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1
Jayaswal, Gaurav. "Spatial confinement of bacterial communities." Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3423866.
Full textAbstract:
The subject of bacterial swimming has intrigued scientists for decades and recently there has been a growing interest in the study of collective swimming behavior of bacteria in a confined geometry. This thesis deals with a systematic experimental investigation of the density distribution of bacterial solutions of different concentration.
Two different types of bacteria, Pseudomonas and E. coli, have been used owing to their diverse propelling mechanism. E. coli behavior has been studied in detail, instead there are no reports in the literature regarding Pseudomonas, to the best of our knowledge.
The experimental set up consisted of two glass plates separated by spacers which define the confinement region. The separation distance ranged from 100 to 250 microns. The two plates were functionalized with bovine serum albumin (BSA) to avoid bacterial adhesion to the glass. The bacterial suspension was subjected to adjustment of buoyancy by addition of a density matching fluid like Percoll.
In agreement with previous studies, we found a significant enhancement of density close to the walls for both bacteria. This effect does not seem to be affected by either the separation distance or the solution concentration. These results were compared with those obtained by numerical simulations of self-propelled rod like particles which do not interact with each other apart from steric interactions. The preliminary data support the experimental outcome suggesting that steric interactions alone are sufficient to produce the observed enhancement effect.Il moto di batteri ha attratto gli scienziati da decenni e, ultimamente, c’è stato un crescente interesse nello studio del moto collettivo di batteri in geometrie confinate. Questa tesi descrive uno studio sperimentale della distribuzione di densità di soluzioni di batteri di concentrazione diversa confinate tra due pareti parallele. Si sono usati due tipi di batteri, Pseudomonas ed E. coli, che presentano diversi meccanismi di propulsione. Il comportamento di E. coli è stato studiato in dettaglio, invece non ci sono lavori in letteratura riguardanti Pseudomonas, per quello che sappiamo. L’apparato sperimentale consisteva di due vetrini separati da spaziatori che definivano la regione confinante. La distanza di separazione variava da 100 a 250 micron. I due vetrini erano funzionalizzati con albumina di serio bovino per evitare l’adesione dei batteri al vetro. Alla sospensione era stato aggiunto del percoll per aggiustare la spinta idrostatica agente sui batteri. In accordo con precedenti studi, abbiamo trovato un significativo aumento di densità in prossimità delle pareti per entrambi i tipi di batteri. Questo effetto non sembra essere influenzato né dalla distanza di separazione, né dalla concentrazione della soluzione. Questi risultati sono stati confrontati con quelli ottenuti da simulazioni numeriche di particelle auto-propellenti c he interagiscono solo mediante interazioni steriche. I dati preliminari supportano l’osservazione sperimentale suggerendo che le sole interazioni steriche sono sufficienti a produrre addensamento dei batteri alle pareti.
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Benskin, Clare McWilliam Haldane. "Bacterial communities in the avian gut." Thesis, Lancaster University, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.539637.
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Fidalgo, Cátia Isabel Assis. "Endophytic bacterial communities of Halimione portulacoides." Doctoral thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/22661.
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Doutoramento BiologiaOs sapais são ecossistemas marinhos altamente produtivos que frequentemente recebem contaminantes de natureza antropogénica. A Ria de Aveiro encontra-se no noroeste de Portugal e contém numerosos sapais. Halimione portulacoides é um dos halófitos mais importantes em sapais Europeus e tem sido amplamente estudada devido ao seu potencial para ser usada em fins de fitorremediação, e como bioindicador de contaminação de sedimentos. Bactérias endofíticas podem apresentar capacidade promotora do crescimento de plantas (PCP), quer diretamente por produção de fito-hormonas e aquisição de nutrientes, quer indiretamente via competição com fitopatogenos. No presente trabalho, a diversidade de bactérias endofíticas da planta de sapal H. portulacoides da Ria de Aveiro é explorada extensivamente. Isolados de bactérias endofíticas foram obtidos e caracterizados quanto à sua taxonomia, capacidade de produzir enzimas e características PCP. As características mais observadas foram atividade celulolítica, xilanolítica e desaminase de 1-aminociclopropano-1-carboxilato, e a produção da auxina ácido indol-3-acético. Os resultados revelaram um enorme potencial da coleção para PCP in vitro e in vivo. A coleção de isolados foi também explorada para procurar diversidade não descrita. Como resultado, dez novas espécies de bactérias foram amplamente caracterizadas e descritas: Microbacterium diaminobutyricum, Saccharospirillum correiae, Altererythrobacter halimionae, Altererythrobacter endophyticus, Zunongwangia endophytica, Salinicola halimionae, Salinicola aestuarina, Salinicola endophytica, Salinicola halophytica e Salinicola lusitana. Consequentemente, o presente trabalho expôs a endosfera de H. portulacoides como um foco de diversidade bacteriana desconhecida. A composição taxonómica da comunidade endofítica foi averiguada via sequenciação do gene 16S rRNA da coleção de isolados, e mais profundamente com a utilização de sequenciação de alto rendimento independente do cultivo. A última abordagem revelou cinco filos principais: Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes e Firmicutes. Destes, apenas Planctomycetes não foi obtido na coleção de isolados. As comunidades diferiram de acordo com o local (no ensaio dependente do cultivo, para locais contaminados e não-contaminado) e tecido (em ambos os ensaios) de amostragem. As principais famílias obtidas no endofitoma nuclear foram Oceanospirillaceae em tecidos de parte aérea, e Enterobacteriaceae e Kiloniellaceae em tecidos de raiz. O trabalho apresentado providenciou uma compreensão profunda das bactérias endofíticas presentes no halófito H. portulacoides, e expôs o seu potencial como foco de bactérias não descritas e bactérias promotoras do crescimento de plantas.
Salt marshes are highly productive marine ecosystems that often act as a sink for contaminants of anthropogenic nature. The Ria de Aveiro lagoon is located in the north-west of Portugal and comprises numerous salt marshes. Halimione portulacoides is one of the most important halophytes in European salt marshes and has been widely researched for its potential for phytoremediation, and as a bioindicator of sediment contamination. Endophytic bacteria can present plant growth promotion (PGP) abilities, either directly by production of phytohormones and nutrient uptake, or indirectly via competition with phytopathogens. In the present work, the diversity of endophytic bacteria from the salt marsh plant H. portulacoides from Ria de Aveiro is extensively explored. Endophytic bacterial isolates were obtained and characterized for their taxonomy, ability to produce specific enzymes and PGP traits. The most observed traits were cellulolytic, xylanolytic and 1-aminocyclopropane-1-carboxylate deaminase activities, and the production of the auxin indol-3-acetic acid. The results revealed an enormous potential of the collection for in vitro and in vivo PGP. The collection of isolates was also explored for undescribed diversity. As a result, ten novel bacterial species were thoroughly characterized and described: Microbacterium diaminobutyricum, Saccharospirillum correiae, Altererythrobacter halimionae, Altererythrobacter endophyticus, Zunongwangia endophytica, Salinicola halimionae, Salinicola aestuarina, Salinicola endophytica, Salinicola halophytica and Salinicola lusitana. Consequently, the present work exposes the endosphere of H. portulacoides as a hotspot of unknown bacterial diversity. The taxonomic composition of the endophytic community was assessed via 16S rRNA gene sequencing of the isolate collection, and with more depth using culture-independent high-throughput sequencing. The latter approach revealed five main phyla: Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes and Firmicutes. From these, only Planctomycetes was not obtained in the isolate collection. The communities differed according to sampling site (for the culture-dependent assay, for contaminated and non-contaminated sites) and tissue (in both assays). The main families found in the core endophytome were Oceanospirillaceae for aboveground tissues, and Enterobacteriaceae and Kiloniellaceae for belowground tissues. The present work provided a deep understanding of the endophytic bacteria present in the halophyte H. portulacoides, and exposed its potential as a hotspot of undescribed bacteria and plant growth promoting bacteria.
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Riddell, Andrew. "Characterisation of bacterial communities within chronic wounds." Thesis, Cardiff University, 2012. http://orca.cf.ac.uk/41930/.
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Chronic wounds are a rapidly growing clinical problem across the world, expensive to healthcare systems and severely injurious to the quality of life of those affected. Such wounds have been shown to contain bacteria within biofilms which can be difficult to identify and treat, and are implicated in the lack of healing. The aim of this study was to improve our understanding of the characterisation of these bacterial communities within chronic wounds. This was achieved through the collection of 18 unique chronic wound samples of various phenotypes and 9 acute wound samples. The two bacterial species, Staphylococcus .aureus and Pseudomonas. aeruginosa, most commonly isolated from chronic wounds and known to be prolific biofilm formers and formidable human pathogens were the focus of this study. Both PCR and culture demonstrated the presence of one or both species in all chronic wound samples and the presence of S. aureus in some acute samples. Novel monoclonal antibodies were developed to TNase (of S.aureus) and LPS (of P. aeruginosa) and their ability to detect the bacteria in vitro in a simulated chronic wound environment was evaluated. The action of these monoclonal antibodies were calibrated and evaluated through the use of fluorescent microscopy, and direct and competition ELISA. Following this biofilms of S.aureus and P. aeruginosa both single species and mixed were evaluated utilising Peptide Nucleic Acid Flourescent In Situ Hybridisation, and the Confocal Laser Scanning Microscope to demonstrate the architecture of the biofilms produced and the locations of the bacteria within the biofilm. Microbiologically using both culture and PCR, the widespread presence of S. aureus and P. aeruginosa throughout human chronic wound samples was demonstrated. The ELISA and fluorescent microscopy illustrated the feasibility of MABs as a rapid and accurate detection system for identifying bacteria within chronic wounds. The PNA FISH accurately identified individual species in mixed biofilms through multiplex staining. It also visually demonstrated the tissue invasion of S. aureus, adhesive properties of P. aeruginosa and the synergy of these virulence factors in mixed biofilms. This study has met its aims in that it has provided further evidence of techniques which could be successfully applied to rapidly identify bacteria within a chronic wound environment, and to characterise the structure and composition of bacterial biofilms formed within these wounds. It provides a basis for the development of future clinically relevant rapid bacterial detection systems, and for the academic study of bacteria within the biofilm phenotype.
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Co, Julia Yin-Ting. "The influence of mucins on bacterial communities." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/99569.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references.
Mucus is the hydrogel layer that coats all wet epithelia in the body. By supporting commensal microbes and preventing pathogenic invasion, mucus maintains host-microbe homeostasis. Mucin polymers, the primary gel-forming component of mucus, are an important mediator of mucus-microbe interactions. In this thesis, I demonstrate that mucins impact bacterial communities in their physical structure as well as microbe-microbe and microbe-host dynamics. In Chapter 2, 1 study the ability of mucin surface coatings to suppress bacterial surface attachment, the first step in biofilm formation, for Streptococcus pneumoniae and Staphylococcus aureus. Mucin-bound glycans were identified as a critical structural component of mucin coatings that are necessary for bacterial repulsion. In Chapter 3, 1 investigate how mucins impact established Pseudomonas aeruginosa biofilms. The data reveal that mucins cause disassembly and structural rearrangement in P. aeruginosa biofilms in a mucin concentration and flow rate dependent manner. In Appendix A, I show evidence for the involvement of the bacterial flagella in mucinmediated biofilm disruption. Deletion of flagellar capfliD or flagellar stators motABCD results in biofilms that are resistant to mucin-mediated dissociation. In Appendix B, I examine how mucins affect dual-species bacterial communities. I show that mucins promote S. aureus survival during co-culture with P. aeruginosa and also suppress the anti-staphylococcal effects of P. aeruginosa pyocyanin. In Appendix C, I explore the impacts of mucins on P. aeruginosa quorum sensing, an important pathogenic determinant in P. aeruginosa infections. I found that mucins suppress the expression of P. aeruginosa Las and Rhl quorum sensing genes as well as downstream virulence factors. In Appendix D, I assess how mucins modulate P. aeruginosa-epithelium interactions. The data show that mucins hinder the ability of P. aeruginosa to attach to epithelial cells in vitro. Additionally, mucins suppressed P. aeruginosa-associatede pithelial cytotoxicity in a mucin concentration dependent manner. Together, this thesis demonstrates that mucins modulate microbial communities in their behavior and interactions. Understanding how mucus and mucins impact microbes provides insight to host-microbe relationships, as well as for the development of novel bacteria-regulating strategies.
by Julia Yin-Ting Co.
Ph. D.
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Kanso, Sungwan, and n/a. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers." Griffith University. School of Biomolecular and Biomedical Science, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20040219.140509.
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16S rRNA gene analysis has shown that bacterial diversity in the GAB bores studied was limited to the genera Hydrogenobacter in the phylum Aquificae, Thermus in the phylum Deinococcus-Thermus, Desulfotomaculum in the phylum Firmicutes, the alpha-, beta- and gamma-classes of the phylum Proteobacteria and the phylum Nitrospirae. There was no clone closely related to members of the delta-proteobacteria and epsilon-proteobacteria classes detected. The number of bacterial strains directly isolated from the Fairlea and the Cooinda bores were far less than the numbers of distinctive phylotypes detected by the 16S rRNA gene characterisation. In addition none of the bacterial strains directly isolated from the water samples were represented in the 16S rRNA gene clone libraries. Similar discrepancies between the bacterial populations obtained from the 16S rRNA gene analysis and those obtained from direct isolation have been reported in the literature (Dunbar et al., 1999; Kampfer et al., 1996; Suzuki et al., 1997; Ward et al., 1998; Ward et al., 1997). However, in general, the phyla with which the isolates were affiliated were the same as those phyla to which the clones belonged. The environmental changes introduced (by bringing the artesian water up to the surface and exposing it to four types of metal coupons made of carbon steels identified by codes ASTM-A53B, ASTM-A53, AS-1074 and AS-1396 and commonly used in bore casings) led to changes in the bacterial community structures. In general, the species which proliferated in the communities before and after the changes were different. The diversity of the bacterial species in the community decreased following the environmental changes. Clones dominating the clone libraries constructed from newly established bacterial communities also differed from the clones dominating the libraries constructed from the bacterial communities which had existed naturally in the bores. These trends toward change in the bacterial communities were observed at both the Fairlea and the Cooinda bore sites. All four metal types incubated in the Fairlea bore water lost between 3.4 and 4.7% of their original weight. In contrast none of the metals incubated in Cooinda bore water lost weight. Clone library A1 showed that the natural population of the Fairlea bore was dominated by clone A1-3, which represented a novel species related to the isolate boom-7m-04. But after metal incubation (and recording of the metal weight loss), the bacterial community was dominated by clone PKA34B, which has a 95% similarity in its 16S rRNA gene sequence with Desulfotomaculum putei. Desulfotomaculum species are known to cause metal corrosion due to their byproduct H2S. But the low level of phylogenetic relatedness found does not provide enough information to speculate on whether the species represented by clone PKA34B is a member of the genus Desulfotomaculum or not. However, the fact that clone PKA34B dominated the PKA clone library by 50% makes the species it represents a suspected candidate likely to be involved with the metal weight loss at the Fairlea bore. In contrast, clone library 4381 showed that the natural population of the Cooinda bore was dominated by clone 4381-15 representing a species distantly related to a hydrogen oxidiser Hydrogenophaga flava (95% similarity). The dominating clone of the new community formed after metal incubation was clone COO25, which has 99% similarity with Thermus species that have not been reported to be involved with metal corrosion to my knowledge. In this project detection, identification and comparative quantification by 16S rRNA gene-targeted PCR probing with probes 23B and 34B were successfully developed for a Leptothrix-like species and for a Desulfotomaculum-like species represented by clones PKA23B and PKA34B respectively. This method of probing permits a fast, sensitive and reproducible detection, identification and at least a comparative quantification of the bacteria in the environment without the need for culturing. Therefore it is extremely suitable for use in bacterial population monitoring. PCR probing with the 34B probe has a potential commercial use as a means of screening for bores with a potential high risk of corrosion due to this Desulfotomaculum-like species. Direct isolation of bacteria from the GAB water has resulted in the isolation of seven strains from the Fairlea bore and eight from the Cooinda bore. Among these isolates, three novel strains were studied in detail. Reports on the characterisation of strain FaiI4T (T=Type strain) from the Fairlea bore (Kanso & Patel, 2003) and strain CooI3BT from the Cooinda bore have been published (Kanso et al., 2002). The data generated during this project add to our current information and extend our knowledge about the bacterial communities of the GAB's sub-surface environment. This information will provide a basis for further ecological studies of the GAB. Studies on involvement of certain groups of bacteria with the corrosion of metals used in bore casings could provide a foundation for further studies to develop maintenance and managing strategies for the GAB bores.
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Kanso, Sungwan. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers." Thesis, Griffith University, 2004. http://hdl.handle.net/10072/366613.
Full textAbstract:
16S rRNA gene analysis has shown that bacterial diversity in the GAB bores studied was limited to the genera Hydrogenobacter in the phylum Aquificae, Thermus in the phylum Deinococcus-Thermus, Desulfotomaculum in the phylum Firmicutes, the alpha-, beta- and gamma-classes of the phylum Proteobacteria and the phylum Nitrospirae. There was no clone closely related to members of the delta-proteobacteria and epsilon-proteobacteria classes detected. The number of bacterial strains directly isolated from the Fairlea and the Cooinda bores were far less than the numbers of distinctive phylotypes detected by the 16S rRNA gene characterisation. In addition none of the bacterial strains directly isolated from the water samples were represented in the 16S rRNA gene clone libraries. Similar discrepancies between the bacterial populations obtained from the 16S rRNA gene analysis and those obtained from direct isolation have been reported in the literature (Dunbar et al., 1999; Kampfer et al., 1996; Suzuki et al., 1997; Ward et al., 1998; Ward et al., 1997). However, in general, the phyla with which the isolates were affiliated were the same as those phyla to which the clones belonged. The environmental changes introduced (by bringing the artesian water up to the surface and exposing it to four types of metal coupons made of carbon steels identified by codes ASTM-A53B, ASTM-A53, AS-1074 and AS-1396 and commonly used in bore casings) led to changes in the bacterial community structures. In general, the species which proliferated in the communities before and after the changes were different. The diversity of the bacterial species in the community decreased following the environmental changes. Clones dominating the clone libraries constructed from newly established bacterial communities also differed from the clones dominating the libraries constructed from the bacterial communities which had existed naturally in the bores. These trends toward change in the bacterial communities were observed at both the Fairlea and the Cooinda bore sites. All four metal types incubated in the Fairlea bore water lost between 3.4 and 4.7% of their original weight. In contrast none of the metals incubated in Cooinda bore water lost weight. Clone library A1 showed that the natural population of the Fairlea bore was dominated by clone A1-3, which represented a novel species related to the isolate boom-7m-04. But after metal incubation (and recording of the metal weight loss), the bacterial community was dominated by clone PKA34B, which has a 95% similarity in its 16S rRNA gene sequence with Desulfotomaculum putei. Desulfotomaculum species are known to cause metal corrosion due to their byproduct H2S. But the low level of phylogenetic relatedness found does not provide enough information to speculate on whether the species represented by clone PKA34B is a member of the genus Desulfotomaculum or not. However, the fact that clone PKA34B dominated the PKA clone library by 50% makes the species it represents a suspected candidate likely to be involved with the metal weight loss at the Fairlea bore. In contrast, clone library 4381 showed that the natural population of the Cooinda bore was dominated by clone 4381-15 representing a species distantly related to a hydrogen oxidiser Hydrogenophaga flava (95% similarity). The dominating clone of the new community formed after metal incubation was clone COO25, which has 99% similarity with Thermus species that have not been reported to be involved with metal corrosion to my knowledge. In this project detection, identification and comparative quantification by 16S rRNA gene-targeted PCR probing with probes 23B and 34B were successfully developed for a Leptothrix-like species and for a Desulfotomaculum-like species represented by clones PKA23B and PKA34B respectively. This method of probing permits a fast, sensitive and reproducible detection, identification and at least a comparative quantification of the bacteria in the environment without the need for culturing. Therefore it is extremely suitable for use in bacterial population monitoring. PCR probing with the 34B probe has a potential commercial use as a means of screening for bores with a potential high risk of corrosion due to this Desulfotomaculum-like species. Direct isolation of bacteria from the GAB water has resulted in the isolation of seven strains from the Fairlea bore and eight from the Cooinda bore. Among these isolates, three novel strains were studied in detail. Reports on the characterisation of strain FaiI4T (T=Type strain) from the Fairlea bore (Kanso & Patel, 2003) and strain CooI3BT from the Cooinda bore have been published (Kanso et al., 2002). The data generated during this project add to our current information and extend our knowledge about the bacterial communities of the GAB's sub-surface environment. This information will provide a basis for further ecological studies of the GAB. Studies on involvement of certain groups of bacteria with the corrosion of metals used in bore casings could provide a foundation for further studies to develop maintenance and managing strategies for the GAB bores.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
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Rodriguez, Caballero Adrian. "STUDY OF BACTERIAL COMMUNITIES : – A WASTEWATER TREATMENT PERSPECTIVE." Licentiate thesis, Mälardalens högskola, Akademin för hållbar samhälls- och teknikutveckling, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:mdh:diva-11884.
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In this thesis, the application of molecular microbiology methods to understand wastewater treatment bio-reactions is described. Two different wastewater treatment systems were chosen for the experimental work. Firstly; the activated sludge processes at two different facilities in Sweden (Västerås and Eskilstuna) were investigated and compared in a context where low temperatures can affect the efficiency of the nitrogen removal performance in terms of nitrification. Initially, fluorescence in situ hybridization (FISH) was utilised in order to quantify some of the species involved in ammonia and nitrite oxidation at Västerås, providing information on how the different communities react to decreasing temperatures. Then, the polymerase chain reaction (PCR), cloning-sequencing method was employed in order to study the composition of the ammonia oxidizing bacteria (AOB) community at the same two wastewater treatment plants (WWTPs). Secondly; the potential use of constructed wetlands for the treatment of winery wastewater was studied. High ethanol concentration artificial wastewater with and without inorganic nutrients (nitrates and phosphates) was fed in a set of pilot-scale constructed wetlands. Pollutant removal performance and enzyme activity tests were carried out. Additionally, the bacterial community structure was investigated by means of denaturing gradient gel electrophoresis (DGGE). In the first set of studies it was shown that the AOB population which plays a major role in nitrifying reactors presented a seasonal shift and a higher diversity at Västerås during winter time, while the nitrification performance maintained stable levels and the ammonia removal efficiency increased. Thus, the higher ammonia removal efficiency at Västerås could be related to the diversity of the AOB population composition. Lastly, when constructed wetlands were in focus, the differential effects of ethanol and nutrients over the chemical oxygen demand (COD) removal performance were proven. In fact, the addition of nutrients on one of the experimental wetlands increased the COD (ethanol) removal and supported the maintenance of a bacterial population similar to the control wetland (no ethanol added). In conclusion, both studies proved a strong relationship between process performance (pollution removal) and the dynamics of the bacterial communities involved.
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Haglund, Ann-Louise. "Attached Bacterial Communities in Lakes – Habitat-Specific Differences." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4627.
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Beeton, S. "Biotransformation of T-2 toxin by bacterial communities." Thesis, University of Kent, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234437.
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Shaw, L. P. "The microbial ecology of human-associated bacterial communities." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10046977/.
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The bacterial communities within the human body have important associations with health and disease. Understanding their complexity requires ecological approaches. In this thesis, I apply ecological techniques and models to explore the microbial ecology of human-associated bacterial communities at multiple scales. In the first half of this thesis, I explore the oral microbiome using 16S rRNA gene sequencing data to characterise the effect of various factors on its diversity. Multiple factors apart from disease can also affect the oral microbiome, but their relative importance remains a matter of debate. In Chapter 2, I use a dataset of saliva samples from a family of related Ashkenazi Jewish individuals to show that host genetics plays much less of a role than shared household in explaining bacterial community composition. In Chapter 3, I use a large dataset of plaque samples from women in Malawi to investigate associations between bacterial taxa and periodontal disease. I show that the signals from gingivitis and periodontitis can be distinguished, and use correlation networks to identify important taxa for the development of disease. The second half of this thesis deals with the effect of antibiotics on the human microbiome. I demonstrate new approaches at two extremes of scale: abstracting the gut microbiome to a single metric, and also investigating the worldwide distribution and diversity of a single resistance gene. In Chapter 4, I develop a new and simple mathematical model of the gut microbiome's response to antibiotic perturbation and fit it to empirical data, showing that in some individuals the gut microbiome appears to return to an alternative stable state, raising questions about the long-term impact of antibiotics on previously healthy bacterial communities. Antibiotic use also selects for resistance, which is a growing concern, particularly as resistance can be transmitted horizontally on mobile genetic elements. In Chapter 5, I describe a global dataset of isolates containing the mobilized colistin resistance gene mcr-1 and use the diversity present within a composite transposon alignment to explore its distribution and spread across multiple bacterial communities.
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Abidov, Amir. "Effects of Hormone Crosstalk on Endophytic Bacterial Communities." Thesis, The University of Arizona, 2015. http://hdl.handle.net/10150/578977.
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The plant hormones salicylic and jasmonic acid (SA and JA, respectively) both play a crucial role in the induction of plant defense system pathways and long-term pathogen resistance. Plants, which do not have an active cellular immune system like animals, instead rely on the release of specific molecules to mediate defense. In general, the SA pathway is activated by biotrophic pathogens and primarily induces antimicrobial responses, while JA is activated by necrotrophic pathogens and herbivory, and induces separate chemical responses. SA and JA are reciprocally antagonistic: activation of one pathway inhibits activation of the other. Here we explore how SA-JA inhibitory crosstalk is used by pathogens or herbivores to combat plant defense. We study the effects of hormone crosstalk on bacterial growth in two plant models: Cardamine cordifolia and Arabidopsis thaliana, which we treated to induce defense pathways. These plants were inoculated with endophytic bacteria isolated from field C. cordifolia plants, and the effects of hormone treatment on bacterial growth rates were measured. We show that JA-induced defenses, which are commonly associated with necrotrophic pathogens, affect varied biotrophic Pseudomonas strains both positively and negatively. Notably, we show that JA-induce defenses affect wild P. fluorescens strains more negatively than SA-defenses.
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Hodder, Karl Russell. "The diversity of soil bacterial communities within the Ecotron." Thesis, University of Liverpool, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343965.
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Meadow, James, Adam Altrichter, Steven Kembel, Maxwell Moriyama, Timothy O'Connor, Ann Womack, G. Brown, Jessica Green, and Brendan J. Bohannan. "Bacterial communities on classroom surfaces vary with human contact." BioMed Central, 2014. http://hdl.handle.net/10150/610203.
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BACKGROUND:Humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the built environment. We sampled 16S rRNA genes from four different surface types throughout a university classroom to determine whether bacterial assemblages on each surface were best predicted by routine human interactions or by proximity to other surfaces within the classroom. We then analyzed our data with publicly-available datasets representing potential source environments.RESULTS:Bacterial assemblages from the four surface types, as well as individual taxa, were indicative of different source pools related to the type of human contact each surface routinely encounters. Spatial proximity to other surfaces in the classroom did not predict community composition.CONCLUSIONS:Our results indicate that human-associated microbial communities can be transferred to indoor surfaces following contact, and that such transmission is possible even when contact is indirect, but that proximity to other surfaces in the classroom does not influence community composition.
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Nieset, Julie E. "The Effect of Protozoan Predation on Four Bacterial Communities." University of Akron / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=akron1145300999.
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Haldar, Kairabi Sadhu. "Profiling of bacterial communities in chronic obstructive pulmonary disease." Thesis, University of Leicester, 2015. http://hdl.handle.net/2381/32292.
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Introduction: It is hypothesized that bacteria are important in the pathogenesis of COPD and exacerbations. Most bacteriological research in COPD has utilised culture based methods. Novel molecular approaches enable detailed evaluation of the airway microbiome that may better inform the role of bacteria in COPD. This project aimed to characterise the microbial community in COPD at stable state and during acute exacerbations through assessment of serial sputa at stable (S), exacerbation (E), follow up (F) and recovery (R) visits. Methods: Sputum from 145 clinical trial COPD patients was collected at multiple stable visits and at each exacerbation (E, F and R visit) over 12 months. Real-time quantitative PCR (qPCR) was performed on sputum DNA using universal 16S gene primers and specific gene targets to quantify total bacterial load and the specific pathogens H. influenzae, S. pneumoniae, M. catarrhalis and S. aureus. In a subgroup of 30 exacerbating patients, 454 high-throughput pyrosequencing of 16S rDNA amplicons was performed at each of the 4 visits. Results: There was no significant difference in total bacterial load or any specific pathogen between longitudinal stable and exacerbation samples. 454 pyrosequencing identified Proteobacteria and Firmicutes to be the dominant groups contributing >80% of the sequence reads at phylum level. Haemophilus, Moraxella and Streptococcus were the dominant groups at genus level. No significant within-subject change in the microbial community was observed across visits. Cluster analysis, based on the ratio of Proteobacteria to Firmicutes (P:F) characterised three subgroups. The high P:F subgroup was characterised by a significant increase in P:F from S to E visits, associated with raised blood CRP and sputum IL-1β levels, suggesting a role for bacteria in exacerbation pathogenesis for this subgroup. Conclusions: Molecular profiling identifies heterogeneity in the airway microbiome of COPD patients, with a role for bacteria suggested in a subgroup.
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Rahalkar, Monali. "Aerobic methanotrophic bacterial communities in sediments of Lake Constance." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-23787.
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Redford, Amanda J. "Interspecies and temporal variation in bacterial leaf surface communities." Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1456691.
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Johnston, Gloria P. "CHARACTERIZATION OF BACTERIAL COMMUNITIES OF RIVERBANK SEDIMENTS CONTAMINATED WITH POLYCYCLIC AROMATIC HYDROCARBONS." Kent State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=kent1397761347.
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Langenheder, Silke. "Links Between Structure and Function of Heterotrophic Aquatic Bacterial Communities." Doctoral thesis, Uppsala : Department of Ecology and Evolution : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4809.
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Gill, Hardeep. "The Effect of Aluminium Industry Effluents on Sediment Bacterial Communities." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23423.
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The goal of this project was to develop novel bacterial biomarkers for use in an industrial context. These biomarkers would be used to determine aluminium industry activity impact on a local ecosystem. Sediment bacterial communities of the Saguenay River are subjected to industrial effluent produced by industry in Jonquière, QC. In-situ responses of these communities to effluent exposure were measured and evaluated as potential biomarker candidates for exposure to past and present effluent discharge. Bacterial community structure and composition between control and affected sites were investigated. Differences observed between the communities were used as indicators of a response to industrial activity through exposure to effluent by-products. Diversity indices were not significantly different between sites with increased effluent exposure. However, differences were observed with the inclusion of algae and cyanobacteria. UniFrac analyses indicated that a control (NNB) and an affected site (Site 2) were more similar to one another with regard to community structure than either was to a medially affected site (Site 5) (Figure 2.4). We did not observe a signature of the microbial community structure that could be predicted with effluent exposure. Microbial community function in relation to bacterial mercury resistance (HgR) was also evaluated as a specific response to the mercury component present in sediments. Novel PCR primers and amplification conditions were developed to amplify merP, merT and merA genes belonging to the mer-operon which confers HgR (Table 5.6). To our knowledge, the roles of merP and merT have not been explored as possible tools to confirm the presence of the operon. HgR gene abundance in sediment microbial communities was significantly correlated (p < 0.05) to total mercury levels (Figure 3.4) but gene expression was not measurable. We could not solely attribute the release of Hg0 from sediments in bioreactor experiments to a biogenic origin. However, there was a 1000 fold difference in measured Hg0 release between control and affected sites suggesting that processes of natural remediation may be taking place at contaminated sites (Figure 3.7). Abundance measurements of HgR related genes represent a strong response target to the mercury immobilized in sediments. Biomarkers built on this response can be used by industry to measure long term effects of industrially derived mercury on local ecosystems. The abundance of mer-operon genes in affected sites indicates the presence of a thriving bacterial community harbouring HgR potential. These communities have the capacity to naturally remediate the sites they occupy. This remediation could be further investigated. Additional studies will be required to develop biomarkers that are more responsive to contemporary industrial activity such as those based on the integrative oxidative stress response.
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Bell, Thomas. "Diversity and functioning of the bacterial communities inhabiting treehole ecosystems." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.427899.
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Chronopoulou, Panagiota-Myrsini. "Impact of crude oil on bacterial communities in marine ecosystems." Thesis, University of Essex, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531559.
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Fevat, Lena. "Biogeography of bacterial, archaeal and picoeukaryotic communities in marine sediments." Thesis, University of Essex, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.428962.
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LASEKE, IAN MATTHEW. "IDENTIFICATION AND CHARACTERIZATION OF BACTERIAL COMMUNITIES IN WARM GROUNDWATER AQUIFERS." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1172086705.
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Mueller, Sabrina R. "Chromium, DNA, and Soil Microbial Communities." Cincinnati, Ohio : University of Cincinnati, 2006. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1141334651.
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Thesis (Ph. D.)--University of Cincinnati, 2008.Advisor: Brian K. Kinkle. Title from electronic thesis title page (viewed Apr. 23, 2009). Keywords: SEC-ICP-MS; Fungal community; bacterial community; DGGE. Includes abstract. Includes bibliographical references.
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Hwang, Chiachi. "Assessment of bacterial communities and an iron-reducing bacterium in relation to an engineered bioremediation system designed for the treatment of uranium-nitric acid contaminated groundwater." Oxford, Ohio : Miami University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=miami1241117969.
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Anitsakis, Erin Colleen. "Dynamics of marine pelagic bacterial communities on the Texas-Louisiana shelf." [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1172.
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Braun, Burga. "Microbiological and molecular analysis of bacterial communities of an urban soil." [S.l.] : [s.n.], 2007. http://opus.kobv.de/tuberlin/volltexte/2007/1525.
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Koch, Isabella. "Assessment of soil bacterial communities with emphasis on the phylum Acidobacteria." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-85547.
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Peter, Hannes. "Diversity and Ecosystem Functioning : Redundancy and Resilience in Freshwater Bacterial Communities." Doctoral thesis, Uppsala universitet, Limnologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-160780.
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Bacteria are immensely diverse and hold key-positions in essentially all biogeochemical cycles. In freshwater ecosystems, bacteria degrade and mineralize organic compounds, linking the pool of dissolved organic matter to higher trophic levels. Aware of the global biodiversity loss, ecologists have started identifying the relationship of diversity and ecosystem functioning. Central to this is the question if species can functionally replace other species, hence being functionally redundant. Functional redundancy might allow communities to maintain functioning when diversity is lost. Due to their large numbers and great diversity, bacterial communities have been suspected to harbor large amounts of redundancy. The central aim of this thesis is to investigate the coupling of diversity and ecosystem functioning of bacterial communities and to understand how environmental perturbation affects this relationship. I manipulated the diversity of complex communities by a dilution technique, and measured the performance of bacterioplankton and biofilm-forming communities at different diversities. Reduction of bacterial diversity differently affected different functions, and that the presence or absence of certain species might be causing this pattern. However, for ecosystems to function, the interplay of multiple functions, i.e. multifunctionality, has to be sustained over long periods of time. In bacterial biofilm communities reduced diversity affected multifunctionality, as reflected by extracellular enzyme activities. A continuous cultivation system was used to address the importance of diversity for resistance and resilience upon environmental perturbation. The analysis of co-occurrence of bacterial taxa showed that the communities form a dense network before the perturbation and that these patterns are disturbed by the environmental perturbation. The final chapter of the thesis presents experimental evidence for the positive effects of temporal and spatial refuges for bacterial communities and the functions they provide. Overall, I found several indications for a lower amount of functional redundancy as previously assumed and it becomes apparent from this thesis that a multifunctional perspective and the consideration of environmental heterogeneity is pivotal.
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Koch, Isabella Heidi. "Assessment of soil bacterial communities with emphasis on the phylum Acidobacteria." kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/8554/.
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Doulgeraki, Agapi I. "Monitoring the succession of bacterial communities during storage of raw meat." Thesis, Cranfield University, 2010. http://dspace.lib.cranfield.ac.uk/handle/1826/5575.
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Fresh meat is exposed to various factors which cause microbiological contamination during handling, processing, packaging and storage. Furthermore, the storage conditions applied may affect the microbial association of the product and consequently the spoilage process. Therefore, the purpose and importance of this study was to identify areas that should be addressed to monitor the succession of bacterial communities during storage of raw meat. The improvement of the microbiological quality and safety of meat was also studied. Cont/d.
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Blanchard, Laurine. "Impact of lightning on evolution, structure and function of bacterial communities." Phd thesis, Ecole Centrale de Lyon, 2013. http://tel.archives-ouvertes.fr/tel-01024190.
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To diversify their genetic material, allowing adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightningrelated electrical phenomena may constitute an additional gene transfer mechanism occurring in nature. The presence in clouds of bacteria capable of forming ice nuclei that lead to precipitations and are involved in the triggering of lightning, such as the global phytopathogen Pseudomonas syringae, led us to postulate that natural electrotransformation in clouds may affect bacteria, by contributing to increase their adaptive potential. We first determined if the ice nucleator bacterium P. syringae could survive when in clouds and acquire exogenous genetic material through lightning shock-simulating in vitro electroporation. In comparison to two other bacteria, P. syringae appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and evolve whilst being transported in clouds. Secondly, we evaluated the impact of lightning shock-simulating in vitro electroporation on the survival, the electrotransformation potential and the diversity of bacteria collected from rain samples. These isolates better resisted lightning than the laboratory strains and some were able to electrotransform exogenous DNA. The rain bacteria we isolated were of different origins and were representative of life modes of the various sources of bacterial emissions on Earth. Our study suggests that bacteria aerosolized from diverse terrestrial ecosystems can spread to new habitats through clouds whilst also being able to acquire new genetic material via lightning-based electrotransformation, thereby potentially enhancing their genetic diversity. The final part of our work consisted of evaluating whether electrotransformation could be applied to the engineering of indigenous soil bacteria in order to develop a tool for the bioremediation of lindane, a once widely used pesticide. Optimized experiments revealed that both natural and electrotransformation contributed to the incorporation of a plasmid harboring a gene encoding the first lindane dechlorination steps by indigenous soil bacteria. In conclusion, we showed that natural electrotransformation mediated by electrical discharges such as those occurring in clouds or reaching soils can be involved in the horizontal gene transfer process among bacteria and, considering the importance of lightning worldwide, may play a role in the adaptation and evolution of these organisms.
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Jones, Meredith Denise Martin. "Oilfield microbiology and the effects of nitrate injection on bacterial communities." Thesis, University of Exeter, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.440338.
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Blow, F. "Variation in the structure and function of invertebrate-associated bacterial communities." Thesis, University of Liverpool, 2017. http://livrepository.liverpool.ac.uk/3009325/.
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Microorganisms are intricately involved in the ecology of many insects, often contributing to host fitness and forming evolutionarily stable associations. The interactions between hosts and microbes can significantly alter their evolutionary trajectories, enabling them to adapt to novel environmental conditions. In this thesis I have examined how host ecology can shape the interactions of bacteria with insects of agricultural and epidemiological importance. I have described the bacterial communities associated with Bactrocera oleae (the olive fruit fly) and generated draft genome sequences for several members of the gut microbiota, including the symbiotic bacterium “Candidatus Erwinia dacicola”. Comparative genomic analyses indicate that Ca. E. dacicola and a novel facultative bacterium Tatumella TA1 may perform key nutritional functions for the host, including the synthesis of essential amino acids and ammonia assimilation from host nitrogenous waste products. Tatumella TA1 is consistently associated with all life stages of populations collected in Israel and Crete at low relative abundance, and encodes large adhesion proteins that may assist in attachment to the host epithelium or other members of the microbiota in the B. oleae gut. I have also examined the variation in frequency and relative abundance of facultative microbes that infect several Glossina spp. (the tsetse fly): the sole vector of African trypanosomes in Sub-Saharan Africa. In addition to three vertically transmitted endosymbionts (Wigglesworthia, Sodalis, and Wolbachia), tsetse flies are infected with two additional potential reproductive manipulators: Spiroplasma and Rickettsia, and a novel strain of Klebsiella. The draft genomes generated for these taxa over the course of this thesis provide the opportunity for future studies in to their role in host biology and how community interactions can shape the transmission and evolutionary dynamics of host-associated microbes.
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GRENNI, PAOLA. "Effects of pesticides and pharmaceuticals on soil and water bacterial communities." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19697.
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Studying soil and water ecosystems using a microbial ecology approach, which analyses the diversity and functioning of microbial communities, can help in evaluating the impact of environmental stressors, such as xenobiotics. In fact, soil and water microorganisms play an important role in maintaining ecosystem environmental quality. For instance, the ability of soil and water to recover from chemical contamination is primarily dependent on the presence of a microbial community with the ability to remove it. Furthermore the microbial community characteristics of an ecosystem can indicate changes in resource availability and the presence of pollution. In this way, the microbial community represents an important key to understanding the impacts of environmental and anthropogenic factors on ecosystems.
This thesis focuses on two groups of xenobiotics frequently detected in soil and water: pesticides and pharmaceuticals. The effects of s-triazine and phenylurea herbicides (terbuthylazine, simazine and linuron) and pharmaceuticals (such as the antiviral drug Tamiflu and two macrolide antibiotics, erythromycin and josamycin) on microbial communities in soil, surface and groundwater were studied. The researches was carried out utilizing innovative molecular techniques in order to identify the natural microbial populations involved in the chemical degradation and evaluate the direct and indirect effects of the herbicides and pharmaceuticals on the microbial community structure and functioning.
For this purpose several investigations involving the selected chemicals in soil and water ecosystems were carried out:
- Research activity regarding s-triazine groundwater contamination caused by diffuse sources. Although the groundwater was considered to have been without life for a long period and unable to recover from herbicide contamination, the experiments performed showed the presence of an autochthonous bacterial community able to degrade the herbicide terbuthylazine. Moreover some bacterial strains such as Janthinobacterium lividum, Advenella incenata and Rhodococcus wratislaviensis, with the capability of growing on various s-triazines were isolated. Among the three isolates, Rhodococcus wratislaviensis was also capable of mineralising the triazine-ring. Finally, an oligonucleotide probe was designed to detect this strain in soil and water samples by applying the in situ fluorescence hybridization technique. This probe can be very useful for monitoring the presence of active R. wratislaviensis populations with the potential to degrade s-triazines in contaminated aquifers and agricultural soils. The research activity was accomplished thanks to active cooperation between IRSA-CNR in Rome and Madrid Complutense University.
- Research activity regarding soil herbicide contamination caused by point sources. The experiments aimed at evaluating the effects of the co-presence of herbicides (linuron and terbuthylazine) and wood amendments on soil bacterial communities. These amendments have recently been proposed for their adsorption capacity, which prevents the mobility of pesticides caused by point sources of contamination. The herbicide degradation and the microbial activity in the presence/absence of pine and oak amendments were assessed and compared. The amendments did not negatively affect bacterial community functioning in terms of dehydrogenase activity. The use of wood amendments can thus be effective in limiting the mobility of herbicides in soils. However the capacity of pine-amended soils to adsorb linuron and terbuthylazine was so high that it hampered herbicide degradation and this should be taken into account since it can modify the persistence of these herbicides. This research was performed by IRSA-CNR together with Spanish CSIC.
- Research on the assessment of the effects of pharmaceutical waste disposal on bacterial communities in soil and groundwater. The research regarded an open quarry contaminated by pharmaceutical residuals (erythromycin and josamycin) owing to its previous improper use for disposal of pharmaceutical waste by a factory producing macrolide antibiotics. The microbiological community characteristics (bacterial abundance, diversity, viability and activity), proposed as microbial indicators, together with chemical investigations of soil and groundwater samples, made it possible to evaluate the quality state of the site.
- Research on the effects of the antiviral drug Tamiflu (recommended for the treatment of cases of avian and swine influenza) on the bacterial community of a surface ecosystem. The role of the bacterial community in the antiviral degradation was demonstrated in microcosm experiments and some bacterial groups, analyzed by fluorescence in situ hybridization, were found to increase in number when there was a halving of the pharmaceutical. This research was performed by IRSA-CNR together with Bologna University.
- Research on variations in bacterial community structure in soil, surface water and groundwater in the presence of herbicides (terbuthylazine, simazine and linuron) or pharmaceuticals (Tamiflu). The research shows that fluorescence in situ hybridization was a useful tool for following the dynamics of individual microbial populations in the ecosystems considered and highlighted the presence of particular groups presumably involved in chemical degradation.
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King, D. H. "Modification of sedimentary communities of nitrate-reducing bacteria by environmental perturbations." Thesis, University of Essex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373211.
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Foster, Jodene. "Characterization of bacterial species in Steinkopf a communal farming area in South Africa: A closer look at pathogenesis." University of the Western Cape, 2019. http://hdl.handle.net/11394/7013.
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Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol)The human population in sub-Saharan Africa has been increasing due to decreases in mortality rates and increases in average human age; in turn increasing poverty and pressure placed on agriculture and agricultural production. However, livestock production in South Africa, and globally, is declining due to disease and parasite prevalence, lack of feed, poor breeding, marketing management, change in nutrition in both livestock and humans, rapid urbanization, encroachment on wildlife and unfavourable climatic conditions brought about by global change. One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic disease. Zoonotic diseases are sicknesses transmissible from animals to humans, resulting from direct contact or environmental reservoirs. Previous studies have identified small-scale farmers as the group most prevalent to contracting zoonotic diseases, especially those working in a communal dispensation. Therefore, this study focused on the communal farming area of Steinkopf in the semi-arid Namaqualand region of South Africa. Steinkopf is one of the largest Act 9 areas, with communal land tenure and a mixed farming system, sheep and goats, on about 759 ha. Steinkopf is divided into two rainfall regions, the Succulent Karoo (winter rainfall region) and the Nama Karoo (summer rainfall region). This study aims to identify and characterise the bacterial microbial communities found in the topsoil layer and faecal matter (dung) within the winter and summer rainfall regions of Steinkopf communal rangeland using Next-generation sequencing. Further, the aim is to assess whether pathogenic bacteria are present within the rangeland and what their potential impact on the local farming community might be if present. A high-throughput sequencing technique (Next-generation sequencing) was used to amplify 16S rRNA targeting the V3-V4 hypervariable regions. The phylotypes produced were 37 phyla, 353 families and 634 genera of which the most abundant bacterial phyla were Planctomycetes, Firmicutes and Bacteroidetes and the most abundant genera were Gemmata, Akkermansia and Arthrobacter. Alpha diversity indices showed a variation in species diversity, evenness and richness between soil and dung samples, it shows a higher species richness, evenness and unique OTUs detected in summer soil samples and at natural water holes. Through these analysis soil samples were regarded as superior to dung samples within this particular environment and for this particular study. Natural water holes were identified as a safer option when compared to man-made water holes as there are natural systems in place that combat the spread and growth of harmful bacterial microbes. It was found that seasonality has a great impact on the development and growth of environmental bacterial microbiota and that the current randomness of grazing routes and migrations within the Steinkopf communal rangeland is not a detriment but instead acts as a benefits to environmental and livestock health. Furthermore, a total of three pathogenic bacteria were identified however, they occurred at relatively low abundances. It can thus be concluded that this study thoroughly describes the usefulness of using a high-throughput sequencing technique such as Next-generation sequencing when amplifying a small sample size in order to achieve a large volume of information; and that currently the Steinkopf communal rangeland is not subjected to or at risk of a potential zoonotic threat.
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FAGORZI, CAMILLA. "The green deal challenge: exploiting biotic interactions from bacterial strains to communities." Doctoral thesis, Università degli studi di Ferrara, 2021. http://hdl.handle.net/11392/2488178.
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One of the main factors behind agricultural sustainability is the effective management of nitrogen (N) inputs, a key element for crop production. Plant growth and agricultural yield is a result of complex interactions between the plant, soil and its microbial communities. An effective way for the management of N inputs resulting in farming practices that are economically viable and environmentally prudent is the use of biologically fixed nitrogen. Symbiotic nitrogen fixing bacteria (rhizobia) represent a promising source of biologically fixed nitrogen, since they provide N inputs directly into the plant (legume). The overarching aim of this thesis is the description, the deciphering and exploitation of the microbial contribution to environmental sustainability.
The first chapter of this thesis focuses on the above-mentioned topic, the symbiosis between legumes and rhizobia, ranging from the most recent discoveries on rhizobia to improve agricultural practices in harsh soils to the choice of the best partnership. Although being species-specific, rhizobia in nature exhibit somewhat large variation in the symbiotic efficiency with different varieties of the same host plant species, which may limit their application to crop as inoculants. While the molecular basis for the species-specificity have been well defined, the molecular basis of the specificity between the variety plant and the bacterial strains belonging to the same species are unknown. In this chapter, the evolutions of the partnership along the genus and its pangenome is dissected and the model species for plant-rhizobium symbiosis, Sinorhizobium meliloti (syn. Ensifer) and Medicago sativa (alfalfa) became our model to investigate the host-symbiont recognition during the initial perception. Next to the novel findings on the evolution of symbiotic nitrogen fixation in the genus, taxonomic revision of the Sinorhizobium/Ensifer genus as well indicates some guidelines for genus delineation in Rhizobiaceae.
The second chapter focuses on the study of the microbiota and its interaction with the environment, analysing the signatures of microbial life in nature. Environmental microbiology can be defined as the study of microbes, their functions, and interactions in all habitats on Earth (and beyond). The papers presented in this chapter are aimed at exploring three different environments sharing the feature of being “extreme”, that is non-conventional for aerobic, mesophilic microbes.
The third chapter reports a systems-biology investigation of metabolic adaptation strategies with a study on the diauxie, showing the metabolic networks of Pseudoalteromonas haloplanktis (a heterotrophic marine bacterium) in complex nutritional conditions encountered in the environment.Uno dei principali fattori alla base della sostenibilità ambientale è la gestione efficace degli input di azoto (N), un elemento chiave per la produzione agricola. La crescita delle piante e la resa agricola sono il risultato di complesse interazioni tra la pianta, il suolo e le sue comunità microbiche. Un modo efficace per la gestione degli input di azoto, che ha come risultato lo sviluppo di pratiche agricole economicamente valide e rispettose dell'ambiente, è l'uso di azoto fissato biologicamente. I batteri simbionti azoto fissatori (rizobi) rappresentano una preziosa fonte di azoto fissato biologicamente, poiché forniscono alla pianta (legume) questo importante elemento direttamente a livello della radice. Il primo capitolo di questa tesi si concentra sull'argomento appena menzionato, la simbiosi tra piante leguminose e rizobi, spaziando dalle più recenti scoperte sui rizobi, volte a migliorare le pratiche agricole in terreni di difficile coltivazione, alla scelta del miglior partenariato. Sebbene siano specie-specifici, i rizobi in natura mostrano una variabilità piuttosto ampia nell'efficienza simbiotica con diverse varietà della stessa specie di pianta ospite, il che può limitare la loro applicazione come inoculanti per le colture. Mentre le basi molecolari della specie-specificità sono state ben definite, quelle che determinano la specificità tra la varietà vegetale e ceppi batterici appartenenti alla stessa specie sono sconosciute. In questo primo capitolo, vengono sezionate le evoluzioni della partnership simbiotica fra pianta e rizobio. Le specie modello Sinorhizobium meliloti (syn. Ensifer) e Medicago sativa (erba medica) sono diventate il nostro modello per studiare il riconoscimento ospite-simbionte durante la percezione reciproca iniziale. Accanto alle nuove scoperte sull'evoluzione della fissazione dell'azoto simbiotico, la revisione tassonomica del genere Sinorhizobium/Ensifer indica alcune linee guida per la delineazione del genere nelle Rhizobiaceae. Il secondo capitolo si concentra sullo studio del microbiota e della sua interazione con l'ambiente, analizzando le “firme” della vita microbica in natura. La microbiologia ambientale può essere definita come lo studio dei microrganismi, delle loro funzioni e interazioni in tutti gli habitat della Terra (e oltre). Gli articoli presentati in questo capitolo hanno lo scopo di esplorare tre diversi ambienti che condividono la caratteristica di essere “estremi”, non convenzionali, per i microbi aerobici, mesofili. Il terzo capitolo riporta un'indagine di biologia dei sistemi delle strategie di adattamento metabolico con uno studio sulla diauxia, che mostra le reti metaboliche di Pseudoalteromonas haloplanktis (un batterio marino eterotrofico) in complesse condizioni nutrizionali incontrate nell'ambiente.
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Nyberg, Karin. "Impact of organic waste residues on structure and function of soil bacterial communities : with emphasis on ammonia oxidizing bacteria /." Uppsala : Dept. of Microbiology, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200620.pdf.
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Thomson, Bruce Craig. "Plant Input Effects on the Diversity and Function of Grassland Bacterial Communities." Thesis, University of Newcastle upon Tyne, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485856.
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By decomposing organic matter, bacterial communities are essential for plant growth and ecosystem functioning. Conversely, aboveground plant communities are known to select for particular bacterial communities by depositing C resources of different palatability belowground. Aboveground communities are known drivers of bacterial community structure which in turn affects soil C cycling. However, the exact mechanisms and feedbacks of this intimate relationship remain unclear. This thesis examines the effects of vegetation on bacterial community structure and whether plant driven differences in bacterial community composition affect soil C cycling and substrate utilisation in a grassland soil at the NERC experimental field site, Sourhope, Scotland. Firstly, the effects of vegetation on bacterial community structure .and soil respiration were examined. Bacterial community structure and function were shown to differ depending on the presence or ab~nce of plants. Particularly, differences in the abundances of certain bacteria were observed and soil respiration rates were higher in vegetated soil 'compared to bare soil. These differences in soil CO2-C efflux were attributed to differences in the physiological traits of the dominant bacterial taxa. Next, an assessment of laboratory soil pre-treatments was carried out to establish a suitable microcosm design for analysing soil bacterial communities. The results from this study were then implemented in the design of subsequent experiments to investigate soil bacterial community structure and C functional responses to added substrates. Using soil microcosms it was then investigated whether plant-induced differences in bacterial community structure affected the decomposition of different substrate types and amounts. Also, whether the presence or absence of plants selected for different bacterial community members responsible for the decomposition of labile and recalcitrant substrates added at a high and low concentration. Functional responses were shown to differ depending on soil type, substrate complexity and loading rate. Respiration responses were thought to be due to differences in bacterial community structure between soil treatments. Taxonomic responses also differed depending on the presence or absence of plants, decomposability of substrate and concentration. However, there were no consistent patterns in community changes. Finally, 13C-Iabelled substrates were added to soil with or without vegetation to accurately measure substrate specific respiration and assess priming effects. Also rRNASIP was performed in an attempt to unambiguously identify bacteria responsible for the assimilation of labelled substrates. Following labelled-substrate additions, mineralisation of substrates differed between soil treatments and was dependent on substrate type. Priming effects were strongest in bare soil as in vegetated soil added substrate was preferentially mineralised over native SOM. Both substrate specific respiration and priming effects were thought to be linked to bacterial community composition. Whilst all substrates were rapidly mineralised and significant differences existed between vegetated and bare soils, 13C was not incorporated into RNA with similar efficiency. Using rRNASIP the entire bacterial community in vegetated and bare soils was shown to have utilised 13C-substrates as a general bacterial community shift into enriched gradient fractions was observed. However, similar to initial bacterial diversity, there were differences in the abundances of functionally active bacteria between vegetated and bare soils.
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Jesus, Indhira I. de (Indhira Immaculada de). "The effects of toluene contamination on epilithic bacterial communities in a stream." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/35985.
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Armstrong, Alacia. "Seasonal dynamics of edaphic bacterial communities in the hyper-arid Namib desert." Thesis, University of the Western Cape, 2014. http://hdl.handle.net/11394/3855.
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>Magister Scientiae - MScThe aim of this study is to investigate the edaphic bacterial community dynamics over short (57 days) and long-term (1 year) sampling intervals using an extensive sampling strategy in combination with community fingerprinting by T-RFLP analyses and micro environmental characterization. The short-term study was conducted on three distinct locations in the Namib Desert gravel plains. Soil bacterial communities were found to be more similar within habitats than between habitats, with the differences likely shaped by soil pH. These findings are consistent with the concept of habitat filtering. Investigation of edaphic bacterial communities over 1 year in an 8100 m2 sampling site revealed seasonal patterns of variation in community structure. Soil moisture, phosphorus, potassium and magnesium were identified as significant abiotic drivers of community temporal dynamics. β diversity was found to increase over time, while the environment remained relatively static. These findings support previous observations that desert communities are likely structured by stochastic and deterministic processes. Taken together, these findings advance understanding of temporal variation of edaphic communities in the Namib desert
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Larouche, Julia. "Environmental Influences on the Genetic Diversity of Bacterial Communities in Arctic Streams." ScholarWorks @ UVM, 2009. http://scholarworks.uvm.edu/graddis/131.
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The National Park Service (NPS) Inventory and Monitoring (I&M) Program is designed to collect baseline data on “vital sign” indicators across the entire NPS system. The project presented in this thesis was designed to supplement to efforts of the Artic Network (ARCN) to catalogue the physical, chemical and biological metrics associated with the Stream Communities and Ecosystems vital sign and to foster a better understanding of the basic structure and function of these remote systems. This data is essential to assess the impacts of current and future environmental change in the ARCN parks. The primary objective of this project was to quantify the genetic diversity of microbial communities of selected arctic stream ecosystems. Microbes are a fundamentally important but poorly understood component of arctic stream ecosystems. They are responsible for recycling organic matter and regenerating nutrients that are essential to the food webs of aquatic ecosystems. Recent research (Jorgenson et al. 2002) in the ARCN parks has shown that two fundamentally different lithologies – ultramafic and non-carbonate – influence terrestrial productivity and impart different geochemical characteristics to stream water. Microbes are found in different stream habitats – sediment (epipssamon) and rock (epilithon) biofilms. In this work we test the hypothesis that these differences in lithology and stream habitat influence the genetic diversity of bacterial biofilm communities in arctic streams and whether these patterns can be correlated to stream biogeochemistry. A microbial community fingerprinting method, T-RFLP, as well as 16S rRNA gene sequencing were used to explore the genetic diversity of microbial communities in sediment and epilithic biofilms in stream reaches that drain watersheds with contrasting lithologies in the Noatak National Preserve, Alaska. Differing patterns in bacterial community composition at both the large-scale (lithology) and small-scale (stream habitat) were observed. Non-metric multidimensional scaling (NMDS) ordination of T-RFLP peaks and Analysis of Similarity (ANOSIM) showed a high degree of separation (ANOSIM P < 0.001) between the non-carbonate and ultramafic lithologies, as well as the two habitats, sediment and epilithon. Significant (P < 0.005, Bonferroni corrected) positive correlations were detected between particular nutrients, base cations, and dissolved organic carbon and bacterial community structure unique to each lithology. Although clone libraries indicated high bacterial OTU diversity within and across stream sites, biogeographical patterns were observed depending on locality type. Rarefaction analyses indicated that streams arising from the non-carbonate lithology may be more diverse than streams arising from the ultramafic lithology. Analysis of MOlecular VAriance (AMOVA) indicated that sediment and epilithon samples had genetically different microbial communities (P = 0.01) and taxonomic identifications revealed markedly different bacterial residents between sediment and epilithon habitats. Our results show relationships at large- and small-scales at the landscape level and in ecological niches within a single stream.
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Dyda, Rachael Y. "Linking phylogeny and lipid composition of natural bacterial communities in arctic waters." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/3252.
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Thesis (M.S.) -- University of Maryland, College Park, 2005.Thesis research directed by: Marine, Estuarine, Environmental Sciences Graduate Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Santmire, Judith Ann. "Bacterial communities in a Northeast Ohio stream effects of substrate size, environmental features and temporal changes /." [Kent, Ohio] : Kent State University, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=kent1113326109.
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Thesis (Ph.D.)--Kent State University, 2005.Title from PDF t.p. (viewed Aug. 23, 2006). Advisor: Laura G. Leff. Keywords: bacterial communities; substrate; lotic; fluorescent in situ hybridization; sediment. Includes bibliographical references.
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Andersson, Martin. "Extent and limitations of functional redundancy among bacterial communities towards dissolved organic matter." Doctoral thesis, Uppsala universitet, Limnologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-331772.
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One of the key processes in the carbon cycle on our planet is the degradation of dissolved organic matter (DOM) in aquatic environments. The use of organic matter by bacteria links energy from DOM to higher trophic levels of the ecosystem when bacteria are consumed by other organisms. This is referred to as the microbial loop. In this thesis I examined if the communities were functionally redundant in their ability to utilize organic matter, or if variation in bacterial composition and richness is of importance. To test this overarching question several experiments were conducted that include methods such as illumina sequencing of the 16S rRNA gene for taxonomic identification of bacterial communities, flow cytometry to follow the growth of communities and spectroscopic measurement to describe the composition of the organic matter pool. Initially we demonstrated how to optimally sterilize organic matter for experimental studies in order to preserve its natural complexity. In further experiments we found that bacterial communities are redundant in their utilization of organic matter and can maintain optimal performance towards a range of organic matter pools. Related to this we found that pre-adaptation to organic matter played a small role as communities performed equally well regardless of their environmental history. We saw a small effect of richness and composition of bacterial communities on the efficiency of organic matter use, but conclude that this is of minor importance relative to abiotic factors. Still, we also show that organic matter can put strong selection pressure on bacterial communities with regards to richness and composition. Additionally we found that the supply rate of a carbon compound greatly influenced the energy utilization of the compound, i.e. a higher growth rate can be maintained if substrate is delivered in pulses relative to a continuous flow. Finally we conclude that the variation in bacterial communities is unlikely to have a major influence on carbon cycling in boreal lakes, but to enable a finer understanding, the genetics underlying the carbon utilization needs to be further explored.
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Mohseni, Mojtaba. "Molecular Characterisation and Horizontal Gene Transfer within 2,4-Dichlorophenoxyacetic Acid Degrading Bacterial Communities." Thesis, University of Exeter, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486770.
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Chlorophenoxyalkanoic acid herbicides, including 2,4-dichlorophenoxyacetic acid (2,4-D), are a group of structurally related compounds which have been extensively applied to the environment for control of broad-leaved weeds. Persistence in the environment presents a serious concern due to environmental toxicity and their impact on human health. Soil microbial communities are capable of total degradation .of these pollutants. Understanding the stability and diversity of the degradative microbial communities, and quantification of sp'ecific catabolic gene expression and dissemination in soil is necessary for the bioremediation of contaminated sites. Environmental soil samples were collected from various sites. A 2,4-D degrading isolate, Burkholderia hospita, was isolated from soil and demonstrated to be predominant in 2,4-D degrading communities using DGGE and clone library analyses of 168 rRNA. This study encompasses the first report of Burkholderia hospita capable of 2,4-D degradation. B. hospita MM1720 contained a large catabolic plasmid which harbours 2,4-D degradative genes. Phylogenetic analysis of tfdA, tfdB and tfdC from B. hospita provided evidence that the acquisition of these functional genes in B. hospita occurred through horizontal gene flow rather than from a common ancestor. In addition, tfdA from B. hospita belonged to the class III tfdA genes and clustered with other tfdA genes recovered from p- and r-Proteobacteria. . A novel GFP system was constructed to study an in vitro biofilm system for plasmid transfer. In vitro biofilms were found to enhance 2,4-D degradation compared to planktonic monocultures. Quantitative PCR (qPCR) was optimised and used to monitor the expression of tfdA transferred into different species within biofilms. Significant upregulation of tfdA gene expression was noted within biofilms compared to planktonic cells. A novel culture-independent method for the detection and quantification of horizontal gene flow among bacteria in soil was developed. All transconjugants acquired the broadhost pMM172::gfjJ, detected by flow cytometry and were determined to belong to a wide range of a-, p- and r-Proteobacteria with high homology to Pseudomonas, Burkholderia, Ralstonia, Variovorax and Sphingomonas genera. This approach shows the detection of a broad transconjugant diversity of a self-transmissible broad-host range plasmid. However, only Pseudomonas, Burkholderia and Ralstonia species were able to grow on 2,4-D as the sole carbon and energy source. Screening for detection of GFP fluorescing transconjugants .by flow cytometry showed greater efficiency compared to methods based on either selective media for detection of culturable transconjugants or DGGE for analysis of microbial community structure. Thus qPCR has been shown to be a suitable approach for assessment of dissemination of catabolic genes in environments and may be developed as a useful tool towards prediction ofthe rate ofxenobiotic degradation. This study provides new insights into the molecular genetics and control mechanisms involved in chlorophenoxy acid herbicide degradation and contribute towards the understanding of the role and potential of horizontal gene transfer for chlorophenoxy acid bioremediation. These new developments in microbial ecology approaches are essential for the assessment and selection of catabolic genes for bioaugmentation optimisation which .may be used for future bioremediation management.
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Brim, Hassan. "Molecular approaches to study bacterial strains and communities of heavy metal polluted soils." Doctoral thesis, Universite Libre de Bruxelles, 1997. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/212200.
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