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Sources of Pollution in the Mataura Freshwater Management Unit

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Sources of Pollution in the Mataura Freshwater Management Unit Sources of Pollution in the Mataura Freshwater Management Unit May 2019 Dr Elaine Moriarty Dr Olga Pantos Dr Sarah Coxon Prepared with support from Nick Ward, Roger Hodson, Rob Williamson and Matt Couldrey from Environment Southland PREPARED FOR: Environment Southland CLIENT REPORT No.: CSC 19007 REVIEWED BY: Dr Brent Gilpin ACKNOWLEDGEMENTS Author Author Author Dr Elaine Moriarty Dr Olga Pantos Dr Sarah Coxon Senior Scientist, Senior Scientist, Scientist, Health and Environment Health and Environment Health and Environment Manager Peer reviewer Mr Wim Nijhof Dr Brent Gilpin Manager, Group Leader, Water and Biowaste Human and Ecological Health Research and Development DISCLAIMER The Institute of Environmental Science and Research Limited (ESR) has used all reasonable endeavours to ensure that the information contained in this client report is accurate. However, ESR does not give any express or implied warranty as to the completeness of the information contained in this client report or that it will be suitable for any purposes other than those specifically contemplated during the Project or agreed by ESR and the Client. Sources of Pollution in the Mataura Freshwater Management Unit i CONTENTS EXECUTIVE SUMMARY ......................................................................... 1 1. BACKGROUND ............................................................................... 4 1.1 MICROBIAL WATER QUALITY ........................................................................... 4 1.2 SOURCES OF POLLUTION AND ROUTES OF TRANSMISSION ..................... 5 1.2.1 Animal faeces .............................................................................................. 5 Cattle .................................................................................................................... 5 Sheep ................................................................................................................... 5 Other ruminants .................................................................................................... 6 Routes of transmission ......................................................................................... 6 1.2.2 Avian faeces ................................................................................................ 7 1.2.3 Human sources ........................................................................................... 8 1.3 FAECAL SOURCE TRACKING ............................................................................ 8 1.4 CAMPYLOBACTER ............................................................................................. 9 1.5 REPORT OBJECTIVES ....................................................................................... 9 2. MATERIALS AND METHODS ....................................................... 11 2.1 SAMPLING SITES ............................................................................................. 11 2.2 MICROBIOLOGICAL ANALYSIS ....................................................................... 13 2.2.1 Coliform and E. coli analysis ..................................................................... 13 2.2.2 Campylobacter isolation ............................................................................ 13 2.2.3 Campylobacter sub-typing and source attribution ..................................... 13 2.2.4 Faecal source tracking .............................................................................. 13 2.2.5 Faecal sterol analysis ................................................................................ 14 2.3 SANITARY SURVEYS ....................................................................................... 14 3. OVERVIEW OF MICROBIAL WATER QUALITY .......................... 15 3.1 OVERVIEW OF MICROBIAL WATER QUALITY IN THE MATAURA FMU ....... 15 3.2 SOURCES OF FAECAL POLLUTION ............................................................... 21 3.3 CHARACTERISATION OF CAMPYLOBACTER ................................................ 23 3.3.1 MBiT source attribution ............................................................................. 23 3.3.2 Genotype analysis and comparison with clinical isolates .......................... 24 4. DISCUSSION ................................................................................. 29 4.1 MICROBIAL SOURCES AND TRANSMISSION ................................................ 29 4.2 HEALTH RISK .................................................................................................... 30 Sources of Pollution in the Mataura Freshwater Management Unit ii 4.3 MANAGEMENT AND MITIGATION ................................................................... 33 4.3.1 Direct deposition ....................................................................................... 33 4.3.2 Indirect sources ......................................................................................... 34 4.3.3 Wildfowl ..................................................................................................... 34 4.3.4 Prioritising mitigations ............................................................................... 35 5. CONCLUSIONS ............................................................................. 36 ABBREVIATIONS ................................................................................. 37 GLOSSARY ........................................................................................... 38 APPENDIX A: MICROBIOLOGICAL METHODS AND REPORTING .. 40 A.1 COLIFORM AND E. COLI ANALYSIS ................................................................ 40 A.2 CAMPYLOBACTER SPP. ISOLATION .............................................................. 40 A.3 CAMPYLOBACTER SUB-TYPING AND SOURCE ATTRIBUTION BY MBIT ... 40 A.4 PCR MARKERS FOR FAECAL SOURCE TRACKING (FST) ........................... 41 A.5 FAECAL STEROL ANALYSIS............................................................................ 46 A.6 PRESENTATION OF RESULTS IN THIS REPORT .......................................... 46 APPENDIX B: SUBCATCHMENT-SPECIFIC INFORMATION AND MICROBIAL WATER QUALITY ..................................................... 50 B.1 MATAURA RIVER AT GORE ............................................................................. 50 B.2 MATAURA RIVER, 200M DOWNSTREAM OF MATAURA BRIDGE ................ 55 B.3 MATAURA RIVER AT MATAURA ISLAND BRIDGE ......................................... 60 B.4 WAIMEA STREAM AT MANDEVILLE ................................................................ 66 B.5 WAIKAIA RIVER AT WAIKAIA ........................................................................... 71 B.6 OTAMITA STREAM AT MANDEVILLE .............................................................. 76 B.7 WAIKAKA STREAM AT GORE .......................................................................... 81 B.8 NORTH PEAK STREAM AT WAIMEA VALLEY ROAD ..................................... 86 B.9 SANDSTONE STREAM AT KINGSTON CROSSING ROAD ............................ 91 B.10 LONGRIDGE STREAM AT SANDSTONE ......................................................... 96 B.11 MIMIHAU STREAM AT WYNDHAM ................................................................ 101 B.12 MOKORETA RIVER AT WYNDHAM RIVER ROAD ........................................ 106 B.13 OTERAMIKA STREAM AT SEAWARD DOWNS ............................................. 111 B.14 WAIKAWA RIVER AT PROGRESS VALLEY ................................................... 116 B.15 TOKANUI RIVER AT FORTROSE OTARA ROAD .......................................... 121 REFERENCES ..................................................................................... 126 Sources of Pollution in the Mataura Freshwater Management Unit iii LIST OF TABLES TABLE 1. SAMPLING SITES SELECTED FOR THE MATAURA FMU ................................ 11 TABLE 2. SUMMARY OF MBIT GENE TARGETS AND THEIR METHODOLOGIES. ........ 42 TABLE 3. SUMMARY OF PCR MARKERS USED IN THIS STUDY .................................... 45 TABLE 4. FAECAL STEROL RATIOS INDICATIVE OF FAECAL POLLUTION. ................. 47 TABLE 5. GUIDELINE FOR GENERAL DATA, MICROBIAL RESULTS AND MBIT INTERPRETATION ............................................................................................................... 48 TABLE 6. EXPLANATION OF PCR-BASED MARKERS ...................................................... 48 TABLE 7. EXPLANATION OF FAECAL STEROL RESULTS AND INTERPRETATION. ..... 49 TABLE 8. RESULTS FOR MICROBIAL AND FST ANALYSIS OF WATER SAMPLES COLLECTED FROM THE MATAURA RIVER AT GORE. .................................................... 51 TABLE 9. NUMBER OF CONSENTED CATCHMENT DISCHARGES TO LAND AND WATER IN THE CATCHMENT FOR THE MATAURA RIVER AT GORE SAMPLING SITE.54 TABLE 10. RESULTS FOR MICROBIAL AND FST ANALYSIS OF WATER SAMPLES COLLECTED FROM THE MATAURA RIVER, 200M DOWNSTREAM OF THE MATAURA BRIDGE. ............................................................................................................................... 56 TABLE 11. NUMBER OF CONSENTED CATCHMENT DISCHARGES TO LAND AND WATER IN THE CATCHMENT FOR THE MATAURA RIVER, 200M DOWNSTREAM OF THE MATAURA BRIDGE. .................................................................................................... 59 TABLE 12. RESULTS FOR MICROBIAL AND FST ANALYSIS OF WATER SAMPLES COLLECTED FROM THE MATAURA RIVER AT MATAURA ISLAND BRIDGE. ................ 61 TABLE 13. NUMBER OF CONSENTED CATCHMENT DISCHARGES TO LAND AND WATER IN THE CATCHMENT FOR THE MATAURA RIVER AT THE MATAURA ISLAND BRIDGE. ..............................................................................................................................
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