Physico-chemical and microbiological data of the Mooi River: A historical perspective HJ Potgieter orcid.org 0000-0002-0683-4183 Dissertation submitted in fulfilment of the requirements for the degree Master of Science in Environmental Sciences at the North- West University Supervisor: Prof CC Bezuidenhout Co-supervisor: Dr JJ Bezuidenhout Graduation May 2019 24133353 i Table of contents DECLARATION ................................................................................................................................... v ABSTRACT ........................................................................................................................................ vi LIST OF FIGURES ...............................................................................................................................vii LIST OF TABLES ..................................................................................................................................ix ABBREVIATIONS ................................................................................................................................ x CHAPTER 1 – INTRODUCTION ................................................................................................... 1 1.1 Background ........................................................................................................................... 1 1.2 Problem statement ............................................................................................................... 2 1.3 Aim and Objectives .............................................................................................................. 3 CHAPTER 2 – LITERATURE REVIEW ........................................................................................ 4 2.1 Aquatic ecosystems ............................................................................................................. 4 2.2 Freshwater ecosystems ....................................................................................................... 5 2.3 Water quality ......................................................................................................................... 6 2.3.1 Africa and developing countries ................................................................................... 6 2.3.2 South Africa.................................................................................................................... 6 2.4 Identifying the problem ......................................................................................................... 7 2.5 Water legislation in SA ......................................................................................................... 7 2.5.1 Ecological Reserve ........................................................................................................ 8 2.5.2 Integrated Water Resource Management (IWRM) ..................................................... 8 2.5.3 Integrated Water Quality Management (IWQM) ......................................................... 9 2.6 Land-use ............................................................................................................................. 11 2.6.1 Urbanisation ................................................................................................................. 11 2.6.2 Agriculture .................................................................................................................... 12 2.6.3 Erosion ......................................................................................................................... 13 2.6.4 Mining ........................................................................................................................... 13 2.7 Data mining ......................................................................................................................... 14 2.8 Data mining techniques ..................................................................................................... 16 2.8.1 Neural networks ........................................................................................................... 16 2.8.2 Evolutionary Algorithms .............................................................................................. 18 2.8.3 Association analysis .................................................................................................... 19 2.8.4 Grouping and clustering .............................................................................................. 19 2.8.5 Regression ................................................................................................................... 19 i 2.8.6 Classification ................................................................................................................ 19 2.9 Physico-chemical parameters ........................................................................................... 20 2.9.1. Physical-Chemical Parameters: Temperature ......................................................... 20 2.9.2 Physical-Chemical Parameters: pH (Acidity and Alkalinity) ..................................... 21 2.9.3 Physical-Chemical Parameters: EC (Electrical Conductivity) .................................. 21 2.9.4 Physical-Chemical Parameters: Sulphate ................................................................. 22 2.9.5 Physical-Chemical Parameters: Nitrate/Nitrite .......................................................... 22 2.9.6 Physical-Chemical Parameters: Phosphate .............................................................. 23 2.9.7 Physical-Chemical Parameters: Calcium .................................................................. 24 2.9.8 Physical-Chemical Parameters: Magnesium ............................................................ 24 2.9.9 Physical-Chemical Parameters: Sodium ................................................................... 24 2.9.10 Physical-Chemical Parameters: Fluoride ................................................................ 25 2.9.11 Physical-Chemical Parameters: Chloride ................................................................ 25 2.10 Microbial monitoring and community composition ......................................................... 26 2.11 Decision making ............................................................................................................... 27 2.11.1 Water Quality index/indices ...................................................................................... 27 2.11.2 GIS .............................................................................................................................. 28 2.12 Summary ........................................................................................................................... 29 CHAPTER 3 – MATERIALS AND METHODS ........................................................................... 30 3.1 Study sites ........................................................................................................................... 30 3.1.1 Mooi River .................................................................................................................... 31 3.1.2 Wonderfonteinspruit River .......................................................................................... 31 3.2 Physico-chemical data ....................................................................................................... 32 3.3 Simplified index ................................................................................................................... 32 3.4 Microbiological data ............................................................................................................ 35 3.4.1 16S rRNA gene amplification and MiSeq sequencing ............................................. 35 3.4.2 Data processing ........................................................................................................... 36 3.5 Statistical analysis .............................................................................................................. 36 3.6 Geospatial analysis ............................................................................................................ 37 CHAPTER 4 – RESULTS ............................................................................................................ 38 4.1 Characteristics of the water quality at the individual sites .............................................. 38 4.1.1 Site C2M11 .................................................................................................................. 38 4.1.2 Site C2M01 .................................................................................................................. 40 4.1.3 Site C2R01 ................................................................................................................... 43 ii 4.1.4 Site C2R04 ................................................................................................................... 44 4.1.5 Site C2R03 ................................................................................................................... 46 4.1.6 Site C2M30 .................................................................................................................. 48 4.1.7 Site C2M32 .................................................................................................................. 50 4.1.8 Site C2M63 .................................................................................................................