By Athi Nkosibonile Mfikili

Influence of sedimentological and hydrological processes on the distribution of the Spartina maritima salt marsh in the Keurbooms Estuary, Western Cape

Athi Nkosibonile Mfikili

Submitted in fulfilment of the requirements for the degree Magister Scientiae in the Faculty of Science, Department of Botany, Nelson Mandela Metropolitan University Port Elizabeth

April 2017

Supervisor: Dr Thomas G. Bornman

Co-supervisor: Dr Derek R. du Preez

I dedicate this thesis to my family,

especially my daughter Lukho Lunathi, this one is for you baby.

Also to my late grandmother Nomnceba Mfikili, mother Vuyokazi Mfikili and cousin sister Zukiswa Mfikili, you will always remain in my heart and I will never forget you.

Declaration In accordance with Rule G5.6.3 [of the Nelson Mandela Metropolitan University], I, Athi Nkosibonile Mfikili (student number: 208016013), hereby declare that the above-mentioned treatise/ dissertation/ thesis is my own work and that it has not previously been submitted for assessment or completion of any postgraduate qualification to another University or for another qualification.

…………………………. (Signature) Athi Nkosibonile Mfikili

Summary Salt marshes are some of the most productive ecosystems in the world and have been the centre of attention over the past few decades, due to their decline as a result of global climate change and anthropogenic impacts. The growth of salt marshes is determined by substrate type, soil conductivity and elevation. The permanently open Keurbooms Estuary along the south-east coast of South Africa is subjected to occasional fluvial flooding and its intertidal area lacks well developed salt marshes, with Spartina maritima restricted to the lower reaches of the Bitou tributary and a few sections of the Keurbooms tributary. Presumeably because of fine sediment habitat in the confluence and lower Bitou tributary. The salinity of the estuarine water ranges between 0.1 – 26.9 and 3.2 – 35.3 in the Bitou and Keurbooms tributaries respectively. A typical salt wedge salinity pattern is common in the Keurbooms tributary where saline water often intrudes underneath the freshwater, especially during high river flows. The following hypotheses were developed and tested in this study: The limited spatial distribution of S. maritima in the Keurbooms Estuary is due to limited availability of fine sediment habitat; and the source of the fine sediment in the estuary is the Bitou tributary rather than the Keurbooms tributary or the sea. It was further postulated that after sediment characteristics, floods are the major hydrological driver determining the distribution of S. maritima in the Keurbooms Estuary.

The results of the surveys of the estuarine channel bottom sediments showed that the Keurbooms tributary was mostly characterized by the sand-size sediment fraction derived from the feldspathic and sandstone with evidence of fine sediment fractions restricted to the upper reaches at the confluence with Whiskey Creek. The Bitou was almost always composed of coarse sized sediments in the upper reaches, fine sediment deposits in the middle and lower reaches and medium sorted sand with almost no clay or calcium carbonate in the estuarine component below the confluence of the tributaries. These findings were further supported by the surface sediment deposited within the S. maritima intertidal salt marsh, which showed finer sediment deposits in the Bitou marsh compared to the Keurbooms marsh surface. Similar results were also found in the sediment cores, with the Keurbooms marsh sediment becoming finer with increasing depth whereas fine sediments reduced with depth in the Bitou marsh. The results of the sediment mineralogy indicated that the increased concentrations of clay minerals in the S. maritima surface

ii sediments are derived from the Bokkeveld shale, siltstone and clay slate exposed above the N2 Bridge in the Keurbooms Estuary.

GIS mapping shows that S. maritima has been declining over the past two decades, with rapid decreases especially evident after big flooding events. The GIS mapping also indicates that the patches of the S. maritima in the Keurbooms tributary are more exposed to big floods than the Bitou marsh. Despite showing an overall decline, S. maritima area coverage remained more consistent in the lower reaches of the Bitou tributary than in the Keurbooms tributary. Despite the larger and more persistent area cover, the S. maritima plants were shorter and less dense than the plants growing in the sandy substrate. The black/grey colouration of soil with increasing depth in the Bitou tributary was an indication of the reduced state of the soil caused by prolonged waterlogged conditions. The roots of S. maritima in both tributaries were mostly restricted to the sub-surface substrate layer (i.e. 0 – 0.25 m), although the Bitou populations showed more vegetative propagation than the Keurbooms populations. This mechanism of reproduction was also demonstrated during the transplant experiment which showed a greater number of new stem production in the fine sediment substrates compared to the sandy silt substrates. Although accretion rates were not determined in this study, the short-term sediment deposition rates revealed that sedimentation is active in the marshes of the Keurbooms Estuary. Therefore, in spite of showing a decline in area cover, the production of viable seed and observed vegetative propagation suggest that the S. maritima is likely to colonize open stable intertidal mudflats / sandflats, thus maintaining its distribution as an intertidal species in the salt marshes of the Keurbooms Estuary.

Keywords: Keurbooms Estuary; sediment dynamics; flooding; salt marshes; Spartina maritima.

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Acknowledgements I would like to thank the Almighty God who gave me strength day-by-day to complete this work, Glory and praise to Him.

This has been a multi-disciplinary study and very challenging experience for me. I was fortunate enough to collaborate with various scientists from different disciplines and I believe my scientific skills and thoughts have through this process improved immensely.

I would like to give special thanks to my supervisor and mentor Dr Tommy Bornman for all the support and input. I am also grateful to Dr Derek du Preez (my co-supervisor) and Prof Maarten de Wit (collaborator/funder) for all their assistance and input.

This work could not have been possible if it was not for the financial support from SAEON Elwandle Node, AEON – ESSRI (Inkaba Ye-Africa) and NMMU Postgraduate scholarship. Thank you very much.

Special thanks to SAEON Elwandle Node staff for all their input, encouragement as well as assisting me on my intensive field trips, especially Tommy, Mfundo Bizani, Sean Bailey and Shaun Deyzel. I was fortunate enough to design the sampling sites and conduct all the field trips with your assistance, thank you very much. Special thanks to Arlene Cobb for all the administrative work required for all the field trips. Throughout my time at SAEON, whether in good times or tough times, I have always had the full support of the entire group. I want to acknowledge this superb group of people for always being there and for supporting me wholeheartedly.

I would also like to thank SAIAB staff for allowing me to use their equipment, especially Francois Lamont and Ryan Palmer.

To the Department of Botany staff and fellow students, I am grateful for all the assistance you gave me. Special mention to Andy Smith, Chan Visagie and Cynthia Tobias, thanks guys. Special thanks to Dr Paul-Pierre Steyn and Prof Janine Adams for all your input and encouragement.

Postgraduate research studies could be a very long and lonely journey, however it was not the case for me, thanks to my AEON friends. Special mention to Lucian, Thomas, Vhuhwavhohau, Abiel and Dr Bastien Linol, thanks guys for all your advice and encouragement and those nice braais.

I am also grateful to Willie (Technician at Department of Geosciences) for all his assistance. Special thanks to Mrs Megan Purchase from the Department Geology in the University of Free State for assisting me with mineralogy analysis. I am also indebted to the Department of Water and Sanitation for providing the flow data of the Keurbooms Estuary, special mention to Nolu Jafta. I am also grateful to the South African Weather Service for providing the weather data. I would also like to thank SANParks Garden Route for providing the Satellite aerial image of the Keurbooms Estuary.

To Mfundo and Phumlile thanks chaps for being there for me, I am grateful for all your assistance and encouragement. My fellow Postgraduate Students Villagers especially Kakuhle, Chinidu, and Ngcali thank you for your input and continued encouragement, you have also made my stay very fun in the village and to the PGSV Football Club, you guys really kept me going, thanks.

To my family, especially my special woman, my mother Sis Ndumi, you have been so patient with me I could not thank you enough, I owe you big time. I thank you for all your support and prayers. Lastly but not least, to my love Bomikazi and our daughter, Lukho thanks for your patience.

Table of Contents Declaration…...... i Summary…...... ii Acknowledgements ...... iv Table of Contents ...... vi List of Figures ...... x List of Tables ...... xv List of Plates ...... xvi Chapter 1. Introduction ...... 1 1.1 General overview ...... 1 1.2 Research aims ...... 2 1.3 Study approach ...... 3 Chapter 2. Literature review ...... 7 2.1 Estuaries ...... 7 2.1.1 Importance of estuaries ...... 8 2.1.2 South African estuaries ...... 9 2.1.3 Keurbooms Estuary ...... 10 2.2 Estuarine sediment dynamics ...... 11 2.2.1 Sedimentation in estuaries ...... 12 2.3 Salt marshes...... 14 2.3.1 Importance of salt marshes ...... 16 2.4 The Spartina salt marsh...... 17 2.4.1 Importance of Spartina spp...... 19 2.4.2 Spartina as an invasive species ...... 20 2.4.3 Spartina maritima (Curtis) Fernald ...... 20 2.4.4 Production of Spartina maritima ...... 21 2.4.5 Habitat requirements of Spartina maritima ...... 22 Chapter 3. Study site ...... 26 3.1 General description ...... 26 3.2 Estuary ...... 28 3.3 Geology ...... 29 3.4 Climate ...... 32

3.5 Socio-economic importance ...... 35 Chapter 4. Spatial and temporal distribution patterns of the bottom sediments of the Keurbooms Estuary ...... 36 4.1 Introduction ...... 36 4.2 Materials and methods ...... 37 4.2.1 Sampling site description ...... 37 4.2.2 Data collection ...... 38 4.2.3 Laboratory analysis ...... 40 4.2.4 Spatial interpolation analysis ...... 42 4.2.5 Statistical analysis ...... 42 4.3 Results ...... 43 4.3.1 Spatial variability of sand and mud distribution ...... 43 4.3.2 Variation in grain size distribution ...... 49 4.3.3 Sediment organic content ...... 60 4.3.4 Hydrographic conditions ...... 66 4.4 General discussion...... 72 4.5 Conclusion ...... 75 Chapter 5. Patterns of sediment deposition within the Spartina maritima salt marsh of the Keurbooms Estuary ...... 77 5.1 Introduction ...... 77 5.2 Materials and methods ...... 78 5.2.1 Site description...... 78 5.2.2 Measurement of sediment deposition ...... 80 5.2.3 Suspended sediment concentration ...... 81 5.2.4 Laboratory analysis ...... 82 5.3 Results ...... 85 5.3.1 Sediment deposition within S. maritima ...... 85 5.3.2 Organic matter deposited on sediment traps within S. maritima ...... 87 5.3.3 Suspended sediment concentration ...... 90 5.3.4 Surface sediment moisture content ...... 93 5.3.5 Surface sediment organic content ...... 95 5.3.6 Surface sediment particle size ...... 98 5.3.7 Sediment types ...... 101

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5.4 General discussion...... 104 5.5 Conclusion ...... 108 Chapter 6. Sediment mineralogy of the Keurbooms Estuary ...... 110 6.1 Introduction ...... 110 6.2 Materials and methods ...... 111 6.2.1 Site description...... 111 6.2.2 Sediment preparation ...... 114 6.3 Results ...... 117 6.3.1 Bottom sediments...... 117 6.3.2 Surface sediment within S. maritima salt marsh ...... 126 6.4 General discussion...... 136 6.5 Conclusion ...... 141 Chapter 7. Growth and distribution of Spartina maritima intertidal salt marsh in the Keurbooms Estuary ...... 142 7.1 Introduction ...... 142 7.2 Materials and methods ...... 143 7.2.1 Site description...... 143 7.2.2 GIS mapping ...... 146 7.2.3 S. maritima seed germination potential ...... 146 7.2.4 S. maritima plant growth...... 150 7.2.5 S. maritima transplant experiment ...... 154 7.2.6 Statistical analysis ...... 156 7.3 Results ...... 157 7.3.1 GIS mapping ...... 157 7.3.2 Seed germination ...... 164 7.3.3 S. maritima plant growth...... 166 7.3.4 Soil analysis ...... 172 7.3.5 Chlorophyll fluorescence of S. maritima ...... 177 7.3.6 S. maritima transplant experiment ...... 179 7.4 General discussion...... 183 7.5 Conclusion ...... 190 Chapter 8. General discussion and conclusion ...... 192 8.1 General discussion...... 192

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8.2 Conclusion ...... 196 References… ...... 197 Appendix 1… ...... 217 Appendix 2… ...... 225

List of Figures Figure 1.1: Flow chart indicating the processes and different stages followed in the study ...... 6 Figure 3.1: A map showing the location of the study, the Keurbooms Estuary ...... 27 Figure 3.2: The geological substrate of the Keurbooms Estuary (Source: Department of Mines, 1979)...... 31 Figure 3.3: Mean minimum and maximum temperatures for the Plettenberg Bay area over the last 12 years (2004 – October 2015) (Mean ± SE)...... 32 Figure 3.4: Mean monthly rainfall at Plettenberg Bay over the past 12 years (2004 – October 2015) (Mean ± SE)...... 33 Figure 3.5: Monthly rainfall at Plettenberg Bay for 2014 and 2015 compared to mean monthly rainfall (Mean ± SE, n = 12 years)...... 34 Figure 3.6: Monthly flow rates in the Keurbooms Estuary for 2014 and 2015 compared to mean monthly flood peaks for the past 12 years (Mean ± SE)...... 35 Figure 4.1: Sampling sites for the bottom sediment of the Keurbooms Estuary...... 38 Figure 4.2: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in June 2014...... 45 Figure 4.3: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in February 2015...... 46 Figure 4.4: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in September 2015...... 47 Figure 4.5: Ternary diagram showing primary sediment types occurring in the bottom sediments of the Keurbooms Estuary...... 49 Figure 4.6: Distribution pattern of (a) mean sediment grain size and (b) sorting in June 2014. . 52 Figure 4.7: Distribution pattern of (a) mean sediment grain size and (b) sorting in February 2015...... 53 Figure 4.8: Distribution pattern of (a) mean sediment grain size and (b) sorting in September 2015...... 54 Figure 4.9: The correlation between mean size and sorting of June 2014 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary...... 57 Figure 4.10: The correlation between mean size and sorting of February 2015 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary...... 58

Figure 4.11: The correlation between mean size and sorting of September 2015 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary...... 59 Figure 4.12: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in June 2014...... 61 Figure 4.13: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in February 2015 ...... 62 Figure 4.14: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in September 2015 ...... 63 Figure 4.15: Sediment organic matter content in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary (Mean ± SE, n = 3)...... 65 Figure 4.16: Flow rate of the Keurbooms tributary recorded on selected days in (a) June, September and October 2014, (b) February, April and June 2015, and (c) July and August 2015...... 67 Figure 4.17: Contour plots showing salinity measured in the lower reaches and Keurbooms tributary...... 69 Figure 4.18: Contour plots showing temperature measured in the lower reaches and Keurbooms tributary...... 71 Figure 5.1: Locality map showing sediment deposition and suspended sediment study sites. ... 79 Figure 5.2: Sediment deposition within the S. maritima in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE, n = 3)...... 86 Figure 5.3: Overall sediment deposition within the S. maritima (Mean ± SE; n = 15)...... 87 Figure 5.4: Organic matter deposited on sediment traps within the S. maritima in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE; n = 3)...... 88 Figure 5.5: Overall organic matter deposited within the S. maritima (Mean ± SE; n = 15)...... 89 Figure 5.6: Correlation between organic matter and sediment deposited on the traps within S. maritima...... 89 Figure 5.7: Suspended sediment concentration in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE; n = 3)...... 91

Figure 5.8: Secchi depth recorded in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide...... 92 Figure 5.9: Overall suspended sediment concentration of the Keurbooms Estuary at the three sources (i.e. Mouth, the Bitou and Keurbooms tributaries) (Mean ± SE; n = 5)...... 93 Figure 5.10: Sediment moisture content of surface sediment deposited during Sept 2014 spring- tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap-tide (Mean ± SE; n = 3)...... 94 Figure 5.11: Overall mean moisture content for S. maritima surface sediment (Mean ± SE; n = 15)...... 95 Figure 5.12: Sediment organic content of surface sediment deposited during Sept 2014 spring- tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap-tide (Mean ± SE; n = 3)...... 97 Figure 5.13: Overall organic matter content for S. maritima surface sediment (Mean ± SE; n = 15)...... 98 Figure 5.14: Sediment particle size deposited on the S. maritima surface during Sept 2014 spring-tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap- tide (Mean, n = 3)...... 100 Figure 5.15: Overall mean sediment particle size deposited on the S. maritima marsh surface (Mean, n = 15)...... 101 Figure 5.16: Ternary diagram showing primary sediment types occurring in the surface sediment of S. maritima stands...... 103 Figure 6.1: Locality map showing both channel bottom and S. maritima surface sediment study sites used to determine sediment mineralogy...... 113 Figure 6.2: XRD peaks showing minerals of estuarine bottom sediments at site K3 in the mouth of the estuary during September 2015 ...... 120 Figure 6.3: XRD peaks showing minerals of estuarine bottom sediments at site K22 in the Keurbooms tributary during June 2014...... 122 Figure 6.4: XRD peaks showing minerals of estuarine bottom sediments at site B6 in the Bitou tributary during (a) June 2014 and (b) September 2015...... 125 Figure 6.5: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 2 in the Bitou tributary during September 2015...... 129

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Figure 6.6: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 4 in the Bitou tributary during September 2014...... 131 Figure 6.7: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 6 in the Keurbooms tributary during September 2015...... 133 Figure 6.8: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 8 in the Keurbooms tributary during February 2015...... 135 Figure 7.1: Locality map showing the S. maritima are coverage and sediment cores sites...... 144

Figure 7.2: Pre-experiment chlorophyll fluorescence (FV/FM) of S. maritima plants (Mean ± SE)...... 153 Figure 7.3: Vegetation and habitat map of the Keurbooms Estuary in 1998...... 160 Figure 7.4: Vegetation and habitat map of the Keurbooms Estuary in 2008...... 161 Figure 7.5: Vegetation and habitat map of the Keurbooms Estuary in 2011...... 162 Figure 7.6: Vegetation and habitat map of the Keurbooms Estuary in 2004 (from Bornman & Adams 2006)...... 163 Figure 7.7: Number of seeds germinated at different salinity treatments over a period of 16 weeks...... 165 Figure 7.8: S. maritima shoot height and root length in the Keurbooms Estuary (Mean ± SE, n = 9)...... 167 Figure 7.9: Correlation between S. maritima plant root length and shoot height...... 168 Figure 7.10: Above-ground and below-ground biomass production of S. maritima in the Keurbooms Estuary (Mean ± SE, n = 9)...... 170 Figure 7.11: Correlation between S. maritima plant above-ground and below-ground biomass...... 171 Figure 7.12: Total biomass production S. maritima in the Keurbooms Estuary (Mean ± SE, n = 9)...... 171 Figure 7.13: Mean soil particle size of the sediment cores collected from selected S. maritima population in the Keurbooms Estuary (n = 3)...... 174 Figure 7.14: Soil moisture content of the sediment cores in the Keurbooms Estuary Mean ± SE, n = 3)...... 175 Figure 7.15: Soil organic content of the sediment cores in the Keurbooms Estuary (Mean ± SE, n = 3)...... 176

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Figure 7.16: Chlorophyll fluorescence (FV/FM) of S. maritima plants at five sites in the Keurbooms Estuary (Mean ± SE; n = 9)...... 178

Figure 7.17: Chlorophyll fluorescence (FV/FM) of S. maritima recorded hourly at site Spar 1 during the incoming tide (Mean ± SE; n = 9)...... 178 Figure 7.18: Stem height of S. maritima plants in different soil treatments (Mean ± SE; n = 4)...... 181 Figure 7.19: The number of produced stems in the different soil treatments (Mean ± SE)...... 182 Figure 7.20: The number of dead stems in different soil treatments (Mean ±SE)...... 182 Figure 8.1: Flowchart indicating the distribution and growth of S. maritima in the Keurbooms Estuary...... 195 Figure A.1.1: Contour plots showing water salinity measured in the selected Bitou tributary sites...... 223 Figure A.1.2: Contour plots showing water salinity measured in the selected Bitou tributary sites...... 224 Figure A.2.1: XRD peaks showing minerals of estuarine bottom sediments at site K3 in the mouth of the estuary during (a) June 2014 and (b) February 2015...... 228 Figure A.2.2: XRD peaks showing minerals of estuarine bottom sediments at site K22 in the Keurbooms tributary during (a) September 2014 and (b) September 2015...... 230 Figure A.2.3: XRD peaks showing minerals of estuarine bottom sediments at site B6 in the Bitou tributary of the estuary during February 2015...... 231 Figure A.2.4: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 2 in the Keurbooms tributary during (a) September 2014 and (b) February 2015...... 235 Figure A.2.5: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 4 in the Keurbooms tributary during (a) February 2015 and (b) September 2015...... 237 Figure A.2.6: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 6 in the Keurbooms tributary during (a) September 2014 and (b) September 2015. ... 239 Figure A.2.7: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 8 in the Keurbooms tributary during (a) September 2014 and (b) September 2015. ... 241

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List of Tables Table 5.1: Primary sediment types found in the surface sediment deposited on the S. maritima marsh surface...... 102 Table 6.1: Sediment mineral species found in the estuarine bottom sediment of the Keurbooms Estuary...... 118 Table 6.2: Sediment mineral species found in the S. maritima surface sediment...... 127 Table 7.1: Area cover of different habitat and vegetation units of the Keurbooms Estuary over time...... 159 Table 7.2: Final seed germination (%), days to first and last germination and mean daily germination of S. maritima at different salinity treatments...... 164 Table 7.3: Mean plant height, root length, above-ground and below-ground biomass of S. maritima clumps in the Keurbooms Estuary (Mean = ± SE)...... 166 Table 7.4: Mean sediment characteristics of sediment collected in the S. maritima study sites at depth intervals (0 – 0.25 m, 0.5 – 0.75 m and 1.0 – 1.25 m herein referred to as top, middle and bottom soil) in the Keurbooms Estuary (mean ± SE; n = 3)...... 173 Table 7.5: Potential quantum yield of S. maritima plants...... 177 Table 7.6: Mean sediment characteristics of sediment used in the transplant experiment of the S. maritima. (Mean ± SE; n = 4)...... 179 Table 7.7: Mean S. maritima plant height, stem production and mortality of the transplant experiment (Mean ± SE)...... 181 Table A.1.1: Grain size parameters for each site in June 2014...... 218 Table A.1.2: Grain size parameters for each site in February 2015...... 219 Table A.1.3: Grain size parameters for each site in September 2015...... 220

List of Plates

Plate 4.1: Cone dredge sampling off the research vessel in the Keurbooms Estuary...... 39 Plate 4.2: Physico-chemical measurements taken from the research vessel (a) and from land (b)...... 40 Plate 4.3: Sediment washing to remove salt...... 41 Plate 5.1: Mouth of the estuary during high tide in April 2015...... 80 Plate 5.2: Sediment trap deployed on the intertidal S. maritima marsh surface...... 81 Plate 6.1: Sandflats at site Spar 6 in the Keurbooms tributary opposite the confluence. Note the sandbanks adjacent to the S. maritima stands...... 114 Plate 6.2: Operating the PANalytical Empyrean machine...... 115 Plate 7.1: S. maritima marsh on a muddy substrate at site Spar 4 in the Bitou tributary...... 145 Plate 7.2: Tall S. maritima stands on the sandy substrate at site Spar 6 in the Keurbooms tributary...... 145 Plate 7.3: Field GIS mapping of S. maritima using a GPS and ArcPad 7 software...... 146 Plate 7.4: Seed spikes on S. maritima...... 148 Plate 7.5: S. maritima seed germination experiment set up...... 149 Plate 7.6: Germinated S. maritima seeds on the filter paper...... 149 Plate 7.7: S. maritima plant collected by hand...... 150 Plate 7.8: S. maritima below-ground and above-ground wet biomass...... 152 Plate 7.9: S. maritima plant with leaf clip...... 154 Plate 7.10: S. maritima transplant experiment set-up in different textural soils...... 156 Plate 7.11: Germinated seeds at the 15 salinity treatment showing retarded growth after 101 days...... 165 Plate 7.12: Non-germinated seeds after 111 days at the 55 salinity treatment...... 166 Plate 7.13: S. maritima plant (a) produced from long rhizome and (b) plant attached on dead rhizome...... 169

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Chapter 1. Introduction

1.1 General overview Coastal salt marshes are some of the most productive ecosystems in the world, in terms of biodiversity and biological productivity (Duarte et al, 2009) and play a significant role also in coastal defence through coastal sedimentation (Marchant, 1967; Neumeier & Ciavola, 2004). Their occurrence is largely controlled by the coastal physiography and they are mostly restricted to relatively low-energy environments (Allen & Pye, 1992). Numerous researchers (Adams & Bate, 1995; Reaper, 1995; Tolley, 1996; Boorman, 2003; Bornman et al. 2008; Hampel, 2003; Vromans, 2010; Bezuidenhout, 2011) have linked the development and distribution of salt marshes to several environmental drivers such as climate, tidal exchange, fresh water inflow, water column salinity, temperature, sedimentation, groundwater, elevation, sediment moisture, sediment organic content and sediment conductivity. Substrate type is one of the most important environmental drivers influencing salt marsh vegetation distribution. Bornman et al. (2004) showed that soil texture plays an important role in seed germination, seedling establishment, root growth and the distribution of salt marsh vegetation along the west coast of South Africa.

Salt marshes are particularly sensitive to changes in sea levels (Day et al. 1999). Sea level has been rising for centuries and the rate of sea level-rise has been anticipated to increase as a result of global warming (IPCC, 2002). It has been reported by Whitfield (1992) that the average sea surface temperature will increase between 2 to 6°C while sea-level will rise by about 0.2 to 1.6 m in the next 100 years due to global climate change. Along the South African coastline, the sea levels have been rising by 1.87 mm/y along the west coast, 1.48 mm/y along the south coast and by 2.74 mm/y along the east coast (Mather et al. 2009). These substantial rise in sea-level will negatively impact on salt marshes and mangroves (Nichols, 2010; Bornman et al. 2016).

Salt marshes develop through sedimentation and their continued existence in the face of global sea level rise is dependent on constant sediment supply from the sea and the river (Stock, 2011). Salt marshes are known to migrate vertically and horizontally in response to sea-level rise. However, Primack (2010) stresses that the rate and extent to which sea-levels are rising may prohibit many species from adjusting to accelerated water levels or from migrating quickly enough. This is often the case for salt marshes where the perimeter is blocked by human developments such as coastal settlements, roads and other hard infrastructure. As the marsh surface elevation declines relative

1 to sea-level, vegetation will undergo a series of changes before it is eventually converted to mud/sandflats due to vegetation die-off (Day et al. 1999). To prevent drowning/flooding, salt marshes must receive continuous sediment input at a rate such that surface elevation gain is sufficient enough to offset the rate of water level rise (Cahoon et al. 1995). Furthermore, impoundments upstream of the estuaries are likely to reduce sediment supply to the estuarine marshes, making the estuaries more dependent on periodic flooding for riverine sediment input.

In South Africa, salt marshes occur only in certain estuaries and in distribution covering an area of approximately 17 000 ha (Adams et al. 1999; Colloty et al. 2002a & b; Veldkornet et al. 2015). A recent study by Schmidt (2013) on the salt marsh distribution of three South African estuaries (i.e. Swartkops, Kromme and Knysna) showed an extensive decrease in area covered by salt marshes. Therefore, the current status of salt marsh area cover in South Africa may have been reduced drastically, mostly as a result of development. The Keurbooms Estuary, in particular, lacks well developed intertidal areas and as a result salt marshes are not extensive and Spartina maritima is limited only to the lower Bitou tributary and the confluence, covering an area of approximately 7.078 ha (Bornman & Adams, 2006). In general, growth of salt marshes is determined by substrate type, soil conductivity and elevation (Reaper, 1995; Bornman et al. 2008; Vromans, 2010; Bezuidenhout, 2011)

It is postulated that the limited distribution of S. maritima in the Keurbooms Estuary is as a result of sediment type, which is largely sand. S. maritima is one of the important primary producers in permanently open estuaries and serves as a sediment trapper for suspended sediment brought in by the daily tides. The sediment entrapment by S. maritima will result in an elevated marsh surface, an action required by coastal salt marshes if they are to keep pace with the predicted rise in sea level.

1.2 Research aims The sedimentary environment of the Keurbooms Estuary has drawn the attention of scientists over the past few decades (Fromme, 1985; Reddering, 1981, 1993 & 1999, Reddering & Rust, 1985, 1988, 1990 & 1994; Huizinga & Slinger, 1999), but the influence of the sediment dynamics of the estuary on the distribution of salt marshes, particularly S. maritima, remains poorly understood. Therefore, the overall aim of this study was to examine the importance of sediment and

2 hydrodynamics on the distribution of the S. maritima salt marsh within the Keurbooms Estuary and further to determine how S. maritima is likely to respond to predicted sea-level rise.

The following hypotheses were developed and tested during the study:

 The limited spatial distribution of S. maritima in the Keurbooms Estuary is due to limited availability of fine sediment habitat;  Fine sediment load in the Keurbooms Estuary comes from the Bitou tributary rather than from the Keurbooms tributary or the sea;  After sediment characteristics, floods are the major hydrological driver determining the distribution of S. maritima.

Specific objectives of the study were:

 To examine sediment distribution of both the Bitou and Keurbooms tributaries (Chapter 4);  To quantify the current sediment load from the following three sources: Keurbooms, Bitou and the sea (Chapter 5);  To determine the importance of each source in terms of sediment load (Chapter 5);  To examine sediment characteristics of the S. maritima salt marsh (Chapter 5);  To examine sediment mineralogy of the estuary (Chapter 6)  To assess the spatial distribution of S. maritima, Zostera capensis, sand and mud banks over time (Chapter 7);  To examine the growth and germination success of S. maritima under different conditions (Chapter 7).

1.3 Study approach The procedure that was followed to examine the influence of sediment and hydrological dynamics on the distribution of S. maritima during this study is explained below and illustrated in the flow diagram in Figure 1.1.

Sediment dynamics is one of the main controlling factors in an estuarine ecosystem (Cunha & Dinis, 2002). The Keurbooms Estuary provides unique sedimentological attributes that will contribute to the understanding of the research topic. The vegetation mapping of the Keurbooms Estuary by Bornman & Adams (2006) indicated that the S. maritima species is restricted mostly to the confluence and Bitou tributary and only covers an area of 7.078 ha in extent. The initial hypothesis developed at the start of this study was that the limited distribution of S. maritima in the Keurbooms Estuary is due to the limited availability of fine sediment habitat in the estuary. Estuaries are known as areas of continuous sedimentation from both marine and riverine sources (Dyer, 1972; Kamaruzzaman et al. 2002; Waznah et al. 2010). The estuarine bottom is important as it may be a source of sediment deposited in the intertidal salt marsh surface as a result of sediment reworking and resuspension, but Burns (1965) suggests that it is unlikely that the bottom itself acts as a source of new sediment in estuaries. Therefore, to understand the importance of both the bottom and suspended sediment characteristics when studying the influence of the sedimentary and hydrological dynamics on the salt marshes, chapter 4 investigated the estuarine bottom sediment distribution of the Keurbooms Estuary.

Spartina maritima is abundant in the confluence and the lower Bitou tributary rather than the Keurbooms tributary. It was then further hypothesised that the fine sediment load in the Keurbooms Estuary comes from the Bitou tributary and not the Keurbooms tributary or the sea. The in situ sediment deposition experiments and surface sediment within S. maritima salt marsh and suspended sediment load from three sources (i.e. the Bitou, Keurbooms tributaries and the sea) were investigated in Chapter 5. However, data analysis and field observations suggest that none of the three sources are the primary source of fine sediment onto the S. maritima marsh surface. To further determine the sediment source of the sediment deposited in the S. maritima intertidal salt marsh surface, selected estuarine channel bottom and S. maritima surface sediments were examined for sediment mineral composition (Chapter 6).

The historical and current distribution of Spartina maritima salt marsh in the Keurbooms Estuary was investigated using a series of GIS maps of historical and recent aerial images to determine whether it is expanding or declining. The results indicate that the S. maritima was declining since 1998 until 2011. Based on field observations and GIS mapping, it appears that sediment and episodic events influence the distribution of the S. maritima in the Keurbooms Estuary. Therefore,

4 in order to ascertain the influence of sediment dynamics on the growth and distribution of S. maritima in the Keurbooms Estuary, sediment cores and plant biomass (i.e. both below- and aboveground) were examined in selected S. maritima stands. S. maritima is the first intertidal salt marsh species found from the water channel in permanently open estuaries and is subjected to twice daily tidal inundation and would therefore be particularly sensitive to prolonged seawater submergence. S. maritima plant stress was examined (adults and seeds) to further determine its response to the predicted rising sea-levels and the resultant increases in inundation and water column salinity.

Research problem: Main hypothesis: GIS Maps Spartina maritima is not Limited distribution of S. extensive in distribution in the maritima is due to limited Keurbooms Estuary availability of fine sediment habitat.

There is progressively finer sediment deposition in the Bitou tributary than the Keurbooms tributary Second hypothesis: Chapter 4: Fine sediment come from the Spatial and temporal distribution Bitou rather than the Keurbooms of bottom sediment of the tributary or the sea. Keurbooms Estuary

None of the tributaries or the sea seem to ?

Chapter 5: transport fines to S. However, surface sediment deposited within S. maritima Patterns of sediment deposition maritima marsh surface suggest predominance of silty within S. maritima sediments. But what is the source of these silty sediments?

Floods are the major hydrological driver determining S. maritima dustribution.

Chapter 7: Chapter 6: Growth and distribution of S. Sediment mineralogy of the maritima salt marsh in the Keurbooms Estuary Keurbooms Estuary

Predicted response of S. maritima to sea level rise using data collected during this study

Figure 1.1: Flow chart indicating the processes and different stages followed in the study

Chapter 2. Literature review

2.1 Estuaries There are many ways in which estuaries have been defined for example (Pritchard, 1967; Day, 1981; Dalrymple et al. 1992; Whitfield, 1992). In general, they have been defined as transitional areas between river environments and ocean environments, where river freshwater meets with saline seawater (Whitfield, 2001; Elliot and McLusky, 2002; Adams, 2004) with a dominance of fine sedimentary materials (McLusky, 1981). There are more than 40 definitions of what an estuary is (Perillo, 1995) but there is still no clear definition that covers all the characteristics of estuaries. The definition by Pritchard (1967) has, for many years, been the most widely used, i.e. “a semi- enclosed coastal body of water which has a free connection with the open sea and within which sea water is measurably diluted with fresh water derived from land drainage.” Although this definition has been the most widely used worldwide, it has been criticized for excluding marine inlets and lagoons without freshwater inflow and those estuaries that are temporarily cut-off and without a free connection to the open sea. Alternatively, new definitions of “estuary” have been proposed by various scientists (Day, 1981; Dalrymple et al. 1992; Perillo, 1995; Wolanski, 2007 and Bird, 2008). Although the definition by Pritchard (1967) has been the most widely used, in a southern African context most estuaries do not have a ‘free connection’ with the sea. Thus, the definition provided by Day (1981) is more commonly accepted and used. Day (1981) defined an estuary as a ‘partially enclosed coastal body of water, which is either permanently or periodically open to the sea and within which there is [significantly] variability of salinity due to the mixture or interaction of sea water with fresh water derived from land drainage.’ This definition implies that an estuary may become temporarily closed and separated from the open ocean and mouth opening largely depends on flooding and/or strong tidal currents.

In sedimentological context, Dalrymple et al. (1992) and Bird (2008) define an estuary as “a seaward part of a drowned valley system subject to tidal fluctuations which receives sediment from both fluvial and marine sources”. Mixture or interaction of sea water with fresh water is the key element of estuarine hydrodynamics (Masselink & Hughes, 2003) and is largely influenced by tidal mechanisms and river flow, and tidal mixing can sometimes be influenced by wind waves, causing considerable erosion. While seawater and river freshwater mix as a result of tidal action

7 and river flow, both marine and fluvial sediment are transported from the sea and the river into the estuary (Dyer, 1997).

Many of South Africa’s estuaries developed during the Holocene period when the coastal river valleys were flooded when the sea-level began to rise 10 000 to 12 000 years ago (Day, 1981). They are still continually evolving, changing their shape, adapting to changes in river flow and to weather patterns (Dyer, 1997) and are particularly affected by the geomorphological and sedimentological changes continuously occurring within or/and around them. Their present position and future evolution largely relies on the variations in sea-level, sediment supply and structural activity, while geomorphologic evolution and biological conditions of the upper reaches is heavily dependent on tidal dynamics, even though the saline seawater may not reach that far upstream (Perrillo, 1995).

2.1.1 Importance of estuaries Estuaries have ecological, social, economic and recreational importance (Colloty et al. 2000a). They have a wide range of forms, each of which has developed as an interaction between riverine and marine processes and constrained by the land. Estuaries are considered among the most productive ecosystems in the world (McLusky, 1981; Martin, 1991; Barbier et al. 2011), but extremely fragile and are easily disturbed by anthropogenic activities (Tyson, 1988). The world’s population is presently living along the coastal areas is increasingly expanding (Wolanski, 2007). As a result, coastal ecosystems and the services they provide are adversely affected by a wide range of human activities such as water quality degradation, destruction of wetlands, overfishing and trawling, deforestation, overgrazing and other poor farming practices, as well as roads, which increase soil erosion and the sediment load in rivers (Wolanski, 2007). It has been further reported that about 50% of salt marshes, 35% of mangroves and 30% of coral reefs and seagrasses are either lost or degraded worldwide as a result of human activities (Waycott et al. 2009; Barbier et al. 2011; Curado et al. 2012; Doney et al. 2012). The loss of biodiversity and ecosystem function in estuarine systems will affect their social, economic and recreational importance, as it would reduce their nursery function, ability to sequester carbon, wastewater treatment and their ability to protect coastal areas against flooding and storm events (McLusky, 1981; Neumeier & Ciavola 2004; Wolanski, 2007).

2.1.2 South African estuaries In general, estuaries have been classified according to their sedimentation, geomorphology, physiography, hydrography, tidal and salinity characteristics (Kennish, 1986). However, in South Africa, estuaries have been classified based on their physiographic, hydrographic and salinity characteristics (Whitfield, 1992). South Africa has approximately 250 functional estuaries (Whitfied, 1998, Adams, 2004). Moreover, Whitfield & Baliwe (2013) identified 41 dysfunctional estuarine systems and approximately 108 extremely small systems connected to the sea but they make very little or no contribution to the overall estuarine biota of the South African estuaries and as a result were not included as functional estuaries of South Africa. South African estuaries are classified into five main types namely: permanently open, temporarily open-closed, river mouths, estuarine lakes and estuarine bays. These estuaries fall within three broad biogeographic regions namely: subtropical, warm-temperate and cool-temperate (Whitfield, 1998; De Villiers & Hodgson, 1999 and Whitfield & Baliwe, 2013). Classification of South African estuaries is dependent largely on where they are situated, i.e. climate of the region but individual systems have changed from one estuarine type to another as a result of anthropogenic influences, e.g. Richards Bay (Whitfield, 1992 & 2001).

According to Day (1981) all South African estuaries occupy river valleys that have become inundated following the most recent sea-level rise. These valleys were filled with sediment and range between youthful and mature stages. Estuaries in South Africa are relatively small in size and shallow with a maximum tidal range of about 2 m between spring high and low tide and may be subject to mouth closure throughout the year. Approximately 70-80% of South Africa’s estuarine systems are temporarily cut-off from the open sea and less than 30% are permanently open to the sea (Whitfield, 1998; Adams, 2004). Temporarily closed estuaries are particularly small compared to permanently open estuaries, and as a result are often blocked off from the sea for varying lengths of time by the sand bars at the mouth (Whitfield, 1998). Closure of South African estuaries are often due to extended periods of dry weather that result in reduced river flow. The influence of the climate is exacerbated by further reductions in river flow due to freshwater abstraction and the construction of dams in the catchment areas of rivers (Whitfield, 1998; Schumann et al. 1999). Furthermore, waves are known to carry marine sediment into estuaries, which are then moved by the incoming/flood tide either into or out of the estuary (Bell et al. 2000). The sediment may settle out as it enters the estuary to form sandbars in the mouth area. However,

9 the effect of waves in determining mouth closure, depends on their intensity, height and period (Schumann et al. 1999). During storm surges, large amounts of sediment can be stirred up in the entrance of estuaries, which can then be moved further into the estuary by the incoming tide, while inside the estuary, smaller waves can scour sediments off the shallow intertidal banks (Theron, 2007; Reddering, 1999). Periodic floods are particularly important to keep the mouth of temporarily closed estuaries open but constrictions caused by road bridges make it difficult for the floods to exercise their function of naturally scouring the sand bars away to keep the mouth open (Whitfield, 1998).

Despite their physical variability, estuaries in South African are still considered one of the country’s most important national assets. They are important for a number of reasons, including ecological, social, recreational and economic purposes (McLusky, 1981; Colloty et al. 2000a; Barbier et al. 2011; van Niekerk & Turpie, 2012). However, their importance, particularly ecological, is threatened by anthropogenic activities and at present there is no pristine estuarine system in South Africa. Estuaries such as Baakens, Ngqurha and Sipingo that were previously functional, are now drastically altered due to canalization, industrialization and urbanization and require rehabilitation to restore their ecological function (Whitfield & Baliwe, 2013).

2.1.3 Keurbooms Estuary The Keurbooms Estuary is one of the few permanently open estuaries along the South African coastline. It was formed during the Pleistocene marine regression and is underlain by poorly consolidated Cretaceous sediment (Duvenage & Morant, 1984). The permanently open Keurbooms Estuary with a floodplain from the Kromme Estuary towards the Knysna Estuary and consists of two tributaries, the Bitou and Keurbooms channels that merge approximately 3.5 km from the mouth. However, these channels differ from each other in terms of physical characteristics, which result in different vegetation communities, sediment and hydrological dynamics. In terms of biological diversity importance, it is ranked 18th from approximately 256 functional South African estuaries (Turpie, 2004).

The Keurbooms channel flows through a steep, often deep forested gorge upstream with no floodplain above the N2 Bridge and as a result, salt marsh vegetation is limited to the confluence with the Bitou, below the N2 Bridge. On the other hand, the Bitou is characterized by a shallow 10 channel and extensive floodplain and as a result, salt marshes are abundant. Although their geomorphological characteristics differ, both channels are classified as blackwater systems because they drain fynbos vegetation that stain the water a dark brown/black. In general, blackwater systems are smaller and are characterized by slow-moving and darkly stained water with less developed floodplain areas that result in a low concentration of suspended sediment (Ross et al. 2004; Utley et al. 2008). Dark, tea-coloured water is attributed to leaching of decaying vegetation leaves and root matter rather than the colour of the soil. Although some rivers that flow through areas of dark-black loam soil have a blackwater colour, they are not considered blackwater systems because the colour of the water is due to the colour of the soil and are referred to as black- mud rivers / estuaries (Ross et al. 2004).

Floodplain areas are important estuarine habitat as they are inundated during flood events and often determine the sediment texture and amount of suspended sediment load (Reed, 1989; Cooper, 1993; Culberson et al. 2004). However, the catchment of the river has a major influence on the nature and quantity of suspended sediment concentration (Ross et al. 2004). Alluvial streams tend to be much larger and have high suspended sediment concentrations, whereas blackwater systems tend to be smaller with less developed floodplains and as a result are characterised by a reduced suspended sediment concentration, often with a high organic content (Ross et al. 2004; Utley et al. 2008). Duvenage & Morant (1984) suggested that the Bitou tributary has a fine-grained sediment with high suspended sediment load compared to the Keurbooms tributary that drains medium to coarse-grained quartzite sand with often a low suspended sediment concentration.

2.2 Estuarine sediment dynamics South African estuaries in their present form were developed during the last Pleistocene Ice age when the rivers and glacial valleys were flooded as the sea-level rose by about 100 metres 10 000 years ago and stabilized about 6000 years ago (Dyer, 1979; Bell et al. 2000). Although most estuaries have kept pace with the gradual inundation, many are still slowly adjusting to the new equilibrium by filling up with sediment. Whether an estuary has been filled-up with sediment or remained deep depends largely on the balance between sediment entering and sediment leaving the estuary (Bell et al. 2000). Sedimentary material is transported into the estuary from both the river and the sea while in some it instances may be washed and blown off from the surrounding

11 land. Organic matter is also considered one of the important sources of sediment but it contributes very little to the total sediment in South African estuaries (Cooper et al. 1999). Although fine sediment deposits are a characteristic feature of estuaries, estuarine sediments are composed of both fine-grained (herein referred to as mud or silt and clay, i.e. those < 63 µm) and coarse-grained (i.e. sand size sediments, those > 63 µm but < 2000 µm), are derived from different sources (Dyer, 1972; Dyer 1986). Sediment movement into and within the estuary is closely related to circulation patterns of the water column (Dyer, 1972). Marine sediment is mainly transported into the estuaries by means of tidal flow, sometimes in conjunction with wave action, while fluvial sediments rely mainly on river flow. However, Theron (2007) emphasized the importance of processes such as wind action and wave over wash in transporting marine sediment directly into the estuary and that tidal flow through the mouth is not necessarily required to facilitate these sediment inputs.

For the most part, estuarine sediments are often made up of terrigenous rock while organic detritus, plants, worms, sea shells are often found if they are of marine origin (Theron, 2007). However, Luternauer et al. (1995) stresses the difficulty to characterise whether the deposited sediment is dominantly marine or riverine since the initial source estuarine sediment is mostly believed to be from riverine waters of the estuary. Present estuaries are mainly floored by recent sediments and their deposition and reworking is more active than the erosion of older rocks in the catchments (Dyer, 1972). As the marine processes of waves and tides rework and redistribute the estuarine sediment it makes it very difficult to determine whether deposited sediment was supplied directly from a riverine or marine source.

2.2.1 Sedimentation in estuaries Estuaries and rivers are often considered as regions of high sedimentation, serving as traps for minerals from inland sources that are transported seaward by rivers, and materials from the ocean transported landward by tidal flow and waves (Kamaruzzaman et al. 2002; Waznah et al. 2010). The study of estuarine sedimentation is complex due to the fact that the main sources of sediment deposited in estuaries are generally from outside of the estuary (Dyer, 1972). For instance, fine sediments in Breton estuaries come from the banks of the estuary, while in selected estuaries in New Zealand, Loire (France), Vigo (Spain) and Apalachicola (USA), the rivers are the main source of clay (McLusky, 1981; Bell et al. 2000). However, whatever the source of the sediments might

12 be, their deposition and distribution within the estuary is largely determined, amongst others, by the grain size characteristics, particularly particle size, and the hydrological dynamics (i.e. speed of the tidal currents and river flow) responsible for transporting the sediments (Dyer, 1972).

Estuarine sediments are composed of both coarse-grained material (mainly sand and gravel) and fine-grained material. Unlike coarse-grained sediments, fine-grained sediments are cohesive in nature and mainly composed of mixtures of clay minerals such as illite, montmorillonite and kaolinite, and small percentage of fine sand and silt (Cancino & Neves, 1999). Grain size analysis still remains a classical sedimentological method widely used to infer transport and deposition within the estuary (Folk & Ward, 1957; Blott & Pye, 2001; Plomaritis et al. 2013; Sanchez & Hernández, 2013). Regardless of the size of sediment, hydrodynamic action is the most important mechanism in determining their transportation and deposition within the estuary (Dyer, 1972; Sanchez & Hernández, 2013).

The grain size distribution pattern of estuarine sediments is energy dependent and controlled by a combination of different modes of transport, such as river discharge, tidal currents and waves (Dyer, 1972, 1979 & 1986; McLaren & Bowles, 1985). Estuarine water column salinity also affects the estuarine sediments, especially the deposition of fine sediment (collectively comprising of silt and clay size fractions). The fine-grained sediments are normally transported in suspension in the water column and because of their cohesive nature, are liable to collide and flocculate in saline water and settle to the bottom quickly as floccules rather than as individual particles (Reddering & Esterhuysen, 1984; Mikes et al. 2002). On the other hand, non-cohesive sand and gravel-sized fractions are mainly transported along the bottom of the estuary as bedload (Dyer, 1986). Usually these coarser sediments are often left behind in the upper reaches of the estuary. However, where conditions are favourable (i.e. during high energy conditions) these coarse- grained sediments may be transported further downstream as suspended material or through saltation but there is often greater probability that they will be deposited prior to the fine-grained sediment when the current slackens (Plomaritis et al. 2013).

The distribution of estuarine sediment is continually changing predictably along the direction of the transport medium (Dyer, 1972; Ong et al. 2012). Several studies have shown that grain size decreases towards the direction of the flow with fine sediment deposits found in the lower reaches while coarse-grained sediment are often found in the upper reaches (Kamaruzzaman et al. 2002;

Waznah et al. 2010; Ong et al. 2012; Okeyonde & Jibiri, 2013; Chauhan et al. 2014). The transportation and deposition of fine sediment in the lower reaches is not always obvious as river flow transporting fine sediments may meet strong incoming tidal currents pushing the fine sediment further upstream in the estuary. Consequently, Kamaruzzaman et al. (2002) suggest that due to the opposing river currents only a small amount of fine sediment may reach further upstream, resulting in large amounts of fine sediment being deposited in the middle and lower reaches.

One of the most important things in dealing with estuarine sediments is that extreme conditions such as heavy rains or/and floods are often more important than normal conditions as they may discharge more sediment in days than what is normally deposited in months or years. For example, it is reported that in 1955 the Delaware River carried more sediment in two days than it carried in any other year between 1950 and 1966 (Dyer, 1979) while in 1972 during a large storm the Susquehanna River discharged more sediment in one week than what was deposited in the previous 50 years (Dyer, 1986). As mentioned earlier, sediment deposited in estuaries is not only riverine but marine sediment entering through the estuarine mouth forms an important part of the estuarine sediments. In estuaries where flood currents are stronger than the ebb currents, marine sand entered through the mouth during the flooding tide cannot all be removed during ebb tide (Beck, 2005). As such, flood-dominated estuaries are dominated by the marine sediment, especially at the mouth. This is often the case for most South African estuaries (e.g. Keurbooms Estuary) (Reddering, 1981, 1993 & 1999).

2.3 Salt marshes Reviews of coastal salt marshes are widely documented, focusing on their ecological, ecophysiological, geomorphological and sedimentological aspects (Ranwell, 1972; Pomeroy & Wiegert, 1981; Adam, 1990; Allen & Pye, 1992; O’Callagham, 1994; Packham & Willis, 1997; Adams et al. 1999; Boorman, 2003). As a result, there is no single definition that defines salt marshes and can therefore be drawn from these and other sources.

In a general sense, salt marshes are defined as transitional areas between land and sea where their environment has some features of both terrestrial and marine habitats. For the purpose of this study, salt marshes are defined as vegetated coastal wetlands dominated by halophytic herbs, grasses and 14 low shrubs that are generally supported by muddy and saline substrates subjected to tidal inundation (Adam, 1990; Allen & Pye, 1992; Packham &Willis, 1997).

Generally, salt marshes are associated with low-energy and gently sloping coasts where fine sediments can be easily transported and trapped in the marsh surface (Allen & Pye, 1992). Ranwell (1972) stressed that salt marsh formation normally begins at a lower elevation that is subjected to tidal inundation twice daily. Salt marshes consist of submerged and emergent marshes. The former are those frequently flooded and adapted to inundated conditions where the soil moisture and salinity conditions are relatively constant, while the latter is less frequently flooded and the environmental conditions are highly variable as result of less inundation and exposure to air (Adam, 1990). Due to their inundation frequency and elevation relative to mean high water, salt marshes have been divided into three zones, the low marsh (subtidal), middle marsh (intertidal) and high marsh (supratidal) (Packham & Willis, 1997; Bornman, 2002). The low marshes are dominated by very few species that are often rooted in both soft subtidal and intertidal substrata, whose leaves and stems are completely submerged for most part of the tidal cycle (Adams et al. 1999). The middle marsh, also referred to as intertidal salt marsh, supports a wide variety of species that are inundated twice daily. The species of the genus Spartina is the most dominant intertidal salt marsh species dominating most salt marshes worldwide whereas, high intertidal marshes including supratidal that are inundated during high spring-tide and flood events are mostly dominated by Sarcocornia spp. (Ranwell, 1972; Packham & Willis, 1997; Bornman et al. 2016). Along the west coast of South Africa, Bornman (2002) found that saline groundwater was important in determining the distribution of supratidal salt marsh species, Sarcocornia pillansii that was not regularly inundated by the tide or river floods.

Salt marshes occur only in certain estuaries and embayments along the coast of South Africa (Adams et al. 1999; Colloty et al. 2002a & b). It has been estimated that salt marshes cover an area of approximately 17 000 ha, with more than 75% confined to five estuaries, i.e. Langebaan Lagoon, Knysna Lagoon, Swartkops Estuary, Berg Estuary and the Olifants Estuary (Adams et al. 1999). However, recently it has been estimated that marshes, and reeds and sedges cover an area of 12 688 ha and 11 806 ha of the total of 90 844 ha of estuarine habitat respectively (van Niekerk & Turpie, 2012). In South Africa, salt marsh distribution follows the same zonation pattern of the subtidal, intertidal (lower and upper intertidal) and supratidal salt marsh as described in other parts

15 of the world (Adams & Bate, 1995; Bornman, 2002; van Niekerk & Turpie, 2012). The presence or absence of salt marsh species is closely related to specific environmental habitats within the systems, which are determined principally by patterns of tidal inundation and salinity (Adams et al. 1999). In permanently open estuaries, where there is adequate tidal exchange, the marshes are well zoned with the seagrass Z. capensis Setchell occurring at the lower water mark subsequently followed by the first intertidal species, Spartina maritima, which is replaced at a higher level by Sarcocornia perennis (Mill.) Scott, Triglochin spp., Limonium scabrum (Thunb.) Kuntze, Bassia diffusa Thunb and ultimately by supratidal species in higher marshes commonly dominated by Sarcocornia pillansii (Adams & Bate, 1995).

2.3.1 Importance of salt marshes Salt marshes are important for a number of reasons, e.g. ecological, economic and social purposes (Colloty et al. 2000b; Castillo et al. 2008). Despite their low plant species richness due to the very stressful environment, salt marshes are among the world’s most productive ecosystems (Adam, 1990; Duarte et al. 2009). Plant communities in estuaries are sources of primary production and serve as nurseries for juvenile fish and invertebrates while they also provide food and habitat to a wide range of species such as migrating and resident birds and fiddler crabs (Coetzee et al. 1996; Wolanski, 2007). The submerged macrophyte, Z. capensis, provides habitat to rare and endangered species such as the seahorse, Hippocampus capensis, mostly abundant in the Knysna and Keurbooms estuaries (Adams et al. 1999). The botanical importance study conducted by Coetzee et al. (1996) in the Kowie Estuary found that submerged salt marsh (collectively consisting of Zostera spp. and Ruppia spp.) was the most important plant community followed by the intertidal salt marsh. Their importance was closely associated with the inundation period and as a result submerged salt marsh supported more diverse and abundant invertebrate and juvenile fish communities than any other marshes.

In the natural environment, estuarine plant communities are known to act as nutrient sinks by removing large amounts of nutrients and organic matter from the water column (Duarte et al. 2009). The results of a phosphate absorption experiment conducted by Lillebø et al. (2007) at two contrasting locations showed that intertidal mudflats colonized by S. maritima had four times higher P absorption capacity than the adjacent mudflats without vegetation. The economic and

16 social significance of salt marshes to nearby communities cannot be ignored. In many coastal communities, salt marshes are the centre of local cultural and community life (Wolanski, 2007; Barbier et al. 2011). Furthermore, in many coastal communities, salt marshes are necessary to sustain commercial fisheries upon which many coastal areas rely, while their diversity attracts interest from tourists and scientists, which contributes to the economy of the area as well as scientific knowledge of the ecosystem (Wolanski, 2007). Salt marsh plant communities are well known for their effectiveness in flood, erosion and storm-water surge control, thus reducing the negative economic implication that these areas would have had to endure (Boorman, 2003; Culberson et al. 2004; Wolanski, 2007. Through their rigid and densely packed stems and leaves Spartina species are known to decrease the speed of tidal flow, causing the deposition of suspended materials and thereby trapping sediment (Sanchez et al. 2001). This sediment acts as a feeding and shelter area for both marine and estuarine organisms (Adams, et al. 1999).

2.4 The Spartina salt marsh The genus Spartina commonly known as cordgrass, is a relatively small genus of halophytic species in the Chloridoideae, a monophyletic lineage of the Poaceae (Grignon-Dubois & Echmak, 2013), which usually grows in dense monospecific stands or colonies on the coastal salt marshes (Strong & Ayres, 2009). The terms Spartina species or plants and cordgrasses will be used interchangeably in the text below. Due to its natural and human-mediated dispersal, the genus Spartina is one of the most abundant and geographically wide spread species of the halophytes (Castillo et al. 2010). Naturally, these plants are limited to the lower intertidal but can also be found sporadically growing among native plants in the higher intertidal zone (Hellquist & Black, 2010; Yannic et al. 2004). Spartina alterniflora Loisel, S. patens (Aiton) Muhl., and S. cynosuroides (L.) Roth are native from the coastal salt marshes along the East Coast of the American continent while S. densiflora and S. argentinensis Parodi grow naturally in Chile and Argentinian coastal salt marshes (White, 2004; Strong & Ayres, 2009; Castillo et al. 2010). Meanwhile, S. maritima (Curtis) Fernald, S. versicolor Fabre and hybrids, S. x townsendii and S. anglica C.E. Hubbard are autochthonous species from the European estuaries (Marchant, 1967; Castillo et al. 2010).

It is believed that Spartina species in many parts of the world were purposefully introduced rather than accidentally (Marchant, 1967; Pierce, 1982; Strong & Ayres, 2009). However, Marchant (1967) and Marchant & Goodman (1969a) speculate that S. alterniflora was accidentally introduced by shipping ballast to the European coast, while Strong & Ayres (2009) assume that European visitors to North America might have purposefully carried the plant species back home due to its usefulness as roofing thatch. Meanwhile, S. densiflora is believed to have been either accidentally or purposefully transported in the sixteenth century to the southwestern corner of Spain, while China introduced S. anglica, S. alterniflora, S. patens and S. cynosuroides as agricultural and ecological bio-engineers since 1963 (Qing et al. 2010). Along the southern African coast, S. maritima is the only natural occurring Spartina species and its earliest record was between 1829 and 1930 on the beach of Port Elizabeth and Cape Recife in Algoa Bay, South Africa (Pierce, 1981). Although its origin is unknown Marchant (1967) and Marchant & Goodman (1969b) postulate that the species is native in South Africa. However, Pierce (1981) believed that the S. maritima was introduced to the southern African coast either accidentally or otherwise by the early settlers from Europe. Most recently, Adams et al. (2012) have found the invasive S. alterniflora in the Great Brak Estuary along the southern coast of South Africa.

Spartina species have the potential to colonize open intertidal areas into dense or individual clumps of plants. However, Packham & Willis (1997) stressed that the salt marsh vegetation is unable to colonize sand or mud flats unless the level of the intertidal zone has been raised to a suitable height relative to that of the tides. Naturally, Spartina species spread through below-ground rhizomes and also through seeds that are carried by the tides (Davis, 2004; Strong & Ayres, 2013). If the seeds are deposited in areas with favourable salinity they could potentially germinate and inhabit these areas. Individuals grow in clumped stands, which then increase in diameter through vegetative rhizome growth (Sloop et al. 2009). The spread of S. anglica, the hybrid of S. x townsendii into France is thought to have happened as a result of seed floating across the English Channel to La Baie des Veys (Strong & Ayres, 2009; Strong & Ayres, 2013). For some Spartina species, seed production is very rare and as a result their spread is either by natural rhizome growth or vegetative transplantation (Kittelson & Boyd, 1997; Castillo et al. 2000; Castillo & Figueroa, 2008). According to Marchant & Goodman (1969a) the British S. alterniflora populations do not produce seeds and its annual increase is through peripheral rhizome growth.

2.4.1 Importance of Spartina spp. The genus Spartina plays an important role in these ecosystems due to their high primary productivity. Spartina plants are regarded as the ecosystems engineers in temperate marshes, just as mangroves are in the tropics (Strong & Ayres, 2009). Beside as coastal shoreline stabilizers, Spartina species can also be influential to other salt marsh species especially when they influence surface elevation of the marsh. Sediment entrapment by Spartina species will result in an elevated marsh, a process necessary for the continued existence of salt marshes in the face of global rising sea levels (Cahoon et al. 1995; Stock, 2011). Redfield (1972) reported that Spartina maintained the equilibrium of the marsh surface with sea level for four thousand years in the marshes of New England. Sanchez et al. (2001) stressed that continued marsh elevation will induce a number of changes in the soil characteristics and perhaps result in the replacement of Spartina by other species. It is reported that primary productivity of S. alterniflora in South Carolina was greatest towards the lower tidal elevation tolerance of Spartina at a depth between 40 cm and 60 cm below mean high tide. According to Strong & Ayres (2009) this is also where most sediment was trapped and the salinity was lowest.

Biomass of cordgrasses play a very important role in the functioning of salt marshes in general. They are known to produce high biomass that result in large necromass generation due to plant senescence (Cacądor et al. 2009). Castillo et al. (2010) showed that production of aerial and subterranean biomass is stimulated by high accretion rate for both S. maritima and S. alterniflora. This is particularly due to an increase in soil fertility and marsh elevation that results in reduced nutrient deficiency and flooding stress. It is reported that Spartina dominated salt marshes of the southern coast of the United States produces up to 3300 g m-2 yr-1 of aboveground dry weight (McLusky 1981). This large amount of necromass are the major contributor to organic matter of rhizosediments (Duarte et al. 2009). According to Castillo et al. (2010) Spartina biomass controls the development of ecological succession and further organizes space occupation for other plants and animals. However, due to its natural vigour and ability to stabilize and protect the coast, in some parts of the world such as China, Spartina species have been deliberately introduced, while in other parts such as Australia, New Zealand and Tasmania, the role of Spartina species as ecosystem engineers is seen as a nuisance to both ecology and human use (Strong & Ayres, 2009).

2.4.2 Spartina as an invasive species In many marshes where Spartina species have been introduced they actively invade other areas of the marsh (Hellquist & Black, 2010; Qing et al. 2010). In the Gulf of Cadiz, S. densiflora spread to eight estuaries and a number of shoreline habitats including dunes, high marsh, salt pans and intertidal flats. S. densiflora in North African salt marshes originated in Spain (Strong & Ayres, 2009; Castillo et al. 2010), whereas at several salt marshes and restoration sites around Humboldt Bay, California where this species has been introduced, its distribution increased significantly (Kittelson & Boyd, 1997). S. densiflora has also been invading S. maritima dominated salt marshes in the south-west of Spain (Castillo et al. 2000; Castillo & Figueroa, 2008). Fertile S. anglica is known as a serious invasive species, it has not been invasive in China since its introduction (Hellquist & Black, 2010). S. patens is invasive in China (Qing et al. 2010), while it is seen as a threat to native high marsh vegetation along the Mediterranean and Iberian coasts (Strong & Ayres, 2009). S. alterniflora is widely recognized as an aggressive invader of salt marshes, and since its introduction in 1979 the species has rapidly spread to other coastal areas in China, outcompeting native plants (Qing et al. 2010). This invasive species was also observed for the first time invading the temporary open/closed Great Brak Estuary on the southern Cape coast of South Africa in 2004 (Adams et al. 2012). This was also the first record in an African salt marsh. The occurrence of this species in the Great Brak Estuary illustrates the adaptive potential of S. alterniflora to southern African conditions and also indicates the possibility of invasion in temporary closed estuaries in other locations around the world (Adams et al. 2012).

2.4.3 Spartina maritima (Curtis) Fernald Spartina maritima (Curtis) Fernald is one of the earliest recorded Spartina species, and was first recorded as early as 1629 in Britain (Marchant, 1967). It is now widely distributed from the coasts of southern and eastern Britain southwards through the low countries of France, Spain and Portugal into the Mediterranean and down to as far as the southern African coast (Marchant, 1967; Marchant & Goodman, 1969b). S. maritima is the smallest European Spartina species, which often grows in tufts of very rigid shoots with strong roots and short, wiry rhizomes and its shoot length ranges from 15 cm up to 80 cm tall (Marchant, 1967; Marchant & Goodman, 1969b). Marchant &

Goodman (1969b) indicated that the shortness of the rhizomes is the reason why the secondary clusters grow close to the parent stock, creating monospecific stands.

The species is widely distributed in warm and cool temperate permanently open estuaries where there is adequate tidal exchange in the intertidal salt marsh (Adams & Bate, 1995). Although natural occurring along African coast, it is believed that S. maritima introduction along the southern African coast is believed to have been by shipping (Mobberly, 1953). The species is grazed by livestock in Britain and Pierce (1982) believed that its introduction could have been accidental or deliberate by early settlers. Unlike in Europe, the southern African populations of S. maritima have shown signs of expansion over the last few decades (Pierce, 1982; Schmidt, 2013; Bornman et al. 2016). However, rates of its expansion are reportedly low with the exception of the Keiskamma Estuary possibly due to the high silt load (Pierce, 1982). It is believed that there is a certain level of marsh elevation in which salt marsh extension may proceed rapidly (Pierce, 1982). Marchant & Goodman (1969b) indicated that the distribution could be limited by summer temperatures. Schmidt (2013) and Bornman et al. (2016) have shown an increase in the distribution of S. maritima by 68.54 ha in Swartkops Estuary between 1939 and 2008. However, the areas obtained from 1939 image were reported with caution due to the poor quality of the image.

2.4.4 Production of Spartina maritima Spartina species spread naturally through below-ground rhizomes and also through seed dispersed by the tides (Davis, 2004). The production of seed is apparently rare in European S. maritima populations (Marchant, 1967) but is more common in the southern African population. Like in many other Spartina populations, the seeds of S. maritima are dispersed by tidal currents, however their germination is not well documented. Bromfield (1836) in Marchant (1967) showed that S. maritima had a greater tendency to set seeds than S. alterniflora, but the seed was seldom well filled and such it would probably be incapable of germinating. Marchant (1964) reported that S. maritima seeds germinated in moist and temperate conditions in a glasshouse but the seedlings soon died. In many areas, the S. maritima plants in populations have been reproduced by vegetative fragments. For example, Castillo & Figueroa (2008) grew S. maritima from clumps for their restoration project of the Odiel mash, Southwest Iberian Peninsula, partly because the natural populations there do not produce seeds and could not be reproduced in nurseries.

2.4.5 Habitat requirements of Spartina maritima Species distributions within salt marshes are controlled amongst others by tidal inundation, salinity gradient, sediment type and amount of oxygen concentration (Adams & Bate, 1994). Growth and distribution of Spartina species along an elevation gradient within salt marshes is not random and is organized in characteristic patches by various abiotic factors such as topography, salinity, tidal inundation, type of sediment and oxygen concentration in the sediment. Growth of S. maritima plants has been widely studied in the field (Castillo et al. 2000; Sanchez et al. 2001; Duarte et al. 2009; Duarte et al. 2013; Duarte et al. 2014) and in glasshouse experiments (Adams & Bate, 1995; Naidoo et al. 2012).

2.4.5.1 Inundation and salinity tolerance Tidal inundation in salt marshes creates a strong salinity gradient that has an influence on the physiology and productivity of the species. The degree of tolerance is important in determining the distribution limit of each species (Long & Mason, 1983). Spartina species, as the first intertidal halophyte subjected to salt water tidal inundation twice daily, are expected to survive a wider range of salinity and much longer periods of submergence than upper marsh species. However, tidal inundation frequency and duration is dependent on the surface elevation range of the marsh. For example, Spartina species found in the lower intertidal zone are expected to be inundated for much longer periods than their upper intertidal counterparts.

Adaptation experiments of Spartina species to different inundation and salinity treatments have been conducted by numerous researchers (Adams & Bate, 1995; White, 2004; Naidoo et al. 2012). Hubbard (1970) showed S. anglica to withstand salt water submergence for at least four months in the laboratory. Adams & Bate (1995) found that S. maritima can withstand submergence in salt water for at least three months. Plant growth was reduced on complete submergence and dry treatment plants showed no significant difference in stem and leaf elongation compare to tidal inundation (Adams & Bate, 1995). Reduced growth in dry treatments explains the absence of S. maritima in temporarily open/closed estuaries indicating their reliance on tidal inundation. S. maritima has been shown by Duarte et al. (2014) to be well-adapted species with an evident

22 photochemical plasticity towards submersion. This allows the species to maintain its photosynthetic activity even during prolonged submergence.

Tidal inundation increases salinity concentrations both in the water column and within the sediment in which the salt marsh plant species grow (Packham & Willis, 1997). Adaptive studies of S. maritima to different salinity concentrations reveal a similar salinity tolerance range to that of S. alterniflora. According to Adams & Bate (1995) S. maritima plants grew equally well at salinities between 0 and 35 but the growth was significantly reduced at salinities of 55 and 75. Naidoo et al. (2012) also found above-ground and below-ground biomass of S. maritima to be higher in 20% sea water than at lower or higher salinities. Koyro & Huchzermeyer (2004) also found that quantum maximum yield was reduced by 50% at 100% seawater while the gas exchange parameters such as net photosynthesis, stomatal conductance, transpiration and water use efficiency of photosynthesis were also lowest under these conditions. It appears that S. maritima is well adapted to salinities between 20 and 35 suggesting that tidal submergence conditions itself is not critical for the survival of this species but more persistent and higher salinities are, which result in reduced biomass and area coverage.

2.4.5.2 Elevation gradient

Salt marsh plant species, Spartina species in particular, have a certain elevation range in which they grow due to their tidal inundation requirement. However, the distribution of a particular Spartina species along the elevation gradient depends on its tolerance to factors such as submergence and inter- and intra-species competition (Castillo et al. 2000). For example, Castillo et al. (2000) and Castillo & Figueroa (2009) found S. maritima tolerate the stressful abiotic environments of the lower intertidal marsh better than S. densiflora but adapted poorly in the presence of competition in the high marsh. Elevation is also a good indicator of the changing environment in salt marshes, with lower elevations expected to have higher salinity and moist substrates due to frequent tidal inundation (Sanchez et al. 1997).

Numerous researchers have shown S. maritima occurring over a wide range of elevation in the intertidal zone where there is frequent inundation (Sanchez et al. 1997; Castillo et al. 2000; Bezuidenhout, 2011; Schmidt, 2013; van der Linden, 2014). In general, S. maritima grows in

23 monospecific stands in the lower intertidal zone and is replaced by other species in the upper intertidal zone or elevated marsh surface even in the lower intertidal area.

In the Kromme Estuary on the southern coast of South Africa, Bezuidenhout (2011) found S. maritima occurring in monospecific stands between 30 – 40 m inshore of the subtidal area. Although Bezuidenhout (2011) did not record any S. maritima in the upper reaches of the Kromme Estuary, Schmidt (2013) found some small patches occurring at 80 m from the high water mark. Similar findings have been reported for the Swartkops Estuary and the Langebaan Lagoon (O’Callaghan, 1994; Schmidt, 2013; Van der Linden, 2014). Although S. maritima appears to occur over a wide elevation range in the intertidal zone, its occurrence is dependent on elevation relative to height above mean sea-level. It has been shown by various researchers (O’Callaghan, 1994; Bezuidenhout, 2011; Schmidt, 2013) that the species becomes abundant at lower elevations above mean sea-level. An experimental study conducted by Castillo et al. (2000) on two different Spartina species, S. maritima and S. densiflora, showed S. maritima to survive better than S. densiflora at elevations between 1.04 and 1.67 m above to Spanish Hydrographic Zero. However, neither species survived for a year at the lowest point of l.04 m above SHZ. Castillo et al. (2000) further noticed that growth rates in surviving clumps of both species increased with elevation, but that of S. densiflora was more sensitive to lower elevation. Santin et al. (2009) noted that S. maritima in Villaviciosa Estuary and the Ria of Ortigueira of the Iberian Peninsula occupied different physiographical positions. S. maritima was found occurring between 1.0 and 2.5 m above mean sea-level. S. maritima appears to have a potentially wide elevation range between 0.3 and 2.5 m above mean sea-level where there is adequate tidal exchange in the intertidal salt marsh.

2.4.5.3 Substrate type It is generally accepted that silt and clay are the main mineral components of salt marsh soils with only small amounts of sand (Lambrinos et al. 2010). However, habitats of S. maritima have been shown to vary from soft mud and sand to firm mud on the fringes (Marchant & Goodman, 1969b; Christian et al. 1983). It is reported that S. maritima grows tallest on sandy silt sediment but that the growth is more satisfactory in pots of salt marsh mud watered with salt solutions (Marchant & Goodman, 1969b). Christian et al. (1983) in their work comparing the growth of S. alterniflora in two contrasting soil textures (i.e. silt-clay and sandy soil) found that plants grew taller on a sandy substrate. However, they found that these two soils supported similar total biomass but with more

24 robust plants in the silt-clay than sandy soil. Substrate type seems to play an important role in Spartina species productivity but differences in plant height are not always attributed to substrate type but also to differences in nutrient levels in the soil (Sanchez et al. 1997). Castillo et al. (2000) ascribe high biomass of Spartina species to soil fertility produced by soil accretion. Both soil fertility and marsh elevation reduce nutrient deficiency and flooding stress of the Spartina species, which result in stimulated growth. Nutrient availability is certainly one of the primary environmental factors limiting plant biomass production in saline environments, which would thus also influence species distribution (Reaper, 1995; Sanchez et al. 1997; Castillo et al. 2000).

Chapter 3. Study site

3.1 General description The Keurbooms Estuary is situated in Plettenberg Bay on the south coast of South Africa, approximately 223 km west of Port Elizabeth (Figure 3.1). The bay of Plettenberg Bay is characterized by a wave dominated shoreline where very high longshore sediment transport rates are recorded during south-easterly storms (Reddering & Rust, 1994). The estuary consists of two contrasting subsystems (rivers), namely the Keurbooms tributary and the Bitou tributary that merge approximately 3.5 km before the mouth opens to the Indian Ocean at 34º 02' S; 23º 23' E (Duvenage & Morant, 1984; Reddering & Rust, 1994). The Keurbooms tributary has its origin in the Outeniqua Mountains, which form part of the Cape Fold Belt, while the drainage system of the Bitou River originates in the Knysna forest (Reddering & Rust, 1985). The total length of the Keurbooms tributary from the mouth to its source at Spitskop in the Outeniqua Mountains is approximately 70 km, while the Bitou tributary from its confluence with the Keurbooms to its source at Buffelsnek is 23 km. Combined, the total catchment area is approximately 1 096 km² (Duvenage & Morant, 1984). The mean annual run-off (MAR) of the Keurbooms tributary is reported to be 102 x 106 m3, while that of the Bitou is given as 32 x 106 m3 (Huizinga & Slinger, 1999) and reflect the rainfall pattern of the Plettenberg Bay area (Bornman & Adams, 2005).

Figure 3.1: A map showing the location of the study, the Keurbooms Estuary

3.2 Estuary The Keurbooms Estuary is classified as a permanently open estuary (Whitfield, 1998; Whitfield & Baliwe, 2013), one of the few along the South African coastline. It is the first permanently open estuary with a floodplain situated in the warm-temperate region between the Kromme Estuary and the Knysna Estuary (Whitfield, 2014 personal communication). In terms of biological diversity, the estuary is ranked 18th from approximately 256 functional South Africa estuaries (Turpie, 2004). Recently Whitfield & Baliwe (2013) listed the estuary as in a good condition but increased freshwater abstraction from the system is the main threat to the functioning of the estuarine ecosystem.

The estuary is influenced by a semi-diurnal, micro-tidal regime, with tidal variation ranging between 0.1 and 1.9 m during spring-tide and 0.4 to 1.6 m during neap-tide (Reddering, 1981; www.windreport.co.za). In the Keurbooms tributary, tidal exchange may reach as far as 14 km upstream during spring high-tide, however because the Bitou tributary is much shallower than the Keurbooms, the tidal amplitude is reduced as a result of the road bridge at Wittedrift, effectively forming the upper limit of the tidal exchange (Huizinga & Slinger, 1999; Bornman & Adams, 2006). Although tidal exchange occurs throughout the estuarine basin during spring high-tide, active tidal exchange, on which the entire water column is flushed, occurs primarily in the lower and middle reaches of the estuary. Bathymetry of the estuary appears to influence the water column salinity (Huizinga & Slinger, 1999). The bathymetry survey of the estuary conducted by Huizinga & Slinger (1999) revealed that the lower reaches were approximately 3 m or less depth and became shallower in the Bitou tributary and towards the middle reaches of the Keurbooms tributary, but then the depth increases again upstream of the N2 Bridge. Huizinga & Slinger (1999) also showed that the western side of Stanley Island was considerably shallower than the eastern channel. The lower reaches was characterized by salinity equivalent to that of sea water while upstream of the N2 Bridge the estuarine water was often characterized by freshwater, often with a clear halocline at depth.

The estuary is separated from the sea by a coastal barrier, which has a tidal inlet connecting it to the sea. The estuary is subjected to substantial flooding (Duvenage & Morant, 1984) and its mouth has the tendency to migrate along the barrier, back and forth, northeast to southwest towards Lookout Rock in response to these floods and oceanic forces. Due to its size and topography, the mouth has never been known to close (Fromme, 1985; Huizinga & Slinger, 1999; Reddering, 1981, 1999; Schutte-Vlok et al. undated). According to Fromme (1985) the mouth of the estuary may migrate at a

28 distance up 1 km along the barrier dune, but Schumann (2015) insisted that breaching of the new mouth depends largely on the flood size and the nature of the exit channel in the back-barrier. The response of the mouth position to floods and oceanic forces is attributed to the fact that the tidal inlet or mouth itself is not anchored in any substrate resistant to erosion (Schumann, 2015). However, the rocks on the southern boundary of the estuary prevent further migration of the mouth beyond Lookout Rock. At present, the mouth is located 0.96 km to the north-east of Lookout Rock. As the mouth migrates along the spit it becomes shallow at times but the strong incoming and outgoing tide keeps it open (Reddering, 1981 & 1999; Schutte-Vlok et al. undated). According to Schumann (2015) the volume of water entering and exiting the estuary over a tidal cycle is estimated to be 1.8 x 106 m3. This is sufficient enough to keep the mouth permanently open. However, there are concerns that increased freshwater abstraction from the system will increase the sedimentation rate in the estuary, especially between the mouth and the N2 Bridge. The estuary would then become progressively shallower, which will result in reduced tidal flow thus increasing the potential for mouth closure (Huizinga & Slinger, 1999). The closure of the mouth would be uncharacteristic for the Keurbooms Estuary.

3.3 Geology The geology of the southern coast of South Africa is dominated by sandstones, quartzites and shale of the Table Mountain, Witteberg and Bokkeveld series (Norman & Whitfield, 2006). The geological substrate and geomorphic morphology of the Keurbooms Estuary differ between its subsystems. They are underlain exclusively by rocks of the Table Mountain and Bokkeveld Group (Duvenage & Morant, 1984; Reddering, 1999). The Keurbooms tributary flows through steep, forested gorges of the Outeniqua Mountains while the Bitou flows through a wide floodplain vegetated with salt marshes and reeds and sedges. The lower reaches of the Keurbooms Estuary are underlain by Tertiary to Quaternary marine and estuarine terrace gravel and partly calcareous sand (Duvenage & Morant, 1984). Bedrock underlying the drainage basin of the Keurbooms River mainly consist of Table Mountain quartzite sandstone (Reddering, 1999). A digitized geological map of the estuary shows that above the N2 Bridge the Keurbooms tributary crosses over a narrow strip of shale and siltstone of the Bokkeveld Group while the drainage basin of the Bitou is underlain mostly by marine and estuarine sandstone, conglomerate and shale of the Enon Formation (Reddering, 1999) (Figure 3.2). More than

29 half of the upper section of the Bitou River is underlain by Table Mountain quartzite but these supply very little sandy sediment to the system because of the resistant nature of the quartzite to erosion (Reddering, 1981; 1999).

The sediment supplied by the geology of the Bitou and Keurbooms tributaries differ. The Bitou tributary supplies more clay and silty sediment compared to quartzites sandy sediment of the Keurbooms tributary (Reddering, 1999). This is partly because the Bokkeveld Group predominately consists of mudstones that weathers more easily than the quartzite, producing fine-grained sediment fractions. In comparison the Bokkeveld slate area underlain by shale and siltstone in the Keurbooms tributary is very small and as a result it supplies very little fines sediment to influence the composition of the estuary. Although the Bitou tributary drains fine-grained sediment fractions, Reddering (1999) stressed that the small size and morphology of the Bitou tributary affects the sediment budget of the estuary. Given the meandering morphology and extensive tidal flats, it would therefore, appear that most of the mud or clay from the Bitou are trapped on the estuarine channel banks or intertidal mudflats near the confluence (Reddering, 1999). Furthermore, Duvenage & Morant (1984) suggests that fluvial sand also contributes very little to the estuarine sediment budget due to the resistant nature of the quartzitic basin to weathering in the Keurbooms. Reddering (1999) believed that the surf zone is the main sediment source of the estuary. River floods are therefore particularly important to temporarily scour and remove accumulated tidal sediment from the lower reaches and to deposit fine sediment onto the salt marshes.

Figure 3.2: The geological substrate of the Keurbooms Estuary (Source: Department of Mines, 1979).

3.4 Climate The climate and run-off data presented in this section were provided by the South African Weather Services and the Department of Water and Sanitation respectively.

The Keurbooms Estuary is located on the warm-temperate region of the south coast of South Africa, close to the Plettenberg Bay area that receives rainfall almost equally throughout the year but it usually peaks in autumn and spring (Duvenage & Morant, 1984). Mean monthly temperatures follow a seasonal pattern and are particularly influenced by both warming and cooling effects of the sea, which creates an overall temperate climate (Bornman & Adams, 2005). The mean maximum and minimum temperatures indicate mild summers and winters with the highest mean maximum recorded in January and February with the lowest mean temperatures recorded in July and August (Figure 3.3). The area predominantly experiences westerly winds during spring and summer and north-westerly winds in spring. Easterly winds are well developed in autumn, particularly in March, with strong easterlies in summer (December) (Bornman & Adams, 2005). Schumann et al. (1982) showed that prevailing strong easterly winds in summer are particularly responsible for the upwelling events along the coastline, which results in plumes of cool water being drawn into the estuary on the flood tides.

26 Maximum 24 Minimum 22

Temperature Temperature (ºC) 14

8 JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC Months

Figure 3.3: Mean minimum and maximum temperatures for the Plettenberg Bay area over the last 12 years (2004 – October 2015) (Mean ± SE).

Literature (Duvenage & Morant, 1986; Bornman & Adams, 2005 & 2006) and South African Weather Services data indicate that the Plettenberg Bay area receives rainfall throughout the year with peaks in winter (Figure 3.4). The passage of cold fronts along the southern coast of South Africa dominate the local weather pattern of Plettenberg Bay. Another factor affecting local rainfall patterns are coastal mountains in the area. As a result, the rain in the area is mainly cyclonic and orographic with comparatively little thunderstorms. According to Duvenage & Morant (1984) rainfall in the Outenique and Tsitsikamma Mountains may exceed 1 100 mm per year. Normally precipitation along this coast occurs with the eastward passage of cyclonic low pressure systems while the autumn rain comes predominately from the east due to the prevailing easterly wind conditions during this period.

The mean monthly precipitation patterns of the area for the past 12 years (2004 – October 2015) are similar to that reported by Bornman & Adams (2005 & 2006) except for the high peaks in winter (i.e. June, July and August) (Figure 3.4). Moreover, precipitation patterns during the study period (i.e. 2014 and 2015) also show similar trends in July, August and September 2015 (Figure 3.5).

120 Mean annual rainfall 2004-2015 = 687 mm 100

40 Mean rainfallMean(mm)

0 JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC Months

Figure 3.4: Mean monthly rainfall at Plettenberg Bay over the past 12 years (2004 – October 2015) (Mean ± SE).

160 2014 140 2015 120 Mean monthly rainfall 2004-2015 100

40 Rainfall(mm) 20

0 JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC Months

Figure 3.5: Monthly rainfall at Plettenberg Bay for 2014 and 2015 compared to mean monthly rainfall (Mean ± SE, n = 12 years).

The mean monthly run-off of the estuary recorded at the Newlands gauging station K8H019 located in the Keurbooms tributary, appears to mirror the rainfall pattern for the same period over the past 12 years (Figure 3.6). However, the monthly flows during the period of this study were low in July and August 2015 despite high rainfalls. This could be related may to the different locations at which water flow and rainfall monitoring systems are situated. Furthermore, the Newlands gauging station is located in the Keurbooms tributary, approximately 13 km from the confluence with the Bitou tributary and as a consequence a large proportion of the catchment is ungauged in terms of area and run-off (Bornman & Adams, 2005).

100

90 Mean month run-off (2014-15)

3 80 Mean monthly run-off 2004-2015

m 6 70

60 off (10 x - 50

10 Mean monthly Meanmonthly run 0 JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC Months

Figure 3.6: Monthly flow rates in the Keurbooms Estuary for 2014 and 2015 compared to mean monthly flood peaks for the past 12 years (Mean ± SE).

3.5 Socio-economic importance The Keurbooms Estuary is relatively undeveloped but a number of proposed or potential developments such as freshwater abstraction (off-channel impoundments) upstream of the estuary as seen to pose a serious threat to the natural character and ecological functioning of the estuary (Bornman & Adams, 2006). The Keurbooms Estuary is an important tourism destination and a source of recreational activities in the Plettenberg Bay area. Tourism and recreational value are both regarded as important by permanent residents and visitors. Tourism value of the estuary is ranked 2nd amongst South African temperate systems with an estimated value of about R400 million per year whereas is ranked 7th in terms of the subsistence value (Turpie & Clarke, 2007). In general, South African estuaries act as nursery areas for linefish species and penaeid prawns caught in the inshore marine environment and the Keurbooms Estuary is ranked 11th amongst temperate system in terms conservation importance on the basis of the estuary size, zonal type rarity and habitat diversity with an estimated value of about R13.8 million per year (Turpie, 2004).

Chapter 4. Spatial and temporal distribution patterns of the bottom sediments of the Keurbooms Estuary

4.1 Introduction Estuaries and rivers are often considered as regions of high sedimentation, serving as traps for minerals from inland and marine sources (Kamaruzzaman et al. 2002; Waznah et al. 2010). However, the study of estuarine sedimentation is complex and requires a broad knowledge of factors affecting sedimentation as the major sources of sediment are generally from outside the estuary (Dyer, 1972). Although it is believed that the initial source of estuarine sediment is from riverine input (Luternauer et al. 1995), sedimentary material is transported into the estuary from both the river and the sea and in some instances may be washed and blown into the estuary from the surrounding land. Sediment transported and deposited within an estuary exhibits a high degree of variability in terms of grain size, mineral type, organic matter content as well as level of sorting (McLaren & Bowles, 1985). This variability is closely related to the sediment source and circulation pattern of the water column, which is controlled at different temporal and spatial scales by periodic phenomena such as semi-diurnal tides and river flow as well as seasonal floods (Dyer, 1972; Cunha & Dinis, 2002).

Sedimentary dynamics are one the main controlling factors of an estuarine ecosystem, structuring estuarine plants and benthic communities. Sediments support a wide range of coastal and marine ecosystems, many of which have economic importance, such as fisheries and shellfish (Rosa et al. 2013). Sediment dynamics also include the formation, distribution and movement of sediments within an estuarine system. Estuarine sediments are mostly transported as suspended, saltation and bedload material (Dyer, 1986). However, the type of sediment transport depends on the size range of sediments, flow rate, and where conditions are favourable a different size range of sediments will settle on the bottom of the estuary (Matoti, 1999). For example, coarse sediments are likely to be deposited first during low flow, whereas fine sediments may continue to remain in suspension and be deposited during a slack water period. Therefore, the observed bottom sediment distribution of a particular estuary is the summation of all the processes acting in the area over time. The distribution of bottom sediment does not only provide valuable information of the source of the sediments deposited in the estuary but also the dynamics of sediment movement. Moreover, the bottom of the estuary is important as it may be a source of sediment introduced into the estuary through turbidity

36 currents, but it is unlikely that the bottom itself acts as a source of new sediment in estuaries (Burns, 1965).

Despite their importance, there is little information available on the sedimentary dynamics of South African estuaries, particularly with regards to their entrainment, transportation and deposition. This lack of information on the sedimentology makes it very difficult to assess environmental change in relation to some of the major pressures such as global climate change and anthropogenic activities such as dam development (van Niekerk & Turpie, 2012). In view of the importance of the bottom sedimentation to various aspects of the estuary, the overall objective of this chapter is to examine sediment distribution of both the Bitou and Keurbooms tributaries of the Keurbooms Estuary at different temporal and spatial scales.

4.2 Materials and methods 4.2.1 Sampling site description The study was conducted at the Keurbooms Estuary, which is made up of two contrasting subsystems, namely the Keurbooms tributary, which is the main channel, and the Bitou tributary that joins the Keurbooms tributary from the west approximately 3.5 km before the mouth opens into the Indian Ocean (Figure 4.1). The Keurbooms tributary flows through steep, forested gorges, often with a deep channel with no floodplain upstream of the N2 Bridge. As a result, salt marsh vegetation is limited only to the confluence and lower reaches of the two tributaries. The Bitou tributary is characterized by a shallow channel, meandering through an extensive floodplain creating habitat for salt marshes above the confluence. According to Reddering (1999) coarse sediments are concentrated in the Keurbooms tributary while fine sediments are deposited in the Bitou tributary, with the lower reaches of the estuary characterized by marine sand (Reddering, 1999). Therefore, sampling sites were selected according to the morphology of the estuary to cover these three sections, i.e. the Bitou tributary, the Keurbooms tributary and the lower reaches (i.e. after the confluence).

Due to shallowness and inaccessibility, the Bitou tributary could only be reached by boat as far as B3, thereafter by car at selected sites. As a result, the Bitou tributary had only 9 sites including 2 additional sites, i.e. Bitou drift and B5 cliff that were sampled during June 2014 and February 2015 (Figure 4.1).

Figure 4.1: Sampling sites for the bottom sediment of the Keurbooms Estuary.

4.2.2 Data collection A total of 92 bottom sediment samples were collected along the Keurbooms Estuary over three sampling periods using a Cone Dredge sampler on board the Research Vessel DWAF 130-E (Plate 4.1). Of these 92 samples, 33 (including additional samples collected at sites K23, K24, K25, K26 and Bitou drift) were collected in June 25, 2014, 30 (including additional samples collected at site B5 Cliff on the cliff opposite B5 in the Bitou) were collected in February 26, 2015 and 29 samples were collected in September 21, 2015. Roughly 0.5 to 2 kg (wet weight)

38 of sediment was collected at each site and stored in sealed plastic bags and transported to the laboratory for grain size and organic matter content analysis.

(a) (b)

Plate 4.1: Cone dredge sampling off the research vessel in the Keurbooms Estuary.

Additionally, water column variables, i.e. temperature (ºC) and salinity were measured at each sampling site using a handheld YSI 600XLM multi-parameter probe. Bathymetry was determined from the YSI’s measured bottom depth. The YSI measurements were taken in June 2014, September 2014, February 2015, April 2015 and September 2015 while Secchi disk measurement were only recorded in April 2015 and September 2015. All YSI measurements were taken by lowering the probe slowly from the surface down to the bottom of the estuary and from the bottom up to the surface (Plate 4.2a). All measurements were taken from the boat except those at sites B5, B6, Bitou drift and Bitou upper (Plate 4.2b).

(a) (b)

Plate 4.2: Physico-chemical measurements taken from the research vessel (a) and from land (b).

4.2.3 Laboratory analysis Upon arrival at the laboratory, the sediment samples were prepared for grain size distribution and organic matter content analysis using the following methods:

4.2.3.1 Grain size analysis The bottom sediments of the Keurbooms Estuary are composed of coarse sand-size to silt-sized fractions and therefore the standard dry sieving method was used to determine particle size. Prior to grain size analysis, sediment samples were washed according to the method described by Buller & McManus (1979) to remove salt from the sediment samples. If the sediment with interstitial saline water were to be dried as received from the field sampling, a white crust deposit of salt would form on the surface and act as cement, binding together the original separate non-cohesive particles (Buller & McManus, 1979). Furthermore, when sediment is dry, deposited salt crystals can be as large as individual particles. Therefore, about 150 to 200 g of wet sediment samples were washed by repeatedly stirring in beakers of tap water, allowing it to settle and thereafter decanting the clear liquid without losing fine particles (Plate 4.3). Three washings in 600 ml of water with thorough stirring were considered sufficient to remove

40 the salt from the weighed sediments (Buller & McManus, 1979). The final wash was left overnight in distilled water. The washed sediments were then oven dried at 70ºC for 24 hours to remove all moisture before analysis.

Plate 4.3: Sediment washing to remove salt.

Shell fragments form an integral part of estuarine sediments (Buller & McManus, 1979). According to them shells in estuarine sediments may be used to indicate transport paths and sources of sediments in the estuary. Therefore, in this study, sediments were analyzed with their shell fragments

Grain size analysis was conducted using a King Test VB 200/300 Sieve Shaker. Mesh sizes used were 2000 µm, 1000 µm, 500 µm, 355 µm, 250 µm, 180 µm, 125 µm, 90 µm, 63 µm and Pan. The sieve sizes were arranged from the coarsest to the lowest mesh size with the pan on the bottom. From the dried samples, 100 g was weighed and poured into the top sieve and closed with the lid. The sample was then mechanically sieved for approximately 15 minutes. The sieved material in each mesh was emptied onto a tray then onto a sheet of paper. Grains stuck on the mesh were loosened by cleaning the mesh with an appropriate brush (i.e. wire for coarse meshes and camel-hair for fine apertures). All the sediment obtained from each sieve mesh was weighed and logged into a datasheet.

Sediment texture and grain size distribution were computed using Gradistat software version 4.0 as developed by Blott & Pye (2001) and primary sediment types were classified according

41 to the method described by Blott & Pye (2012). For the purpose of this study only mean sediment size and sorting have been reported using the Folk & Ward (1974) method. The grain size statistical parameters are given using Folk & Ward (1957) phi (ϕ).

The coarse sediment grain size is represented by lower phi (ϕ) value, which increases when the sediment particle size becomes finer.

4.2.3.2 Organic matter content The sediment organic matter content was determined according to the method described by Briggs (1977) and Duarte et al. (2013). About 20 g of sediment sample from each site was weighed and placed in a drying oven at 70ºC for a period of 24 hours. The dried sediment samples were placed in a muffle furnace (ashing oven) at 550ºC for 8 hours. The crucibles were removed from the ashing oven and reweighed after cooling down. Organic matter content was determined as a loss of mass during ashing of the initial dry mass and expressed as a percentage using the following equation:

푀푑 − 푀푎 ( ) ∗ 100 푀푑

Where Md is the initial dry sediment mass and Ma is the mass of the sediment after ashing.

4.2.4 Spatial interpolation analysis For the purpose of spatial representation of the sediment data, spatial interpolation analysis was conducted using ArcGIS 10.2. By using the Kriging method of the Geostatistical analyst tool, an interpolated surface map of grain size and organic content was developed for each sampling period.

4.2.5 Statistical analysis One-way ANOVA was conducted to determined significant differences between sampling sites and periods. Where a significant difference was found a Tukey post – hoc test was carried out and correlation analyses between mean sediment size and sorting were also run. All statistical analyses were conducted using STATISTICA (Statistical software developed by Statsoft, Inc.) version 13.0.

4.3 Results 4.3.1 Spatial variability of sand and mud distribution Spatial distributions of the sand and mud fractions are illustrated in Figures 4.2, 4.3 and 4.4. The mud fraction collectively includes the silt and clay sized fractions (i.e. those <63µm in size). The sediment textural distribution pattern of the Keurbooms Estuary is exclusively composed of sand-sized fractions with the exception of the Bitou tributary which, shows evidence of mud fractions.

In June 2014, the sand content ranged from 99.8% to 100% in the lower reaches (i.e. below the confluence) and from 91.8% to 100% in the Keurbooms tributary. The Bitou tributary had lower sand content readings than the rest of the estuary and ranged from 68.2% to 99.9% (Figure 4.2a). The estuary is almost free of mud fractions in the lower reaches compared with other parts of the estuary. The mud content ranged from 0% to 0.2% by weight percentage in the lower reaches and from 0% to 8.2% in the Keurbooms tributary. A higher mud fraction was found in the Bitou tributary where they made up 0.1% to 31.8% (Figure 4.2b). The sites B1, B4 and Bitou_drift had the highest content at 10.2%, 22.7% and 31.8% respectively (Figure 4.2b). Bitou upper also showed a fair amount of mud fraction, i.e. 1.8%. Overall, the entire estuary comprised of 97.5% sand and 2.5% mud fraction during June 2014 sampling period.

February 2015 showed similar results to that of June 2014 but with increased sand fraction content in the Keurbooms and Bitou tributaries. Sand content ranged from 99.7% to 100% in the lower reaches and from 99.1% to 100% in the Keurbooms tributary (Figure 4.3a). Although the mud fraction content was still constrained to the Bitou tributary, it was reduced considerably with contents ranging from 0% to 3.4%. However, sites B1 and B4 remained the sites with the highest mud fraction content (i.e. 3.4% and 2.8% respectively) (Figure 4.3b). The additional site, B5_Cliff (which is on the bank opposite B5) appears to be the source of the mud fraction for site B5 and B4. Bitou_upper continued to have a fair amount of mud fraction, i.e. 1.5%. Although the number of sites sampled in February 2015 were reduced from 33 to 30 sites, the average values of sand for the entire estuary increased to 99.4% while the mud fraction decreased to 0.6% during February 2015.

Similar to the February 2015 results, sediment texture in September 2015 had a high sand fraction with considerably reduced amounts of mud sized fractions in the Keurbooms and Bitou tributaries (Figure 4.4a and b). Sand content ranged from 99.7% to 100% in the lower reaches and from 98.4% to 100% in the Keurbooms tributary. The Bitou tributary continued to have

43 lower sand content readings than the rest of the estuary. Sand content in the Bitou tributary ranged from 92.7% to 99.8% (Figure 4.4a) while the mud fraction ranged from 0.1% to 7.3% with the highest at B1 (i.e. 7.3%) (Figure 4.4b). The lower reaches were almost free of the mud fraction while it was considerably reduced in the Keurbooms tributary. In the lower reaches, the mud fraction ranged from 0% to 0.3% and from 0% to 1.6% in the Keurbooms tributary. The highest mud content in the Keurbooms tributary was recorded at site K15 just above the N2 Bridge (Figure 4.4b). There was little change in the average sand and mud fraction in September 2015 from those recorded in the February 2015 sediments. On average the September 2015 sediments comprised of 99.5% sand and 0.5% mud fraction.

(a) (b)

Figure 4.2: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in June 2014.

(a) (b)

Figure 4.3: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in February 2015.

(a) (b)

Figure 4.4: Spatial distribution of (a) sand-fraction content and (b) mud-fraction within the Keurbooms Estuary in September 2015.

According to Pye & Blott (2012) four primary sediment types occur in the Keurbooms Estuary namely: sand, very slightly silty sand, very slightly clayey slightly silty sand and slightly clayey silty sand (Figure 4.5). The primary sediment type, sand was the most dominant (comprising 79% of all 92 collected sediment samples) and was primarily deposited in the lower reaches (i.e. after the confluence) and in the Keurbooms tributary. Very slightly silty sand (15%), very slightly clayey slightly silty sand (9%) and slightly clayey silty sand (3%) were present in the Bitou tributary and at some selected sites in the upper reaches of the Keurbooms tributary (i.e. sites K12, K18, K20 and K21) which were deposited during June 2014 sampling period (Figure 4.5).

The sediment type, slightly clayey silty sand, was only deposited in 2014 at the Bitou_drift site (Figure 4.1.). In February 2015, the sediment textural distribution was exclusively sand in the lower reaches and the Keurbooms tributary while the Bitou tributary was dominated by the very slightly silty sand sediment type. In September 2015, sediment textural distribution showed no change with the exception of site B1 in the Bitou tributary that became very slightly clayey slightly silt sand.

S sand (s) slightly sandy SI silt (si) slightly silty Jun-14 C clay (c) slightly clayey C Feb-15 s sandy (vs) very slightly sandy 100 (vsi)C si silty (vsi) very slightly silty c clayey (vc) very slightly clayey (vs)C (vs)(vsi)C Sep-15 90 (s)C (si)C

(s)(si)C 70 sC siC

(si)sC (s)siC

ssiC 40 cS cSI (si)cS (s)cSI

30 sicS scSI

20 (c)S

(si)(c)S (c)siS (c)sSI (s)(c)SI 10 (vs)(vc)SI (vsi)(vc)S (vc)SI (vc)S (vc)(si)S (vc)siS (vc)sSI (vc)(s)SI 0 SI S (vsi)S (si)S siS sSI (s)SI (vs)SI % sand

Figure 4.5: Ternary diagram showing primary sediment types occurring in the bottom sediments of the Keurbooms Estuary.

4.3.2 Variation in grain size distribution Grain size is one of the fundamental physical properties of sediment, and as such it is very useful in identifying the depositional environment and pattern of sediment transport (Folk & Ward, 1957; Rabiu et al. 2011). Results obtained from Gradistat with respect to grain size parameters, namely

49 mean size and sorting, are presented in Appendix 1 (i.e. Tables A.1.1, 1.2 and 1.3) and illustrated in Figures 4.6, 4.7 and 4.8.

The grain size distribution of the Keurbooms Estuary tends to vary spatially and temporally. In June 2014, the mean size ranged from 2.009 to 1.337 ϕ (i.e. fine to medium sand) (Figure 4.6a) while sorting varied from 0.722 to 0.393 ϕ (i.e. moderately to well sorted) in the lower reaches (Figure 4.6b). The distribution pattern in the Keurbooms tributary showed mixed medium-fine- coarse trends from the confluence to the upper reaches. The mean size ranged from 2.344 to 0.736 ϕ (i.e. fine to coarse sand) (Figure 4.6a) while sorting varied from 1.301 to 0.405 ϕ (i.e. poorly to well-sorted). The sediment in the Bitou tributary showed evidence of finer sediment fractions. This was clearly shown by the high mean values that are indicative of very fine to fine sand grain (Figure 4.6a). The mean values ranged from 3.915 to 0.969 ϕ (very fine to coarse sand) while in terms of sorting the sediment varied from 1.839 to 0.799 ϕ (poorly to moderately-sorted). The fine sediment fractions were more poorly sorted than the coarse fractions (Figure 4.6b).

In February 2015, the sediment mean size varied from 1.999 to 1.467 ϕ (i.e. medium sand) (Figure 4.7a) while sorting ranged from 0.544 to 0.388 ϕ (i.e. moderately to well-sorted) (Figure 4.7b) in the lower reaches. In the Keurbooms tributary, mean size ranged from 1.810 to 0.765 ϕ (i.e. medium to coarse sand) (Figure 4.7a), while sorting ranged from 1.315 to 0.440 ϕ (poorly to moderately-sorted). In general, the grain size distribution was mostly characterized by moderately to well-sorted medium sand (Figure 4.7b). Only sites K19 and K21 were characterized by moderately-sorted coarse and poorly-sorted medium sand respectively. During February 2015, the sediment in the Bitou tributary was much coarser than the June 2014 sediment. The mean size ranged from 2.213 to 0.879 ϕ (i.e. fine to coarse sand) and the sorting from 1.363 to 0.433 ϕ (i.e. poorly to well-sorted). It is also notable that B1 remained the only site with fine-grained sediment (Figure 4.7a). This could be related to decreased energy of the transporting medium and saline waters in this deep site, resulting to fine sediment grains (Folk, 1974).

In September 2015, the sediment in the lower reaches did not change except for site K2 that became fine and very well-sorted while K3 at the mouth became very well-sorted (Figure 4.8a). The variation in the mean size in the lower reaches ranged from 2.014 to 1.593 ϕ (i.e. fine to medium sand) while sorting ranged from 0.570 to 0.336 ϕ (i.e. moderately to very well-sorted) (Figure 4.8b). The sediment in the Keurbooms tributary remained unchanged. The mean size varied from

1.618 to 0.116 ϕ (i.e. medium to coarse sand) while sorting ranged from 0.871 to 0.366 ϕ (moderately to well-sorted sand). It was also notable that site K19 remained coarse while K22 in the upper reaches of the Keurbooms tributary became coarse sand with the lowest phi (ϕ) value of 0.116 ϕ (Figure 4.8a). Similar to February 2015, the sediment in the Bitou tributary became much coarser during the September 2015 period. However, it was notable that site B1 remained the only site with fine-grained sediment, while sites Bitou_upper and B6 were characterized by coarse and very coarse sand respectively (Figure 4.8a). The mean size therefore ranged from 2.427 to -0.014 ϕ (i.e. fine to very coarse sand) while sorting ranged from 1.316 to 0.437 ϕ (i.e. poorly to well- sorted).

Overall, in June 2014, the sediment mean size ranged from 0.736 to 3.916 ϕ with an average of 1.550 ± 0.118 ϕ while in February 2015 it ranged from 0.765 to 2.213 ϕ with an average of 1.522 ± 0.063 ϕ. In September 2015, the mean size decreased slightly, ranging from -0.014 to 2.427 ϕ with an average of 1.416 ± 0.099 ϕ. In terms of sorting, the June 2014 samples ranged from 0.410 to 1.839 ϕ with an average of 0.805 ±0.065 ϕ while February 2015 ranged from 0.364 to 1.363 ϕ with an average of 0.696 ± 0.052 ϕ. In September 2015, sorting ranged from 0.336 to 1.316 ϕ with an average of 0.628 ± 0.049 ϕ.

4.5 4 Mean size (ɸ)

) 3.5 ϕ 3 2.5 2 1.5

Meangrain size ( 1 0.5

B1 B2 B4 B5 B6

K2 K4 K5 K6 K7 K9

K21 K10 K11 K12 K13 K14 K15 K16 K17 K18 K19 K20 K23 K24 K25 K26

Bitou drift

K3_Mouth

K22_Upper

Bitou_Upper

K1_Blind arm K8_Confluence Sites

(a)

2 1.8 Sorting (ɸ) 1.6

1.4 )

ϕ 1.2 1

0.8 Sorting ( 0.6 0.4 0.2

B2 B1 B4 B5 B6

K4 K2 K5 K6 K7 K9

K16 K10 K11 K12 K13 K14 K15 K17 K18 K19 K20 K21 K23 K24 K25 K26

Bitou drift

K3_Mouth

K22_Upper

Bitou_Upper K1_Blind arm K8_Confluence Sites

(b)

Figure 4.6: Distribution pattern of (a) mean sediment grain size and (b) sorting in June 2014.

2.5

2 Mean (ɸ) ) ϕ 1.5

1 Mean size Meansize (

0.5

B3 B1 B2 B4 B5 B6

K7 K2 K4 K5 K6 K9

K10 K11 K12 K13 K14 K15 K16 K17 K18 K19 K20 K21 K22

B5_Cliff

K3_Mouth

Bitou_Upper

K1_Blind arm K8_Confluence Sites

(a)

1.6 1.4 Sorting (ɸ) 1.2

) 1 ϕ 0.8

Sorting ( 0.6 0.4 0.2

B1 B2 B3 B4 B5 B6

K2 K4 K5 K6 K7 K9

K12 K10 K11 K13 K14 K15 K16 K17 K18 K19 K20 K21 K22

B5_Cliff

K3_Mouth

Bitou_Upper

K1_Blind arm K8_Confluence Sites

(b)

Figure 4.7: Distribution pattern of (a) mean sediment grain size and (b) sorting in February 2015.

3 Mean (ɸ) 2.5

) ϕ 1.5

Mean size Meansize ( 0.5

-0.5

B1 B2 B3 B4 B5 B6

K2 K4 K5 K6 K7 K9

K10 K11 K12 K13 K14 K15 K16 K17 K18 K19 K20 K21 K22

K3_Mouth

Bitou_Upper

K1_Blind arm K8_Confluence Sites

(a)

1.4 Sorting (ɸ) 1.2

1 ) ϕ 0.8

0.6 Sorting ( 0.4

0.2

B4 B1 B2 B3 B5 B6

K2 K4 K5 K6 K7 K9

K12 K10 K11 K13 K14 K15 K16 K17 K18 K19 K20 K21 K22

K3_Mouth

Bitou_Upper K1_Blind arm K8_Confluence Sites

Figure 4.8: Distribution pattern of (a) mean sediment grain size and (b) sorting in September 2015.

The mean and sorting value is the preferred tool to indicate the sediment distribution pattern (Waznah et al. 2010). An attempt to highlight the mode and environment of deposition will be made from this data. The scatter plots of the correlation between the mean size and sorting of all sampled periods (i.e. June 2014, February 2015 and September 2015) in the Keurbooms Estuary are shown in Figures 4.9, 4.10 and 4.11.

Generally, the sediment in the lower reaches was dominated by well-sorted sand in June 2014 and there was significant negative correlation (i.e. r=-0.865; p < 0.05)) between mean sediment grain size and sorting (Figure 4.9a). The plot shows that when the mean size phi (ϕ) values decrease the sediment become less sorted. There was positive correlation between mean sediment grain size and sorting in the Keurbooms tributary, but significant (i.e. r=0.221; p > 0.05). The Keurbooms tributary comprised mostly of moderately sorted medium sand and sorting showed not trend with mean sediment grain size (Figure 4.9b). The moderately sorted nature of sediments in the Keurbooms tributary could be due to the relatively constant energy of the transport medium. The scatter plot (Figure 4.9c) for the sediment in the Bitou tributary shows a strong positive correlation (r=0.738) between mean sediment grain size and sorting, but not significant (p > 0.05). The plot indicates that the finer the sediments the more poorly-sorted they become.

During February 2015, the sediment in the lower reaches was entirely composed of moderately to well-sorted medium sand. However, the scatter plot (Figure 4.10a) showed a negative correlation between mean sediment grain size and sorting, but not significant (r=-0.0680, p > 0.05). Although the sediment was mostly moderated well sorted medium sand, but became less sorted with decreasing mean size phi values. Sediments deposited in the Keurbooms tributary were mostly dominated by moderately well to moderately-sorted medium sand. There was a weak negative correlation between mean size and sorting, but not significant (r=-0.016; p > 0.05) and the sediment sorting showed no increasing trend with mean sediment grain size (Figure 4.10b). There was strong negative correlation between mean sediment grain size and sorting, but not significant for the sediment deposited in the Bitou tributary during February 2015 period (r=-0.619; p > 0.05). The sediment became less sorted with decreasing mean grain size (Figure 4.10c).

During September 2015, the sediment in the lower reaches was mostly well sorted and very well sorted at site K2 behind the mouth and K3 at the mouth. There was significantly strong negative correlation between mean sediment grain size and sorting (r=-0.726; p < 0.05). The scatter plot

55 showed sediments to be less sorted with decreasing mean size phi values (Figure 4.11a). There was also negative correlation between mean sediment grain size and sorting, but not significant for sediment deposited in the Keurbooms (r=-0.411; p > 0.05) and Bitou tributaries (r=-0.130; p > 0.05). The scatter plots (Figure 4.11b & c) showed that the sediments became less sorted with decreasing mean size phi values. However, in few circumstances, coarse sediment at site K22 and B6 (low mean size phi values) were moderately-sorted. This could be related to change in energy of the transport medium, which may suggest that the sediments were deposited under moderately low energy conditions.

4 )

ϕ 3 r = -0.865

1 Meangrain size (

0 0 0.5 1 1.5 2 (a) Sorting (ϕ)

4 )

ϕ 3 r = 0.221

1 Meangrain size (

0 0 0.5 1 1.5 2 (b) Sorting (ϕ)

r = 0.738

) ϕ

1 Meangrain size (

0 0 0.5 1 1.5 2 (c) Sorting (ϕ)

Figure 4.9: The correlation between mean size and sorting of June 2014 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary.

r = -0.680 )

ϕ 3

1 Meangrain size (

0 0 0.5 1 1.5 2 (a) Sorting (ϕ)

r = -0.016 )

ϕ 3

1 Meangrain size (

0 0 0.5 1 1.5 2 (b) Sorting (ϕ)

r = -0.619 )

ϕ 3

1 Meangrain size (

0 0 0.5 1 1.5 2 (c) Sorting (ϕ)

Figure 4.10: The correlation between mean size and sorting of February 2015 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary. 58

) r = -0.726 ϕ 3

1 Meangrain size (

0 0 0.5 1 1.5 2 (a) Sorting (ϕ)

4 )

ϕ 3 r = -0.411

1 Meangrain size (

0 0 0.5 1 1.5 2 (b) Sorting (ϕ)

3.5

) r = -0.130 ϕ 2.5

1.5

Meangrain size ( 0.5

-0.5 0 0.5 1 1.5 2 Sorting (ϕ) (c)

Figure 4.11: The correlation between mean size and sorting of September 2015 sediment deposited in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary. 59

4.3.3 Sediment organic content Spatial distribution trends of sediment organic matter in the Keurbooms Estuary are shown in Figures 4.12, 4.13 and 4.14. In June 2014, organic matter was high in the lower reaches and at selected sites in the Bitou tributary (i.e. B1, B2 & Bitou drift) (Figure 4.12). Notably, site K18 in the Keurbooms tributary had a reasonable amount of organic matter content. In February 2015, the amount of organic matter was reduced with the highest content found at site K21 in the Keurbooms tributary and at site B1 and B5_Cliff in the Bitou tributary (Figure 4.13). Furthermore, sites in the upper Bitou had increased amounts compared with those in the lower reaches and the Keurbooms tributary. September 2015 showed reduced organic matter trends in the Keurbooms tributary but increased trends in the Bitou tributary while the lower reaches similar trends as in February 2015. Notably, the highest organic matter contents were observed at site B1 and B6 (Figure 4.14).

Figure 4.12: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in June 2014.

Figure 4.13: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in February 2015

Figure 4.14: Spatial distribution of sediment organic matter content of the Keurbooms Estuary in September 2015

The mean organic matter concentrations are shown in Figure 4.15. Figure 4.15a indicates that the mean sediment organic matter content was almost uniform at all sites in the lower reaches. Although not significantly so, sites K3 at the mouth and K8 below the confluence had lower organic matter content. The organic matter content varied with sampling location in the Keurbooms tributary and sites K18 and K21 had the highest organic content (Figure 4.15b). The mean organic matter content in the Keurbooms tributary varied from 0.70 ± 1.12% to 5.71 ± 4.08% but did not vary significantly with sampling period (p > 0.05). In the Bitou tributary, the mean organic content varied from 0.82 ± 0.06% to 8.58% ± 2.03% (Figure 4.15c). However, the highest organic content was recorded at the once-off site, Bitou drift (i.e. 15.1%) while it remained high at sites B1, B4 and B5 throughout the study period (Figure 4.15c).

(a)

(b)

(c)

Figure 4.15: Sediment organic matter content in the (a) lower reaches, (b) Keurbooms tributary and (c) Bitou tributary (Mean ± SE, n = 3) (NB: squares without bars were only sampled once). 65

4.3.4 Hydrographic conditions Flow rate results for selected days recorded at the K6H019 gauge farther upstream of the Keurbooms tributary are presented in Figure 4.16. Water salinity and temperature profiles of the lower reaches and Keurbooms tributary are illustrated in Figure 4.17 and 4.18 respectively.

45 40 Flow rate (m³/s) 35 30 25 20 sampled day 15 Flowrate(m³/s) sampled days 10 5 0

(a) Dates

15 sampled day Flowrate(m³/s) Sampled day 10

(b) Dates

45 40 35 30 25 20

15 Flowrate(m³/s) 10 5

2015072

20150720 20150722 20150723 20150724 20150725 20150726 20150727 20150728 20150729 20150730 20150731 20150801 20150802 20150803 20150804 20150805 20150806 20150807 20150808 20150809 20150810 20150811 20150812 20150829 20150830 20150831 (c) 20150719 Dates

Figure 4.16: Flow rate of the Keurbooms tributary recorded on selected days in (a) June, September and October 2014, (b) February, April and June 2015, and (c) July and August 2015.

Water column salinity showed marked trends both spatially and temporally (Figure 4.17). In June 2014, the salinity ranged from 11.9 to 34.2. The salinity profile shows that from the confluence, the Keurbooms tributary was characterised by fresh surface water and became more saline with depth (Figure 4.17). The lower reaches (i.e. after the confluence) was mainly characterised by saline water of up to 34. The salinity on the 9 and 10 September 2014 was recorded during high spring-tide. The salinity ranged from 1.5 to 35.4 on 9 September 2014 and from 5 to 35.1 on 10 September 2014. During both periods, the salinity contour plots show that the estuarine water was characterised by saline water as far as site K17 in the upper reaches (Figure 4.17). In both periods, up to site K17 (September 9, 2014) and K12 September 10, 2014), the bottom salinity exactly equaled the surface salinity (i.e. 26.5) (Figure 4.15). During both periods, the estuary was characterized by fresh surface water flowing over the bottom saline water in the upper reaches (i.e. from K17 and K14 farther upstream during 9 and 10 September 2014 respectively) (Figure 4.17). This well-mixed water column was due to weak river inflow (i.e. 0.544 and 0.549 m³/s on 9 and 10 September respectively – Figure 4.16a) and strong stirring action of the tidal currents. The contour plot for February 2015 period shows a typical salt wedge salinity profile (Figure 4.17). The salinity ranged from 0.3 to 35.2. Similar to June 2014, the salinity in the lower reaches was

67 characterised by saline water of up to 34.3. Although in February 2015 the salinity recordings were conducted during incoming neap-tide, site K8 in the confluence showed decreased salinity values. Farther upstream, the Keurbooms tributary was characterised by fresh surface water flowing over the saline bottom water. This salinity pattern was due to weak tidal currents complimented by strong river inflow (i.e. 4.749 and 8.482 m³/s on 25 and 26 February 2015) (Figure 4.16b). On April 21, 2015 the salinity ranged from 0 to 33. The contour plot shows that estuary was consistently characterised by freshwater inflow as far as at site K6 in the lower reaches (Figure 4.17). Increased salinity values were only evident at sites K3_the mouth, K4, and K5 where the sea water enters the estuary. Although the salinity recordings were taken during the incoming spring-tide, it appears that river inflow was larger than the flooding tidal current. The river inflow recorded at the K6H019 gauging station was 26.473, 22.395, 11.406, 7.582 and 5.613 m³/s on 17, 18, 19, 20 and 21 April 2015 (Figure 4.16b). In September 2015, the salinity ranged from 0.09 to 34.8. Similar to April 2015, the contour plot shows (Figure 4.17) that high saline water was constrained to the lower reaches as far as site K5 while K6, K7 and K8 were characterised by slightly fresh water flowing over the bottom saline water. Although river inflow data for September 2015 were not available at the time of writing up this study, this salinity pattern could be related to strong river inflow and weak stirring action by tidal currents.

Figure 4.17: Contour plots showing salinity measured in the lower reaches and Keurbooms tributary.

In June 2014, the water temperature ranged from 12.6 to 16.3ºC. The upper reaches were characterised by cold surface water with slightly warm water underneath, while the estuarine regime was slightly warmer throughout (Figure 4.18). The water temperature became slightly warmer on September 9 and 10 2014 compared to that recorded in June 2014. On September 9, 2014, the temperature ranged from 16.8 to 20.3ºC and from 16.5 to 19.3ºC on 10 September 2014. In the upper reaches both periods were characterised by slightly warm surface water with cold water underneath (Figure 4.18). On 9 September 2014, the lower reaches were mainly characterised by cold water throughout compared to warm water on 10 September 2014.

The water temperature in February 2015 was warm compared to the previous recorded periods. The temperature ranged from 21.0 to 23.5ºC. The estuarine regime was characterised by warm water throughout the recorded period (Figure 4.18). From site K15 above the N2 bridge towards the head of the estuary with cold water flowing on top of warmer water (Figure 4.18). In April 2015, the water temperature ranged from 14.6 to 17.1ºC. The contour plot shows (Figure 4.18) that the estuarine regime was slightly warmer while the Keurbooms tributary was characterised by cold water with slightly warmer bottom water in the deep sites. In September 2015, water temperature ranged from 12.1 to 18.2ºC. The estuarine regime was characterised by cold marine water with slightly warmer surface water at site K1 and K2 in the blind-arm and K6, K7 and K8 at the confluence (Figure 4.18). The Keurbooms tributary was mostly characterised by warm water with some patches of cold bottom water in deep sites upstream (Figure 4.18).

Figure 4.18: Contour plots showing temperature measured in the lower reaches and Keurbooms tributary.

4.4 General discussion It is commonly believed that grain size distribution is generally related to the sediment source and hydrodynamics during the time the sediment was transported and deposited in the estuary (Mason & Folk, 1958; Ong et al. 2012). However, Dyer (1986) suggested that relating the grain size distributions to the fluid flow relies mainly on how the different sediment grains have been transported and deposited. Normally, fine sediment grains are more easily moved than coarser grains, and as a result tend to be transported in suspension and eventually settle when the flow diminishes, while coarse sediment fractions are transported closer to the bed as bedload and are more likely to be deposited first when the flow diminishes (Dyer, 1979, McLaren, 1981; McLaren & Bowles, 1985; Rosa et al. 2013). In this study, textural analysis was carried out for the purposes of description, comparison and interpretation of sediment, while grain size distribution trends were analysed to differentiate environments of deposition as well as to trace the potential sediment sources.

The sediment textural distribution of the Keurbooms Estuary was exclusively composed of sand-size fractions throughout the study period, except in the Bitou and in few sites in the Keurbooms tributary where fine deposits were evident. Although neither sand/mud nor grain size distribution varied significantly over time, the general grain size distribution trends suggested that spatial sediment distribution of the Keurbooms Estuary is affected by different local sediment sources and hydrodynamic conditions.

The characteristics of sediment deposits are inherited from its source and are dependent on the sedimentary processes such as, winnowing, selective or partial deposition of grain size distribution in transport, and total deposition of the grain size distribution in transport (McLaren, 1981). However, McLaren (1981) suggested that once established, these trends indicate a transport path for sediment movement, which may suggest a model identifying the environment of deposition. With that in mind, relative textural changes between a deposit and its source can be interpreted using three assumptions as described by McLaren (1981), i.e. 1) that a deposit is the product of a single sediment source where a source includes provenance as well as all deposits or facies that might occur between the provenance and the deposits; 2) the assumption that fine grains have a greater probability to be moved by transporting processes than coarser grains, and 3) the greater probability of coarse grains being deposited from sediment in transport than finer grains. The sediment distribution pattern of the Keurbooms Estuary appeared to display a combination of these assumptions.

Similar to the findings of the Amatikulu Estuary by Le Vieux (2010), the sediment distribution pattern in the lower reaches of the estuary was uniform throughout the period of the study and was characterized by well sorted medium sand with almost no mud deposits. Small mud deposits in the lower reaches were mostly found at sites K1 and K2 suggesting that, if by any chance fine sediments have been transported farther down, they are washed away to the sea without having been deposited. This is also an area where tidal action is very active, therefore deposition of fine sediments is unlikely since they are normally deposited in less turbulent conditions (Tucker, 1982). This could have been the reason why sites K1 and K2 (i.e. in the blind arm of the mouth) had evidence of mud compared with the other sites in the lower reaches. Furthermore, visual inspection of the sediment in the lower reaches, indicated shell fragments suggesting marine influence. The uniform nature of sorting in the lower reaches is due to the continual reworking of the sediment by the tidal and river currents combined with a single sediment source (Le Vieux, 2010). Sediment in the lower reaches appear to be mature rather than recently deposited sediment. According to Tucker (1982) a degree of sorting can also contribute towards the textural maturity of the sediment. He explained that texturally immature sandstones are mostly characterized by poorly sorted angular grains while texturally mature sandstone sediments are well sorted with well-rounded grains. Texturally maturity of sediments generally increases with the amount of reworking or distance travelled. The sediment supplied to the estuary either by the rivers or tidal action contribute to the evolution of estuarine morphological structures, such as channel-bank systems, shoals, mouth bars and subaqueous deltas (Liu et al. 2010). In the lower reaches islands of sand banks were from time-to-time evident upstream of the mouth. This could be due to transported sand from the sea and back- barrier but not from the river itself.

Both the Bitou and Keurbooms tributaries were characterized by either medium or coarse sand with fine deposits at selected sites. However, the Bitou tributary appears to be the primary source and depositional centre of fine-grained sediments in the Keurbooms Estuary, while a few sites in the upper reaches of the Keurbooms tributary also showed evidence of fine-grained deposits. The abundance of fine deposits was particularly evident in deeper environments (e.g. sites B1, K18 and K21) and near or on the banks (e.g. sites B4, B5, Bitou_drift and B5_cliff). The four primary sediment types identified using the method of Pye & Blott (2012) were related to the grain size distribution trends. The sand sediment type was mostly confined to the lower reaches and the Keurbooms tributary, where the sediments were mostly well to moderately well sorted medium sand, while the Bitou tributary was characterised by a mixture of very

73 slightly clayey slightly silty sand to very slightly silty sand. The increased range of fine deposits at sites near or on the banks suggest the influence of bank erosion as an important source of fine sediment input in the Bitou tributary. Continuous fine deposits at site B1 in the Bitou tributary could be related weak currents in this deep site as well as the constant high salinity recorded throughout the study (see Appendix 1). Fine sediments (i.e. composed of the clay mineral illite, kaolinite and montmorillonite) are liable to collide and flocculate into large aggregates in high salinity water (Dyer, 1979). This process enhances the settling rates of the sediment particles as they no longer settle as individual particles but as flocculants. Slightly clayey silty sand at the Bitou_drift once-off site was mostly muddy but the site seemed to be influenced by grazing cattle. It is also unclear whether this sediment is transported any farther down the channel. Fine sediment deposits in the upper reaches of the Keurbooms tributary (i.e. sites K18, K20 and K21) appear to have been sourced from Whiskey Creek. The sediment at these sites were slightly darker in colour compared to the yellow – brown sand found at the other sites. McLaren & Bowles (1985) demonstrated that the sediment can become finer in the direction of transport with an increasing energy regime. This could explain the fine deposits at sites K15 and K18 in the Keurbooms tributary. Although sediment mixing is possible at deeper sites, it would require stronger currents for re-suspension and further transport of the fine deposits. Absence of fine deposits farther down in the lower reaches suggest that there is not enough fine sediment resuspension beyond the deeper fine deposit sites.

The majority of the sediments in the Keurbooms tributary were characterized by moderately to well-sorted medium sand with some coarse and poorly sorted sand in the upper sites. Due to decreasing energy of the transport medium, sediments in transport may undergo selective deposition (McLaren, 1981). Although fine sediments are normally deposited during the period of slack water (Kamaruzzaman et al. 2002), but coarse sediments are always likely to be deposited first when the energy of the transport medium decreases (McLaren, 1981). This could explain the observed poorly sorted sediment at K19 followed by poorly sorted fine sand at K18 in the June 2014 sediments. Furthermore, the moderately to well sorted medium sand nature of the Keurbooms tributary suggest that they were deposited during moderate energy conditions (Kamaruzzaman et al. 2002; Waznah et al. 2010) and the coarse sand was deposited during high energy conditions, i.e. floods (Folk & Ward, 1957; Tucker, 1982; Waznah et al. 2010).

The decrease in mean grain size both in February and September 2015 could be related to strong flow rates recorded in September 2014, October 2014, April, June and July 2015. Since fine sediments are easily transported in suspension, it is likely that these sediments were

74 washed out the mouth of the estuary without settling down due to the high flow rates. Furthermore, freshwater floating over the saline bottom water in the Keurbooms tributary could also be attributed to strong river inflow farther upstream in the upper reaches, than in the lower reaches, which is strongly influenced by tidal inflow. However, this saline bottom waters can also explain the deposition of fine sediments at sites K15, K18 and K21. Water column salinity of the Keurbooms Estuary is influenced by very strong tidal mixing in the lower reaches but weak vertical mixing farther upstream in both the Keurbooms and Bitou tributary. Although the Keurbooms tributary was from time to time characterized by freshwater floating over saline bottom waters, the Bitou tributary was entirely fresh up until site B1 (see Appendix 1). This could also be because of the shallow nature of the Bitou tributary and the sandbanks at the N2 Bridge over the Bitou preventing the upstream movement of saline water.

The distribution of organic matter was closely associated with the texture of the sediments. However, water column circulation can also influence the amount of organic matter in the sediment (Burone et al. 2003). Although sediment organic matter of the Keurbooms Estuary varied significantly between sampling periods, the organic content appeared to be dependent on the percentage mud fraction in the sediment (Burone et al. 2003; Kamaruzzaman et al. 2010). High organic content was mainly restricted to the Bitou tributary sites. Organic content as high as 15% was evident at the Bitou drift site. This could be related to a high mud fraction and dense plant material at this site. The abundance of organic matter in the Bitou tributary indicates that the sediments are immature and of riverine origin (Burone et al. 2003; Venkatramanan et al. 2010). Notably, the lower reaches in June 2014 showed a significant increase in organic matter content compared to the February and September 2015 sampling period. High organic matter content in the lower reaches during June 2014 could be due to higher river flows prior to sampling. However, the organic matter usually remains suspended in the water column, it would therefore appear that it is washed away during high flows. The decrease in organic content recorded during subsequent sampling suggests that the organic content and fines were subsequently flushed out of the estuary.

4.5 Conclusion The sediment textural distribution of the Keurbooms Estuary is exclusively composed of sand- size fractions throughout the study period except in the Bitou and at a few deeper sites in the Keurbooms tributary where fine deposits were evident. The spatial sediment distribution of the Keurbooms Estuary is influenced by different local sediment sources as well as hydrodynamic conditions. Although river inflow is fairly strong throughout the estuary, the sediment grain

75 size trends in the lower reaches reflect less or no direct influence from the Keurbooms and Bitou tributaries. Although fine sediment deposits were restricted mostly to the Bitou tributary and at selected sites in the upper Keurbooms tributary, they were unevenly distributed, displaying selective deposition characteristics. This suggests that the fine sediments do not necessarily originate from the rivers themselves but from other sources such as the estuarine channel banks. Furthermore, the amount of organic matter content in the sediment appear to be closely related to the two inputs (i.e. marine and terrestrial inputs). The organic matter content in the Bitou tributary is correlated to the mud fraction while in the lower reaches, the estuarine circulation was important in determining the distribution patterns.

Mohan (1990) found that morphology to have played an important role in the grain size reduction of the Vellar river sediments. Selective fine deposits in the Bitou may indicate the influence of morphology of the Bitou tributary on the transportation and deposition of fine sediment farther down in the tributary. The sediment may be trapped on the banks or creeks but eroded during high flow, thus the banks appear to be the source of fine sediment deposits in the Bitou tributary. Although, flocculation of fine cohesive sediment was not tested in this study, it is probable that the abundance of fine sediment at site B1 and other sites in the Keurbooms tributary were deposited as flocs because of the higher water salinity (Dyer, 1979). Furthermore, deposition of poorly sorted coarse sand in the upper reaches, but moderately to well-sorted medium sand in the middle reaches of the Keurbooms tributary indicate changing transport medium conditions. Although sediment distribution became coarser through the period, the absence of coarse grained sediment farther down the estuary suggest that both the tributaries do not have the capacity to transport coarse grained sediment farther down. This could be due to moderate energy conditions of the river flow during the study period. Although the circulation pattern may not have the capacity to transport coarse sediment farther down the estuary it will remain an important mechanism for size sorting of the sediment (Dyer, 1979). To conclude, it would therefore appear that coarse sediment in the Keurbooms Estuary is moved only during strong floods. Naturally, high flows tend to flush fine sediment out of the estuary to the sea. Therefore, the only place for the fines to remain within the estuarine system is on the estuarine banks, where they can be flushed out during higher flows, or trapped by intertidal salt marsh such as Spartina maritima, where the fines has a greater chance to remain, even during higher flows. Bornman et al. (2016) found S. maritima to play an important as a sediment trap in the intertidal salt marsh of the Swartkops Estuary. The importance of trapping of sediment by the vegetation will be studied and discussed in Chapter 5 of this study.

Chapter 5. Patterns of sediment deposition within the Spartina

maritima salt marsh of the Keurbooms Estuary

5.1 Introduction Salt marshes are among the most productive ecosystems, second after tropical rain forests in term of biodiversity and biological productivity, but their survival is threatened by global sea- level rise and anthropogenic activities (Duarte et al. 2009; Kelly et al. 2011). Generally, salt marshes are characterised by muddy and saline substrates subjected to tidal inundation (Allen & Pye, 1992; Packham & Willis, 1997). Moreover, salt marshes are associated with low-energy and gently sloping coasts where fine sediments can be easily transported and trapped on the marsh surface. The Keurbooms Estuary lacks well developed intertidal areas and as a result the salt marshes are not extensive and S. maritima in particular is limited to the Bitou tributary and the confluence covering an area of 7.078 ha (Bornman & Adams, 2006).

Spartina species are regarded as the main ecosystems engineers in salt marshes (Strong & Ayres, 2009). Through their rigid and densely packed stems and leaves, Spartina species play a significant role in coastal defence by reducing the speed of tidal flow and/or wave energy, causing the precipitation of suspended sediments (Sanchez et al. 2001; Neumeier & Ciavola, 2004; Strong & Ayres, 2009). Sediment entrapment by Spartina does not only stabilize the bank but provide feeding and shelter areas for both marine and estuarine organisms (Adams et al., 1999). S. maritima only occurs in South African warm and cool temperate permanently open estuaries (Adams & Bate, 1995). Sediment entrapment by Spartina species will result in an elevated marsh surface, a process necessary for the continuous existence of salt marshes in the face of global rising sea levels (Cahoon et al., 1995; Stock, 2011). Marsh elevation will induce a number of changes in the soil characteristics and perhaps replacement of Spartina by other species (Sanchez et al. 2001) should elevation exceed their tolerance range.

S. maritima is the first species to occupy the lower intertidal zone in South African permanently open estuaries. It is believed that increased rates of sedimentation are achieved through the establishment of vegetation at low tidal elevation (Culberson et al. 2004). Therefore, the genus Spartina species are particularly important in facilitating sediment accretion which will then result in an elevated marsh surface necessary for continuous survival of coastal salt marshes.

The overall objective of this chapter was to examine patterns of sediment deposition within the S. maritima salt marsh. However, past studies by Christiansen et al. (2000), Temmerman et al. (2003) and Stock (2011) showed that spatial sedimentation patterns are affected by tidal frequency, surface elevation, suspended sediment within the water column, distance from the sediment source and difference in vegetation structure of the marsh. Results from the sediment distribution study of the Keurbooms Estuary (Chapter 4) suggest that fine sediment is more prevalent in the Bitou than the Keurbooms tributary. It was then hypothesized that the fine sediment in the estuary originate from the Bitou tributary rather than the Keurbooms tributary or the sea. To test this hypothesis, suspended sediment concentrations were examined from these three sources (i.e. the sea, Bitou and Keurbooms tributaries).

5.2 Materials and methods 5.2.1 Site description Sediment deposition was examined on the intertidal S. maritima salt marsh surface of the Keurbooms Estuary (Figure 5.1). The estuary is influenced by semi-diurnal, micro-tides and the mean tidal range vary between 0.1 to 1.9 m and 0.4 to 1.6 m during spring-tide and neap- tide respectively (Reddering, 1981; www.windreport.co.za). In the Keurbooms tributary the tidal exchange may reach as far as 14 km upstream during high spring-tide, however because the Bitou tributary is much shallower than the Keurbooms, the tidal amplitude is reduced as a result of the road bridge at Wittedrift, effectively forming the upper limit of the tidal exchange (Huizinga & Slinger, 1999; Bornman & Adams, 2006). Due to the geomorphology of the system, salt marshes, and S. maritima species in particular, are not extensive in the Keurbooms Estuary. The dominant intertidal salt marsh species in the Keurbooms Estuary are; S. maritima, Sarcocornia perennis, Sarcocornia decumbuns, Bassia diffusa and Triglochin species. Bornman & Adams (2006) has calculated area cover by S. maritima to be 7.078 ha in the Keurbooms Estuary. S. maritima is most abundant in the Bitou tributary and the confluence while few stands are also evident in the Keurbooms tributary just above the confluence. Abundance of S. maritima in the Bitou could be related to the presence of large intertidal habitat and appropriate sediment type compared with the limited floodplain area as well as sandy substrate in the Keurbooms tributary.

Suspended sediment concentrations were examined from the mouth (i.e. the sea) and the upper reaches of both tributaries (Figure 5.1). The Bitou tributary is smaller and shallower than the

Keurbooms tributary and its banks are more easily eroded during high flows and/or floods. The mouth has a tendency to migrate along the barrier, northeast to southwest towards Lookout Rocks in response to these floods and oceanic forces (Reddering, 1981; Fromme, 1985). However, there was no major flood event during the study period and the mouth remained more-or-less in the same position although a sand bank was from time-to-time evident immediately upriver of the mouth (Plate 5.1).

Figure 5.1: Locality map showing sediment deposition and suspended sediment study sites.

Plate 5.1: Mouth of the estuary during high tide in April 2015.

5.2.2 Measurement of sediment deposition Pre-weighed 47 mm diameter Whatman Glass Fibre (GF/F) filter papers with a nominal pore diameter of 0.45 µm were used as sediment traps to determine sediment deposition patterns in the salt marshes of the Keurbooms Estuary. Short-term sediment deposition rates allow more frequent sampling and avoids problems such as compaction as experienced during vertical profile measurement. A total of eight sites were selected in the intertidal Spartina maritima salt marsh and three filter papers secured on plastic petri-dishes were deployed at each site (Figure 5.1) over a 24-hour tidal cycle for five tidal periods (i.e. spring-tide on 9 Sept 2014, neap-tide on 22 Oct 2014, neap-tide on 26 Feb 2015, spring-tide on 21 April 2015 and neap-tide on 21 Sept 2015). Using a method modified after Reed (1989, 1992) and Culberson et al. (2004) filter papers were secured on 70 mm diameter plastic petri-dishes. Filter papers were anchored to the marsh surface sediment with two bamboo sticks through the two holes drilled into each dish (Plate 5.2). The bamboo sticks held the filter paper on the edges with very little or no damage to the filter paper during deployment. All the traps were deployed and collected during low tide. After each collection period of 24 hours, the traps were individually capped with a lid for transportation to the laboratory. The filter traps were analysed for sediment deposition and organic matter content.

In addition, approximately 0.5 to 1 kg of surface sediment deposited within the S. maritima zone was collected at each site and stored in sealed plastic bags and transported to the laboratory for particle size, moisture content and organic matter content analysis.

Plate 5.2: Sediment trap deployed on the intertidal S. maritima marsh surface.

5.2.3 Suspended sediment concentration The amount of sediment supply depends on several factors such as suspended sediment concentration in the water body, hydrodynamic conditions, inundation frequency, duration and height/depth (Stock, 2011). Suspended sediment concentration was examined from three sources, i.e. from the sea, the Keurbooms tributary and the Bitou tributary. Three replicates of two litres of water were collected from 0.5 m depth using a Niskin sampling bottle from each station during all sampling periods. Collected waters were then transported in their labelled bottles to the laboratory and analysed for suspended sediment concentration. Secchi readings were also taken at each site as a measure of the transparency of the water. The measurements were taken using a method described by the EPA (2006). The Secchi disk hanged horizontally off the side of the vessel was lowered slowly into the water until it disappeared from the view and then slowly raised until it reappeared. The sequence was repeated at least four times until the exact limit of visibility point was found.

5.2.4 Laboratory analysis Upon arrival at the laboratory, all the samples were sorted and prepared for analysis. The process to analyze the sediment deposition and organic matter on the traps as well as the suspended sediment load and particle size of surface sediment is explained in more detail below.

5.2.4.1 Sediment deposition rates The method to determine sediment deposition rates depends on the type and amount of sediment deposited in the trap. Usually fine sediment takes longer to dry than sandy sediment. The methods used in this study is modified after Culberson et al. (2004). The sediment content deposited on the pre-weighed filter papers was determined after oven drying at 70 ºC for 24 hours. The dried filter paper was then weighed and sediment accumulation rate was then expressed as g/cm². The amount of organic matter was determined by ashing the filter papers at 550 ºC for eight hours as described by Briggs (1977) and Duarte et al. (2013). The filters were then reweighed and organic matter content was determined as a percentage.

5.2.4.2 Suspended sediment concentration Suspended sediment load was determined using the filtering method as described by McCave (1979) through pre-weighed 47 mm in diameter G/F filter papers with a nominal pore diameter of 0.45 µm using a Rocker vacuum pump. The filter paper was then oven dried at 70 °C for 24 hours and reweighed to determine sediment load. The suspended sediment concentration was expressed as g/l.

5.2.4.3 Surface sediment moisture and organic content The sediment moisture and organic matter content were determined according to the method described by Briggs (1977) and Duarte et al. (2013). Approximately 20 g of sediment sample was weighed from each site in crucible and placed in a drying oven at 70ºC for a period of 24 hours. The dried sediment samples were weighed again before placement in a muffle furnace (ashing oven) at 550ºC for 8 hours. The crucibles were removed from the ashing oven and reweighed after cooling down. The percentage organic matter content was determined as a loss of mass during ashing of the initial dry mass using the following equation:

푀푑 − 푀푎 ( ) ∗ 100 푀푑

Where Md is the initial dry sediment mass and Ma is the mass of the sediment after ashing.

5.2.4.4 Surface sediment particle size The hydrometer method, as set out by Gee and Bauder (1986) was used to determine sediment particle size due to the dominance of fine material. Approximately 50 g of air-dried sediment was weighed out in a pre-weighed beaker and allowed to equilibrate with the atmosphere overnight. The air-dried sediment was then placed in a 1 litre measuring cylinder. To this -1 sample 100 ml of 50 g.l solution of Sodium Hexametaphosphate (Na3PO)6 was added. Due to the nature of the Keurbooms Estuary sediment, the sediment mixture was left overnight prior to the start of the experiment to allow sufficient time for the clay conglomerates to break apart. The mixture was then filled up to 1 litre with distilled water. The cylinder was closed off at the mouth and shaken by hand for at least 1 minute. A hydrometer was inserted and readings were taken after 30 seconds, 60 seconds, 3 minutes, 1.5 hours and 24 hours. A blank containing a similar liquid was also prepared without any sediment. The readings were then placed in the following equations to calculate the percentage size fraction in the samples.

C = R-RL

Where C is the concentration of soil in suspension in g.l-1, R is the uncorrected hydrometer reading (in g.l-1) and RL is the hydrometer reading of the blank solution.

퐶 푃 = ( ) ∗ 100 퐶표

Where P is the summation percentage for the given time interval and Co is the oven dried weight of the sample.

X = θt-½

Where X is the mean particle diameter in suspension in µm at time t. θ is the sedimentation parameter (µm min½) and is a function of the hydrometer settling depth, solution viscosity and particle and solution density.

18휂ℎʹ 휃 = ½ [g(휌푠−휌푙)]

3 Where h’ is the hydrometer settling depth (cm). ps =soil particle density (g/cm ), pl = solution density (g/cm3), g = gravitational constant (cm.s-2) and η = fluid viscosity in poise (g.cm-1.s-1).

The relationship of the settling depth to the hydrometer dimensions were approximated by: hʹ = -0.164R + 16.3

Where R is the uncorrected hydrometer reading.

The summation percentage was then calculated as follows:

2 푃2휇m = 푚In ( ) + P24 푋24

Where X24 is the mean particle diameter in suspension at 24 hours, P24 is the summation percentage at 24 hours, and m was determined using the following equation:

푃 −푃 푚 = 1.5 24 ln(푋1.5−푋24)

Where m is the slope of the summation percentage curve between X at 1.5 hours and X at 24 hours. X1.5 is the particle diameter in suspension at 1.5 hours, and P1.5 is the summation percentage at 1.5 hours. This procedure was repeated for the 30 second and 60 second readings.

The sediment was classified subjectively into three main categories, i.e. sand, silt and clay (Zoutendyk & Bickerton, 1999; Mateos-Naranjo et al. 2011).

5.2.4.5 Statistical analysis Analysis of variance between sampling sites and periods was conducted to determined significant differences. Where significant difference was found a Tukey post – hoc test was carried and correlation analyses were also run. All statistical analyses were conducted using STATISTICA (Statistical software developed by Statsoft, Inc.) version 13.0.

5.3 Results 5.3.1 Sediment deposition within S. maritima 5.3.1.1 September 2014 spring-tide Sediment deposited during the September 9, 2014 spring-tide ranged from 0.133 ± 0.0015 g/cm² to 0.287 ± 0.034 g/cm² but there was no significant difference between the sites (p > 0.05). The sediment deposition pattern (Figure 5.2) showed increasing trends away from the mouth (i.e. sites Spar 3, Spar 4, Spar 7 and Spar 8).

5.3.1.2 October 2014 neap-tide During the October 22, 2014 neap-tide the sediment deposition varied from 0.124 ± 0.011 g/cm² to 0.478 ± 0.117 g/cm². The neap-tide resulted in a significant increase (p < 0.05) in deposition compared to September 2014. Sediment deposition at site Spar 8 was significantly higher than those close to the mouth (i.e. Spar 1, Spar 2 and Spar 5) and Spar 7 (p < 0.05) while there was not significant difference in other sites (p > 0.05) (Fig. 5.2) (Figure 5.2).

5.3.1.3 February 2015 neap-tide Sediment deposited during the February 26, 2015 neap-tide was significantly less than September and October 2014 (p < 0.05). The sediment deposition ranged from 0.017 ± 0.007 g/cm² to 0.333 ± 0.096 g/cm² during the February 2015 neap-tide. Sediment deposition was homogenous at all sites except at site Spar 8 (Figure 5.2). Sediment deposited at site Spar 8 was significantly higher than at sites Spar 1, 2, 3, 4, 5, 6 and 7 (p < 0.05).

5.3.1.4 April 2015 Spring-tide The sediment deposition during the April 21, 2015 spring-tide ranged from 0.044 ± 0.003 g/cm² to 0.234 ± 0.184 g/cm². Although, the sediment deposition pattern showed changes compared to the other periods, there was no significant difference between sites and tidal cycles (p > 0.05). The highest deposition was recorded at site Spar 6 in the Keurbooms tributary while the lowest were at site Spar 2 (Figure 5.2).

5.3.1.5 September 2015 neap-tide During the September 21, 2015 neap-tide, sediment deposition ranged from 0.031 ± 0.008 g/cm² to 0.146 ± 0.1 g/cm². Similar to April 2015, there was no significant difference between sites (p > 0.05) and high sediment deposition rates were recorded at sites Spar 3 and Spar 8 (Figure 5.2). For the first time in this study, one filter paper was entirely washed away at site Spar 6. This was as a result of a branch from a tree that was transported and fell on the trap,

85 breaking the petri-dish. Although, there was no significant difference between sites, sediment deposited in September 21, 2015 was significantly lower than that deposited in September and October 2014 (p <0.05).

0.7 Sep-14 0.6

Oct-14 cycle (g/cm²) cycle (g/cm²) - 0.5 Feb-15

0.4 Apr-15 Sep-15 0.3

0.2

0.1

Sediment Sediment deposited per tidal 0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.2: Sediment deposition within the S. maritima in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE, n = 3).

5.3.1.6 Overall deposition Although sediment deposition varied between sampling period and sites it followed the same pattern for almost all tidal cycles. The overall sediment deposition ranged from 0.085 ± 0.024 g/cm² to 0.267 ± 0.066 g/cm² with no significant difference between sites (p > 0.05). Overall sediment deposition rates (Fig. 5.3) suggest that the deposition were highest furthest from the mouth. However, field observations noted that at sites furthest from the mouth (i.e. site Spar_8), not only sediment was deposited on the traps but other organic materials (Zostera capensis leaves, etc.) as well. Although disturbance to the filter traps was small, some sites such Spar 2 and 7 were damaged by mobile marine organisms, e.g. crabs.

0.4

0.35

0.3

0.25

0.2

0.15

0.1

Sediment Sediment deposition (g/cm²/tide) 0.05

0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.3: Overall sediment deposition within the S. maritima (Mean ± SE; n = 15).

5.3.2 Organic matter deposited on sediment traps within S. maritima 5.3.2.1 September 2014 spring-tide Organic matter content deposited on the sediment traps ranged from 24.56 ± 4.82% to 48.96 ± 2.67% during spring-tide of September 9, 2014. Although, there was no significant difference between the sites, high organic matter content was recorded at site Spar 1, 2 and 6 while the lowest content was found at those sites furthest from the mouth, i.e. mainly at sites Spar 3, 7 and 8 (Figure 5.4).

5.3.2.2 October 2014 neap-tide Deposited organic matter content during the October 22, 2014 neap-tide showed similar trends to those found during September 2014 spring-tide. Organic matter content ranged from 22.38 ± 1.25% to as high as 49.24 ± 11.07% with was no significant difference (p > 0.05) between sites. Opposite to the September 2014 samples, increased organic content were observed at site Spar 5 and decreases at Spar 6 during October 2014 (Figure 5.4).

5.3.2.3 February 2015 neap-tide During the February 26, 2015 neap-tide the deposited organic matter ranged from 20.68 ± 8.52% to as high as 49.85 ± 12.33%. Although there was no significant difference (p > 0.05) between sites, high organic matter content was observed at site Spar 6 and 3 while decreased

87 content was observed at site Spar 1 and 2 compared to those recorded during both September and October 2014 (Figure 5.4).

5.3.2.4 April 2015 spring-tide Deposited organic matter content during the spring-tide of April 21, 2015 ranged from 21.72 ± 5.08% to 37.2 ± 6.27%. It was noticeable that sites furthest from the mouth (i.e. Spar 3, 4, 7 and 8) showed a lower organic matter content than those closer to the mouth (Figure 5.4).

5.3.2.5 September 2015 neap-tide Deposited organic matter content during the neap-tide of September 21, 2015 ranged from 20.71 ± 9.43% to as high as 55.95 ± 8.82%. Figure 5.4 shows increased trends at sites Spar 1, 6 and 7 while sites furthest from the mouth, whereas sites Spar 3, 4 and 8 continued to have low organic content.

80 Sep-14 70

Oct-14 cycle(%)

- 60 Feb-15 Apr-15 50 Sep-15 40

Organic matter Organicmatter deposited per tidal 0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.4: Organic matter deposited on sediment traps within the S. maritima in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE; n = 3).

5.3.2.6 Overall deposition The overall sediment organic matter content deposited on the sediment traps during the study period ranged from 24.78 ± 2.31% to 42.39 ± 5.55%. Sites furthest from the mouth showed a lower organic matter content than those closer to the mouth (Figure 5.5). The overall sediment

88 organic matter deposited at site Spar 6 was significantly higher than that at Spar 8 (p < 0.05). Although sediment particle size was not determined due to insufficient sediment deposition on the traps, it was noted that sites furthest from the mouth were composed of mostly fine sediment while those closer to the mouth were entirely composed of sand-sized particles. There was a negative correlation between deposited sediment and organic matter content on the traps, but not significant (r = -0.689; p > 0.05). Scatter plot indicates that the high organic matter in small amount of sediment deposition (Figure 5.6).

10 Organic matter Organicmatter deposited (%)

0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.5: Overall organic matter deposited within the S. maritima (Mean ± SE; n = 15).

50 R = -0.689 40

Organic matter Organicmatter (%) 10

0 0 0.05 0.1 0.15 0.2 0.25 0.3 Deposition (g)

Figure 5.6: Correlation between organic matter and sediment deposited on the traps within S. maritima.

5.3.3 Suspended sediment concentration 5.3.3.1 September 2014 spring-tide The suspended sediment concentration measured from three sources (i.e. the mouth, Bitou and Keurbooms) varied from as little as 0.004 ± 0.001 g/l to 0.03 ± 0.0004 g/l during the spring- tide of September 9, 2014. Increased suspended concentrations were recorded at the mouth of the estuary with significantly lower (p < 0.05) concentrations at both the Bitou and Keurbooms tributaries (Figure 5.7). Despite the high suspended concentrations at the mouth, the Secchi depth indicate (Figure 5.8) that the water was clear to the bottom at the mouth as well as at both the Bitou and Keurbooms tributaries. The suspended material is therefore of such a low concentration as to not influence water clarity in shallow water.

5.3.3.2 October 2014 neap-tide During the October 22, 2014 neap-tide, suspended concentrations ranged from 0.005 ± 0.0001 g/l to 0.019 ±0.003 g/l. In October 22, 2014, the mouth of the estuary had significantly higher concentrations (p<0.05) than the Keurbooms tributary (Figure 5.7). The Bitou had higher concentrations than the Keurbooms tributary but was not significant. Secchi disk readings were to the bottom for both the mouth and the Bitou tributary and close to the bottom at the Keurbooms tributary (Figure 5.8). The reduced clarity for the Keurbooms is likely because of the high concentration of tannins in the water in the upper reaches, rather than an increased suspended sediment load.

5.3.3.3 February 2015 neap-tide The suspended concentrations ranged from 0.0049 ± 0.0008 g/l to 0.013 ± 0.001 g/l during the February 26, 2015 neap-tide sampling period. Similar to September 2014, the mouth had significantly higher (p < 0.05) concentrations than both the Bitou and Keurbooms tributaries (Figure 5.7). Similar to the October 2014 sampling period, Secchi readings were at the bottom at the mouth and the Bitou and at the one-meter mark in the Keurbooms tributary (Figure 5.8).

5.3.3.4 April 2015 spring-tide During the April 21, 2015 spring-tide, the suspended concentrations ranged from 0.009 ± 0.001 g/l to 0.036 ± 0.003 g/l and followed the same pattern as recorded during the other sampling periods. The mouth had significantly higher concentrations (p < 0.05) than both the Bitou and Keurbooms tributaries (Figure 5.7). In terms of water transparency, the Secchi disk was visible

90 to the bottom of both the mouth and the Bitou (i.e. 1.1 and 0.5 m respectively) while in the Keurbooms tributary it was only visible to 1.1 m of the 3 m depth (Figure 5.8).

5.3.3.5 September 2015 neap-tide The suspended concentrations ranged from 0.02 ± 0.0001 g/l to 0.03 ± 0.008 g/l during the September 21, 2015 neap-tide sampling period. Although there was no significant difference (p>0.05) between sites, the mouth of the estuary continued to show an increased suspended concentration compared to the Bitou and Keurbooms tributaries (Figure 5.7). Secchi disk readings were at the bottom for both the mouth and the Bitou while it was at 0.9 m in the Keurbooms tributary (Figure 5.8).

0.05

cycle 0.045 Sep-14 - 0.04 Oct-14 0.035 Feb-15 Apr-15 0.03 Sep-15

(g/l) 0.025 0.02 0.015 0.01

0.005 Suspended Suspended concentrationper tidal 0 Mouth Bitou Keurbooms Sites

Figure 5.7: Suspended sediment concentration in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide (Mean ± SE; n = 3).

3 Sep-14 2.5 Oct-14 Feb-15 2 Apr-15 Sep-15 1.5

1 Secchi disk Secchi disk depth (m) 0.5

0 Mouth Bitou Keurbooms Sites

Figure 5.8: Secchi depth recorded in September 2014 spring-tide, October 2014 neap-tide, February 2015 neap-tide, April 2015 spring-tide and September 2015 neap-tide.

5.3.3.6 Overall suspended concentration During the study period the mean overall suspended sediment concentration ranged from 0.01 ± 0.002 g/l to 0.02 ± 0.004 g/l. Although Duvenage & Morant (1984) stated that the Bitou tributary is likely to have high suspended sediment load than the Keurbooms tributary that drains mostly medium to coarse quartzite sand but the suspended sediment data in this study showed no difference between these tributaries. The suspended sediment data as shown in Figure 5.9 indicates low suspended sediment concentration from the Bitou and Keurbooms tributaries and a significantly (p < 0.05) higher concentration at the mouth, presumably because of re-suspension in the surf zone. The suspended sediment at the mouth however consisted of large sand particles.

0.035

0.03

Suspended sediment 0.025

0.02

0.015

0.01

0.005 Suspended sediment Suspended sediment concentration(g/l) 0 Mouth Bitou Keurbooms Sites

Figure 5.9: Overall suspended sediment concentration of the Keurbooms Estuary at the three sources (i.e. Mouth, the Bitou and Keurbooms tributaries) (Mean ± SE; n = 5).

5.3.4 Surface sediment moisture content 5.3.4.1 September 2014 spring-tide Sediment moisture contents ranged from 24.73 ± 5.52% to 51.2 ± 8.36% during the September 9, 2014 spring-tide with no significant differences between sites (p > 0.05). Noticeably, sites in the Bitou tributary had higher moisture contents than those found in the Keurbooms although not significant (p > 0.05) (Figure 5.10).

5.3.4.2 October 2014 neap-tide The sediment moisture content ranged from 23.57 ± 0.24% to 53.32 ± 1.52% (p < 0.05) during the October 22, 2014 neap-tide. Significantly higher (p < 0.05) moisture contents were recorded at site Spar 2 in the Bitou marsh with a noticeable, but not significant (p > 0.05), increase at site Spar 7 in the Keurbooms tributary compared to the September 2014 spring-tide (Figure 5.10).

5.3.4.3 February 2015 neap-tide Similar trends to those found in October 2014 was recorded during the February 26, 2015 neap- tide sampling period. Sediment moisture content ranged from 23.31 ± 1.8% to 53.33 ± 3.07%. Significantly increased moisture contents were recorded at site Spar 1 and 2 (p < 0.05) while

Spar 6 continued to have lower moisture contents (Figure 5.10). Statistically, site Spar 6 was significantly lower than both sites Spar 1 and 2 while Spar 3 and 5 were lower than Spar 2 (p < 0.05).

5.3.4.4 April 2015 spring-tide The sediment moisture content ranged from 22.64 ± 0.37% to 53.38 ± 2.61% during the April 21, 2015 spring-tide. Sites Spar 2 and 6 continued to have high and low moisture contents respectively (Figure 5.10). Statistically, site Spar 2 was significantly higher than sites Spar 1, 3, 5, 6, 7 and 8 while Spar 6 was significantly lower than Spar 1, 2, 4 and 7 (p < 0.05).

5.3.4.5 September 2015 neap-tide The patterns of the sediment moisture content across sites during the September 21, 2015 neap- tide followed the same trend as reported for October, February and April periods (Figure 5.10). The sediment moisture content ranged from 27.93 ± 0.53% to as high as 54.9 ± 0.67%. Site Spar 2 was significantly higher than Spar 1, 3, 5, 6 and 8 (p < 0.05). Meanwhile, sites Spar 4 and 7 were the same with no significance difference (p > 0.05) recorded (Figure 5.10).

70 Sep-14 60 Oct-14 Feb-15 50 Apr-15 40 Sep-15

Sediment Sediment moisture content(%) 10

0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.10: Sediment moisture content of surface sediment deposited during Sept 2014 spring-tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap-tide (Mean ± SE; n = 3).

5.3.4.6 Overall sediment moisture content During the study period, the overall sediment moisture content ranged from 25.63 ± 2.09% to 52.58 ± 1.19%. Sites at the Bitou marsh (Spar 1, 2, 3 and 4) appear to have a higher moisture content than those at the Keurbooms marshes (Fig. 5.11). Statistically, sediment moisture content at site Spar 2 was significantly higher than at all other sites (p < 0.05) while Spar 1 was significantly higher than Spar 5, 6 and 8 (p < 0.05). Site Spar 6 was significantly lower than site Spar 4 and 7 (p < 0.05).

10 Sediment Sediment moisture content(%)

0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.11: Overall mean moisture content for S. maritima surface sediment (Mean ± SE; n = 15).

5.3.5 Surface sediment organic content 5.3.5.1 September 2014 spring-tide Sediment organic matter content ranged from 3.66 ± 0.28% to 14.88 ± 2.40% during the September 9, 2014 spring-tide. Site Spar 1 and 2 had a significantly (p < 0.05) higher organic matter content than site Spar 3, 4 and 5 while site Spar 6, 7 and 8 had uniform sediment organic matter (p > 0.05) (Figure 5.12). Significantly lower organic matter contents were recorded at site Spar 3 in the Bitou tributary.

5.3.5.2 October 2014 neap-tide Similar trends of sediment organic matter content to those found during September 9, 2014 were also recorded for the October 22, 2014 neap-tide sampling period (Figure 5.12). Organic

95 matter content ranged from 4.48 ± 0.91% to 16.67 ± 3.63% during the October 2014 neap-tide. Site Spar 1 had a significantly higher (p < 0.05) organic matter content than sites Spar 3, 4 and 5 while Spar 2 had significantly higher contents than site Spar 3. Similar to the September 2014 spring-tide period, site Spar 6, 7 and 8 had uniform organic matter with no statistical difference (Figure 5.12).

5.3.5.3 February 2015 neap-tide Sediment organic matter content ranged from as little as 1.56 ± 0.56% to as high as 21.68 ± 8.05% during the February 26, 2015 neap tide period. Site Spar 2 had significantly higher contents than Spar 3, 4, 5, 6 and 8 (p < 0.05). Organic matter content at site Spar 1 was reduced compared to other sampling periods (September and October 2014) but not significantly (p > 0.05). Furthermore, Spar 6 in the Keurbooms marsh had the lowest content compared with other sites and periods (Figure 5.12).

5.3.5.4 April 2015 spring-tide During the April 21, 2015 spring-tide period the sediment organic matter content ranged from 1.97 ± 0.22% to 12.53 ± 1.49%. A similar pattern to that of February 2015 was recorded, with significant differences between sites but not between sampling periods. Site Spar 2 had a significantly higher organic matter content than site Spar 3, 4, 5, 6 and 8 (p < 0.05) while site Spar 6 continued with a low organic content (Figure 5.12). Statistically, site Spar 6 was significantly lower than Spar 1 and 2 (p < 0.05).

5.3.5.5 September 2015 neap-tide Sediment organic matter content ranged from 3.32 ± 0.10% to 15.71 ± 0.92% during the September 21, 2015 neap-tide sampling period. Similar to the other periods (i.e. February 2015 and April 2015) site Spar 2 had a significantly higher (p < 0.05) organic content than other sites (i.e. Spar 1, 3, 4, 5, 6 and 8) while a noticeable increased, but not significant, content was recorded at site Spar 7 (Figure 5.12).

30 Sep-14 Oct-14 25 Feb-15 20 Apr-15 15 Sep-15

Sediment Sediment organiccontent (%) 5

0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.12: Sediment organic content of surface sediment deposited during Sept 2014 spring- tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap-tide (Mean ± SE; n = 3).

5.3.5.6 Overall sediment organic matter content The overall sediment organic matter content ranged from 4.12 ± 0.47% to 15.68 ± 1.60% during the study. During the period of this study, sediment organic matter content followed the same pattern of the sediment moisture content. Sites Spar 1 and 2 had significantly higher (p < 0.05) organic matter content compared to the other sites (Figure 5.13). Sites Spar 3, 4, 5, 6, 7 and 8 showed no significant difference in their organic matter contents (Figure 5.13).

2 Sediment Sediment organicmatter content (%) 0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Figure 5.13: Overall organic matter content for S. maritima surface sediment (Mean ± SE; n = 15).

5.3.6 Surface sediment particle size 5.3.6.1 September 2014 spring-tide During the September 2014 spring-tide the mean contribution of sand was 52.7 ± 10.6%, silt 40.3 ± 10.4% and clay 2.02 ± 0.58% (p < 0.05). Generally, silt and clay contents were high at sites in the Bitou marsh surface (i.e. Spar 1, 2, 3 and 4) and at the confluence (i.e. Spar 5) (Figure 5.14). However, sites further upstream of the Bitou (i.e. Spar 3 and 4) showed increased sand content (Figure 5.14). Sites in the Keurbooms marsh surface were mainly composed of sand size fractions with some evidence of silt fractions at site Spar 7 (Figure 5.14).

5.3.6.2 October 2014 neap-tide The silt and clay content increased during the October 2014 neap-tide sampling period. The mean sand percentage contribution decreased to 49.7 ± 4.73% while silt and clay fraction increased to 47.9 ± 4.8% and 2.3 ± 0.38%. Significant (p < 0.05) increases in the silt and clay fraction was evident in sites in the Keurbooms marsh surface (Figure 5.14). Site Spar 6 in the Keurbooms marsh had significantly (p < 0.05) higher silt content (i.e. 72.14 ± 4.74%) with concomitant low clay content (i.e. 1.27 ± 0.62%). Noticeably, site Spar 5 in the confluence had the highest clay content (i.e. 4.13 ± 1.38%) compared to other sites. Despite evidence of silt and clay fraction, site Spar 8 had the highest sand size contribution at 67.9 ± 11.6% (Figure 5.14).

5.3.6.3 February 2015 neap-tide The sediment particle size pattern changed significantly during the February 2015 neap-tide sampling period. The mean sand percentage contribution decreased to 42.02 ± 5.21% while the silt and clay fraction increased to 55.65 ± 5.6% and 2.31 ± 0.52% respectively (Figure 5.14). Sites Spar 1 and 2 in the Bitou marsh surface and Spar 8 farther up the Keurbooms marsh surface had significantly higher (p < 0.05) silt contributions than sites Spar 5 and 6 (Figure 5.14). Although sites in the Keurbooms marsh surface had low silt contents (except site Spar 8), the clay fraction was evident in all sites compared to the Bitou sites (Figure 5.14). Notably, site Spar 6 had significantly higher (p < 0.05) clay content than sites Spar 2 and 3 (Figure 5.14).

5.3.6.4 April 2015 spring-tide Mean silt and clay percentage contribution were 67.3 ± 4.7% and 3.4 ± 0.9% respectively while the sand fraction was reduced to 29.34 ± 4.59% during the April 2015 spring-tide. Site Spar 6 in the Keurbooms marsh surface showed a significantly reduced sand content (p < 0.05), but significantly increased silt content compared to other sites (Spar 1, 2, 4 and 7) and to the February 2015 period (Figure 5.14). Notably, site Spar 8 had significantly higher clay content than Spar 5 and 6 while sites Spar 1, 2, 3 and 7 showed no significant difference in clay content (Figure 5.14). Furthermore, clay content was reduced at site Spar 4, although not significantly so (p > 0.05).

5.3.6.5 September 2015 neap-tide During the September 2015 neap-tide, the mean contribution of the sand size fraction was 40.7 ± 5.23%, silt 57.6 ± 5.35% and clay 1.7 ± 0.57%. Site Spar 7 had a significantly higher (p < 0.05) sand-sized fraction but lower silt content than Spar 2 (p < 0.05). Generally, the silt content was higher in the Bitou marsh surface sites with a noticeable clay fraction at sites Spar 3, 4, 5 and 6 (Figure 5.14). Site Spar 4 had a significantly higher (p < 0.05) clay fraction than Spar 1.

100 90 80 70 60 50 40 30 20 10

Sediment Sediment particle size contribution (%) 0

Oct. Oct. 14 Oct. 14 Oct. 14 Oct. 14 Oct. 14 Oct. 14 Oct. 14 Oct. 14

Feb. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Sep. 15 Sep. 14 Feb. 15 Sep. 15 Sep. 14 Feb. 15 Sep. 15

Apr. Apr. 15 Apr. 15 Apr. 15 Apr. 15 Apr. 15 Apr. 15 Apr. 15 Apr. 15 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites Sand Silt Clay

Figure 5.14: Sediment particle size deposited on the S. maritima surface during Sept 2014 spring-tide, Oct 2014 neap-tide, Feb 2015 neap-tide, April 2015 spring-tide and Sept 2015 neap-tide (Mean, n = 3).

5.3.6.6 Overall sediment particle size The overall mean contribution of sand was 40.60 ± 5.23%, silt 56.48 ± 5.35 % and clay 1.70 ± 0.57% during the study period. Although, neither sand nor silt varied significantly between sites (p > 0.05), increased silt but reduced sand-sized fraction was restricted to the Bitou marsh surface sites (Figure 5.15). Notably, sites in the Bitou had higher clay content than the Keurbooms marsh surface sites, although not significantly so (p > 0.05).

100

10 Sediment Sediment particle size contribution (%) 0 Spar 1 Spar 2 Spar 3 Spar 4 Spar 5 Spar 6 Spar 7 Spar 8 Sites

Sand Silt Clay

Figure 5.15: Overall mean sediment particle size deposited on the S. maritima marsh surface (Mean, n = 15).

5.3.7 Sediment types According to the Pye & Blott (2012) particle size classification method, out of the 120 collected sediment samples, roughly 16 primary sediment types were recorded in the surface sediment deposited within the S. maritima stands. These are presented in Table 5.1 and illustrated in Figure 5.16. Very slightly clayey sandy silt is the most dominant sediment type (25% of the 120 collected sediment samples) and was primarily deposited during the February 2015 neap- tide, the April 2015 spring-tide and the September 2015 neap-tide (Figure 5.16). Sandy silt (22.5%) and very slightly clayey sandy silty sand (14.71%) were the most occurring primary sediment types after very slightly clayey sandy silt (Figure 5.16). Although a high sand fraction was reported in September 2014, October 2014 and September 2015 (Figure 5.14), the Pye & Blott (2012) particle size classification indicate that sand, as the primary sediment type was the least (only 5%) found sediment type on the surface sediment deposited in the S. maritima of the Keurbooms Estuary. Although the sediment appears to be pure sand at sites Spar 1, 5, 6 and 7, field observation further suggest that the sediment was composed of fine sand rather than coarse sand and as a result was mostly classified as silty sand.

101

Table 5.1: Primary sediment types found in the surface sediment deposited on the S. maritima marsh surface.

Sediment types No. of sediment samples % of sediment samples Sand 5 4.17 Very slightly clayey sand 2 1.67 Sandy silt 27 22.5 Very slightly clayey sandy silt 30 25.0 Very slightly clayey silty sand 17 14.17 Slightly clayey sandy silt 7 5.83 Very slightly clayey slightly sandy silt 6 5.0 Slightly sandy silt 6 5.0 Slightly clayey silty sand 6 5.0 Very slightly clayey slightly silty sand 2 1.67 Silty sand 6 5.0 Very slightly sandy very slightly clayey 1 0.83 Slightly sandy slightly clayey silt 1 0.83 Very slightly sandy very slightly clayey silt 1 0.83 Slightly silty slightly clayey sand 1 0.83 Slightly silty sand 2 1.67 Total sediment samples 120

102

S sand (s) slightly sandy 09-Sept-2014 (Spring-tide) SI silt (si) slightly silty C clay (c) slightly clayey 22-Oct-2014 (Neap-tide) C 26-Feb-2015 (Neap-tide) s sandy (vs) very slightly sandy (vsi)C si silty (vsi) very slightly silty 100 c clayey (vc) very slightly clayey (vs)C (vs)(vsi)C 21-Apr-2015 (Spring-tide) 21-Sept-2015 (Neap-tide) 90 (s)C (si)C

(s)(si)C

70 sC siC

60 (si)sC (s)siC

ssiC

40 cS cSI (si)cS (s)cSI

30 sicS scSI

20 (c)S

(si)(c)S (c)siS (c)sSI (s)(c)SI (vs)(vc)SI (vsi)(vc)S10 (vc)SI (vc)S (vc)(si)S (vc)siS (vc)sSI (vc)(s)SI

0 SI S (vsi)S (si)S siS sSI (s)SI (vs)SI % sand

Figure 5.16: Ternary diagram showing primary sediment types occurring in the surface sediment of S. maritima stands.

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5.4 General discussion Salt marshes develop through sedimentation and their continued existence in the face of rising sea-levels depends on continuous sediment supply which will result in increases in surface elevation (Cavatorta et al. 2003; Stock, 2011). Short-term sediment deposition rates are important to predict whether or not salt marshes will accrete sufficient sediment to offset the rate of sea-level rise (Cahoon et al. 1995). However, past studies on short-term sediment deposition patterns suggest that sediment supply to the marsh surface is controlled by factors such as distance to the sediment source (Reed et al. 1999; Cavatorta et al. 2003; Temmerman et al. 2003), wind-wave activity (Sheldon, 1968; Reed, 1989) and frequency, height and duration of tidal inundation (Reed, 1989; Christiansen et al. 2000; Rooth & Stevenson, 2000, Temmerman et al. 2003; Culberson et al. 2004; Stock, 2011) while vegetation has been also reported to influence the rate of deposition (Cavartorta et al. 2003; Culberson et al. 2004). In the micro-tidal Keurbooms Estuary, the availability of local sediment and tides appear to be important factors governing the sediment deposition pattern in the S. maritima salt marsh surface. The sediment deposition patterns were in agreement with the Temmerman et al. (2003) integrated spatio-temporal model which explains the deposition according to elevation differences which are in fact equivalent to differences in tidal inundation and height. The spatio-temporal sediment deposition rates were higher further from the mouth while suspended sediment concentrations were high at the mouth and decreased towards the upper reaches of the Bitou and Keurbooms tributaries.

Reed (1989) suggested that sediment deposition on the marsh surface requires both the availability of suspended sediment and the opportunity for that sediment to be transported onto the marsh surface. Sediment deposition is important to maintain marsh surface elevation, but sediment reworking is probably of greater importance in the shorter term (Sheldon, 1968; Reed, 1989). Wind generated wave action is responsible for the reworking of sediment in the intertidal mudflats (Sheldon, 1968) and to resist potential reworking and resuspension, deposited sediments must be consolidated in the marsh surface (Reed, 1989). Temporal variation in sediment deposition rates on the marsh surface showed no obvious pattern but differences in sedimentation between sites suggest a combination of accessibility to the sediment source and tidal inundation frequency and magnitude. The main contemporary source of sediment deposited on the Keurbooms Estuary S. maritima marsh surface appear to be the banks or/and adjacent estuarine channel. Both estuarine channels adjacent to the monitored salt marshes are shallow, commonly less than 3 m deep. It would therefore appear that as the tide

104 advances, smalls waves generated by local winds over the estuarine waters remobilizes the sediment from the bottom or/and the banks of the estuarine channel which is then transported in suspension into the S. maritima marsh surface. Although, sediment particle size was not quantified, field observation suggests that the marsh surface at sites Spar 1, 3 and 6 were composed of unconsolidated sediment, therefore, sediment deposited on filter traps in these sites might have been remobilized by the tidal action from the marsh surface itself rather than from the open channel bed or from the water column.

Apart from the sediment source, marsh surface elevation and frequency of tidal inundation could be attributed to differences in sediment deposition rates on the S. maritima marsh surface. Due to a higher frequency and much longer tidal inundation, lower soil surface elevation marshes are expected to receive higher rates of sediment deposition (Culberson, et al. 2004) while a shorter flooding duration may reduce the opportunity of the suspended sediment to be transported onto higher soil surface elevations (Reed, 1989). Due to limited S. maritima habitat in the Keurbooms Estuary, distance from the estuarine channel was not considered as an important factor when selecting monitoring sites but sites Spar 3, 5, 6, 7 and 8 located close to the main channel while Spar 1, 2 and 4 had a more elevated interior marsh surface. Notably, sites along the channel (i.e. Spar 3, 6 and 8 except Spar 5 and 7) had higher sediment deposition rates than the interior sites at Spar 1, 2 and 4. These sediment deposition differences could be related to the combination of sediment resuspension and longer tidal inundation at the sites closest to the channel. Reed et al. (1999) and Temmerman et al. (2003) found that proximity to the creeks had affected the rate of sediment deposition. Although, site Spar 2 was near the creek, the high marsh elevation and insufficient tidal waters to re-suspend consolidated sediment from the marsh surface reduced the sediment deposition (Wang et al. 1993).

The presence of vegetation, particularly aboveground plant biomass is known to reduce the energy in the water column of the flooding water, thus increasing the rate of short-term sediment deposition and decreasing erosion and remobilization of sediment (Christiansen et al. 2000; Culberson et al. 2004; Butzeck et al. 2015). Although all sediment traps for this particular study were deployed in S. maritima stands, the vegetation itself did not appear to influence the rate of sediment deposition but rather the local sediment source. The scatter plot indicates a strong negative correlation (r = -0.689) between sediment deposition and organic matter content on the traps. Although sediment particle size was not determined due to insufficient sediment deposition in the traps, it was noted that sites furthest from the mouth were composed mostly of fine sediment while those closer to the mouth were entirely

105 composed of sand-sized particles. Litter accumulation was responsible for the observed higher depositional patterns, especially at sites Spar 6 and 8, and this was due to S. maritima and Z. capensis leaves deposited on the filter paper rather than the sediment itself. The low sediment deposition rates at Spar 2 and 7 could also be attributed to damage to the edges of the filter paper by crabs. However, the amount of organic matter content revealed a curious anomaly. The organic matter was high close to mouth especially at those sites in the interior marsh surface. Reed et al. (1999) also found organic matter content of the Hut marshes, North Norfolk, to increase with distance away from the creek. Organic matter tends to float and is more readily transported by tides and is more likely to reach interior marsh sites than their original sources or low-lying sites (Reed et al. 1999; Culberson et al. 2004). High organic matter contents at sites Spar 1, 2, 6 and 7 could have been due to the combination of this process and deposited plant litter, while at Spar 4 and 5 it is more likely due to the contribution of the fine-grained sediment deposited on the filter traps. At sites Spar 3 and 8 the organic matter content suggest that plant litter makes up the most of the organic matter rather than transported organic matter with the suspended sediment.

Effects of wind waves on suspended sediment is well studied (Reed, 1989; Wang et al. 1993). Although not significant, differences in suspended sediment concentrations at the mouth could be related to the different prevailing winds generated in the Plettenberg Bay coast rather than the tidal cycles alone. Notably, wind wave action was great during the September 2015 neap- tide period, and could explain the high suspended sediment concentrations recorded during that period. However, suspended sediments from the mouth are characterized by large sand particles, and therefore are unlikely to be transported further up to the S. maritima marsh surface without settling out of the water column. On the other hand, low suspended sediment concentrations in both the Bitou and Keurbooms tributaries could be due to low flow rates and lack of available sediment sources. Although sediment particle size was not quantified due to small sediment concentration, visual observation indicate that suspended concentrations were characterized by the small fine fraction and the organic fraction. Furthermore, Secchi disk measurements further indicated that the water column of both tributaries were clear, further suggesting small suspended concentrations carried by these two tributaries. It would therefore appear that the only available sediment for these tributaries is transported along the estuarine bottom and the river flow is insufficient to re-suspend sufficiently to be transported as suspended sediment further down the estuary. Alternatively, fine sediment may be transported

106 as suspended load during medium to large floods and the fines that remain in the system are then reworked onto the marsh surfaces through various erosion and depositional processes.

The intertidal areas in estuaries are often known as the main areas for the deposition of muddy sediments but sediment distributions in estuaries are continually changing with the changing river flow and tidal range and will therefore never achieve a true steady state (McLusky, 1981). The sediment particle size of the surface sediments deposited within the S. maritima marsh was both spatially and temporally variable but indicated that fine sediments were deposited mostly on the Bitou marsh rather than on the Keurbooms marsh surface. The deposition of sediments within the S. maritima marsh surface is related to two main factors, i.e. the availability of sediment to the marsh surface and the ability of these sediments to be transported to the marsh surface by the hydrodynamic conditions i.e. both tidal and river flow. Overall the particle size of the surface sediment at sites Spar 1, 2 and 3 in the Bitou marsh had a high silt content but reduced sand fractions (less than 37%) while site Spar 4 had uniform silt and sand concentrations but with a higher clay fraction (i.e. > 3%) compared to the other sites in the Bitou section. Deposition of fine sediment in the Bitou marsh could be due to resuspension of the intertidal mudflat (especially at sites Spar 2 and 4) which are then trapped by the vegetation (Reed, 1989; Culberson et al. 2004). The relatively high sand and decreased silt content in the Keurbooms marsh sites (i.e. Spar 5, 6, 7 and 8) could be attributed to the combination of sediment source and active tidal action and strong river flow compared to the Bitou marsh sites. Evidence of small fractions of clay-sized sediments in the Keurbooms marsh surface show ability of these marshes to trap fine sediments regardless of the source.

There is a general assumption that sedimentary organic matter is related to the grain size composition of the sediment. In particular, a higher content of organic matter tends to occur in sediment with a higher mud content (i.e. silt and clay content) due to a greater surface area (Magni et al. 2008). Magni et al. (2008) found that the fine sediments were more organic enriched than coarser sediments in the Cabras lagoon, Italy. Indeed, sediment organic matter content of the S. maritima surface sediment in the Keurbooms Estuary increased in the fine sediments (i.e. silt and clay fraction). Furthermore, the surface sediments of the intertidal S. maritima salt marsh in the Keurbooms Estuary were relatively moist throughout, probably due to frequent tidal inundation and the presence of a shallow water table (Bornman et al. 2004) but followed the same pattern as the sediment organic matter. The silty sediment nature of these sediments has also influence their water holding capacity thus they were moist throughout. Sediment texture is known as an important factor influencing sediment moisture content

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(Gomez-Plaza et al. 2001), while organic matter content has also been shown to increase the water holding capacity of the sediments (Bornman et al. 2004; Shaw, 2007). Normally, sediment moisture content is contained in the interstitial pore spaces of sediment particles where the size of the pores depends on the size of the sediment grains (Shaw, 2007). Although large sediment grains may accumulate large quantities of water, the large spaces and irregular shapes means water is easily transferable through a hydraulic gradient (Gomez-Plaza et al. 2001). Meanwhile, fine sediments (i.e. clay and silt particles) retain the most moisture due to its small particle sizes and interstitial spaces.

Storm or flood events are known to be an important sediment transporting agent for the long- term accretionary budgets of the marsh surface (Rooth & Stevenson, 2000). However, neither was recorded during the study period and therefore their influence and contribution to short- term sediment deposition remain unknown. However, spatial and temporal variability of the surface sediment deposited on the S. maritima marsh indicate that the processes responsible for sediment deposition are currently active. Therefore, the initial null-hypothesis of this study (Chapter 5), that the fine sediment in the estuary originate from the Bitou but rather from the Keurbooms tributary and the sea could not be proven. However, the results of the surface sediment deposited on the S. maritima salt marsh suggest active sedimentation of fines does take place on the marsh surface, although the source is more likely re-suspended sediment from the banks or the mudflats rather than from the tributaries.

5.5 Conclusion Although S. maritima plants are known to trap sediment from daily tidal deposition, there was no clear influence on the sediment deposition rates. Similar to earlier studies (Reed, 1989; Reed et al. 1999; Rooth & Stevenson, 2000; Temmerman et al. 2003; Culberson et al. 2004) sediment deposition rates appear to be influenced by the sediment source, marsh surface elevation and frequency of tidal inundation which is affected by spring and neap-tides. The source of the sediment being deposited on the marsh is unlikely to be directly from the rivers themselves or the sea. The increase in organic matter content in the interior marsh sites were attributed to the combination of transported organic matter by tides which was retained in the interior areas and the fallen plant litter (Culberson et al. 2004).

Although, the particle size of both short-term sediment deposition and suspended sediment was not quantified due to insufficient sediment on the filters, the surface sediment deposited within the S. maritima marsh surface indicated that continuous fine sediments are deposited in the

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Bitou marsh surface but less so in the Keurbooms marsh. The source of the sediments is not necessarily from the tributaries as it was hypothesized but might have been scoured by the tidal and river waters from the banks or the mudflats. Regardless of the source of the sediments deposited in the S. maritima surface, the results of both short-term sediment deposition and the surface sediment studies suggest that the processes responsible for the sediment deposition on the Keurbooms Estuary salt marshes are currently active. However, frequent sediment deposition monitoring is needed to gain a better understanding of the role of floods and storm surges and whether these salt marshes receive sufficient quantities of sediment to keep pace with the rising sea-level.

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Chapter 6. Sediment mineralogy of the Keurbooms Estuary

6.1 Introduction Estuaries are often known as areas of high sedimentation, serving as traps for minerals from inland sources which are transported seaward by rivers as well as materials from the ocean that are transported landward by tidal flow and waves (Kamaruzzman et al. 2002; Waznah et al. 2010). The nature of sedimentary material may vary in terms of its origin, size, shape and composition (Nichols, 2009). Nichols (2009) suggest that almost any mineral which is stable under surface conditions is likely to occur as a detrital grain in a sedimentary rock. However, Macintosh (1976) indicated that although all minerals occur in rocks, only a few are rock forming minerals. Minerals that are most commonly found in the make-up of rocks include, but are not limited to, quartz, feldspar, mica, calcite, olivine, garnet; pyroxenes and amphiboles (Ernst, 1969; Macintosh, 1976; Nichols, 2009). Minor rock-forming minerals include topaz, beryl, apetite, talc, rutile, kyanite and halite. Both these types of rock-forming minerals could be introduced into the sediment as a result of soil weathering from the parent rock and may be transported into an aquatic system with sediment by river flow, tidal flow and wind (Nichols, 2009).

Transformation of clay minerals in sediments are controlled by the sediment source. Abdullah et al. (2015) suggest that sediment from acidic base type rocks will have an abundance of quartz, plagioclase, and alkaline feldspar minerals. Meanwhile, the presence of clay minerals like illite and kaolinite may suggest their derivation from crystallite rocks containing feldspar and mica (Chaudri & Singh, 2012; Abdullah et al. 2015). However, deducing the transportation and deposition of minerals in estuaries is not obvious. As the freshwater interacts with seawater, flocculation may occur, which increases the settling velocity of sediment particles and changes the properties of the particles themselves (Edzwald & O’Melia, 1975). Edzwald & O’Melia (1975) suggest that deposition of minerals depends on the type of mineral and its stability in saline water. Clay minerals, which are relatively stable in low saline waters, are destabilized to a greater degree in water of a higher salinity (Edzwald & O’Melia, 1975). For instance, if illite is present in the parent rock it is most likely to be deposited downstream of an estuary while kaolinite is most likely to be deposited in the freshwater sediments. This is partly because illite is more stable in saline water than kaolinite and as a result it has a slower rate of flocculation than kaolinite (Edzwald & O’Melia, 1975). Therefore, the presence of different minerals in estuarine sediments can be used to trace their provenance and depositional environments (Abdullah et al. 2015).

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The bottom sediments of the Keurbooms Estuary revealed (Chapter 4) coarse-grained size sediment in the upper reaches of both tributaries but the S. maritima surface sediment (Chapter 5) indicated a dominance of fine sediments. However, the sources of these sediments are unclear.

Due to the importance of the salt marsh surface as a depositional environment for fines and clay minerals, the sediment mineralogical composition of the Keurbooms Estuary was investigated to determine the origin and source of fine sediment in the S. maritima surface sediments. The study will form the baseline sediment mineralogy of the Keurbooms Estuary against which future changes could be measured.

Specific objectives of this chapter are:

 To identify the estuarine bottom and Spartina maritima surface sediment mineralogy (including clay minerals);  To determine whether mineral components found in the S. maritima sediments are related to those found in the bottom sediments of the Keurbooms and Bitou tributary;  To determine the main source of the S. maritima surface sediment.

6.2 Materials and methods 6.2.1 Site description Sub-samples of the bottom sediments (i.e. sites K3, K22 and B6) collected in June 25, 2014, February 26, 2015 and September 21, 2015 as well as surface S. maritima sediments at sites Spar 2, Spar 4, Spar 6 and Spar 8 collected in September 9, 2014, February 26, 2015 and September 21, 2015 were selected for this study. The S. maritima surface sediment were part of the sediment deposition study within the S. maritima surface and were therefore only collected from September 2014 as opposed to the bottom sediments which were collected seasonally from June 2014. The selection of these sites were based on their source and depositional environment importance. Site K3 is situated at the mouth of the estuary while K22 and B6 are situated in the Keurbooms and Bitou tributaries respectively (Figure 6.1). Site K22 is in the upper reaches of the Keurbooms tributary while B6 is situated just below the Bitou upper site. B6 was chosen over Bitou upper because it is a more natural site compared to Bitou upper, which is situated at the small bridge with evidence of eroded sediment from the gravel road.

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Sites Spar 2 and 4 were located in the Bitou tributary S. maritima marsh surface while sites Spar 6 and 8 were in the Keurbooms tributary S. maritima marsh surface. Site Spar 8 was approximately 400 metres below the N2 road bridge while site Spar 6 was situated on the S. maritima marsh surface on large sandflats just opposite the confluence in the Keurbooms section (Plate 6.1).

The two tributaries differ with respect to geomorphology and geology. The Keurbooms tributary, as the main tributary of the estuary, flows through deep, forested gorges of quartzite mountains while the smaller Bitou tributary flows through extensive floodplains vegetated with salt marshes, reeds and sedges as well as agricultural land. In terms of geology, the lower reaches are underlain by Tertiary to Quaternary marine and estuarine terrace gravel and partly calcareous sand (Duvenage & Morant, 1984), while the Keurbooms tributary is underlain mainly by the Table Mountain quartzite sandstone bedrock with a narrow strip of shale and siltstone of the Bokkeveld Group above the N2 Bridge (Figure 3.2).

The Bitou tributary is underlain mostly by marine and estuarine sandstone, conglomerate and shale of the Enon Formation (Figure 3.2) (Reddering, 1993; 1999). More than half of the upper section of the Bitou River is underlain by Table Mountain quartzite but these supply very little sandy sediment to the system because of the resistant nature of the quartzite to erosion (Reddering, 1999)

Due to the distinctive nature of their geology, the sediment supplied by the Bitou and Keurbooms tributaries should differ. The Bitou tributary supplies more clay and silty sediment compared to quartzite sandy sediment of the Keurbooms tributary (Reddering, 1999). This is partly because the Bokkeveld Group predominantly consists of mudstones that weathers more easily than the quartzite, producing fine-grained sedimentary fractions. Although a strip of shale and siltstone is evident crossing the Keurbooms tributary, it is very small and as result the sediment supply should also have a limited influence on the sediment composition of the estuary.

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Figure 6.1: Locality map showing both channel bottom and S. maritima surface sediment study sites used to determine sediment mineralogy.

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Plate 6.1: Sandflats at site Spar 6 in the Keurbooms tributary opposite the confluence. Note the sandbanks adjacent to the S. maritima stands.

6.2.2 Sediment preparation A total of 21 sub-samples, nine bottom sediments and 12 S. maritima surface sediments collected from sites K3, K22 and B6, and Spar 2, 4, 6 and 8 respectively during June 2014, February 2015 and September 2015 sampling periods were prepared for sediment mineralogy analysis. All samples were oven-dried at 70ºC for 24 hours. After drying, the sediments were pulverized into powder using a ball mill. Measures were taken to avoid any kind of contamination by cleaning the pan of the mill several times as well as rinsing with alcohol after each sample.

X-ray diffraction (XRD) was used to identify the mineralogical components in the sediment samples. The sediment samples were randomly mounted in aluminium powder holders using the back-loaded method as described by Moore & Reynolds (1989). The sample loader was cleaned and placed into the sample changer according to the label and placed in the XRD machine for analysis.

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6.2.2.1 X-Ray Diffraction analysis The XRD analysis was conducted using a PANalytical Empyrean machine (Plate 6.2) of the Department of Geology at the University of the Free State. The machine was set to run for 42 minutes from 3.5 – 70 degrees for each sample. The computer (PC) connected to the PANalytical Empyrean machine was used to collect the sediment mineral data using Panalytical data collector. The sediment minerals were then identified on the PC using the Panalytical High Score desktop software (version 4.5).

Plate 6.2: Operating the PANalytical Empyrean machine.

6.2.2.2 The analytic identification of minerals Both qualitative and semi-quantitative analyses were conducted. The method described by Moore & Reynolds (1989) was used to identify the minerals available in each sediment sample. Mineral identification was conducted by searching for the mineral that explain the strongest peak or peaks. The identified mineral was confirmed by finding the positions of weaker peaks for the same mineral. Once a set of these peaks were confirmed as belonging to a particular mineral, these peaks were eliminated from the consideration. For example, quartz has its strongest peak at 26.65 º2θ for Cu Kɑ radiation, therefore if this peak is present, it is ideal to check the 20.85 º2θ position as it is where the second most intense peak of quartz occurs. This procedure was repeated until all peaks were identified. Identified minerals were verified using

115 the Handbook of Mineralogy Powder Diffraction Files (www.handbookofmineralogy.org/index.html).

The semi-quantitative analysis of the minerals was determined according to the diffraction pattern. Only the percentage of the minerals was calculated. The percentage content of the minerals was calculated using peak height values of the mineral divided by the total count of the peak values of all minerals multiplied by 100 to obtain the percentage content of the respective mineral. Analysis of variance between sampling sites and periods was conducted to determined significant differences. Where significant difference was found a Tukey post – hoc test was carried out. All statistical analyses were conducted using STATISTICA version 13.0.

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6.3 Results 6.3.1 Bottom sediments Table 6.1 shows the presence of 11 minerals found in the bottom sediment of the Keurbooms Estuary. These minerals were: quartz, mica (i.e. muscovite), halite, rutile, clinochlore, chalcopyrite, K-feldspar (i.e. microcline), plagioclase (i.e. albite), aragonite, kaolinite and anatase. Quartz is by far the most common of the silica minerals in sedimentary rocks (Moore & Reynolds, 1989). Quartz was the most abundant mineral found in the bottom sediment of the Keurbooms Estuary. On average, quartz comprised 76.7% of the bottom sediments of the Keurbooms Estuary. However, site K3 at the mouth had a significantly lower quartz content than B6 in the Bitou (p < 0.05) but not significantly lower than K22 in the Keurbooms tributary. Muscovite, a member of the mica group, was the second most abundant silicate mineral found in the bottom sediments of the Keurbooms Estuary. On average, mica comprised 4.3% of the bottom sediments with the majority found in the Keurbooms tributary (i.e. 6.8%), 6.1% in the Bitou tributary and none of this mineral was evident at site K3 in the mouth of the estuary. Halite was found at all the sites, i.e. 6% at K3, 3.1% at K22 and 1.6% at B6. Site K3 had a significantly higher content than at B6 (p < 0.05). There are several series of feldspars found in South Africa (Macintosh, 1976) and monoclinic K-feldspar was the only feldspar identified in the sediments of the Keurbooms Estuary. On average, K-feldspar made up 2.5% of all the bottom sediment (Table 6.1) but site K3 in the mouth had a significantly higher content than B6 (p < 0.05) but not significantly higher than K22. Rutile and plagioclase were found in almost all the sites throughout the period of the study. On average, the content of rutile and plagioclase comprised 2.7% and 2.4% respectively (Table 6.1).

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Table 6.1: Sediment mineral species found in the estuarine bottom sediment of the Keurbooms Estuary.

Quartz Mica Halite Rutile Clinochlore Chalcopyrite K-Feldspar Plagioclase Aragonite Kaolinite Anatase Sites % % % % % % % % % % %

K3_June 2014 77.5 0.0 7.0 4.2 0.0 0.0 4.2 3.3 3.8 0.0 0.0

K3_Feb 2015 71.1 0.0 5.0 3.6 0.0 10.3 3.6 3.1 3.3 0.0 0.0

K3_Sept 2015 67.3 0.0 6.0 4.1 0.0 11.2 4.1 3.6 3.6 0.0 0.0

K22_June 2014 77.1 6.7 3.6 1.8 4.7 0.0 1.8 0.0 0.0 4.1 0.0

K22_Feb 2015 75.4 6.8 3.8 3.2 4.8 0.0 3.2 2.9 0.0 0.0 0.0

K22_Sept 2015 78.9 6.9 1.9 2.7 4.5 0.0 2.7 2.4 0.0 0.0 0.0

B6_June 2014 80.2 6.6 2.4 2.0 4.9 0.0 0.0 0.0 0.0 0.0 3.8

B6_Feb 2015 83.2 3.5 0.0 2.8 5.1 2.0 0.0 3.4 0.0 0.0 0.0

B6_Sept 2015 79.1 8.3 2.4 0.0 0.0 0.0 3.1 2.5 0.0 4.6 0.0

Average 76.7 4.3 3.6 2.7 2.7 2.6 2.5 2.4 1.2 1.0 0.4

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6.3.1.1 Site K3 Moore & Reynolds (1989) suggested that non – clay minerals are almost always present in the sediments, even if in a small amount, and are always identified by more intense peaks than that of the clay minerals. The XRD peaks for the site K3 in the mouth of the estuary reveal intense non – clay mineral peaks with no evidence of clay minerals during all three sampling periods (Figure 6.2). There were only seven minerals found at site K3, i.e. quartz, chalcopyrite, halite, rutile, K- feldspar, plagioclase and aragonite (Figure 6.2). Quartz, as shown by very sharp peaks at the 26.65 º2θ and 20.85 º2θ positions, was the most abundant mineral found at K3. K-feldspar (i.e. microcline) and plagioclase (i.e. albite) combined were the second most abundant mineral at K3. The presence of K-feldspar is confirmed by the intense peak at 27.45 º2θ close to the sharp quartz main peak, while plagioclase is indicated at the 27.95 º2θ position (Figure 6.2). Moore & Reynolds (1989) suggest that peaks at 23.50 º2θ are not useful to identify the presence of plagioclase since it is very close to the peaks from the alkali series. Feldspars are among the most important rock- forming minerals of the Cape soils derived from the granites (Macintosh, 1976). Halite was also evident throughout as shown by the XRD peaks (Figure 6.2). Reddering (1981) suggest that poor calcium carbonate (CaCO3) sediment enters the estuary from the rivers but up to 35% carbonate rich sediment enters the estuary from the sea through the tidal inlet. However, only a small proportion of calcium carbonate, in particular aragonite (i.e. 3.5%), was found in the K3 sediments (Figure 6.2). The copper mineral, chalcopyrite, was also evident in the February and September 2015 sediments (Figure 6.2).

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Figure 6.2: XRD peaks showing minerals of estuarine bottom sediments at site K3 in the mouth of the estuary during September 2015

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6.3.1.2 Site K22 Of the 11 minerals found in the analysed bottom sediments, eight were found at site K22 (upper reaches). Quartz was the most dominant mineral with reduced concentrations of K-feldspar and plagioclase (2.6% and 1.8% respectively; p > 0.05) compared to the K3 sediments. Furthermore, concentrations of halite and rutile were also reduced to 3.1% and 2.6% respectively although also not significantly (p > 0.05) different to K3. There were three clay mineral species found in the K22 sediments, namely mica, clinochlore and kaolinite. Mica, represented by muscovite, was the most abundant clay mineral found at site K22 in all the samples as shown by the broad XRD reflection peaks (Figure 6.3). Clinochlore is one of chlorite minerals and was the second most abundant clay mineral species found at K22 while kaolinite was only identified in the June 2014 sediments (although XRD peaks did not show it) (Figure 6.3). This is probably due to clay mineral interference. Aragonite was absent in all analysed samples.

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Figure 6.3: XRD peaks showing minerals of estuarine bottom sediments at site K22 in the Keurbooms tributary during June 2014.

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6.3.1.3 Site B6 Quartz, mica, halite, rutile, clinochlore, chalcopyrite, K-feldspar, plagioclase, kaolinite and anatase were the main identified minerals found at site B6 in the Bitou tributary (Table 6.1). Site B6 had significantly higher concentrations of quartz than K3 at the mouth (p < 0.05) but not significantly different to site K22 in the Keurbooms tributary. Similar to K22 sediments, mica, clinochlore and kaolinite were the main clay mineral species found at site B6. Although their concentrations were lower compared to those recorded at site K22 there were not significant (p > 0.05) difference in the mineral content. Clinochlore was identified in June 2014 and February 2015 but not in September 2015. Anatase was detected in the June 2014 sediments as shown by the reflection peaks at the 25.85 º2θ position to the left of the quartz main peak for the first time in this study (Figure 6.4a). Anatase is associated with rutile and is usually derived from other titanium bearing minerals (Anthony et al. 2001). Although quartz was the abundant mineral found in June 2014 but neither K-feldspar nor plagioclase were detected. Furthermore, only one clay mineral i.e. clinochlore was detected in June 2014 whereas kaolinite was only identified in the September 2015 sediment (Figure 6.4b)

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Figure 6.4: XRD peaks showing minerals of estuarine bottom sediments at site B6 in the Bitou tributary during (a) June 2014 and (b) September 2015.

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6.3.2 Surface sediment within S. maritima salt marsh A total of 12 minerals, namely quartz, mica (i.e. muscovite), halite, K-feldspar (i.e. microcline), plagioclase (i.e. albite), kaolinite, rutile, clinochlore, calcite, pyrite, aragonite and chalcopyrite were identified in surface sediment deposited within the S. maritima salt marsh (Table 6.2). Although quartz remained the most abundant mineral, its concentrations were reduced to an average of 67.4% in the surface sediment deposited within the S. maritima marsh surface compared to the channel bottom sediments. Notably, site Spar 2 in the Bitou marsh surface had significantly lower quartz concentrations than those at sites Spar 4, 6 and 8 (p < 0.05) while no difference was found between sites Spar 4, 6 and 8 (p > 0.05). Mica, kaolinite and clinochlore were the three main clay mineral species found throughout the different sites. Although the same clay minerals identified in the bottom sediments were also found in the S. maritima surface sediment, their concentrations were higher compared to the bottom sediments. There was no mica found at site K3 at the mouth of the estuary and therefore Spar 2, 4, 6 and 8 had significantly higher mica concentrations than K3 while Spar 2 had significantly higher concentrations than site B6 in the Bitou (p < 0.05). Furthermore, Spar 2 had significantly higher concentrations of clinochlore than site K3 (p < 0.05) while no significant difference was found between the S. maritima marsh surface and the estuarine bottom sediment for the kaolinite mineral species (p > 0.05).

K-feldspar and plagioclase were also evident in the surface sediment samples with average values of 4.2% and 4.1% respectively. Spar 2 had significantly higher concentrations of K-feldspar and plagioclase than those found at sites K22 and B6 (p < 0.05). Notably, calcite and aragonite only occurred in the surface sediment found at sites in the Keurbooms tributary, while almost uniform concentrations of pyrite were evident at all the sites. Low concentrations of chalcopyrite were found in the June 2014 sediments at site Spar8. Halite and rutile were the characteristic minerals of surface sediment deposited within the S. maritima salt marsh. Spar 2 had significantly higher concentrations of halite than K22 and B6 while Spar 4 was significantly higher than B6 (p < 0.05). No significant difference was found between S. maritima marsh surface and estuarine bottom sediment for the rutile species (p > 0.05).

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Table 6.2: Sediment mineral species found in the S. maritima surface sediment.

Quartz Mica Halite K-feldspar Plagiclase Kaolinite Rutile Clinochlore Calcite Pyrite Aragonite Chalcopyrite Sites % % % % % % % % % % % % Spar 2_September 2014 53.9 8.6 7.9 8.4 5.0 0.0 8.4 6.1 0.0 1.7 0.0 0.0 Spar 2_February 2015 60.1 11.4 9.1 4.4 5.8 0.0 0.0 7.4 0.0 1.8 0.0 0.0 Spar 2_September 2015 56.8 9.8 6.9 5.9 6.5 0.0 5.9 6.5 0.0 1.7 0.0 0.0 Spar 4_September 2014 71.4 8.0 6.3 3.0 4.5 5.6 0.0 0.0 0.0 1.2 0.0 0.0 Spar 4_February 2015 72.7 6.6 4.4 3.2 3.7 0.0 3.2 4.9 0.0 1.1 0.0 0.0 Spar 4_September 2015 71.6 7.2 4.3 5.4 4.7 5.5 0.0 0.0 0.0 1.3 0.0 0.0 Spar 6_September 2014 70.0 7.3 4.7 3.3 3.0 0.0 3.3 4.9 2.3 1.2 0.0 0.0 Spar 6_February 2015 74.8 6.9 3.6 3.9 3.1 0.0 0.0 0.0 4.4 1.4 1.8 0.0 Spar 6_September 2015 64.0 7.9 3.9 3.9 3.5 5.3 3.9 0.0 4.0 1.4 1.9 0.0 Spar 8_September 2014 68.9 7.2 4.4 3.2 3.1 5.3 0.0 0.0 4.7 1.2 0.0 2.0 Spar 8_February 2015 71.2 6.4 3.2 3.4 2.8 4.7 3.4 0.0 3.3 0.0 1.5 0.0 Spar 8_September 2015 72.8 7.1 2.4 2.5 3.2 4.9 2.5 0.0 3.3 1.3 0.0 0.0

Average 67.4 7.9 5.1 4.2 4.1 2.6 2.6 2.5 1.8 1.3 0.4 0.2

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6.3.2.1 Site Spar 2 Quartz, mica, halite, rutile, clinochlore, K-feldspar, plagioclase and pyrite were found at site Spar 2 (Figure 6.5). Quartz was the most abundant mineral with an average of 57.0%. K-feldspar and plagioclase were the two feldspar group species associated with the quartz with an average concentration of 6.2% and 5.8% respectively. Mica (i.e. muscovite) and clinochlore were the only clay mineral species found at site Spar 2 with no kaolinite found throughout the period of the study. Mica was represented by muscovite as shown by the broad XRD reflection peaks at 8.7 º2θ (Figure 6.5). Site Spar 2 had significantly higher concentrations of halite than sites Spar 4, 6 and 8 (p < 0.05) with an average of 7.9%. Additionally, pyrite was also found at site Spar 2 as shown by the reflection peaks at 33 º2θ position (Figure 6.5). Pyrite is the most common and widely distributed sulphide mineral which occurs in ore veins and as isolated crystals in sedimentary rocks (Macintosh, 1976). Meanwhile, rutile occurred only in the September 2014 and September 2015 sediments.

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Figure 6.5: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 2 in the Bitou tributary during September 2015.

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6.3.2.2 Site Spar 4 Quartz concentrations increased significantly at site Spar 4 compared to site Spar 2 (p < 0.05) to an average of 71.9% while K-feldspar and plagioclase were less abundant with average concentrations of 3.9% and 4.3% respectively. Mica, clinochlore and kaolinite were the three clay mineral species found at site Spar 4 with evidence of kaolinite in the September 2014 (Figure 6.6) and September 2015 sediment as shown by the reflection peaks at the 12.4º 2θ position. Muscovite and kaolinite reflections interfere with each other in the September 2014 (Figure 6.6) and September 2015 XRD peaks diagrams. Although they are not clay minerals but Moore & Reynolds (1989) suggest that interference between clay minerals could be caused by quartz and feldspars since some clays are associated with them. Clinochlore was only found in February 2015.

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Figure 6.6: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 4 in the Bitou tributary during September 2014.

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6.3.2.3 Site Spar 6 The XRD diagram (Figure 6.7) show quartz, mica, halite, K-feldspar, plagioclase, kaolinite, rutile, calcite, pyrite and aragonite as the main minerals found at site Spar 6 during September 2015 with no clinochlore. Quartz was the most abundant mineral with an average of 69.6%. Although concentrations of feldspar and plagioclase were lower compared to those reported for sites Spar 2 and 4, no significant (p > 0.05) difference was found. Site spar 6 had significantly lower concentrations of halite than Spar 2 (p < 0.05). Mica, clinochlore and kaolinite remained the only clay mineral species. Kaolinite was only found in September 2015 while clinochlore was restricted to the September 2014 sediment sample (Table 6.2). Calcite was evident at site Spar 6 during all the sampling periods, while aragonite was only found in the February and September 2015 sediments (Figure 6.7).

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Figure 6.7: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 6 in the Keurbooms tributary during September 2015.

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6.3.2.4 Site Spar 8 Quartz, mica, halite, K-feldspar, plagioclase, kaolinite, rutile, calcite, pyrite and chalcopyrite were the main minerals found at site Spar 8 (Table 6.2). The XRD peak diagram (Figure 6.8) reveal sharp peaks, suggesting a dominance of non-clay minerals with mica and kaolinite the only occurring clay minerals. Quartz was still the most abundant mineral with an average percentage of 71.0% while concentrations of halite, K-feldspar and plagioclase were lower compared to sites spar 2, 4 and 6, with average concentrations of 3.3%, 3.1% and 3.0% respectively. Clinochlore was absent during all the sampling periods at Spar 8. Although concentrations of kaolinite were higher compared to other sites (i.e. K3, K22, B6, Spar 2, Spar 4 and Spar 8), it was not significant (p > 0.05). However, concentrations of mica were significantly lower than those reported for Spar 2 (p < 0.05), reduced to an average of 6.9%. Furthermore, calcite remained the characteristic mineral of the S. maritima surface sediment of the Keurbooms tributary. Aragonite was only found during February 2015 at site Spar 8 (Figure 6.8). Pyrite was absent in February 2015 but present in September 2014 and September 2015 while chalcopyrite was only present in September 2014 (Table 6.2).

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Figure 6.8: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 8 in the Keurbooms tributary during February 2015.

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6.4 General discussion Sediment minerals play an important role in understanding the weathering and soil forming process of sediments and by studying their distribution, one will be able to infer the sediment source and depositional environments, especially in estuarine environments (Abdullah et al. 2015). The introduction of sediment minerals into the estuarine environment are a result of weathered soil from the parent rock that is transported by either water currents or wind into their respective depositional environments. The mineralogy of the sediments of the Keurbooms Estuary reflects the geological substrate of the estuary and its tributaries, which are underlain by sandstones, quartzite and shale of the Table Mountain, Witteberg and Bokkeveld series (Figure 3.2). Reddering (1993 & 1999) suggest that the Table Mountain quartzite underlying the Keurbooms Estuary basin supply small amount of sediment to the systems due to its resistance to weathering. However, quartz was the most abundant mineral in both the estuarine bottom and S. maritima surface depositional environments, although concentrations were reduced in the S. maritima surface sediments. Quartz is the most abundant and widespread of all rock-forming minerals found mostly in the igneous, granitic and metamorphic rocks (Ernst, 1969; Macintosh, 1976). Abundance of quartz in the sediments of the Keurbooms Estuary suggest that the underlying sandstone is composed mostly of quartz grains. Furthermore, quartz lacks cleavage and as a result is fractured with difficulty and therefore its grains are only slightly reduced in size during erosion and transportation (Ernst, 1976; Macintosh, 1976). The estuarine bottom sediments at sites B6 and K22 in the upper reaches of the Bitou and Keurbooms tributaries respectively, were characterised by coarse grained sediments (Chapter 4). The abundance quartz in the coarse grained bottom sediments of the Keurbooms Estuary could also be due to its resistance to weathering.

Quartz are normally closely associated with the feldspar minerals (Figure 6.8), one of the most abundant mineral group of the Earth’s crust (Ernst, 1969). Feldspars are abundant in most sediments, in almost all igneous and metamorphic rocks and is the chief constituent of many sandstones and slightly fine-grained sediments (Ernst, 1969). K-feldspar and plagioclase are the main series of feldspars occurring in South Africa (Macintosh, 1976). Both K-feldspar and plagioclase were the only detected feldspars in the Keurbooms Estuary. Interestingly, higher concentrations of K-feldspar were found in the S. maritima surface sediments compared to both B6 and K22 (K3 had higher concentrations than both B6 and K22). The abundance of K-feldspar and plagioclase in the S. maritima surface sediments appear to have been derived from the

136 feldspathic sandstone passing above the slate of shale and siltstone above N2 Bridge (Figure 3.2). Although there is evidence of feldspathic sandstone in the upper reaches of the Keurbooms tributary (Figure 3.2), the lower concentrations of the K-feldspar at site K22 suggest that the resulting sediments are transported further down into the estuary. It is highly possible that high concentration of K-feldspar at site K3 were transported from the upper reaches during previous floods and retained in the mouth.

The bottom sediments of the Keurbooms Estuary revealed (Chapter 4) coarse-grained size sediments in the upper reaches of both tributaries but the S. maritima surface sediments (Chapter 5) showed a dominance of fine sediments. However, the source of these sediments is unclear. Fine grained sediments are known to be transported in suspension and deposited further down the estuary during slack water. Naturally, clay minerals are the main constituents of fine-grained sedimentary rocks such as shale, mudstone, siltstone and fine-grained metamorphic slate and phyllite (Li et al. 2012). Clay minerals in estuarine and ocean sediments are generally formed through weathering processes that is depended on the parent rock types, though they may also be formed in their depositional environments as diagenetic clays as a result of climatic conditions (Edwald & O’Melia, 1975; Lan et al. 2012). However, Edwald & O’Melia (1975) suggest that clays formed through diagenesis are important in deeper sediments and less important for surface sediments. Mica, clinochlore and kaolinite were the only three occurring clay minerals found in both estuarine bottom sediments and S. maritima surface sediments. Although the same clay minerals identified in the bottom sediments were also found in the S. maritima surface sediment, their concentrations were higher compared to the bottom sediments and their distribution was also more representative of the underlying geological rocks supplying the sediment to the estuary.

Mica (muscovite) is a common rock-forming clay mineral associated with quartz, plagioclase and K-feldspar as shown in Figure 6.5 (Anthony et al. 2001). Mica was the most abundant clay mineral in the sediments of the Keurbooms Estuary, especially in the S. maritima surface sediments, but was entirely absent in the mouth. The abundance of mica has been used to elucidate the energy levels of the depositional environments (Rasul & Basaham, 2002). Rasul & Basaham (2002) found that mica was abundant within the high mud concentration areas. Although mica was detected at both sites B6 and K22 in the upper reaches of the Bitou and Keurbooms tributaries respectively, their abundance in the S. maritima surface sediments could be directly related to the fine sediments

137 deposited in these environments, while absence of mica in the mouth was due to absence of the fine sediment fraction.

According to Lan et al. (2012) chlorite and kaolinite are the main minerals making up terrigenous fine particulate matter. Clinochlore was the only occurring chlorite group mineral found in the Keurbooms sediments and naturally, chlorite is the product of physical weathering of metamorphic rocks (Lan et al. 2012) and it has been reported to occur in abundance in old and deeply buried shales (Moore & Reynold, 1989). Li et al. (2012) suggested that if high percentages of illite and chlorite are found, there is also a high likelihood of an abundance of kaolinite as a result of strong chemical weathering. The average concentration of clinochlore in the estuarine bottom sediments were 4.7% and 3.3% while for kaolinite were 1.4% and 1.5% at sites K22 and B6 respectively. Therefore, according to the distribution of these clay minerals in the Keurbooms Estuary, they were mostly likely derived through physically weathering of the shale outcrops. Furthermore, kaolinite is considered to require > 10 000 years to form and it therefore probably developed on old and reworked geomorphic surfaces (Wilson, 1999).

Kaolinite clay minerals species was abundant in the upper reaches sites of the S. maritima surface sediments (i.e. sites Spar 4 and 8) while its concentration was reduced upstream in the upper reaches of both tributaries and entirely absent at those sites close to the mouth (Spar 2 and 6) and at the mouth. Nelson (1960) found kaolinite to occur in abundance in the upper reaches of the Rappahannock Estuary while Edwald & O’Melia (1975) have explained longitudinal distribution of clays in the surface sediments of the Pamlico River Estuary in terms of clay stabilities. Edwald & O’Melia (1975) conducted a series of clay experiments that showed that illite aggregates at a slower rate than either kaolinite or montmorillonite in solutions with a salinity of 17.5. Their results suggest that kaolinite have a high rate of flocculation and as a result are much more likely to be deposited when the water salinity increases. The abundance of kaolinite in the upper sites of the S. maritima surface sediments suggest that the salinity of the estuarine water consistently ranging between 6.3 – 21.3 is most likely responsible for the flocculation of the clay minerals at these sites.

According to Reddering (1999), the slate of the Bokkeveld Group crossing the estuarine channel in the upper reaches of the Keurbooms tributary is so small that it would contribute very little fine- grained sediment to the estuary. Reddering (1999) further stressed that natural traps (deep areas) in the upper reaches of Keurbooms tributary would capture the shale component of the sediment.

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This could explain the evidence of fine-grained sediment at site K21, K18 and B4 (Chapter 4) and the lower abundance of kaolinite at site B6 and K22 in the upper reaches of both the Bitou and Keurbooms tributaries, thereby further restricting the transportation of clay sized sediments onto S. maritima surface. Although, fine-grained sediments are known to be transported in suspension by the river no clay mineral species was detected at site K3 in the mouth of the estuary throughout the study period. These results correspond with the sediment size distribution of the lower reaches, which was almost devoid of fine grained sediments (Chapter 4).

In most rivers around the world, sediment contamination is becoming more of a problem and clay minerals are known to be important traps for heavy metals (Abdullah et al. 2015). The results of the sediment mineralogy in the Keurbooms Estuary show no evidence of contamination in both estuarine bottom sediments or in the S. maritima surface sediments. There were no heavy minerals detected in the Keurbooms Estuary sediments during the study period except for rutile and anatase. Rutile is the most common natural form of titanium dioxide commonly found in igneous, granitic and metamorphosed limestone as well as in clays and shales (Macintosh, 1976; Anthony et al. 2001). On the other hand, anatase is usually derived from other titanium-bearing minerals as a result of hydrothermal solution (Anthony et al. 2001). Mohan (1990) suggest that high density zircon and rutile minerals are always abundant in fine sized sediments, while pyroxenes are mostly found in coarser sediments. Rutile and anatase are often associated with quartz and their presence in the Keurbooms Estuary could be due to the dominance of quartzitic sandstone.

Chalcopyrite is one of the most widely occurring copper minerals and is associated with pyrite, galena, sphalerite, calcite and other copper compounds (Macintosh, 1976). Pyrite was widely found in the S. maritima surface sediments, but not in the estuarine bottom sediments. It is therefore very unlikely that it was derived from its associated mineral, the chalcopyrite, because chalcopyrite was only detected once during September 2014 at site Spar 8 and at the mouth of the estuary during February and September 2015. As the sulphide mineral, pyrite is normally associated with other sulphides in quartz veins of sedimentary and metamorphic rocks (Macintosh, 1976). According to Ernst (1969) both pyrite and chalcopyrite are common accessary minerals of igneous, sedimentary and metamorphic rocks. Ernst (1969) further reported pyrite to be abundant in the sediments of mudstone rich in organic material in the Santa Barbara Basin, California, Zuider Zee at the heads of Norwegian fjords and in the Dead Sea. On average, S. maritima surface

139 sediments had silt and clay contents ranging between 39.03 – 70.78% and 1.48 – 3.35% respectively, while organic matter contents ranged between 4.12 to 15.68%. According to Reddering (1993) pyrite is a common trace component of the sandstone facies on the Robberg Formation but however, he stated that it was absent in the shale facies. In this study, the absence of pyrite in the estuarine bottom sediments and its abundance in the S. maritima surface sediments could be related to common occurrence of Fe – sulphide in the shallow sub-surface of the modern coastal sedimentary environments (Reddering, 1993). Reddering (1993) associated the presence of pyrite in the Robberg Formation with plant debris, therefore its abundance in the S. maritima surface sediment could have been complimented by plant debris from the S. maritima plants.

Halite typically occurs in sedimentary rocks of evaporate association (Ernst, 1969; Battey, 1972; Anthony et al. 2001) and in South Africa halite is commonly found in salt pans and the sea (Macintosh, 1976). Therefore, abundance of halite at site K3 in the mouth of the estuary was no surprise, while occurrence of this mineral species at both K22 and B6 in the Keurbooms and Bitou tributaries suggests that the areas are or were influenced was by the sea. It is possible that as sea levels decreased, marine deposits containing a large proportion of salt remained behind (Macintosh, 1976). The abundance of halite in the S. maritima surface sediment may suggest continuous marine influence as a result of daily tidal inundation.

Calcite and aragonite were the only two calcium carbonate compounds found in the Keurbooms Estuary sediments. But, however, these species were only detected at site K3 in the mouth and at Keurbooms marsh surface sediments (i.e. Spar 6 and 8). These results correspond with Reddering

(1981) and Bornman & Adams (2006) statement that poor calcium carbonate (CaCO3) sediment enters the estuary from the rivers but up to 35% carbonate rich sediment enters the estuary from the sea through the tidal inlet. However, only a small proportion of calcium carbonate, in particular aragonite (i.e. 3.5%), was found in the K3 sediments. Although aragonite is associated with calcite, it is a much rarer mineral than calcite, and can be distinguished from calcite by its hardness, higher relative density and lack of cleavage (Macintosh, 1976). Furthermore, aragonite is a very unstable mineral which readily reverts to calcite at a temperature of 400 °C or at ordinary temperatures if in contact with water or a solution of calcium carbonate (Macintosh, 1976). Although there was evidence of aragonite at site K3 in the mouth, there were no evidence of calcite. Abundance of aragonite in the mouth of the estuary could be related to marine influence in the form of sea shells

140 while calcite in the S. maritima surface sediments, especially at sites Spar 6 and 8, could have been derived from the conglomerate just above the N2 bridge of the Bitou tributary (Figure 3.2) which may contain calcite minerals. The selective occurrence of aragonite could also be due to the fact that it is a rarer mineral than calcite and is only found in few localities in South Africa, e.g. in caves, some near Mossel Bay (Macintosh, 1976).

6.5 Conclusion The sediment minerals found in the Keurbooms Estuary varied both temporally (i.e. June/September 2014, February and September 2015) and spatially (depositional environments, i.e. estuarine bottom and S. maritima surface sediments) and is a good reflection of the underlying geology of the estuary and its tributaries. Although concentration of quartz was reduced in the S. maritima surface sediments, it remained the most abundant mineral in both depositional environments of the Keurbooms Estuary. Furthermore, the abundance of quartz, K-feldspar and plagioclase in both the estuarine bottom sediments and S. maritima surface sediments suggest that the sediments of the Keurbooms Estuary is derived mostly from acidic base rock types. The distribution of clay mineral species shows a selective distribution pattern in both the estuarine bottom and S. maritima surface sediments. Mica was the most abundant clay mineral, while kaolinite was less abundant, especially in the S. maritima surface sediments closer to the mouth (i.e. Spar 2 and 6). Although on average the S. maritima surface sediments had higher concentrations of kaolinite than the estuarine bottom sediments, the overall low abundance of this clay mineral species in the sediments of the Keurbooms Estuary indicate that the sediments are relatively young. The results from the estuarine bottom sediments suggest that main source of these clay mineral species is not necessarily from the catchments but rather from the Bokkeveld shale and siltstone slate crossing the channel above the N2 Bridge. Despite intensive agriculture activities, especially along the Bitou tributary, there was no evidence of anthropogenic influence on the sediment mineralogy of both estuarine bottom and S. maritima surface sediments. The sediment minerals reveal natural geological influences rather than anthropogenic impacts. This may change if large in-channel impoundments are constructed to supply the growing population with freshwater in Plettenberg Bay.

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Chapter 7. Growth and distribution of Spartina maritima intertidal salt marsh in the Keurbooms Estuary

7.1 Introduction The Spartina species are important primary producers occurring in most salt marshes worldwide. Through rigid and densely packed stems and leaves, species of this genus are highly efficient at trapping sediment and protecting the coast against erosion (Neumeier & Ciavola, 2004). The species have a high tolerance for flooded conditions which allows it to colonize bare open intertidal areas to form dense or individual clumps of Spartina populations (Santin et al. 2009). Spartina species increase its distribution through below-ground rhizomes as well as through seed dispersed primarily by the water (Davis, 2004; Sloop et al. 2009; Strong & Ayres, 2009; Strong & Ayres, 2013). S. maritima is the only Spartina population naturally occurring along the southern African coast. The species was first recorded between 1829 and 1930 on the beach of Port Elizabeth and Cape Recife in Algoa Bay (Pierce, 1982) and is now known to be widely distributed in warm and cool temperate permanently open estuaries where there is adequate tidal exchange in the intertidal salt marsh (Adams & Bate, 1995). Even though production of a seed set is common for the southern African S. maritima population, germination of the seed and establishment of seedlings is not well documented. It is believed that after the species has established itself in a new area it will spread through below-ground rhizomes rather than through the germination and establishment of seedlings (Marchant, 1967).

As the main species to be found in the lower intertidal zone, it is expected to be inundated for longer periods than the upper intertidal areas, but ultimately the tidal inundation frequency and duration is dependent on the surface elevation range relative to mean sea level. The substratum in which S. maritima grows may vary from soft mud and sand to firm mud on the fringes (Marchant & Goodman, 1969b; Christian et al. 1983). Marchant & Goodman (1969b) suggest that S. maritima species grows well on mud soil but will grow taller on sandy silt sediment. Christian et al. (1983) reported similar findings for S. alterniflora.

The Keurbooms Estuary lacks well developed intertidal areas and as a result the area covered by S. maritima is not extensive and is limited only to the lower Bitou tributary, the confluence and a few patches in the Keurbooms tributary, covering an area of approximately 7.078 ha (Bornman & Adams, 2006). Our understanding of the distribution of S. maritima in the Keurbooms Estuary is 142 based on the GIS mapping efforts by Bornman & Adams (2006). Field observations indicated two distinct S. maritima populations, i.e. those occurring in the muddy Bitou tributary and those growing on a sandy substrate in the Keurbooms tributary. It was hypothesized that the limited distribution of the S. maritima in the Keurbooms Estuary was related to sediment type. Additionally, we further hypothesized that after sediment type, floods are the major hydrological driver determining the distribution of S. maritima in the Keurbooms Estuary. The overall aim of this chapter was to examine the growth and distribution of S. maritima in the Keurbooms Estuary and relate that to physical habitat and perceived drivers.

The specific objectives of this study were:

 To assess the spatial distribution of S. maritima, Zostera capensis, sand and mudbanks over time;  To examine seed germination and seedling success and;  To further examine the growth of S. maritima under different soil textural conditions.

7.2 Materials and methods 7.2.1 Site description The study was conducted on the S. maritima intertidal salt marsh in the Keurbooms Estuary. The estuary is influenced by semi-diurnal, micro-tidal regime and with the mean tidal range of about 1.6 m (Reddering, 1981). The estuary is also subject to periodic flooding, transporting sediment into the estuary which result in major changes in mouth position, sediment and vegetation of the estuary. The S. maritima in the Keurbooms Estuary is limited only to the lower Bitou tributary, the confluence and a few patches in the Keurbooms tributary. The S. maritima population in the confluence and Bitou tributary often occur in waterlogged muddy substrate (Plate 7.1) while the Keurbooms tributary population grow on a sandier substrate. The Bitou and confluence area are characterised by dense but short S. maritima populations while those in the Keurbooms tributary are tall, with thick stems. But, the S. maritima stands in the Keurbooms tributary appear shorter on the side facing the channel than the main body of the stand behind.

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Figure 7.1: Locality map showing the S. maritima are coverage and sediment cores sites.

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Plate 7.1: S. maritima marsh on a muddy substrate at site Spar 4 in the Bitou tributary.

Plate 7.2: Tall S. maritima stands on the sandy substrate at site Spar 6 in the Keurbooms tributary.

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7.2.2 GIS mapping Georeferenced aerial photographs of the Keurbooms Estuary (i.e. 1998, 2008 and 2011) were obtained from South African National Parks. The spatial distribution of S. maritima, Z. capensis, estuarine water, mudflats, sandflats and the sandy beach were digitized using ArcGIS software 10.3. Several of the habitats in the Keurbooms Estuary (i.e. Z. capensis, mud and sandbank as well as S. maritima) can change rapidly in response to floods, so ground-truthing were conducted using a GPS and ArcPad 7 software to verify the presence of these habitats for the most recent GIS map (Plate 7.3). The mapped habitat areas were calculated and compared between the different years.

Plate 7.3: Field GIS mapping of S. maritima using a GPS and ArcPad 7 software.

7.2.3 S. maritima seed germination potential The ripe spikes of S. maritima were randomly collected from different populations of S. maritima in the salt marshes of the Keurbooms Estuary (Plate 7.4). Seeds were collected on the 26 and 27 of February 2015 and transported to the laboratory for preparation. Upon arrival in the laboratory, the caryopses were stripped from the spikes and those containing seeds were selected and stored at room temperature without exposing them to sunlight. 146

The S. maritima seed germination experiment was conducted in the glasshouse facility of the Nelson Mandela Metropolitan University. The experiment consisted of five salinity treatments (0, 15, 25, 35 and 55) with five replicates in each treatment (Plate 7.5). The seeds were inspected and those seeds that were damaged were set aside and were not used for the germination experiment. Fifty S. maritima seeds were placed in 9 cm Petri-dishes containing two sheets of Whatman #2 filter paper. The petri-dishes were covered with lids to limit evaporation and placed in the glasshouse under normal day-night conditions as described by Kittelson & Boyd (1997) and Biber & Caldwell (2008). The filter papers were watered with their respective salinity treatment to keep the seeds moist in the closed Petri-dishes. The Petri-dishes were inspected and filter papers were moistened with respective salinity treatments daily until the first seeds germinated and thereafter weekly. The seeds were considered to have germinated after the appearance of the cotyledon (Plate 7.6). The experiment was started on 21 May 2015 and the experiment was terminated after 16 weeks (111 days) on 10 September 2015 after there were no further seed germination occurring. After the experiment was terminated, the germinated seeds were removed and transplanted into pots with salt marsh soil collected in the Keurbooms Estuary. The seedling growth experiment was watered twice daily with water with a salinity of 18.

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Plate 7.4: Seed spikes on S. maritima.

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Plate 7.5: S. maritima seed germination experiment set up.

Plate 7.6: Germinated S. maritima seeds on the filter paper.

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7.2.4 S. maritima plant growth Growth is not easy to define in halophytes, since fresh weight is considerably increased through succulence and extra dry weight may be related to an increase in solute uptake (Packham & Willis, 1997). Therefore, due to the contrasting nature of the two S. maritima populations (in the two tributaries), the decision was taken to measure the root length and shoot height of the S. maritima collected from different areas, as well as above- and below-ground biomass. A total of nine S. maritima plants were collected by hand from site Spar 1, 2, 4 and 6 on the 21st – 23rd September 2015 (Plate 7.7). Although there is no detailed study conducted to assess growth of S. maritima in terms of soil texture, field observations suggested that growth of this species in the Keurbooms Estuary is governed by different sediment types. Therefore, to better understand the growth of S. maritima in both the Bitou and Keurbooms tributaries, three replicate sediment cores were collected from each plant collection site at depth intervals of 0 – 0.25 m (surface), 0.5 – 0.75 m (middle) and 1.0 – 1.25 m (bottom), using a hand auger.

Plate 7.7: S. maritima plant collected by hand.

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7.2.4.1 S. maritima plant measurements Nine S. maritima clumps collected from site Spar 1, 2, 4 and 6 were measured for root length and shoot height on the same day as the collection, while the plant was still alive and supple. The plants were collected by hand with their sediment, so the roots had to be gently washed in the field to remove the sediment. Root length and shoot height of the S. maritima plants were then measured using a tape measure while they were still wet. Below-ground and above-ground sections of the plants were separated, sealed in plastic bags and transported to the Nelson Mandela Metropolitan University laboratory for biomass analysis. Although utmost care was taken to remove as much of the root system as possible, an unknown quantity of root biomass, especially the fine hair-like roots, remained in the soil. The chances of roots remaining in the soil were also greater in the muddy sediment compared to the sandy sediment.

7.2.4.2 S. maritima biomass Upon arrival at the laboratory, the plants were washed off with tap water to remove secreted salt on the plant shoots and to further remove any remaining soil on the roots as described by Naidoo et al. (2012). Biomass was determined by separately oven drying plant below-ground and above- ground sections at 60 ºC until a constant weight is reached as described by Duarte et al. (2013) (Plate 7.8). Aboveground and belowground biomasses were then determined by weighing the material using a balanced scale, accurate to two decimal places. Biomass was expressed in grams (g).

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Plate 7.8: S. maritima below-ground and above-ground wet biomass.

7.2.4.3 Soil analysis The sediment cores were analyzed for moisture, organic matter content and particle size. To determine sediment moisture content, approximately 20 g of soil from each site was weighed into a crucible and oven dried at 70 ºC for a period of 24 hours (Duarte et al. 2013).

The sediment organic matter was determined using the loss on ignition method after ashing the oven dried sediment samples in a muffle furnace at 550 ºC for a period of 8 hours as described by Briggs (1977) and Duarte et al. (2013).

The sediment particle size was determined using the hydrometer method as described in Chapter 5 (i.e. section 5.2.4.4). The sediment particle size was classified into three main categories, i.e. sand, silt and clay (Zoutendyk & Bickerton, 1999; Mateos-Naranjo et al. 2011).

7.2.4.4 S. maritima plant adaptation Chlorophyll fluorescence of the S. maritima plants was determined in the field on 22 and 23 September 2015 using a field portable plant efficiency analyser (Handy PEA – Hansatech). Dark adaptation times for S. maritima plants is not well documented, therefore, dark adaptation times were experimentally determined by placing nine leaf clips on the leaves of the S. maritima plants.

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The shutter plates were closed immediately and measurements were taken from each leaf clip in sequence at 2 minute intervals. The process was repeated for 4, 6, 8, 10, 12, 14, and 16 minute intervals as described in the Hand PEA Field Reference Guide (2002). The plant chlorophyll a fluorescence was determined as the ratio FV/FM, after the dark adaptation period, that reflects the potential quantum yield of photosystem II (PSII) where FV is the difference between the maximum fluorescence and the minimum fluorescence period level F0 (Druva-Lusite et al. 2008). Normally, the ratio should plateau at the minimum dark adaptation period. The pre-experiment showed that the FV/FM readings reached peaks at 12 minutes. Therefore, 12 minutes was an adequate minimum dark adaptation period for the S. maritima plant species in the Keurbooms Estuary on the day of sampling.

0.8

0.78 Dark Adaptation

0.76

0.74

0.72

0.7

0.68

0.66 Maximum Maximum PSII efficiency (Fv/Fm)

0.64 2 4 6 8 10 12 14 16 18 20 Time (Minutes)

Figure 7.2: Pre-experiment chlorophyll fluorescence (FV/FM) of S. maritima plants (Mean = ± SE).

Nine S. maritima plants were selected at each site, i.e. Spar 1, 2, 6 and 8. The chlorophyll fluorescence measurements were taken in sequence after darkening of the leaves with leaf clips for 12 minutes (Plate 7.9). All measurements were taken at low tide on the 22nd of September 2015. Furthermore, chlorophyll fluorescence measurements were taken at site Spar 1 on the incoming

153 high-tide on the 23rd of September 2015 to investigate whether the tides had any influence on S. maritima efficiency. Measurements were made on nine S. maritima plants hourly (for four hours).

Plate 7.9: S. maritima plant with leaf clip.

7.2.5 S. maritima transplant experiment To help understand the causes of the observed morphological differences in the S. maritima populations in the Keurbooms Estuary, replicated pot experiments were conducted in the glasshouse to identify the potential effects of soil type on the growth of this species. S. maritima plants were collected with their soil from the Bitou and Keurbooms populations (i.e. site Spar 2

154 and 6 respectively) on the 21 and 22 of September 2015 for glasshouse transplant experiments. Efforts were made to collect plants of more or less the same height.

The S. maritima plant experiment was established in the glasshouse, with four soil (Clayey Sand soil, Unmodified Clayey Sand soil, Silty soil and Unmodified Silty soil) treatments. S. maritima were transplanted into pots containing these different textural soils. Four replicate pots were used for each soil treatment (Plate 7.10). Clayey Sand soil was prepared by mixing up soil collected from site Spar 2 and 4, while unmodified Clayey Sand soil and unmodified Silty soil were the soils collected with the plants from the Keurbooms Estuary. Field observation and laboratory results of sediment cores indicated that the sediment changes at 0.5 – 0.75 m to silty sand in the Keurbooms S. maritima population. Therefore, the bottom of the Silty soil treatment was layered with a mud soil and overlaid with sand soil collected at site Spar 6 to emulate the natural conditions of the S. maritima populations in the Keurbooms tributary. Sub samples of the soil were taken from these experiments to determine sediment moisture, organic content and particle size.

Studies on adaptation to salinity (Adams & Bate, 1995; Naidoo et al. 2012; Duarte et al. 2014) indicate that S. maritima is well adapted to seawater between 20 and 35. Therefore, the decision was taken to water the plants daily with a salinity treatment of 18. The experiment began on the 8th of October 2015 and terminated after 8 weeks on the 13th of December 2015. Four stems from each treatment were selected and growth rate was monitored by measuring their height with a tape measure while the number of newly produced and dead stems were also counted on weekly intervals.

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Plate 7.10: S. maritima transplant experiment set-up in different textural soils.

7.2.6 Statistical analysis Analysis of variance between sampling sites and periods was conducted to determined significant differences. Where significant difference was found a Tukey post – hoc test was carried out. All statistical analyses were conducted using STATISTICA version 13.0.

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7.3 Results 7.3.1 GIS mapping GIS mapping of 1998, 2008 and 2011 aerial photographs are provided in Figure 7.3, 7.4 and 7.5 and the area cover of habitats are compared in Table 7.1. Beach sand was mapped separately due to its importance in influencing the distribution of sandflats. Analysis of the 1998 aerial photograph indicates that the area covered by Z. capensis and S. maritima was 49.22 hectares (ha) and 5.09 ha respectively (Table. 7.1). Estuarine water covered 134.39 ha of the mapped area (which excluded the upper parts of the Keurbooms tributary) (Figure 7.3) while sandflats, mudflats and beach sand covered 94.89, 17.76 and 36.96 ha respectively (Table 7.1). Z. capensis was mostly found in the lower reaches of the estuary while the S. maritima was restricted mostly to the Bitou tributary and at a few sites in the confluence and middle reaches of the Keurbooms tributary (Figure 7.3). Notably, the S. maritima in the Bitou occur around mudflats while those in the Keurbooms tributary and confluence are closely associated with sandbanks. Sandbanks were the dominant habitat in the lower reaches of the Keurbooms tributary.

The 2008 aerial photograph was taken after the November 2007 flood which resulted in the mouth opening in a new position adjacent to Lookout Rocks. The analysis of the 2008 aerial photograph indicate a decrease in area covered by estuarine water to 122.48 ha, but increased beach sand (38.47 ha), sandbanks (128.68 ha) and mudflats (30.63 ha) (Table 7.1). The sandbanks were most abundant in the lower reaches (i.e. towards the southwest) of the Keurbooms tributary while mudflats were still mostly restricted to the Bitou tributary (Figure 7.4). The additional sand appears to have been transported from the Keurbooms tributary rather than from the Bitou tributary. The area covered by Z. capensis and S. maritima was reduced to 22.45 and 3.93 ha (i.e. by 26.76 and 1.16 ha between 1998 and 2008) (Table 7.1). Notably, the area that was previously Z. capensis in 1998 was covered by sand or converted to mudflat, especially in the lower reaches of the Keurbooms tributary (Figure 7.4). Areas that were previously S. maritima in the Keurbooms tributary were replaced by sandbanks in 2008 (Figure 7.4).

The estuarine water area covered 191.72 ha in the 2011 aerial photograph (i.e. increased by 69.24 ha between 2008 and 2011) (Table 7.1). Although it is not clear when the 2011 aerial photograph was taken, it appears that it was taken during high tide which could be the reason for the increased estuarine water area coverage. Notably, beach sand was increased by 11.5 ha between 2008 and

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2011 (to 49.97 ha) while mudflats and sandbanks were reduced to 22.87 and 67.07 ha (i.e. 7.76 and 61.61 ha less) respectively (Table 7.1). The increased beach sand could possibly be due to the shift of the mouth further south-westwards towards Lookout Rocks as a result of a flood (Figure 7.5). The distribution of Z. capensis increased to a total of 31.87 ha while the S. maritima area was reduced by 1.02 ha to cover 2.91 ha in 2011 (Table 7.1). Sandbanks were mostly found at the mouth and in the Keurbooms tributary (Figure 7.5). Furthermore, the aerial photograph (Figure 7.5) shows that areas that were previously sandbanks in 2008 were successively replaced by the Z. capensis in the lower reaches. S. maritima was replaced by mudflats or estuarine water in the Bitou tributary and by either sandbanks or Z. capensis in the confluence and in the Keurbooms tributary (Figure 7.5).

Although the distribution of S. maritima show a decline with time, its geographic location in the Keurbooms Estuary remained the same to that mapped by Bornman & Adams (2006) (Figure 7.6). According to the Bornman & Adams (2006) vegetation and habitat map of the Keurbooms Estuary, the S. maritima covered an area of approximately 7.078 ha with extensive distribution of Z. capensis beds but reduced mudflats as illustrated in Figure 7.6.

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Table 7.1: Area cover of different habitat and vegetation units of the Keurbooms Estuary over time.

Difference Difference Bornman between between & Adams 1998 & 2008 & Habitat 1998 (ha) (2006) 2008 (ha) 2011 (ha) 2008 2011

Beach sand 36.92 38.47 49.97 1.54 11.50 Estuarine water 134.39 159.42 122.48 191.72 -11.90 69.24

Mudflats 17.76 5.33 30.63 7.76 12.87 -22.87

Sandbanks 94.89 80.47 128.68 61.61 33.79 -67.07 Z. capensis 49.22 88.73 22.45 31.87 -26.76 9.41

S. maritima 5.09 7.078 3.93 2.91 -1.16 -1.02

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Figure 7.3: Vegetation and habitat map of the Keurbooms Estuary in 1998.

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Figure 7.4: Vegetation and habitat map of the Keurbooms Estuary in 2008.

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Figure 7.5: Vegetation and habitat map of the Keurbooms Estuary in 2011. 162

Figure 7.6: Vegetation and habitat map of the Keurbooms Estuary in 2004 (from Bornman & Adams 2006).

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7.3.2 Seed germination The first seed of S. maritima germinated after 6 weeks (i.e. after 42 days) exposed to the 15 salinity treatment. Only five seeds germinated (Table 7.2). The next seed germination at the 15 salinity treatment was evident after 8 weeks (i.e. after 60 days) while one seed each germinated at a salinity of 25 and 35 after 7 weeks (i.e. 42 days) after which there were no further seed germination for these treatments until the experiment was terminated (Figure 7.7). Germinated seeds at both 25 and 35 salinity treatment appeared whiter in colour rather than green as it would have been expected and showed signs of retarded growth. Last germination at the 15 salinity treatment occurred after 14 weeks when one additional seed germinated after 89 days bringing the total number of seeds germinated to 8 seeds (i.e. final germination percentage of 3.2%) (Table 7.2; Figure 7.7). However, germinated seeds at 15 salinity treatment showed signs of retarded growth after 15 weeks (i.e. 101 days) (Plate 7.11). There was no seed germination recorded at the 0 and 55 salinity treatment (Plate 7.12). Mean daily germination as shown in Table 7.2 was 0, 0.036, 0.009, 0.009 and 0 for the 0, 15, 25, 35 and 55 salinity treatment which indicated a very low germination rate. After the termination of the experiment (i.e. after 111 days), a total of 10 seeds germinated out of 1 250 seeds in all the treatments.

Table 7.2: Final seed germination (%), days to first and last germination and mean daily germination of S. maritima at different salinity treatments.

Salinity Final germination Days to first Days to last Mean daily germination treatment after 111 days (%) germination germination (MDG)

0 0 (0) 0 0 0

15 8 (3.2) 42 89 0.036

25 1 (0.4) 46 46 0.009

35 1 (0.4) 46 46 0.009

55 0 (0) 0 0 0

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9 0 ppt 8 15 ppt 7 25 ppt 6 35 ppt 5 55 ppt

2 Number Number germinated of seeds 1

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Time (weeks)

Figure 7.7: Number of seeds germinated at different salinity treatments over a period of 16 weeks.

Plate 7.11: Germinated seeds at the 15 salinity treatment showing retarded growth after 101 days.

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Plate 7.12: Non-germinated seeds after 111 days at the 55 salinity treatment.

7.3.3 S. maritima plant growth S. maritima growth measurements are presented in Table 7.3 and illustrated in Figure 7.8, 7.9, 7.10, 7.11 and 7.12.

Table 7.3: Mean plant height, root length, above-ground and below-ground biomass of S. maritima clumps in the Keurbooms Estuary (Mean = ± SE).

Plant characteristics Shoot height Root length Above-ground Below-ground Sites (cm) (cm) biomass (g) biomass (g)

Spar 1 65.67 (± 3.91) 23.69 (± 1.82) 37.91 (± 6.27) 44.58 (± 9.49)

Spar 2 58.08 (± 1.97) 23.61 (± 1.71) 17.31 (± 2.58) 17.42 (± 4.22)

Spar 4 42.32 (± 2.51) 19.91 (± 1.47) 5.42 (± 1.05) 7.46 (± 2.15)

Spar 6 56.51 (± 3.85) 23.50 (± 1.79) 24.11 (± 3.73) 18.46 (± 3.60)

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7.3.3.1 Shoot height and root length The mean S. maritima shoot height ranged from 42.32 ± 2.51 to 65.67 ± 3.91 cm (n = 9) (Table 7.3). Although the Keurbooms tributary S. maritima populations appeared somewhat taller in the field, the shoot height measurements indicate that site Spar 6 plants are shorter than those in the Bitou tributary (i.e. Spar 1 and 2) (Figure 7.8). Plants at sites Spar 4 were significantly shorter than those at sites Spar 1, 2 and 6 (p < 0.05). Root length were uniform at all sites with no significant difference (p > 0.05) in terms of root length. The roots of collected S. maritima exhibited extensive branched rhizomes showing evidence of vegetative propagation of this species. Branched rhizomes were as long as 42 cm from the parent plant (Plate 7.13a). In some cases, S. maritima clumps from the Bitou tributary were attached to dead root rhizomes suggesting below-ground vegetative reproduction and this may result in their roots appearing shorter compared to the plants collected from the Keurbooms tributary (Plate 7.13b). A strong positive correction (r = 0.926) was found between S. maritima plants root length and shoot height (Figure 7.8 & 7.9). The correlation indicates that the longer the S. maritima roots, the taller they become (Figure 7.9).

80 Shoot height 70 Root length 60

20 Averagerootlength (cm) 10

0 Spar 1 Spar 2 Spar 4 Spar 6 Sites

Figure 7.8: S. maritima shoot height and root length in the Keurbooms Estuary (Mean ± SE, n = 9).

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30 r = 0.926 25

15 plant rootlength(cm) 10

5 S. S. maritima

0 0 10 20 30 40 50 60 70 S. maritima plants shoot height (cm)

Figure 7.9: Correlation between S. maritima plant root length and shoot height.

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Plate 7.13: S. maritima plant (a) produced from long rhizome and (b) plant an attached from dead rhizome.

7.3.3.2 Plant biomass production The biomass production of S. maritima plants appear to follow the same pattern as that of the shoot height and root length. The mean above-ground biomass production varied from 5.42 ± 1.05 to 37.91 ± 6.27 g (no = 9) while below-ground ranged from 7.46 ± 2.15 to 44.58 ± 9.49 g (no = 9) (Table 7.3). Site Spar 1 had significantly higher above-ground biomass than Spar 2 and 4 while Spar 6 had significantly higher above-ground biomass than Spar 4 (p < 0.05) (Figure 7.10). In terms of below-ground biomass, site Spar 1 had a significantly higher below-ground biomass than Spar 2, 4 and 6 (p < 0.05) while other sites showed no significant in biomass (p > 0.05) (Figure

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7.10). A scatter plot diagram (Figure 7.11) showed a strong positive correlation (r = 0.951) between above-ground and below-ground biomass. Total biomass production showed similar trends to those of the above-ground and below-ground biomass (Figure 7.12). Notably, site Spar 1 had significantly higher total biomass than Spar 2, 4 and 6 (p < 0.05) while Spar 4 had a significantly lower total biomass than Spar 6 (p < 0.05).

50 Aboveground biomass Belowground biomass 40

30 ground biomass biomass (g)ground - 20

Below 10

0 Spar 1 Spar 2 Spar 4 Spar 6 Sites

Figure 7.10: Above-ground and below-ground biomass production of S. maritima in the Keurbooms Estuary (n = 9, Mean ± SE).

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50 r = 0.951 40

Belowground biomass Belowgroundbiomass (g) 10

0 0 5 10 15 20 25 30 35 40 Aboveground biomass (g)

Figure 7.11: Correlation between S. maritima plant above-ground and below-ground biomass.

100 90 Total biomass 80 70 60 50 40

Total biomass Totalbiomass (g) 30 20 10 0 Spar 1 Spar 2 Spar 4 Spar 6 Sites

Figure 7.12: Total biomass production S. maritima in the Keurbooms Estuary (n = 9, Mean ± SE).

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7.3.4 Soil analysis Soil characteristics of the areas where S. maritima plants were collected are presented in Table 7.4 and the soil particle size, moisture and organic matter content are illustrated in Figure 7.13, 7.14 and 7.15 respectively. The soil at site Spar 2 and 4 in the Bitou tributary was dark in colour while those at site Spar 1 and 6 in the lower part of the Bitou tributary (i.e. after the confluence) and the Keurbooms tributary respectively appeared to change colour with depth especially at 0.5 – 0.75 m. Marine shell fragments were often evident at 1.0 m depth.

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Table 7.4: Mean sediment characteristics of sediment collected in the S. maritima study sites at depth intervals (0 – 0.25 m, 0.5 – 0.75 m and 1.0 – 1.25 m herein referred to as top, middle and bottom soil) in the Keurbooms Estuary (mean ± SE; n = 3).

Soil texture

Site Sand % Silt % Clay % Moisture % Organic %

Spar 1 Top 48.22 (± 20.53) 49.05 (± 22.37) 2.73 (± 1.86) 39.95 (± 2.73) 7.4 2(± 1.68)

Spar 1 Mid 48.29 (± 14.70) 49.36 (± 14.49) 2.35 (± 1.72) 25.56 (± 1.87) 1.64 (± 0.03)

Spar 1 Bot 34.34 (± 7.81) 64.78 (± 7.39) 0.88 (± 0.54) 25.28 (± 2.62) 1.57 (± 1.13)

Spar 2 Top 50.23 (± 1.26) 43.38 (± 1.37) 6.39 (± 0.64) 49.44 (± 3.68) 11.21 (± 1.90)

Spar 2 Mid 56.48 (± 4.46) 39.70 (± 4.64) 3.82 (± 0.96) 37.57 (± 7.82) 7.28 (± 3.02)

Spar 2 Bot 53.57 (± 9.94) 44.21 (± 10.60) 2.22 (± 0.85) 33.06 (± 5.15) 5.39 (± 2.09)

Spar 4 Top 58.69 (± 5.97) 35.39 (± 8.35) 5.91 (± 2.49) 33.90 (± 1.59) 4.43 (± 0.07)

Spar 4 Mid 34.40 (± 8.63) 62.18 (± 6.71) 3.43 (± 2.13) 24.23 (± 2.23) 2.78 (± 1.14)

Spar 4 Bot 32.54 (± 3.21) 63.08 (± 4.81) 4.39 (± 1.61) 22.80 (± 0.84) 2.48 (± 0.17)

Spar 6 Top 25.76 (± 3.96) 72.63 (± 4.29) 1.61 (± 0.38) 29.09 (± 3.51) 4.06 (± 1.46)

Spar 6 Mid 49.45 (± 20.89) 48.13 (± 2.17) 2.43 (± 1.17) 21.20 (± 1.27) 1.55 (± 0.27)

Spar 6 Bot 32.19 (± 9.53) 63.46 (± 10.58) 4.35 (± 2.59) 21.19 (± 0.85) 1.16 (± 0.07)

7.3.4.1 Sediment particle size The mean sand contributions for sites Spar 1, 2, 4 and 6 were 48.22%, 50.23%, 58.69% and 25.76% while silt contributions were 49.04%, 43.38%, 35.39% and 72.63% respectively in the surface layer (0 – 0.25 m) (Table 7.4). Meanwhile, the mean clay contribution for sites Spar 1, 2, 4 and 6 were 2.73%, 6.39%, 5.91% and 1.61% respectively (Table 7.4). Although site Spar 6 had lower sand and high silt concentrations than Spar 1, 2 and 4, it was not significant (p > 0.05). Site Spar 1 showed uniform amounts of sand and silt fractions, with lower clay fractions than those of sites Spar 2 and 4, although not significantly so (p > 0.05) (Figure 7.13). Neither sand, silt nor clay varied significantly between sites in the surface layer (0 – 0.25 m).

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The overall mean concentration of silt and clay in the middle layer was slightly lower compared to that of the surface layer, while sand was higher, although not significantly so (p > 0.05). The mean sand contributions for sites Spar 1, 2, 4 and 6 were 48.29%, 58.48%, 34.40% and 49.45%. The mean silt contents for sites Spar 1, 2, 4 and 6 were 49.36%, 39.70%, 62.18% and 48.13% respectively. Site Spar 4 had a lower sand and higher silt content than Spar 1, 2 and 6 although not significantly so (p > 0.05) (Figure 7.13). The sediment particle size of the 0.50 – 0.75 m depth was uniform at site Spar 1 compared to the surface layer (Figure 7.13). Sites Spar 1, 2, 4 and 6 in the middle layer had no significant change in the clay fraction between sites (Figure 7.13).

The mean contribution of sand for sites Spar 1, 2, 4 and 6 was 34.34%, 53.37%, 32.54% and 32.19% while silt was 64.78%, 44.21%, 63.08% and 63.46 respectively in the bottom layer (i.e. 1.0 – 1.25 m depth). The mean clay contribution for sites Spar 1, 2, 4 and 6 were 0.88%, 2.22%, 4.39% and 4.35% (Table 7.4). The mean overall sand and clay contributions were lower while contents of silt were higher compared to both the surface and middle layers although neither was significant (p > 0.05). All sites showed an increased silt fractions while sand contribution was lower at all sites (Figure 7.13). Furthermore, site Spar 2 had significantly higher clay content in the surface layer than the bottom layer (p < 0.05). Spar 4 and 6 had higher clay fractions than sites Spar 1 and 2 clay fraction but no significantly so (p > 0.05).

100 90 80 70 60 50 40 30 20 10 0 Spar 1 Spar 1 Spar 1 Spar 2 Spar 2 Spar 2 Spar 4 Spar 4 Spar 4 Spar 6 Spar 6 Spar 6 Top Mid Bot Top Mid Bot Top Mid Bot Top Mid Bot Sediment Sediment particle size contribution (%) Sites

Sand Silt Clay

Figure 7.13: Mean soil particle size of the sediment cores collected from selected S. maritima population in the Keurbooms Estuary (n = 3).

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7.3.4.2 Sediment moisture content The mean sediment moisture content ranged from 29.09 ± 3.51% to 49.44 ± 3.68% in the 0 – 0.25 m depth (i.e. surface layer). Notably, site Spar 2 had a significantly higher moisture content than sites Spar 4 and 6 (p < 0.05) (Figure 7.14).

In the 0.5 – 0.75 m depth the mean sediment moisture content ranged from 21.20 ± 1.27% to 37.27 ± 7.82% (Table 7.4). Although there was no significant difference found between sites (p > 0.05), site Spar 2 continued to have a higher moisture content than sites Spar 1, 4 and 6. (Figure 7.14). Site Spar 6 had significantly lower moisture contents in the 0.5 – 0.75 m depth than the surface layer (i.e. 0 -0.25 m depth) of sites Spar 1 and 2, whereas Spar 1 and 4 had significantly lower moisture content in the 0.5 – 0.75 m depth than the surface layer of Spar 2 (p < 0.05).

The mean moisture ranged from 21.19 ± 0.85% to 33.06 ± 5.15% in the bottom layer (i.e. 1.0 – 1.25 m depth) with no significant difference recorded between sites (p > 0.05). However, sites Spar 1, 4 and 6 in the 1.0 – 1.25 m depth had significantly lower moisture contents than the 0 – 0.25 m depth in site Spar 2 (i.e. surface layer) and the 1.0 – 1.25 m depth sediment in Spar 6 had a significantly lower moisture content than that of the surface layer at site Spar 1 (p < 0.05).

0.0 - 0.25 m 50 0.5 - 0.75 m 40 1.0 - 1.25 m

20 Moisturecontent(%) 10

0 Spar 1 Spar 2 Spar 4 Spar 6 Sites

Figure 7.14: Soil moisture content of the sediment cores in the Keurbooms Estuary Mean ± SE, n = 3).

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7.3.4.3 Sediment organic matter content The mean sediment organic matter content ranged from 4.06 ± 1.46% to 11.21 ± 1.90% in the surface layer (i.e. 0 – 0.25 m depth) (Table 7.4). Site Spar 2 had significantly higher (p < 0.05) organic matter content than both sites Spar 4 and 6 (Figure 7.15).

The mean organic matter content ranged from 1.55 ± 0.27% to 7.28 ± 3.02% in the 0.5 – 0.75 m depth (Table 7.4). Site Spar 2 continued to have a higher organic matter content than sites Spar 1, 4 and 6 (Figure 7.15) but there was no significant difference found between sites (p > 0.05). However, in terms of depth the organic matter content in the 0.5 – 0.75 m depth was lower compared to that of the surface layer (0 – 0.25m depth). Spar 1, 4 and 6 had significantly lower organic matter contents than those of site Spar 2 in the 0 – 0.25 m depth range (p < 0.05).

In the bottom layer (i.e. 1.0 – 1.25 m depth) the mean sediment organic matter ranged from 1.16 ± 0.07% to 5.39 ± 2.09% (Table 7.4). Similar, to the organic matter of the middle layer (i.e. 0.5 – 0.75 m depth), Spar 2 had a higher organic matter content than sites Spar 1, 4 and 6, although not significantly so (p > 0.05) (Figure 7.15). Sites Spar 1, 4 and 6 had a significantly lower organic matter content at depth than the surface layer (0 – 0.25 m depth) of site Spar 2 (p < 0.05).

12 0.0 - 0.25 m 10 0.5 - 0.75 m 8 1.0 - 1.25 m

Organic matter Organicmatter content (%) 2

0 Spar 1 Spar 2 Spar 4 Spar 6 Sites

Figure 7.15: Soil organic content of the sediment cores in the Keurbooms Estuary (Mean ± SE, n = 3).

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7.3.5 Chlorophyll fluorescence of S. maritima

The mean chlorophyll fluorescence potential quantum yield of PSII (FV/FM) for S. maritima after the dark adaptation period ranged from 0.694 ± 0.023 to 0.773 ± 0.006 (Table 7.5). Site Spar 4 located in the Bitou had significantly lower PSII (FV/FM) values than site Spar 8 located in the

Keurbooms (Figure 7.16). The minimum FV/FM values were recorded at site Spar 4 (i.e. 0.530) while maximum values were recorded at site Spar 2 (i.e. 0.809) (Table 7.5).

Hourly chlorophyll fluorescence potential quantum yield of PSII of S. maritima recorded at site Spar 1 during the incoming tide ranged from 0.690 ±0.025 to 0.717 ±0.019. There was no significant difference found between the recorded hours (p > 0.05). During the first and second hour at low and incoming tide, the potential yield values of PSII (FV/FM) were uniform but declined during the third hour when the sediment surface of the plants was completely submerged, indicating some photo-inhibition of photosynthesis (Fig 7.17). Although the plants were still submerged during the fourth hour, the potential yield values of PSII (FV/FM) increased to similar values as during the first and second hour recordings (Figure 7.17). This may suggest good adaptation of S. maritima species during normal tidal submergence.

Table 7.5: Potential quantum yield of S. maritima plants.

FV/FM

Sites Minimum Maximum Mean ± SE

Spar 1 0.613 0.756 0.717 ± 0.018

Spar 2 0.632 0.809 0.736 ± 0.018

Spar 4 0.530 0.775 0.694 ±0.023

Spar 6 0.614 0.791 0.744 ± 0.015 Spar 8 0.747 0.801 0.773 ± 0.006

177

0.8 Dark Adaptation 0.76

0.72

0.68

0.64 Maximum Maximum PSII efficiency (Fv/Fm) 0.6 Spar 1 Spar 2 Spar 4 Spar 6 Spar 8 Sites

Figure 7.16: Chlorophyll fluorescence (FV/FM) of S. maritima plants at five sites in the Keurbooms Estuary (Mean ± SE; n = 9).

0.76 Dark Adaptation 0.74

0.72

0.7

0.68

0.66

0.64 Maximum Maximum PSII efficiency (Fv/Fm)

0.62 1 2 3 4 Time (Hourly)

Figure 7.17: Chlorophyll fluorescence (FV/FM) of S. maritima recorded hourly at site Spar 1 during the incoming tide (Mean ± SE; n = 9).

178

7.3.6 S. maritima transplant experiment Table 7.6 presents the average soil particle size of the sediment used in the transplant experiment. Unmodified Clayey Sand pots had a significantly higher sand contribution than both Silty and Unmodified Silty pots (p < 0.05). Furthermore, both Silty and Unmodified Silty pots had significantly higher silt soil fraction than both Clayey Sand and Unmodified Clayey Sand pots (p < 0.05). Clayey Sand and Unmodified Clayey Sand pots had a higher clay fraction than both Silty and Unmodified Silty pots, although not significantly so (p > 0.05).

Clayey Sand soil had a significantly higher moisture content than soils in both the Silty and Unmodified Silty pots while Unmodified Clayey Sand pots had a significantly higher moisture content than soils in Unmodified Silty pots (p < 0.05). Moreover, Clayey Sand pots soil had a significantly higher organic matter content than both Silty and Unmodified Silty soils (p < 0.05).

Table 7.6: Mean sediment characteristics of sediment used in the transplant experiment of the S. maritima. (Mean ± SE; n = 4).

Soil texture

Pot Sand % Silt % Clay % Moisture % Organic %

Clayey Sand 46.32 (±3.96) 48.42 (±3.76) 5.25 (±0.62) 36.12 (±0.52) 5.80 (±0.16) Unmodified Clayey Sand 48.60 (±0.20) 47.08 (±0.55) 4.30 (±0.47) 31.45 (±3.47) 3.95 (±1.07)

Silty 29.44 (±6.57) 67.31 (±6.38) 3.24 (±0.83) 21.29 (±0.97) 2.17 (±0.18) Unmodified Silty 29.21 (±3.74) 66.60 (±3.41) 4.18 (±0.38) 24.29 (±0.73) 2.20 (±0.14)

Initial measurements at the start of the experiment indicate that S. maritima plants in the Clayey Sand and Unmodified Silty pots were shorter than those in the Unmodified Clayey Sand and Silty pots (Table 7.7). Although efforts were made to collect more or less plants of the same height, those transplanted into the Unmodified Clayey Sand pots were much taller than the others. Although pots were watered daily, plants in the Clayey Sand and Unmodified Clayey Sand pots showed evidence of waterlogged conditions the next day, i.e. not draining. This could be related

179 to the higher contribution of clay fraction in these pots resulting in a higher water holding potential compared to the other pots.

Final tiller height of the recorded plants ranged from 36.26 ±0.34 to 42.44 ±1.69 cm (Table 7.7). Figure 7.18 shows that plants in the Clayey Sand pots were shorter than those in the Unmodified Clayey Sand, Silty and Unmodified Silty pots, although not significantly so (p > 0.05). The tallest plant (75.2 cm) was recorded in the Silty soil pot and more stems were also recorded in this soil treatment.

The plants in the Silty and Unmodified Silty soil treatments appeared healthy for most of the experiment, but the Clayey Sand and Unmodified Clayey Sand soil treatments produced more stems (Figure 7.19). The mean initial count of new stems at the beginning ranged from 0.75 ± 0.31 to 3.0 ± 0.72 while final count after the experiment ranged from 9.25 ± 1.77 to 13.5 ± 1.03 (Table 7.7). There was however no significant difference in stem production (p > 0.05) between treatments. Despite producing more new stems, Unmodified Clayey Sand treatment had a large number of dead stems (Figure 7.19).

Table 7.7 shows that the mean initial count of dead stems at the beginning of the experiment ranged from 1.25 ± 1.10 to 7.25 ± 0.94 while final dead stems ranged from 9.25 ± 2.05 to 19.25 ± 1.03. Unmodified Clayey Sand soil had s significantly higher number of stem mortality than Clay Sand, Silty and Unmodified Silty soils (p < 0.05) (Figure 7.20). In most cases, stem mortality in the Clayey Sand and Unmodified Clayey Sand soil treatment pots included newly produced stems. Results of stem production and mortality suggest that Clayey Sand soil produces more stems but may not survive longer if submerged for a longer period while Silty soils support a higher growth rate in terms of height rather than stems production, and is not prone to prolonged saturated soil conditions.

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Table 7.7: Mean S. maritima plant height, stem production and mortality of the transplant experiment (Mean ± SE).

Mean plant height (cm) Produced stems Dead stems

Pot Initial Final Initial Final Initial Final

Clayey Sand 24.32 (± 0.73) 36.26 (± 0.34) 0.75 (± 0.31) 12 (± 2.01) 2.5 (± 0.28) 9.25 (± 2.05) Unmodified Clayey Sand 30.57 (± 2.26) 42.08 (± 2.99) 3 (± 0.72) 13.5 (± 1.03) 7.25 (± 0.94) 19.25 (± 1.03)

Silty 31.06 (± 1.17) 42.44 (± 1.69) 1 (± 0.38) 10 (± 1.18) 1.75 (± 1.10) 5.75 (± 2.39) Unmodified Silty 25.56 (± 0.96) 41.17 (± 1.77) 1.75 (± 0.5) 9.25 (± 1.77) 3.5 (± 1.04) 9.5 (± 2.5)

50 45 Stem height 40 35 30 25 20 15

10 Mean stem Meanstem height (cm) 5 0 Clayey Sand Unmodified Clayey Sand Silty Unmodified Silty

Sites

Figure 7.18: Stem height of S. maritima plants in different soil treatments (Mean ± SE; n = 4).

181

14 Stem production

Number Number stems of produced per week 0 Clayey Sand Unmodified Clayey Sand Silty Unmodified Silty

Sites

Figure 7.19: The number of produced stems in the different soil treatments (Mean ± SE).

20 Dead Stems

5 Number Number deadofstems per week 0 Clayey Sand Unmodified Clayey Sand Silty Unmodified Silty

Sites

Figure 7.20: The number of dead stems in different soil treatments (Mean ±SE).

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7.4 General discussion Many studies have been conducted on Spartina species across the world, ranging from their growth (both from seedlings and vegetative) (Christian et al. 1983; Kittelson & Boyd, 1997; Sanchez et al. 1997; Castillo et al. 2000; White, 2004; Biber & Caldwell, 2008; Curado et al. 2010; Mateos- Naranjo et al. 2011) to their physiology and adaptation to various stressful environments (Sanchez et al. 2001; Castillo et al. 2000; Nieva et al. 2003; Nieva et al. 2005; Castillo et al. 2008; Castillo & Figueroa, 2008; Castillo & Figueroa, 2009; Duarte et al. 2009; Santin et al. 2009 & Duarte et al. 2013; 2014). The S. alterniflora species was detected in the Great Brak Estuary in South Africa (and promptly eradicated), but the S. maritima population remains the only native Spartina species occurring along the southern African coast. There is no evidence of how the S. maritima species was introduced to southern African coast but it is believed that it was introduced accidentally or otherwise by early settlers (Pierce, 1982). Despite its origin, the distribution of S. maritima along the southern African coasts has been explained primarily on the basis of its salinity and inundations tolerance ranges (Adams & Bate, 1995; Naidoo et al. 2012). Our understanding about its distribution along the elevation gradient is based on field studies and GIS mapping efforts (Pierce, 1983; Bornman & Adams, 2006; Bezuidenhout, 2011; Schmidt, 2013; Veldkornet et al. 2014; van der Linden, 2014; Bornman et al. 2016).

Unlike in Europe, southern African populations of S. maritima have reportedly been increasing in extent over the last decades (Pierce, 1982; Naidoo et al. 2012; Schmidt, 2013). However, the distribution of S. maritima in the Keurbooms Estuary is not abundant, only covering an area of approximately 7.078 ha according to Bornman & Adams (2006). Zoutendyk & Bickerton (1999) reported S. maritima populations to have covered an area of 4.868 ha accounting for only 2.2% of the total mapped area in the Keurbooms Estuary. In this study, the GIS mapping of the 1998 aerial photograph indicate an increase of the S. maritima (i.e. 5.09 ha) compared to the distribution reported by Zoutendyk & Bickerton (1999) but less area cover compared to Bornman & Adams (2006). The 2008 and 2011 aerial photographs further showed decreases in distribution of S. maritima to 3.93 and 2.91 ha respectively (Table 7.1). Furthermore, the habitat covered by the Zostera capensis beds was also reduced in the 1998, 2008 and 2011 aerial photographs compared to the 2004 aerial photograph mapped by Bornman & Adams (2006). Although salt marshes are known to develop through sedimentation, most species are sensitive to flooding and increased sediment deposition. Colloty et al. (2000b) has shown reeds and submerged macrophyte plant 183 community types to have been removed by the large floods in the Swartkops Estuary as a result of bank erosion. Pierce (1982) also reported large-scale removal of Zostera beds in the Swartkops Estuary as a result of floods, although Spartina stands remained intact. The Keurbooms Estuary is subject to periodic flooding, transporting large quantities of sediment further down in the lower reaches of the estuary and resulting in major changes in the mouth position, sediment composition and the estuarine vegetation. Although the 1998 and 2004 aerial photographs were not taken soon after flooding events, the flow data (www.dwa.gov.za) reveals several flood peaks between 2000 and 2003. However, these flood peaks do not seem to have had an influence on the vegetation and habitat distribution of the estuary except for reduced mudflats between the 1998 aerial photograph and Bornman & Adams (2006). The Spartina species, especially S. maritima, can colonize low- lying intertidal mudflats somewhat below their current natural distribution (Castillo et al. 2000). Therefore, the extensive intertidal mudflats in the 1998 aerial photograph could have been colonized by the S. maritima vegetation resulting in increased S. maritima cover while estuarine water area also replaced the mudflats in 2004 (Bornman & Adams, 2006) due to high flows. The 2008 aerial photograph was taken after the November 2007 flood (Schumann, 2015) that had a major influence on the vegetation and habitat distribution in the Keurbooms Estuary. The S. maritima area was reduced by nearly half while Z. capensis was reduced by two-thirds compared to Bornman & Adams (2006). Due to large-scale sediment deposition in the estuary as a result of the flooding, S. maritima was evidently replaced by either sandbanks or mudflats while Z. capensis was mostly covered by mudflats in 2008 (Figure 7.4).

In 2011, the area covered by the S. maritima salt marsh was further reduced by 1.02 ha from 2008 while Z. capensis increased by 9.41 ha (Table 7.1). The estuarine water area covered 191.72 ha in the 2011 aerial photograph (i.e. increased by 69.24 ha between 2008 and 2011) (Table 7.1). Although it is not clear when the 2011 aerial photograph was taken, it appears that it was taken after the May and June 2011 minor floods (www.dwa.gov.za) which could be the reason for the increased estuarine water area coverage, the reduced sandbanks, and increased area covered by Z. capensis in 2011. Although these minor floods reportedly do not have a major impact on the estuarine system, the appreciable increase in the water level of up to 1.5 m could have scoured the sand and mudflats (Schumann, 2015), creating more Zostera habitat. Furthermore, the estuarine open water area had covered the area previously covered by S. maritima in 2008, resulting in a reduction of S. maritima in 2011. The mudflats of the Bitou marsh (i.e. site Spar 2 and 4) is

184 characterized by tidal creeks and the S. maritima marsh area also showed evidence of anthropogenic impact (local fishermen digging for mud prawn) resulting in a decline of the Spartina area cover.

Furthermore, observations during ground-truth mapping indicate that the area previously mapped as S. maritima by Bornman & Adams (2006) along the edges of the Island in the Keurbooms tributary is presently covered with Triglochin spp. Although the changes of S. maritima distribution in the Keurbooms Estuary were remarkable compared to the 2004 map (Bornman & Adams, 2006), the results should be interpreted with caution as all three aerial photographs used in this study (i.e. 1998, 2008 and 2011) did not show the small clumps of S. maritima area below the N2 in the Keurbooms tributary recorded during field observations and in Bornman & Adams (2006). Despite its decline, 1998, 2008 and 2011 maps showed that S. maritima was still in the same geographical area as mapped by Bornman & Adams (2006), i.e. restricted mostly in the Bitou tributary and the confluence with patches found below the N2 Bridge in the Keurbooms tributary. Zoutendyk & Bickerton (1999) reported S. maritima further down in the blind arm of the estuary but neither this study nor Bornman & Adams (2006) recorded it. This S. maritima was likely eroded due to the southwest migration of the mouth in response to big floods.

The southern African populations of S. maritima species are known to produce viable seeds, however, their production from seeding germination is unknown (Marchant & Goodman, 1969b; Packham & Willis, 1997; Yunnic, 2004). The earliest record of the S. maritima species in the southern Africa was between 1829 and 1930 on a beach between Port Elizabeth and Cape Recife in Algoa Bay, South Africa (Pierce, 1982). This study showed that the southern African populations of S. maritima have the potential to germinate under low salinities despite the low germination rates. The history and establishment of S. maritima in the Keurbooms Estuary is unknown but in all likelihood it may have been in existence prior to the first southern African recording in Algoa Bay. Lambrinos et al. (2010) found that a muddy substrate had a greater seedling potential than sandy or mixed substrate for the S. alterniflora populations in Willapa Bay, Washington, while Mateos-Naranjo et al. (2011) showed that S. densiflora also had a better seedling survival and growth rate on mud soil than on sand soil in the Gulf of Cadiz. Although the reasons for the enhanced growth in muddy soils are still unclear, it may explain the limited

185 distribution of S. maritima in the Keurbooms tributary that is characterized by a sandy substrate, probably with nutritional limitations (Ranwell, 1972; Lambrinos et al. 2010).

S. maritima spread through below-ground rhizomes and also through seed dispersed by tides that then germinates when conditions are favourable (Marchant, 1967; Davis, 2004). However, the rate and conditions in which the seeds germinate suggest that the spread of S. maritima salt marsh in the Keurbooms Estuary is not the dominant form of reproduction. Furthermore, S. maritima seedling establishment in the Keurbooms Estuary could also be limited by competition with matured conspecific or annual marsh species as shown by Kittelson & Boyd (1997) for S. densiflora populations.

The S. maritima salt marsh of the Keurbooms Estuary exhibits growth forms described by Marchant & Goodman (1969b). The results showed that the muddy substrate of the Bitou tributary (especially at site Spar 4) was characterized by short S. maritima while the silty sand substrate especially at site Spar 1 in the lower reaches of the Bitou was characterized by tall plants. Although the scatter plot (Figure 7.9) indicated that the plant roots followed the same shoot height pattern but the roots were uniform. Similar results were recorded by Marchant & Goodman (1969b) on the roots of S. maritima. The distinct differences between plant characteristics, especially between streamside and inland plants shoots, are well documented for species of Spartina (Pierce, 1983; Sanchez et al. 1997; Tsuzaki, 2010; Naidoo et al. 2012). The sediment characteristics, especially sediment texture is regarded as one of the important factors influencing salt marsh colonization and growth (Christian et al. 1983; Bornman et al. 2004; Shaw, 2007). The sediment texture determines the amount of water available in the sediment for plant growth. For example, due to reduced interstitial pore space created by the small particle size, the soils with a high concentration of silt and clay-sized fractions and small amounts of sand are likely to have a higher water holding potential than soil mostly composed of sand (Christian et al 1983). Sanchez et al. (1997) attributed differences in growth of S. maritima in the northwest of Spain to waterlogging conditions and variation in sediment redox potential and sulfide concentration whereas intra- and inter-species competition was important in determining the growth of S. maritima in the Odiel marshes on the Atlantic coast of southwest Spain (Castillo et al. 2000).

The differences in S. maritima plant growth in the Keurbooms Estuary are due to drainage exchange and sediment particle size of the salt marshes. The sub-surface of the Bitou marsh were

186 characterized by mostly the clay-sized fraction compared to the Keurbooms marsh (i.e. site Spar 6), although the clay content was reduced within both marsh habitats. However, due to the majority of plant roots being restricted to the surface layer, the Bitou marsh (i.e. Spar 2 and 4) plants would be negatively affected by the poor drainage (water logged) conditions. Although the moisture content was high at site Spar 2, the growth of the S. maritima plants at Site Spar 4 were influenced by the continuous waterlogged substrate conditions throughout the study period. The S. maritima salt marsh plants of the Keurbooms Estuary displayed a typical “guerilla” species growth form as the plants were evidently attached to their parent stock but the plants in the Bitou marsh (especially at site Spar 2 and 4) clearly showed more below-ground vegetative reproduction than the plants at site Spar 1 in the lower Bitou and Spar 6 in the Keurbooms marsh. Prolonged waterlogging inhibit plant growth of S. maritima, however, under these stressful environmental conditions, our findings suggest that the species allocate proportionally more resources to vegetative propagation rather than to shoot height or sexual reproduction (Castillo & Figueroa, 2009). Despite showing evidence of vegetative reproduction, the plants in the Bitou marsh (i.e. Spar 2 and 4) showed reduced below- ground and above-ground biomasses compared to the plants at sites Spar 1 in the lower Bitou marsh and Spar 6 in the Keurbooms marsh. The production of below-ground and above-ground biomass of S. maritima has been shown to be stimulated by high accretion rates, increases in soil fertility and stress while on the other hand marsh age reduce the biomass (Castillo et al. 2000; 2010). Although the results of the sediment deposition rates reveal that continuous sedimentation takes place in the salt marshes of the Keurbooms Estuary, reduced biomass in the Bitou marsh could be due to decreased sediment aeration as a result of the waterlogged conditions (Castillo et al. 2008). It is possible that the short growth form of S. maritima in the Bitou tributary could be due to the age of the marsh. Recently established marshes show a greater growth rate than older marshes (Castillo et al. 2000). The high biomass of dead roots in the Bitou marsh indicate that the marsh could be much older than the new S. maritima clumps established in the Keurbooms tributary.

This was also demonstrated by Adams & Bate (1995) who recorded a lower stem production when the S. maritima plants were grown under submerged conditions compared to growth under normal tidal inundation or dry treatments. Although redox potential and sulphide concentration in the sediment were not determined in this study, variations in redox potential and sulphide concentration could further explain the reduced plant growth and biomass production in the

187 waterlogged substrate conditions in the Bitou marsh. Prolonged waterlogged conditions has been found to reduce redox potential and increase sulphide concentration in the sediment, leading to reduced plant growth as result of reduced nitrogen uptake (Sanchez et al. 1997; White, 2004).

The morphological differences observed in the field were also demonstrated by the transplant experiments. The S. maritima plants grown in the clayey sand soils had shorter stems than those in the silty soils but had produced a greater number of new stems. Pierce (1983) reported a maximum of 78 tall flowering culms and 40 medium flowering culms from November to March in the S. maritima populations of the Swartkops Estuary. In this study, at least two S. maritima plants had flowered in the silty soil treatment in November 2015. As opposed to plants in stressful environmental conditions, the tall growth form in the silty sand suggests that the plants allocate most of its energy or resources into stem elongation rather than vegetative propagation. This could be due to the differences in the nutrient content of the different soil types.

These two contrasting growth forms of S. maritima plants could be related to the soil texture and variation in nutrients available to plants. Although clayey sand soils had significantly lower silt content than silty soils, they had a significantly higher amount of clay, and as a result these soils exhibited a higher moisture content and organic matter content than the silty soils. Despite producing a greater number of stems, the plants grown on clayey sand soil had also a greater number of stem mortality than those in the silty soil. Mateo–Naranjo et al. (2011) also reported S. densiflora plants to produce a greater percentage of new stems in mud soil than those grown on lower clay and higher sand content soil. Furthermore, S. maritima plants grown on silty soil treatments appeared healthy for most part of the experiment while those in the clayey sand soil treatments showed evidence of discolouration on their leaves, a sign of physiological stress. These high mortality rates in the clayey sand soil could be related to rich organic matter clayey sand. The high organic matter is expected to increase the oxygen demand of the soil which further reduces the redox potential of the waterlogged soils resulting in plant die-back (Tsuzaki, 2010).

The chlorophyll fluorescence was used in past studies to screen plant stress in response to various environmental factors such as salinity especially in the face of rising sea levels (Castillo et al. 2000; Duarte et al. 2014). Past studies have shown that the optimum plant growth of S. maritima is between 18 and 25 (Adams & Bate, 1995; Naidoo et al. 2012) and these findings were supported by high below- and above-ground biomass at 20% sea water than they were in lower or higher

188 salinity. Considering the present predictions of sea level rise in the coastal systems (IPCC, 2002), it is very likely that the frequency and magnitude of higher than current tide levels will be increased, thus subjecting the lower marsh vegetation to increased submersion periods (Duarte et al. 2014). Although S. maritima species have been shown to colonize lower intertidal mudflats (Castillo et al. 2000), they are particularly sensitive to rising sea levels and it is expected that they will not survive if they are submerged with seawater for extended periods of time (Duarte et al. 2014). However, the degree of stress experienced by S. maritima plants as measured by changes in chlorophyll fluorescence may provide valuable information as to how well they are adapted to stressful environmental conditions in the field. The chlorophyll fluorescence potential quantum of

PSII (FV/FM) of the S. maritima plants of the Keurbooms Estuary populations did not show any signs of stress, except for site Spar 4 located in the waterlogged mudflats in the Bitou marsh where the FV/FM were significantly lower than the plants at the other sites. Duarte et al. (2013) showed evidence of the interaction between pore water salinity, precipitation and air humidity with the PSII efficiency of S. maritima. Although, soil salinity was not determined in this study, the photo- inhibition of photosynthesis of the plants at site Spar 4 could be related to longer saline waterlogging conditions as pointed out by Duarte et al. (2014). This waterlogged conditions could have been promoted by the surface sediment type, which was characterized by a high amount of clay-sized fraction compared to the other sites (i.e. Spar 1, 2 and 6). Tidal inundation experiment showed that the potential yield of PSII (FV/FM) were reduced during the incoming tide when the sediment surface was completely submerged, but increased again thereafter indicating that the species is highly adapted to short-term submerged conditions. These results suggest that waterlogged conditions itself does not prohibit plant growth of S. maritima but prolonged waterlogging does.

The tidal chlorophyll fluorescence experiment showed that the potential quantum of PSII (FV/FM) declined when the sediment substrate was submerged, indicating temporary photo-inhibition of photosynthesis. Although the sediment substrate was still submerged during the fourth hour, the potential yield values of PSII (FV/FM) increased to similar values as during the first and second hour. The observed reduction in PSII quantum yield (FV/FM) values during submergence were in agreement to those reported by Duarte et al. (2014). The increase in the PSII quantum yield

(FV/FM) values during the outgoing tide indicated good adaptation ability of S. maritima species to short-term tidal submergence.

189

7.5 Conclusion The Spartina species are usually dominant in the lower intertidal salt marsh, however, this habitat is particularly vulnerable to sea level rise as result of global climate change. It is postulated that rising sea levels will result in prolonged waterlogged conditions in the lower intertidal marsh leading to die-backs of the lower intertidal species, especially the Spartina species. Although the S. maritima has been reportedly increasing in extent in other parts of the southern African coast (Pierce, 1982; Naidoo et al. 2012; Schmidt, 2013; Bornman et al. 2016), this study showed that the distribution of S. maritima salt marsh in the Keurbooms Estuary has been declining over the past two decades. Aerial photographs showed that floods scoured and deposited the sand on the S. maritima stand resulting in reduced coverage. Therefore, the hypothesis that after sediment type, the floods are the major hydrological driver determining distribution of S. maritima in the Keurbooms Estuary was supported.

The differences in plant growth forms support the main hypothesis that the distribution and growth of S. maritima in the Keurbooms Estuary is related to the sediment type of the estuary. The growth form of S. maritima populations in this study, both field investigations and laboratory experiments, showed similar growth mechanisms as described by Marchant & Goodman (1969b). The muddy sub-surface substrate, especially in the Bitou marsh at sites Spar 2 and 4 were characterized by short form S. maritima populations while the silty sand substrate (especially in the lower Bitou marsh at site Spar 1) was characterized by taller plants. Interestingly, the plants in the Keurbooms tributary at site Spar 6 showed no significant difference in shoot height between those in the Bitou, despite the initial observation. Despite these contrasting observations, the roots were almost uniform at all site despite differences in sediment types. The short form S. maritima in the Bitou marsh (especially at site Spar 4) was exposed to prolonged waterlogged substrate conditions, resulting in a low potential yield of PSII (FV/FM) (photo-inhibition). Despite these stressful conditions, the short growth form of the Bitou populations displayed more extensive branched rhizomes (evidence of below-ground vegetative reproduction) than those plants in the lower Bitou marsh and the Keurbooms tributary. This growth form suggests that under stressful conditions, S. maritima allocate almost all its energy into vegetative reproduction rather than shoot height.

190

Potential yield of PSII (FV/FM) were reduced during prolonged waterlogged conditions and during the incoming tide when the sediment surface was completely submerged. The yield however increased thereafter indicated that the S. maritima species is highly adaptive to short-term submerged conditions. These results suggest that waterlogged conditions itself does not prohibit plant growth of S. maritima but prolonged waterlogging does. Although the S. maritima population showed potential for seed germination, the slow rate and strong evidence of below-ground propagation further suggest that the S. maritima populations maintain their presence in the salt marshes of the Keurbooms Estuary mostly through below-ground vegetative reproduction expansion rather than through seedling establishment. Strong evidence of below-ground vegetative reproduction suggested that the S. maritima is likely to colonize exposed intertidal mudflats and sandbanks using this method. The small clumps of S. maritima in the Keurbooms were in all likelihood established through seedlings and are now expanding through vegetative growth. The high accretion rates in the main Keurbooms channel would act to stimulate the vegetative process and flooding events would therefore be important in transporting sediments onto the marsh surface despite having a negative impact on the S. maritima area cover.

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Chapter 8. General discussion and conclusion

8.1 General discussion Sedimentary dynamics are one of the main controlling factors of an estuarine ecosystem, structuring vegetation and benthic communities. Although the sedimentary environment of the Keurbooms Estuary has drawn the attention of scientists (especially geologists) over the past several decades, the influence of the sediment dynamics on the distribution of salt marshes were poorly understood. The sediment supplied by the Bitou and Keurbooms tributaries differs partly due to the distinctive nature of the underlying geology through which they drain. The sediment survey of the estuarine bottom revealed that the Keurbooms tributary is mostly characterized by a whitish sand-size sediment fraction derived from feldspathic and quartzite sandstone with evidence of finer sediment fraction in the upper reaches opposite Whiskey Creek. Although an outcrop of shale and siltstone passes the Keurbooms tributary between Whiskey Creek and the N2 road bridge, this geological substrate supply limited fine sediment to the estuary. Although the upper Bitou was almost always composed of coarse sized sediments, the middle and lower reaches of this tributary were mostly characterized by finer sediment deposits. The lower reaches of the estuary, after the confluence were characterized by marine medium sorted sand. These results corroborated the findings by Reddering (1981) that fluvial sand sediment with practically no clay or calcium carbonate is transported into the estuary does not reach the lower reaches. These results supported our earlier statement that the fine sediment required by the Spartina maritima for growth comes from the Bitou rather than the Keurbooms tributary or the sea.

The intertidal areas are known to be the main sites of fine sediment deposits in estuaries and similar results were recorded in this study, i.e. fine sediment deposits within the S. maritima marshes, especially in the Bitou marsh (Chapter 5). Similar results were also recorded in the sediment cores, although the Keurbooms marsh sediment became finer with increasing depth (i.e. 0.50 – 0.75 and 1.0 – 1.25 m depth) while the fine fraction in the sediment of the Bitou marsh were reduced with depth. The sediment mineralogy of the estuary indicated reduced quartz concentrations and increased clay mineral concentrations in the S. maritima marsh surface sediments compared to the estuarine channel sediments. Generally, clay minerals in the sediments can be either inherited or derived from pre-existing parent rocks as a result of transformation processes (Wilson, 1999). Although the clay minerals found in the S. maritima surface sediment were also the same detected

192 in estuarine bottom sediments, the increased concentrations of these clay minerals in the S. maritima surface sediments suggest that their main source is not necessarily the upper catchments of the tributaries, but rather derived from the Bokkeveld shale and siltstone slate crossing the channel above the N2 road bridge.

The permanently open Keurbooms Estuary located in the warm-temperate climatic region is one of the few estuaries in which intertidal salt marshes occur along the southern African coast. Intertidal salt marshes occur only in certain estuaries (Adams et al. 1999; Colloty et al. 2002) that maintain a permanent connection with the sea and are characterized by a low-energy and a gently sloping coast (Allen & Pye, 1992; Whitfield, 1998). The Keurbooms Estuary lacks extensive floodplain areas and as a result the salt marshes are mainly restricted to the Bitou and small patches in the Keurbooms tributary. Different salt marsh plant species can occur over a wide range of sediment substrate types, e.g. the habitat for Spartina species vary from soft muddy to a sandy silt substrate (Marchant & Goodman, 1969b; Christian et al. 1983). The diagram below (Figure 8.1) summarises the growth and the distribution of the S. maritima in the Keurbooms Estuary. Growth of S. maritima in the Keurbooms Estuary is restricted to the confluence, lower Bitou and a few parts of the Keurbooms tributary. Two growth forms of S. maritima were evident in two contrasting sediment substrates. The muddy sub-surface substrate of the Bitou was characterized by short monospecific stands of S. maritima populations whereas the sandy silt substrate of the Keurbooms tributary was characterised by taller isolated clumps.

A high soil moisture content is another characteristic feature of salt marsh sediment and soil moisture content is generally expected to decline from the low marsh to the high marsh due to a lower inundation frequency and magnitude (Reaper, 1995). Although sites Spar 1 in the lower Bitou and Spar 6 in the Keurbooms tributary were located at the edge of the channel, a lower moisture content was recorded than the inland (further form the channel) Bitou sites. This was largely attributed to differences in the soils rather than inundation frequency. Soils which are waterlogged on a regular or permanent basis are known to present an extremely hostile environment for plant growth as they limit the rate in which oxygen diffuse (i.e. redox potential) into the soil, thus causing anaerobic conditions (Reaper, 1995; van der Linden, 2014). The short form S. maritima in the Bitou marsh, especially at Spar 2 and 4, could be as a result of the prolonged waterlogged substrate conditions in which they grow (Sanchez et al. 1997). The

193 black/grey colouration of the soil with increasing depth was also an indication of the reduced oxygen state of the soils.

S. maritima plants are known to grow tallest on a sandy silt substrate but growth is more satisfactory on a muddy substrate (Marchant & Goodman, 1969b). Therefore, with change in sediment texture with depth, we expected that the roots of plants in the sandy silt sediment substrate (sites Spar 1 and 6) would locate their active part of its root system in the deeper finer soils which would then result in more productive growth. However, that was not the case as all plants located the majority of their roots in the sub-surface soil layer (i.e. 0 – 0.25 m). Despite similar root lengths to the Keurbooms tributary populations, the Bitou population was characterised by short and dense wiry rhizomes, evidence of belowground vegetative reproduction. Due to the shortness of the rhizomes, the plants grew close to their parent stock displaying typical monospecific growth of “guerilla” species (Marchant & Goodman, 1969b; Castillo et al. 2010). Less below-ground vegetative reproduction in the Keurbooms tributary may suggest that the sandy silt nature of the soil in these S. maritima populations lack the necessary nutrients to promote vegetative reproduction.

Despite showing the ability of vegetative propagation, the mapped aerial photographs showed that the distribution of the S. maritima in the Keurbooms Estuary has been declining over the last three decades (Chapter 7). This decline in distribution could be related flooding rather than normal prolonged waterlogged conditions. The GIS mapping and aerial images clearly showed that large scale sediment deposition on the marsh surface as a result of flooding had replaced the S. maritima habitat with sandbanks or mudflats, especially after the 2007 (i.e. 1 in 20 years) big flood event (Figure 7.4). These results supported the hypothesis that after sediment dynamics, floods are the major hydrological driver determining the distribution of the S. maritima in the Keurbooms

Estuary. However, reduced chlorophyll fluorescence potential quantum of PSII (FV/FM) values for plants growing in the prolonged waterlogged conditions may result in the further decline of S. maritima. This decline could be due to the age of the population (clearly evident in all the aerial images over the past three decades) or that the flood may have impacted the Bitou marsh by scouring away the surface layer, thereby reducing the surface elevation and subjecting the plants to a higher frequency and magnitude of inundation. The ability of S. maritima to accrete sediment in the intertidal zone may reverse these water logged conditions over time.

194

Figure 8.1: Flowchart indicating the distribution and growth of S. maritima in the Keurbooms Estuary.

195

8.2 Conclusion The distinctive nature of the sediment substrate of the Keurbooms tributaries (i.e. the Bitou and Keurbooms) affect the growth and distribution of S. maritima in the system. Despite showing signs of photo-inhibition in prolonged waterlogged conditions, S. maritima grew well in the muddy Bitou marsh. Although a decline in S. maritima surface area is reported here, the production of viable seed and observed vegetative propagation suggest that the S. maritima is able to colonize open stable intertidal mudflats and sandbanks, which will result in the expansion in distribution of this species in the Keurbooms Estuary. Although accretion rates were not determined in this study, the short-term sediment deposition rates reveal that sedimentation in the marshes of the Keurbooms Estuary remains active, and will, over time, result in elevated marsh surfaces. Although floods have been shown to reduce the distribution of S. maritima in the Keurbooms Estuary, they are an important sediment transporting mechanism to the salt marsh surface, which, in turn, may further stimulate S. maritima growth.

The S. maritima plant species is known to protect channel banks against erosion during floods or storms (Neumeier & Ciavola, 2004). Despite the Keurbooms Estuary being subjected to regular flooding (at least after every 2 years), the continued decline in the distribution of S. maritima is of concern, as it reduces the ecosystem functioning of the intertidal salt marsh and may make the coast more vulnerable to bank erosion. These impacts will be accelerated by human activities, especially ongoing bait digging by local fishermen in the lower intertidal zone. It is therefore, recommended to continue monitoring of the sedimentation and the distribution S. maritima in this estuarine system, especially through the use of Rod Set Elevation Tables (Cahoon et al. 1995).

196

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Appendix 1 Chapter 4: Sediment and hydrodynamics distribution

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Table A.1.1: Grain size parameters for each site in June 2014.

Site Depth (m) Mean (ϕ) Sorting (ϕ) Sediment name

K1_Blind arm 0.892 1.779 0.419 Well sorted medium sand K2 1.655 2.009 0.393 Well sorted fine sand K3_Mouth 1.457 1.813 0.41 Well sorted medium sand K4 1.071 1.337 0.722 Moderately sorted medium sand K5 1.189 1.661 0.489 Well sorted medium sand K6 1.189 1.638 0.471 Well sorted medium sand K7 2.389 1.508 0.513 Moderately well sorted medium sand K8_Confluence 1.049 1.752 0.532 Moderately well sorted medium sand K9 1.205 1.89 0.533 Moderately well sorted medium sand K10 1.217 1.586 0.405 Well sorted medium sand K11 2.077 1.259 0.673 Moderately well sorted medium sand K12 0.573 1.652 0.684 Moderately well sorted medium sand K13 1.863 1.013 0.802 Moderately sorted medium sand K14 0.588 1.058 0.804 Moderately sorted medium sand K15 0.820 1.735 0.709 Moderately sorted medium sand K16 1.971 0.99 0.626 Moderately well sorted coarse sand K17 3.633 0.876 0.644 Moderately well sorted coarse sand K18 1.850 2.344 1.301 Poorly sorted fine sand K19 7.611 0.775 0.779 Moderately sorted coarse sand K20 2.478 1.498 0.859 Moderately sorted medium sand K21 3.219 1.858 0.919 Moderately sorted medium sand K22 4.424 0.935 0.547 Moderately well sorted coarse sand K23 1.052 1.091 0.583 Moderately well sorted medium sand K24 4.764 1.251 0.593 Moderately well sorted medium sand K25 2.869 0.81 0.762 Moderately sorted coarse sand K26 0.262 0.736 1.113 Poorly sorted coarse sand B1 1.274 2.438 1.292 Poorly sorted fine sand B2 1.092 1.773 0.799 Moderately sorted medium sand B4 3.091 1.781 Poorly sorted very fine sand B5 1.089 1.098 1.402 Poorly sorted medium sand B6 3.923 0.969 0.902 Moderately sorted coarse sand Bitou drift 0.417 3.915 1.839 Poorly sorted very fine sand Bitou upper 0.355 1.037 1.266 Poorly sorted medium sand

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Table A.1.2: Grain size parameters for each site in February 2015.

Site Depth (m) Mean (ϕ) Sorting (ϕ) Sediment name K1_Blind arm 2.252 1.467 0.544 Moderately well sorted medium sand K2 2.523 1.999 0.364 Well sorted medium sand K3_Mouth 2.450 1.665 0.388 Well sorted medium sand K4 1.488 1.567 0.524 Moderately well sorted medium sand K5 1.180 1.804 0.444 Well sorted medium sand K6 1.760 1.828 0.521 Moderately well sorted medium sand K7 1.799 1.828 0.409 Well sorted medium sand K8_Confluence 1.148 1.675 0.510 Moderately well sorted medium sand K9 1.728 1.810 0.596 Moderately well sorted medium sand K10 2.106 1.666 0.408 Well sorted medium sand K11 0.890 1.304 0.651 Moderately well sorted medium sand K12 2.119 1.471 0.702 Moderately sorted medium sand K13 0.970 1.404 0.839 Moderately sorted medium sand K14 0.426 1.325 0.652 Moderately well sorted medium sand K15 2.008 1.663 0.653 Moderately well sorted medium sand K16 4.165 1.205 0.617 Moderately well sorted medium sand K17 2.328 1.418 0.734 Moderately sorted medium sand K18 7.547 1.319 0.922 Moderately sorted medium sand K19 2.170 0.765 0.725 Moderately sorted coarse sand K20 4.220 1.737 0.440 Moderately sorted medium sand K21 5.714 1.652 1.315 Poorly sorted medium sand K22 1.625 1.004 0.550 Moderately well sorted medium sand B1 3.823 2.213 0.921 Moderately sorted fine sand B2 1.141 1.809 0.437 Well sorted medium sand B3 0.493 1.809 0.433 Well sorted medium sand B4 1.723 0.948 Moderately sorted medium sand B5 1.010 1.612 1.119 Poorly sorted medium sand B5_Cliff 0.973 1.363 Poorly sorted coarse sand B6 1.733 1.068 0.973 Moderately sorted medium sand Bitou upper 0.260 0.879 1.193 Poorly sorted coarse sand

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Table A.1.3: Grain size parameters for each site in September 2015.

Site Depth (m) Mean (ϕ) Sorting (ϕ) Sediment name

K1_Blind arm 2.244 1.634 0.470 Well sorted medium sand K2 1.815 2.014 0.336 Very well sorted fine sand K3_Mouth 2.649 1.970 0.336 Very well sorted medium sand K4 1.946 1.653 0.383 Well sorted medium sand K5 1.105 1.634 0.396 Well sorted medium sand K6 1.504 1.837 0.376 Well sorted medium sand K7 2.703 1.593 0.570 Moderately well sorted medium sand K8_Confluence 1.390 1.817 0.437 Well sorted medium sand K9 1.374 1.664 0.418 Well sorted medium sand K10 1.527 1.608 0.366 Well sorted medium sand K11 0.880 1.255 0.658 Moderately well sorted medium sand K12 1.969 1.389 0.639 Moderately well sorted medium sand K13 0.957 1.302 0.706 Moderately sorted medium sand K14 1.212 1.571 0.494 Well sorted medium sand K15 2.813 1.263 0.871 Moderately sorted medium sand K16 3.774 1.100 0.693 Moderately well sorted medium sand K17 2.175 0.919 0.579 Moderately well sorted medium sand K18 7.380 1.712 0.721 Moderately sorted medium sand K19 1.870 0.817 0.789 Moderately sorted coarse sand K20 6.349 1.598 0.431 Well sorted medium sand K21 5.907 1.618 0.565 Moderately well sorted medium sand K22 1.863 0.116 0.647 Moderately well sorted coarse sand B1 2.404 2.427 1.185 Poorly sorted fine sand B2 1.616 1.828 0.437 Well sorted medium sand B3 0.407 1.971 0.446 Well sorted medium sand B4 1.091 1.184 Poorly sorted medium sand B5 1.412 1.126 1.316 Poorly sorted medium sand B6 1.495 -0.014 0.730 Moderately sorted very coarse sand Bitou upper 0.245 0.558 1.047 Poorly sorted coarse sand

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Water column salinity and temperature of the Bitou tributary

In June 2014, measurements were only taken at sites B1, B2 and B6. Salinity at sites B1 and B2 were characterized by saline water (i.e. ranging between 24.7 and 26.3) whereas saline water (i.e. 24.1) intrudes underneath the freshwater (i.e. 7.1) displaying a form of a wedge at site B6 upstream of the Bitou tributary (Figure A.1.1). The saline water at sites B1 and 2 were cold throughout all depths whereas bottom water at site B6 were slightly warmer (at 15 ºC than surface water (at 12ºC) (Figure A.1.2).

In September 2014 the salinity was measured on 9 and 10. Only site B1 and B2 were recorded on the 9th and the salinity was extremely saline with very little or no freshwater influence. This was partly due to high tidal exchange and low river discharge. Water temperature was almost the same at both sites but at B1 was slightly warmer (at 18ºC) than bottom water (at 17ºC), at B2 temperature was the same (at 18ºC) (Figure A.1.2). The salinity on the following day (i.e. 10 September 2014) declined but sites B1 and B2 remained saline with warm water at 19ºC. Sites Bitou drift and Bitou upper upstream of the Bitou (in the salinity profile referred as sites 3 and 4) were extremely cold and fresh with no tidal influence. This was partly because on the 10 September 2014 recordings were taken during low tidal as oppose to the recording taken during incoming high tide on the 9 September 2014.

Sites B1 B2, B3, B5, B6 and Bitou upper (in the salinity profile referred as sites 1, 2, 3, 4, 5, and 6) were recorded during February 2015. The salinity profile showed two salinity patterns during February 2015 (Figure A.1.1). Site B1 in the lower reaches and B5 and B6 further upstream the N2 Bridge display a typical salt wedge salinity profile with saline water following underneath the freshwater. But, however, because of depth and tidal mixing at sites B2 and B3 the salinity was the same top to bottom at ~ 19. Meanwhile, site Bitou upper was extremely characterised by freshwater with no tidal exchange whatsoever. Water temperature ranged between 21 – 24ºC. The freshwater at site Bitou upper were characterized by slightly cold water at 21ºC than other sites. Despite site B5 and B6 displayed typical salt wedge salinity profile but the water temperature was the same at all depth (Figure A.1.2). Site B1 was characterised by slightly cold bottom water at 21ºC.

Although the Bitou tributary is not gauged but, according to Keurbooms tributary flow rate data, measurements in April 2015 were taken after 5 days high river discharge. Site B1, B2, B3, B6 and

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Bitou upper (in the salinity profile referred as sites 1, 2, 3, 4 & 5) were recorded during April 2015. Saline water flows underneath freshwater, displaying salt wedge salinity pattern whereas at site B3 the salinity was almost the same top to bottom, partly because of well mixing due to low bathymetry. Meanwhile, sites B6 and Bitou upper further upstream were extremely characterised by freshwater with no tidal exchange whatsoever (Figure A.1.1). Despite showing different salinity patterns, the water temperature was the same at all sites at 16ºC (Figure A.1.2).

Sites B1 B2, B3, B5, B6 and Bitou upper (in the salinity profile referred as sites 1, 2, 3, 4, 5, and 6) were recorded during September 2015. Similar to April 2015 salinity profile, site B1 and B2 were characterised by saline bottom water following underneath fresh surface water. Again due to shallow bathymetry at site B3 the salinity was almost the same from surface to bottom. There appears to be very little or no mixing further upstream as a result the salinity at B5, B6 and Bitou upper was extremely fresh (Figure A.1.1). Similar water temperature to that reported during February 2015 was observed in September 2015 (Figure A.1.2).

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Figure A.1.1: Contour plots showing water salinity measured in the selected Bitou tributary sites.

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Figure A.1.2: Contour plots showing water salinity measured in the selected Bitou tributary sites.

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Appendix 2 Chapter 6: Sediment minerals

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Estuarine bottom sediments

Site K3

Site K3 in the mouth of the estuary had no evidence of clay minerals as shown by intense XRD peaks during all three sampling periods. Aragonite remained as a characteristic feature of the sediment in the mouth during June 2014 and February 2015 periods but chalcopyrite was notably absent in June 2014 (Figure A.2.1).

Site K22

Chalcopyrite was entirely absent at site K22. Quartz, feldspars (i.e. both K-feldspars and plagioclase) were the main minerals whereas, mica and clinochlore were the only detected clay minerals during February 2015 and September 2015 sediment samples with no evidence of kaolinite (Figure A.2.2). Absence of kaolinite at K22 could be due to the fact that it occurs on fine- grained sediments < 0.002mm (Dyer, 1979). Furthermore, halite and rutile were commonly occurring throughout the study period (Figure A.2.2).

Site B6

Concentration of quartz were increased whereas mica was reduced at B6 in February 2015 compared to both June 2014 and September 2015. Interestingly, chalcopyrite was detected during February 2015 (Figure A.2.3).

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Figure A.2.1: XRD peaks showing minerals of estuarine bottom sediments at site K3 in the mouth of the estuary during (a) June 2014 and (b) February 2015.

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Figure A.2.2: XRD peaks showing minerals of estuarine bottom sediments at site K22 in the Keurbooms tributary during (a) September 2014 and (b) September 2015.

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Figure A.2.3: XRD peaks showing minerals of estuarine bottom sediments at site B6 in the Bitou tributary of the estuary during February 2015.

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Surface sediments deposited within the S. maritima salt marsh.

Site Spar 2

Quartz remained as the major mineral site Spar 2 despite its concentration were reduced compared to those found in the bottom sediments. We expected that if Bitou tributary drain fine sediments, the S. maritima surface sediment would have more clay minerals but, however, only mica and clinochlore were detected with no kaolinite. Despite this, the concentrations of these clay minerals were increased compare to those found in the bottom sediments (Table 6.2). Halite was consistently present throughout while rutile was absent in February 2015 (Figure A.2.4b). Neither aragonite nor chalcopyrite were detected in this site (Figure A.2.4).

Site Spar 4

Quartz, K-feldspar and plagioclase were the major occurring minerals at site Spar 4. Clinochlore was detected during February 2015 but with no evidence of kaolinite whereas an opposite occurred in September 2015 sediment samples while mica was consistently present throughout (Figure A.2.5). It should be noted that Figure A.2.5 showed kaolinite as occurring on the same peaks as clinochlore. This is partly due to interference of clay minerals with each other. Meanwhile, pyrite and halite were consistently occurring in the Bitou marsh sediments.

Site Spar 6

Quartz, K-feldspar and plagioclase remained as the major minerals at site Spar throughout (Figure A.2.6). Mica was the only occurring clay mineral found in both September 2014 and 2015 whereas clinochlore and kaolinite were detected only during September 2014 and September 2015 respectively. Notably, calcite was detected throughout (Figure A.2.6) and this may suggest marine origin of these sediments. Furthermore, halite and pyrite was also detected throughout while aragonite was only detected in September 2015 (Figure A.2.6b).

Site Spar 8

Similar to site Spar 6 results, quartz, K-feldspar and plagioclase, mica and halite were the commonly occurring minerals throughout the period of the study. Notably, kaolinite was detected throughout whereas clinochlore was entirely absent (Figure A.2.7). Furthermore, calcite remain as

232 the only CaCO3 mineral while pyrite was also detected throughout and chalcopyrite was found only in September 2014.

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Figure A.2.4: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 2 in the Keurbooms tributary during (a) September 2014 and (b) February 2015.

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Figure A.2.5: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 4 in the Keurbooms tributary during (a) February 2015 and (b) September 2015.

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Figure A.2.6: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 6 in the Keurbooms tributary during (a) September 2014 and (b) September 2015.

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Figure A.2.7: XRD peaks showing minerals of surface sediment deposited within S. maritima at site Spar 8 in the Keurbooms tributary during (a) September 2014 and (b) September 2015.

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