM-4 gene was found to be part of the gene cassette in the class 1 integron associate with complex ISCR1. Two of the Egyptian isolates had a detectable plasmid, ~300kb in size, which carried both blaCTX-M-14 and blaVIM-4 genes. All the blood culture isolates were examined to ascertain the persistence of sulphonamide resistance despite the long-term prescribing reduction on this antibacterial. PCR was performed to detect sul1, sul2 and sul3 genes in all the isolates. Of the sulphonamide resistant isolates 25 carried the sul1, 27 carried the sul2 and none carried the sul3 genes. Eight isolates had both the sul1 and sul2 genes. Most of the isolates carried sul1 had Int1 as part of the same class 1 integron. Interestingly three isolates were PCR negative for sul1 but positive for sul2 and int1. Int2 and 3 were found in 3 and 2 isolates respectively. The class 1 integron contained different insert gene cassettes; dfrA (dfrA17, dfrA16, dfrA15), aadA (aadA5, aadA2, aadA1) and blaOXA-1 families in addition to the resident sul gene. In conclusion this thesis shows the diversity of the genetic environment and carriers of the CTX-M β-lactamases within the same hospital. Sulphonamide resistance in Gram-negatives persists despite the prescribing reduction of this antibacterial in a Scottish hospital and the recommended constraint on the use of sulphonamide.
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Matobole, Relebohile Matthew. "Matrix comparison of isolation conditions for secondary metabolite producing marine sponge associated bacteria." University of the Western Cape, 2015. http://hdl.handle.net/11394/4754.
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>Magister Scientiae - MScThe discovery of novel secondary metabolites has declined significantly in recent years whereas there is a rise in the number of multi-drug resistant pathogens and other types of diseases. The decline in natural product discovery was due to high rediscovery of already known compounds and the costs in developing natural products. As a result pharmaceutical companies lost interest in investing in natural product discovery. However, there is a renewed interest in marine sponge associated microorganisms as a rich and untapped source of secondary metabolites. The objective of this study was to design a matrix to investigate the extent to which the One Strain-Many Compounds (OSMAC) approach applies to a collection of marine sponge isolates harvested from two South African marine sponge samples. Terminal restriction fragment length polymorphisms (T-RFLP) analysis was used to investigate and ascertain the two marine sponges which hosted the highest microbial diversities to be used for further culture-dependent studies. The culture-dependent studies, using 33 media which included liquid enrichment, heat treatments and antibiotic treatments, resulted in 400 sponge isolates from the two marine sponges Isodictya compressa and Higginsia bidentifera. Using antibacterial overlay assays, 31 dereplicated isolates showed antibacterial activity. Bioactivities were also exhibited against E. coli 1699 which is genetically engineered for resistance against 52 antibiotics which implies that some of the bioactive compounds could be novel. The 16S rRNA gene sequences revealed that the microbial phyla isolated from the marine sponges belonged to Actinobacteria, Firmicutes and Proteobacteria (Alphaproteobacteria and Gammaproteobacteria).Thirty isolates were selected for an OSMAC-based matrix study, 17 of which showed noantibacterial activities in preliminary screening. The application of the OSMAC approach using co-culture and 36 culture conditions resulted in 6 isolates showing antibacterial activities, three of which did not show activities in preliminary screening. One of these, a Bacillus pumilus isolated from I. compressa displayed antibacterial activity against 5 indicator strains whereas in preliminary screening it had not shown activity. The results show that marine sponges can host novel microbial species which may produce novel bioactive compounds. The results also confirm that traditional methods employing a single culture condition restricts the expression of some biosynthetic pathways of microorganisms and as a result many metabolites have yet to be identified.
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Beukes, Chrizelle Winsie. "Characterisation of bacteria associated with the root nodules of Hypocalyptus and related genera." Diss., University of Pretoria, 2012. http://hdl.handle.net/2263/31148.
Full textAbstract:
Until recently, most of the legumes that have been studied in South Africa were known to be
nodulated by diverse alpha-rhizobia in the class Alphaproteobacteria. Our knowledge
regarding the occurrence of so-called beta-rhizobia were limited and restricted to Aspalathus
and Cyclopia species. The aim of this study was, therefore, to explore the diversity and
evolution of the root-nodule bacteria of various papilionoid legumes indigenous to southern
Africa. By making use of housekeeping gene sequence information, the research presented
here showed that all 69 of the bacteria isolated from the root-nodules of species in the genera
Hypocalyptus, Virgilia, Podalyria and Cyclopia represented beta-rhizobia in the genus
Burkholderia (class Betaproteobacteria). Based on these DNA sequences, the isolates could
be assigned to 25 independent lineages that most probably represent distinct species. With
the exception of one group that tended to associate with B. tuberum in my phylogenies, the
majority of these lineages or species appeared to be new to science as they did not group
with any of the known diazotrophic and/or nodulating species. Phylogenetic analyses of the
nifH and nodA gene sequences also separated the isolates into a number of groups, but
surprisingly the groups recovered with these two gene regions did not match, nor did they
match with those inferred using housekeeping gene sequences. In general, there was only
one exception where the same group of isolates were recovered from phylogenies inferred
for the various loci. These findings thus suggested a significant impact of horizontal gene
transfer on the evolutionary histories of the determinants of nodulation and nitrogen-fixation
in these bacteria. The phylogenetic groups recovered from the various sequences also did not
match those expected based on the host or geographic origin of the isolates. However,
isolates from the South African legumes generally appeared to group separate from those
isolated in other parts of the world. The distinctness of the South African isolates was most
pronounced in the nifH and nodA gene trees, where they formed a well-supported cluster
separate from all of isolates associated with Mimosa species elsewhere, which suggest a
unique and possibly African origin for the root-nodule bacteria examined in this study. The
findings presented in this dissertation thus present an important contribution to our
understanding of the diversity and evolution of these bacteria from both a Southern African
and a global perspective.Dissertation (MSc)--University of Pretoria, 2012.
Microbiology and Plant Pathology
MSc
Unrestricted
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Devine, Carol A. "16S ribosomal DNA analysis of microbial populations associated with hydrocarbon reservoirs." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312360.
Full textAbstract:
The sulphate-reducing bacteria (SRB) are a diverse group of organisms which use sulphate as a terminal electron acceptor and produce the highly toxic gas, hydrogen sulphide. The deleterious effects of this include hydrocarbon reservoir souring, formation damage and microbial corrosion. The SRB are of major economic importance to the oil industry. However, knowledge of the microbial ecology of the deep subsurface remains limited. The aim of this project was to investigate whether organisms are indigenous to the hydrocarbon formation and/or are introduced during drilling operations. A range of molecular techniques such as 16S rDNA sequence analysis, probing with labelled oligonucleotides, and denaturing gradient gel electrophoresis (DGGE) were employed to investigate the microbial diversity in oil field samples. A wide range of bacterial 16S rDNA sequences were identified using these molecular methods. An analysis of drilling mud samples revealed a diverse range of bacterial 16S rDNA sequences confirming that bacteria, including SRB, can be introduced to the reservoir during drilling operations. A number of bacterial 16S rDNA sequences were recovered from a geological core sample taken from a depth of 9,770 feet. The microbial diversity was remarkable in such a high temperature, high pressure environment. This lends credence to the theory that certain bacteria may be indigenous to the subsurface environment. Scanning electron micrographs of core which had been incubated in growth medium indicated the presence of 'nannobacteria'. These tiny coccoids, with a diameter of only 0.1 μm are far smaller than the generally accepted minimum size for cellular life forms. The nannobacteria grew in regular colony shaped structures and were seen only in sections taken from inside the rock. This study indicates that hydrocarbon reservoirs provide an environment in which bacteria, if introduced during drill operations, may become established. However, the subsurface also contains complex indigenous microbial populations that demonstrate considerable species diversity and may include unrecognised life forms.
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Davenport, Russell James. "The detection and monitoring of mycolic acid containing actinomycetes associated with foaming in activated sludge plants." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313240.
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Morrissey, Ember. "Environmental regulation of tidal wetland microbial communities and associated biogeochemistry." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3300.
Full textAbstract:
Microbial communities play an essential role in carrying out the biogeochemical cycles that sustain life on Earth, yet we know very little about their ecology. One question of particular interest is how environmental conditions shape microbial community structure (i.e., the types of organisms found in the community and their relative abundance), and whether such changes in structure are related to biogeochemical function. It is the aim of this dissertation to address this question via the examination of carbon (C) and nitrogen (N) cycling in wetland ecosystems, which due to their diverse hydrology have a profound influence on biogeochemical cycles. With respect to N cycling, the community structure of denitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-capable organisms was evaluated in response to changes in resource availability, specifically organic matter (OM) and nitrate (NO3-), using an in situ field manipulation. Interactive regulation of microbial community composition was exhibited in both groups, likely due to variation in C substrate preferences and NO3- utilization efficiency. Subsequent experimentation considering only denitrification revealed that resource regulation of activity rates was mediated through changes in denitrifier community composition. The resource regulation of wetland C cycling also was evaluated using an in situ OM manipulation. OM characteristics (e.g., degree of decomposition) affected microbial extracellular enzyme activity (EEA) and changed the community structure of bacteria, archaea, and methanogens. These changes were linked with carbon dioxide and methane production via a conceptual model diagramming the importance of microbial community structure and EEA in greenhouse gas production. The investigation of C cycling in wetlands was extended to consider an important global change threat: saltwater intrusion into freshwater tidal wetlands. Bacterial community structure and EEA were examined along a natural salinity gradient. Salinity was strongly associated with bacterial community structure and positively correlated with EEA. These results suggested that salinity-induced increases in decomposition were responsible for reduced soil OM content in more saline wetlands. This work demonstrates that microbial communities in wetlands are structured by environmental conditions including resource availability and salinity. Further, the research provides evidence that environmental regulation of important biogeochemical processes in wetlands (e.g., methanogensis, denitrification, etc.) is mediated through changes in microbial community structure.
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Tujula, Niina Amanda Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "Analysis of the epiphytic bacterial community associated with the green alga Ulva australis." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Sciences, 2006. http://handle.unsw.edu.au/1959.4/25197.
Full textAbstract:
Epiphytic bacterial communities on the surfaces of marine algae are poorly characterised. Most information available on marine bacterial epiphytes is derived from culture-based studies. With the rapid development of molecular community analysis technologies, it is now possible to obtain a more comprehensive picture of marine microbial populations on living surfaces. The intertidal macroalga Ulva australis, belongs to the cosmopolitan group of green marine algae (Ulvales) known to require the presence of bacteria for normal growth and has been suggested to employ specific bacteria for the defence against fouling by micro- and macro-organisms. This thesis has examined the composition and structure of the surface associated bacterial community on Ulva australis using 16S rRNA gene clone library, denaturing gradient gel electrophoresis (DGGE), and catalysed reporter deposition ??? fluorescence in situ hybridisation (CARD-FISH) analysis. The 16S rRNA gene clone library revealed that the five main bacterial groups present in the surface associated community were Bacteriodetes, Planctomycetes, Alpha-, Gamma-, and Delta-Proteobacteria. Twenty-two sequence phylotypes were identified, suggesting that the epiphytic community was of relatively low diversity. A clone similar to an algal morphogenesis inducing Cytophaga strain was identified, indicating that U. australis harbours bacteria important for thallus structural maintenance. DGGE analysis showed that while the bacterial community varied over spatial and temporal (seasons) scales it also included a stable subpopulation consistently associated with the seaweed surface. Sequencing of selected DGGE bands suggested that members of the Alphaproteobacteria and the Bacteriodetes belonged to the stable subpopulation. Using CARD-FISH with different phylogenetic probes demonstrated that Alphaproteobacteria (~ 70%) and Cytophaga-Flavobacteria (~13%) constituted the majority of bacterial cells on the surface of U. australis. A comparison of the results provided by the molecular community analysis methods, employed in this thesis, and those of culturing of epiphytic bacteria from U. australis revealed that each approach provides different patterns of phylogeny and extent of diversity. For example, the culture collection and the clone library detected a relatively high amount of Gammaproteobacteria, however, DGGE and CARD-FISH did not. Also, low species diversity clone sequences and isolates of Alphaproteobacteria contrasted with the high numbers detected by the DGGE analysis. In addition to the phylogentic determination of the epiphytic bacterial community, CARDFISH was also used to assess the organisation and distribution of bacterial cells across different zonal regions on seaweed surface. It was found that approximately 40% of bacterial cells clustered in aggregates, or microcolonies. These aggregations were considered to be heterogeneous in composition and were mainly comprised of multiply species. The occurrence of more non-viable solitary single rather than aggregated cells suggests that aggregates might offer greater protection to bacterial cells from the harsh conditions in the intertidal zone. More broadly, CARD-FISH was found to be a useful tool for studying microcolonies and was also successfully applied to detect slow growing soil microcolonies cultivated using a novel soil substrate membrane system culturing technique without the need to perform an rRNA enrichment incubation. The findings in this thesis, as described from the application of a number of molecular community analysis techniques such as clone library, DGGE and CARD-FISH, have improved our understanding of the diversity and structure of the epiphytic bacterial community associated with U. australis. Morevover, the information provided may to design future studies in the ecology of bacteria-seaweed interactions, including symbiotic interactions, and aid in marine biotechnology applications such as identifying bacteria which produce bioactive secondary metabolites.
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Botham, Crystal Marie. "Molecular and genetic dissection of host pathways disrupted by Helicobacter pylori's virulence factor, cytotoxin associated gene A /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1417800931&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.
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Thesis (Ph. D.)--University of Oregon, 2007.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 60-66). Also available for download via the World Wide Web; free to University of Oregon users.