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Bacterial Diversity of South African Soils AR Sholeye Orcid.Org 0000-0003-2109-503X Bacterial diversity of South African soils AR Sholeye orcid.org 0000-0003-2109-503X Dissertation submitted in fulfilment of the requirements for the degree Master of Science in Biology at the North West University Supervisor: Prof OO Babalola Graduation ceremony: July 2020 Student number: 31415695 DECLARATION I, the undersigned, declare that this thesis submitted to the North-West University for the degree of Master of Science in Biology in the Faculty of Natural and Agricultural Sciences, School of Environmental and Health Sciences, and the work contained herein is my original work with the exceptions to the citations and that this work has not been submitted at any other University partially or entirely for the award of any degree. Name: Abisola Regina Sholeye Signature: ……………………………………………. Date: …………………………………………………. Co-Supervisor: Dr. Omena Ojuederie Signature: ……………………………………………. Date: …………………………………………………. Supervisor: Professor Olubukola Oluranti Babalola Signature: ……………………………………………. Date: …………………………………………………. ii DEDICATION This work is dedicated to the Almighty God the source of life and every good thing. iii ACKNOWLEDGEMENTS I would like to sincerely appreciate my supervisor Professor Olubukola Oluranti Babalola and Dr. Omena Bernard Ojuederie for their kind and encouraging words, their invaluable suggestions, advice, and guidance which really gave me the push I needed to carry on and complete the degree. I acknowledge the National Research Foundation, South Africa for a grant awarded. I also thank the North-West University Postgraduate Bursary for awarding me the bursaries throughout the duration of my MSc programme, the NWU library staff Mr. Siviwe Bangani, Ms Dina Mashiyane for assisting with online research tools and also for scheduling relevant trainings. I would also like to appreciate my big mum Cecilia Modupe Adejumo, my uncle Peter Nwoko, my mum Anne Nwoko, my dad Olayinka Sholeye, my brothers Oladipo Sholeye, Timilehin Sholeye, my sisters Remi Sholeye and Damilola Sholeye and to every member of my family, I love you all so much. Special thanks to all those who assisted with guidance, technical aspects, review and correction of this work: Professor Munyati, Dr. Nicholas Igiehon, Dr. Aremu Rhoda, Dr. Caroline Ajilogba, Dr. Adenike Amoo, Mr. Simon Isaiah, Mr. Ben Enagbonma, Ms. Anelda Van der Walt. Also to Dr. Esther Fayemi and Professor Helen Drummond for their contributions. I would also like to appreciate members of the laboratory, Dr. Ayansina Ayangbenro, Mr. Kehinde Abraham, Mr. Tayo, and Mrs. Mamsi Khantsi. Appreciation also goes to Sister Gloria Uwaya, Pastor Mark Ajilogba, Miss Fiyinfoluwa Giwa, Victoria Ajilogba, Emmanuel Ajilogba, Demilade Ajilogba and Damilola Ajilogba and all the members of Deeper Life Campus Fellowship and RCCG Fountain of Life Parish who make my stay in South Africa fun and enjoyable. iv I also thank Dr. Olaleru Akin and Mr. Timothy Quadri for their assistance in the admission process. I appreciate the Almighty God who reigns from age to age, the ancient of days for the breath of life and His uncountable blessings on my life. My deepest appreciation goes to Him. v TABLE OF CONTENTS DECLARATION ........................................................................................................................ ii DEDICATION ........................................................................................................................... iii ACKNOWLEDGEMENTS ...................................................................................................... iv TABLE OF CONTENTS .......................................................................................................... vi LIST OF MANUSCRIPTS SUBMITTED FOR PUBLICATION ........................................ x LIST OF TABLES .................................................................................................................... xi LIST OF FIGURES ................................................................................................................. xii LIST OF ABBREVIATIONS ................................................................................................. xiv GENERAL ABSTRACT ........................................................................................................ xvi CHAPTER ONE ......................................................................................................................... 1 1.1 General Introduction ........................................................................................................ 1 1.2 Problem Statement ........................................................................................................... 5 1.3 Research Hypothesis......................................................................................................... 5 1.4 Research Questions........................................................................................................... 5 1.5 Research Aim .................................................................................................................... 6 1.6 Research Objectives ......................................................................................................... 6 CHAPTER TWO ........................................................................................................................ 7 2.1 Soil Quality Indicators; Their Correlation and Role in Enhancing Agricultural Productivity (Review Paper).................................................................................................. 7 2.2 Introduction ...................................................................................................................... 7 2.3 Soil Quality Assessment ................................................................................................. 11 vi 2.4 Importance of Soil Quality to Ecosystem Services ...................................................... 13 2.5 Indicators of Soil Quality ............................................................................................... 14 2.5.1 Physical indicators ................................................................................................................. 16 2.5.2 Chemical indicators ............................................................................................................... 19 2.5.1 Biological indicators .............................................................................................................. 21 2.6 Roles of Microorganisms in Soil Quality Assessment ................................................. 24 2.7 Conclusion ....................................................................................................................... 26 2.8 Acknowledgements ......................................................................................................... 26 CHAPTER THREE ................................................................................................................. 27 3.1 Bacterial Diversity and its effect on Agricultural Productivity (Review Paper) ...... 27 3.2 Introduction .................................................................................................................... 27 3.3 Soil Microbiome .............................................................................................................. 30 3.4 Insights into the Soil Microbiome ................................................................................. 31 3.5 Evolution and Distribution of Bacteria ........................................................................ 32 3.6 Importance of Microbial Diversity in the Soil ............................................................. 32 3.7 Factors Affecting Microbial Distribution in the Soil ................................................... 33 3.7.1 Soil texture and structure ..................................................................................................... 33 3.7.2 Soil physicochemical properties ........................................................................................... 34 3.7.3 Land use practices ................................................................................................................. 36 3.7.4 Influence of termite activity on microbial diversity ........................................................... 40 3.8 Methods used for Microbial Diversity Analysis........................................................... 41 3.9 Conclusion ....................................................................................................................... 43 3.10 Acknowledgements ....................................................................................................... 44 CHAPTER FOUR .................................................................................................................... 45 vii 4.1 Land Use and Its Influence on Soil Bacterial Diversity (Research Article) .............. 45 4.2 Introduction .................................................................................................................... 46 4.3 Materials and Methods .................................................................................................. 48 4.3.1 Description of soil sample collection sites: .......................................................................... 48 4.3.2 Soil sample collection ............................................................................................................ 49 4.3.3 DNA extraction and PCR amplification of bacteria
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