COPYRIGHT AND CITATION CONSIDERATIONS FOR THIS THESIS/ DISSERTATION o Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. o NonCommercial — You may not use the material for commercial purposes. o ShareAlike — If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original. How to cite this thesis Surname, Initial(s). (2012) Title of the thesis or dissertation. PhD. (Chemistry)/ M.Sc. (Physics)/ M.A. (Philosophy)/M.Com. (Finance) etc. [Unpublished]: University of Johannesburg. Retrieved from: https://ujcontent.uj.ac.za/vital/access/manager/Index?site_name=Research%20Output (Accessed: Date). An assessment of the aquatic macroinvertebrate diversity within the Nyl River Floodplain system, Limpopo, South Africa. By Nathan Jay Baker DISSERTATION Submitted in Fulfilment of the Requirements for the Degree MAGISTER SCIENTIAE In Aquatic Health In the FACULTY OF SCIENCE At the UNIVERSITY OF JOHANNESBURG Supervisor: Dr. R Greenfield January 2018 The financial assistance of the National Research Foundation (NRF) towards this research is hereby acknowledged. Opinions expressed, and conclusions arrived at are those of the author and are not necessarily to be attributed to the NRF. “An understanding of the natural world and what’s in it is a source of not only a great curiosity but great fulfilment.” ─David Attenborough ACKNOWLEDGEMENTS I would like to dedicate this dissertation to my parents, Dean and Mercia Baker, who inspired my love for nature and encouraged me to always strive for greatness. Without your support, guidance and dedication, I would not be the person I am today. Thank you for always being there for me, especially when I needed it most. I would like to extend my further gratitude and thanks to the following people and organisations: The University of Johannesburg for its financial support and for the use of its infrastructure and equipment. The National Research Foundation (NRF) for the financial support provided. The University of Johannesburg’s Spectrum facility and its staff for the use of equipment and their assistance with analyses. Dr Richard Greenfield for his mentorship, support and guidance throughout this project. I am honoured to have worked under your supervision. Mr Gregg Jansen van Rensburg and Mr Ryaz Musa for their valued friendships and their assistance with fieldwork and statistical interpretation, I couldn’t have done it without you. Mrs Simone Dahms-Verster for her cherished friendship and her consistent effort in assisting me with laboratory work and proof reading. Team Ginger-Brown (GB) for life! Ms Kelly Shannon Dyamond and Ms Lizaan de Necker for their assistance with the identification of some macroinvertebrate taxa. My colleagues in the University of Johannesburg’s EcoTox Laboratory, thank you for the support, motivation and endless supply of coffee you provided throughout this project. All my friends and family, your continued love, support and encouragement is what kept me going. I am lucky to have such a special group of people in my life, I cannot begin to express my gratitude. Lastly, a special thanks to Dr Olena Kudlai for your support, guidance and encouragement which motivated me every step of the way and continued to keep me positive. Your wealth of knowledge, advice and constructive criticisms were always welcomed and have made me a better scientist. i SUMMARY South Africa is a water scarce country with uneven distributions of rainfall both spatially and temporally. With the proposed pressures of climate change, it has been foreseen that within the coming decades, water availability may become a limiting factor for further development in South Africa. Regardless of the usable conversion rate of catchment runoff to riverine surface water flow, most of South Africa’s surface water resources are provided by rivers. Due to over exploitation, anthropogenic influences and mismanagement, all river systems within South Africa are impacted to some extent. Due to a lack of knowledge regarding much of the biota supported by freshwater systems, specifically in semi-arid countries such as South Africa, it is of utmost importance to study freshwater ecosystems to determine the full extent of the biodiversity supported by such systems and how this biodiversity may become affected through anthropogenic impacts and its use as ecological indicators. Macroinvertebrate taxa form much of the global freshwater biodiversity and due to their wide taxonomic diversity, they show adaptations to extremely variable environments, ubiquitous distributions and varying sensitivities to stressors. Therefore, macroinvertebrate taxa are readily used as bioindicator test organisms for many biomonitoring and management studies. The Nyl and Mogalakwena Rivers are important water sources for the semi-arid Limpopo Province and despite this, they are continually being stressed through increased urbanisation, industrial and mining development as well as intensive agricultural activities. The Nyl River flows through and provides water for the towns of Modimolle (population of >68 513), Mookgophong (population of >35 640) and Mokopane (population of >30 151). The Nyl River provides water resources for the internationally acclaimed Nyl River Floodplain including the RAMSAR accredited Nylsvley Wetland, a recognised biodiversity hot spot. Notwithstanding its importance to aquatic fauna and flora, the Nylsvley Wetland provides suitable habitat and breeding grounds to over 400 avian species, the endangered Roan antelope Hippotragus equinus (É. Geoffroy Saint-Hilaire, 1803) and South Africa’s only wild rice Oryza longistaminata A. Chev. & Roehrich. The wetland also aids in flow attenuation, water retention and water purification during periods of flooding and drought. After the floodplain, the name of the river changes to the Mogalakwena River which becomes an important source of water for many large- and small-scale agricultural and industrial activities established within the Mogalakwena municipality. The Mogalakwena River then flows downstream into the transboundary Limpopo River. ii Many facets of the Nyl and Mogalakwena River ecosystem have been characterised, however, information regarding the state (i.e. structure and function) of the macroinvertebrate assemblages is outdated. The study aimed to comprehensively assess the macroinvertebrate community assemblages within the Nyl and Mogalakwena Rivers and their associated wetlands. Additionally, it aimed to identify possible anthropogenic impacts on these rivers by correlating physico-chemical water parameters and sediment characteristics to that of the macroinvertebrate community assemblage distributions. Ten sites along the Nyl and Mogalakwena Rivers were chosen according to their relative positions to point sources of pollution of the system. Two sampling surveys were conducted, one during the low flow season (July 2016) and one during the high flow season (February 2017) of the system. Macroinvertebrate taxa were collected using ‘kick, stir, sweep’ methods, fixed using 10 % neutrally buffered formalin and stained using Rose Bengal. In addition to macroinvertebrate sampling, in situ water quality parameters were measured and a water and sediment sample were collected from each sampling site and analysed at the University of Johannesburg’s laboratories. Laboratory work included the enumeration and identification of macroinvertebrate taxa to the lowest taxonomic level possible using available taxonomic guides. The physical characteristics (organic content and grain size distributions) of the collected sediments were evaluated according to standard United States Environmental Protection Agency (USEPA) methods and the results were used to supplement the water and macroinvertebrate analysis data. Water nutrients were analysed using standard test kits and light spectrophotometry, whereas, water metal contamination was determined using inductively coupled plasma optical emission spectrometry (ICP – OES). Univariate diversity indices, multivariate statistics and correlation analyses were conducted using ComEcoPaC version 1 (Drozd 2010) and Canoco version 5 (Šmilauer & Lepš 2014) and IBM SPSS Statistics 24 software (IBM Corporation, Armonk, NY, USA), respectively. The water quality at the sites in the upper reaches of the Nyl River was ideal, thereafter deteriorating downstream of the Modimolle wastewater treatment facility (WWTF). Statistical analyses revealed spatial variations between impacted sites and the unimpacted sampling sites for both sampling seasons. These spatial variations were driven by increases to chemical oxygen demand concentrations (decreased dissolved oxygen) and elevated nutrient levels (nitrites, nitrates, ammonia, ammonium, orthophosphates and total nitrogen). The water at the sites adjacent and downstream to iii the Modimolle WWTF was strongly correlated to and had higher concentrations of most of the tested nutrients, environmental parameters and metal concentrations, indicating that polluted effluent being discharged from the Modimolle WWTF affected the water quality at these sites. The water quality at the Nylsvley Wetland site (NYL) included a potential recovery, seemingly due to the assimilative ability of wetland environments. The sites within the Mogalakwena and Limpopo Rivers had good water quality, however, drought