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Title: Use of multiple displacement amplification based approaches for detection and analysis of environmentally significant and contaminating bacteria in fresh water
Author: Akinbami, Omolola Adetola
Awarding Body: Queen's University Belfast
Current Institution: Queen's University Belfast
Date of Award: 2013
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One of the great challenges of microbial analysis in natural environments derives from the fact that a large proportion of microorganisms present is not culturable in standard conditions. To overcome this, various molecular approaches are widely used. Multiple Displacement Amplification (MDA) is especially useful as it can be applied in conjunction with other techniques to identify genes derived from individual microbial cells. The aim of this project was to study freshwater samples obtained from various environments in Ireland in order to identify dominant bacterial species and key genes associated with them that were likely to be involved in biodegradation of contaminating compounds. In order to do this, various molecular approaches were applied, with the most important being MDA assisted PCR. The tlree fresh water environments studied were: commercial bottled water, agriculturally contaminated ground water obtained from Co. Kilkenny, Ireland and ground water samples obtained from a diesel-contaminated site in Northern Ireland. In these environments, dominant bacterial strains were identified using MDA assisted PCR. Strains related to Rhodoferax ferrireducens were identified in commercial bottled water; Pseudomonas fluorescens and Polaromonas sp. in agriculturally-contaminated ground water samples; Dechloromonas aromatica and Pseudomonas putida in diesel-contaminated ground water samples. Functional genes (nitrate reductase and naphthalene dioxygenase) which are known to be involved in biodegradation were shown to be present in some of the strains. It was shown that the narG gene (nitrate reductase) was associated with strains related to Pseudomonas fluorescens, Alicycliphilus denitrificans and Polaromonas naphthalenivorans detected in agricultural-contaminated ground water. Naphthalene dioxygenase gene (nahAc) was associated with strains related to Pseudomonas fluorescens, Pseudomonas putida and nagAc (another naphthalene dioxygenase gene) with Ralstonia pickettii detected III ground water samples obtained from a diesel-contaminated site in Northern Ireland. To achieve a more comprehensive characterization of the studied environments corresponding 16S rRNA gene libraries were obtained and analysed. Sequences found in these libraries were affiliated with Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Actinobacteria and Cyanobacteria
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available