The Rhizobiome of Vachellia (Acacia) Woodlands Surrounding Witwatersrand Gold and Uranium Mine Tailings
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The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings Michelle Toni Buck A Thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment for the degree of Doctor of Philosophy Declaration I, Michelle Toni Buck (Person number: 322062), am a student registered for the degree of Doctor of Philosophy (PhD) in the academic year 2018. I hereby declare the following: I am aware that plagiarism (the use of someone else‟s work without their permission and/or without acknowledging the original source) is wrong. I confirm that the work submitted for assessment for the above degree is my own unaided work except where I have explicitly indicated otherwise and acknowledged. In this context, I understand that the use of editing services is considered airded work and must be declared. I have not submitted this work before for any other degree or examination at this or any other University. The informationing used in the Thesis HAS NOT been obtained by me while employed by, or working under the aegis of, any person or organization other than the University. I have followed the required conventions in referencing the thoughts and ideas of others. I understand that the University of the Witwatersrand may take disciplinary action against me if there is a belief that this is not my own unaided work or that I have failed to acknowledge the source of the ideas or words in my writing Signature: Date: 8th August 2018 i Abstract Phytoremediation of mine tailings and surrounding areas provide the most cost-effective means of alleviating their pollutant effects. Research has shown that successful revegetation of mine tailings and surrounding areas can be optimised by providing appropriate microbial symbionts for the plants. Microorganisms are beneficial to plant growth and health which is essential for revegetation and phytoremediation of contaminated sites. The aim of this study was to assess the microbial status of Vachellia karroo rhizosphere currently growing on the surrounding areas of two mining operations, namely Vaal River (VR) and West Wits (WW) Operations. Metataxonomy is the study/use of genetic material isolated from field/environmental samples. It has been reported from metataxonomy studies that a large amount of microbial biodiversity had been missed by cultivation-based methods. Metataxonony allows for an unbiased genetic analysis from all members of the sampled community since it is a PCR directed sequencing approach for identification. Root and soil samples were collected in spring, roots were removed and physio-chemical analyses were preformed on the soil, including pH, conductivity, cation exchange capacity and XRF analysis. The soil samples were then prepared for DNA extraction by mixing/bulking 5 g of soil for each niche site and control. Then 500 mg of soil was used to extract DNA using the DNeasy® PowerSoil® Kit (Qiagen). Target genes, namely the 16S rRNA V1-V3 hypervariable region and the ITS2 hypervariable region, were sequenced at Molecular Research LP MR DNA (http://www.mrdnalab.com), Texas. The rhizosphere bacterial communities of V. karroo from VR Operations was predominantly comprised of Acidobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, Planctomycetes, Gemmatimonadetes, (between 1 % and 47 % depending on the niche sites and controls) and the remainder of the phyla (Chloroflexi, Armatimonadetes, Nitrospirae, Candidatus Saccharibacteria, candidate division WPS-1 and candidate division WPS-2) were less than 1 %. The numbers all represent the average percentage of sequences across 14 phyla. For WW Operations the bacterial communities were predominantly comprised of Actinobacteria, Acidobacteria, Planctomycetes, Verrucomicrobia, Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, (between 0.7 % and 41.4 % depending on the niche sites and controls) and the remainder of the phyla (candidate division WPS-1, candidate division WPS-2, Armatimonadetes, Candidatus Saccharibacteria, Nitrospirae and Cyanobacteria/Chloroplast) were around 1 %. The numbers all ii represent the average percentage of sequences across 15 phyla. The rhizosphere fungal communities of V. karroo from VR Operations was predominantly comprised of Ascomycota (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Ascomycota_unidentified, Leotiomycetes and Incertae_sedis_14); Zygomycota (Incertae_sedis_10); Basidiomycota, Agaricomycetes, Atractiellomycetes, Tremellomycetes (between 0.01 % and 77.1 % depending on the niche sites and controls) and to a lesser degree Glomeromycota (Glomeromycetes) and Fungi_unidentified (between 0.2-6 % depending on the niche sites and controls). The numbers all represent the average percentage of sequences across 12 classes. For WW Operations the fungal communities were predominantly comprised of Ascomycota (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Ascomycota_unidentified, Leotiomycetes and Archaeorhizomycetes), Zygomycota (Incertae_sedis_10), Basidiomycota, Agaricomycetes, Tremellomycetes, Atractiellomycetes, Basidiomycota_unidentified, Fungi_unidentified and Glomeromycota (Glomeromycetes) (between 0.01 % and 91.42 % depending on the niche sites and controls). The numbers all represent the average percentage of sequences across 13 classes. The study represents a first report utilising metataxonomic tools in the analysis of the rhizobiome of V. karroo from areas around mine tailings. The results will assist in making decisions about future microbial surveys and applying microbial inoculum in revegetation of mine waste sites and the affected areas. Key words: mine tailings, revegetation, Vachellia karroo, metataxonomy, ITS2, 16S rRNA iii Dedication I would like to dedicate this project to Alexander Spruyt (fondly known as Lexx) who thought up the initial project and who I wish was here to continue his own research. “This day is remembered and quietly kept, No words are needed, we shall never forget, For those we love don't go away, They walk beside us every day. Unseen and unheard, but always near, So loved, so missed, and so very dear.” – Author unknown iv Acknowledgements I would like to to take this opportunity to express my deepest gratitude to people who have been immensely supportive during the course of completing this difficult research project First and foremost I would like to thank my supervisor, Professor Vincent M. Gray, who supported me every step of the way financially, intellectually and emotionally, and for his always welcoming and understanding attitude for discussion, his advice and enthusiasm throughout the course of this study. To Dr Pieter De Maayer, without whom the project would not have been completed. For his time spent brainstorming and always willing presence in assisting me. To Professor Crissie Rey for all her advice and financial assistance. To Stephen Naegeli, without whom I would never have had the courage to continue this research project. He was my rock and support and he always encouraged me to complete my research that I had started. To my beloved parents who always believed in me and were always willing to listen to my troubles. To my friend Joshua Hazzan, who always had something encouraging to do or say and who assisted with cataloguing my vast quantity of results. To my family and friends who always had encouraging things to say and kept me positive. To Isabel Weiersbye for her advice, assistance and support in collection of samples, sample analysis and compiling results. v Finally I would like to thank the National Research Foundation (NRF), the University of the Witwatersrand for the Postgraduate Merit Award (PMA), THRIP, Professor M. E. C. Rey and Professor V. M. Gray for financial assistance. vi Research output Conference attendance Poster presentations Molecular Biosciences Research Thrust Research Day 8 December 2016 Wits Club, West Campus, University of the Witwatersrand Title: Identification of arbuscular mycorrhizal (AM) fungal genes associated with the tolerance, transport and/or accumulation of non-micronutrient metals found in gold and uranium mine tailings Authors: M. T. Buck, V. M. Gray and A. J. Valentine 8th Cross Faculty Postgraduate Symposium 25-26 October 2017 Auditorium at the School of Public Health, Education Campus, 27 St Andrews Road, Parktown Title: The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings Authors: M. T. Buck, V. M. Gray, P. De Maayer, I. Weiersbye and M. E. C. Rey Molecular Biosciences Research Thrust Research Day 30 November 2017 Wits Club, West Campus, University of the Witwatersrand Title: The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings Authors: M. T. Buck, V. M. Gray, P. De Maayer, I. Weiersbye and M. E. C. Rey vii Table of contents Declaration......................................................................................................................... i Abstract .............................................................................................................................. ii Dedication .......................................................................................................................... iv Acknowledgements ........................................................................................................... v Research output ...............................................................................................................