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A Metagenomic Insight Into the Role Of A METAGENOMIC INSIGHT INTO THE ROLE OF WASTEWATER TREATMENT PLANTS AS POTENTIAL HOTSPOT FOR ANTIBIOTIC RESISTANT BACTERIA AND ANTIBIOTIC RESISTANCE GENES by PO-CHENG TANG Submitted in fulfilment of the academic requirements for the degree of Master of Science (MSc) in the Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science at the University of KwaZulu-Natal, Durban, South Africa. June 2016 As the candidate’s supervisor, I have approved this dissertation for submission. Name: ____________________Prof. A. O. Olaniran Signed: ____________________ Date: _______________ i Abstract The magnitude of the global freshwater crisis is underestimated. Although international and national efforts have implemented strategies to safeguard these precious resources, the consequential effect of continued deterioration of water quality on the available options for water usage is still a major area of concern. Contamination of surface water resources resulting from inadequate treated effluent discharge from wastewater treatment plants (WWTPs) has previously been indicated as an important topic requiring continued investigations. Often, these discharges introduce large amounts of organic matter and nutrients which could lead to eutrophication and temporary oxygen deficiencies, ultimately disrupting the natural biotic community structure and its important ecological functions. In addition, pathogenic bacteria and antibiotic resistance genes (ARGs) present in the wastewater discharged increases public health risks due to their disease causing potential and dissemination of resistance determinants, respectively. This could result in increased cases of diseases such as dysentery, cholera, skin infections and typhoid, leading to higher rates of mortality and morbidity, placing further stresses on the public health system. Hence, better management and minimisation of microbial pathogens and antibiotic resistant bacteria in WWTPs is crucial to prevent the dissemination of potential pathogens and ARGs into the environment. The overall objective of this study was to provide metagenomic insights into the bacterial diversity as well as the ARGs associated with the communities present in wastewaters and to establish the impact of the discharged effluents on the receiving river bodies. Samples were collected from two urban WWTPs receiving distinctive raw sewage, with combinations of domestic, industrial and hospital, in the city of Durban, South Africa. Metagenomic sequencing were conducted on the Roche 454 platform and shotgun generated pyrosequences were analysed using established pipelines ii (MG-RAST) and a plethora of bioinformatic tools (IDBA_UD, MaxBin, CheckM, etc.) and databases (VFDB and CARD). The findings of this study suggest that there is a substantial shift between the bacterial communities in the raw wastewater and the treated wastewater in terms of abundance, composition and diversity. Similarly, this was observed in the functional genes determined and the overall metabolic potential of the associated bacterial communities. Additionally, putative genes encoding for resistance to most classes of antibiotics were identified in all samples and encompassing the three major resistance mechanisms. Although shotgun sequencing and subsequent analysis only provides qualitative and semi-quantitative data, we were able to establish a list of the bacterial communities and antibiotic resistance genes across all the water samples, identified the potentially pathogenic bacteria causing human disease in the treated wastewaters of both plants that need to be considered during treatment management decisions, as well as the functional potential of the communities. Overall, results from this study demonstrated the usefulness of a metagenomic approach in initial stages of water quality assessments. The results of this work also provide significant and novel information that will contribute to our understandings of water quality which could lead to sustainable wastewater management decisions. iii “If you take care of the small things, the big things take care of themselves.” – Emily Dickinson (1830-1886) iv Preface The experimental work described in this dissertation was carried out in the Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville campus), Durban, South Africa from February 2014 to August 2015, under the supervision of Professor Ademola O. Olaniran. These studies represent original work by the author and have not otherwise been submitted in any form for any degree or diploma to any tertiary institution. Where use has been made of the work of others, it is duly acknowledged in the text. v Declaration 1 - Plagiarism I, Po-Cheng Tang declare that: 1. The research reported in this dissertation, except where otherwise indicated, is my original research. 2. This dissertation has not been submitted for any degree or examination at any other university. 3. This dissertation does not contain other persons’ data, pictures, graphs or other information, unless specifically acknowledged as being sourced from other persons. 4. This dissertation does not contain other persons’ writing, unless specifically acknowledged as being sourced from other researchers. Where other written sources have been quoted, then: a. Their words have been re-written but the general information attributed to them has been referenced b. Where their exact words have been used, then their writing has been placed in italics and inside quotation marks, and referenced. 5. This dissertation does not contain text, graphics or tables copied and pasted from the Internet, unless specifically acknowledged, and the source being detailed in the dissertation and in the References sections. Signed: ______________________________ vi Declaration 2 - Publications and Conferences For all publications, P. Tang and A.O. Olaniran both conceptualized and designed the research project as well as contributed equally in the preparation of all the listed manuscripts; P. Tang implemented and analyzed experimental work. Publication 1: P. Tang and A.O. Olaniran (2016). Fate of bacterial pathogens, community composition and antibiotic resistance genes in two full-scale wastewater treatment plants as revealed by metagenomic analysis. Science of the Total Environment (Submitted). Publication 2: P. Tang and A.O. Olaniran (2016). Chlorination effects on bacterial diversity, functional potential and antibiotic resistome during urban wastewater treatment: A metagenomic insight. Water Research (Submitted). Publication 3: P. Tang and A.O. Olaniran (2016). Antibiotic resistance genes, bacterial community structure and metabolic potential in two rivers impacted by wastewater treatment plant discharges: a metagenomic approach. Environmental Science and Pollution Research (Submitted). Publication 4: P. Tang and A.O. Olaniran (2016). Bacterial community dynamics of two rivers receiving treated urban wastewater effluents: a T-RFLP assessment. World Journal of Microbiology and Biotechnology (Submitted). Publication 5: P. Tang and A.O. Olaniran (2016).Draft genome sequence of an Acinetobacter sp. PT1 reconstructed from metagenomic sequences of wastewater effluent samples from a wastewater treatment plant in Durban, South Africa. Genome Announcement (in preparation). Publication 6: P. Tang and A.O. Olaniran (2016). Draft genome sequence of a Polynucleobacter necessarius PT2 reconstructed from metagenomic sequences of wastewater effluent samples from a wastewater treatment plant in Durban, South Africa. Genome Announcement (in preparation). vii Declaration 2 - Publications and Conferences Conference Presentations: P. Tang and A.O. Olaniran (2015). Chlorination effects on bacterial diversity and antibiotic resistance gene profiles of treated wastewater: A metagenomic insight. VI International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld 2015); Barcelona, Spain. Signed: ______________________________ viii Contents Abstract ..................................................................................................................................... ii Preface ....................................................................................................................................... v Declarations ............................................................................................................................. vi List of figures ......................................................................................................................... xiv List of tables......................................................................................................................... xxiv Acknowledgements ........................................................................................................... xxviii Chapter 1 Introduction and literature review ............................................................ 1 1.1 Introduction ............................................................................................ 2 1.2 Microbial water quality assessments ..................................................... 6 1.3 Next-generation sequencing and water quality assessments ............... 12 1.3.1 Technologies, experimental design and analysis methods for metagenomic studies .............................................................. 13 1.3.1.1 Next-generation sequencing technologies ................ 13 1.3.1.2 Experimental design ................................................
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