ResearchOnline@JCU This file is part of the following reference: Bainbridge, Zoe T. (2015) Tracing the sources, transport and dispersal of suspended sediment from the Burdekin River catchment into the Great Barrier Reef lagoon. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/42312/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/42312/ Tracing the sources, transport and dispersal of suspended sediment from the Burdekin River catchment into the Great Barrier Reef lagoon PhD thesis submitted by Zoe T. Bainbridge B.App.Sc (Hons) in May 2015 for the degree of Doctor of Philosophy in the College of Marine and Environmental Sciences James Cook University Statement on the Contribution of Others Research funding James Cook University/CSIRO Tropical Landscapes Joint Venture and School of Earth and Environmental Sciences co-funded scholarship JCU Graduate Research School JCU TropWATER North Queensland Dry Tropics Australian Government’s Marine and Tropical Sciences Research Facility CSIRO (Petra Kuhnert/Rebecca Bartley) Thesis committee Associate Professor Scott Smithers, College of Marine and Environmental Sciences, James Cook University Dr Stephen Lewis, TropWATER, James Cook University Jon Brodie, TropWATER, James Cook University Dr Scott Wilkinson, Land and Water Flagship, CSIRO Dr Petra Kuhnert, Computational Informatics, CSIRO Editorial support Scott Smithers Rebecca Bartley Stephen Lewis Grant Douglas Scott Wilkinson Stephen Hillier Jon Brodie Jim Wallace Petra Kuhnert Brent Henderson Eric Wolanski Peter Hairsine Jorge Álvarez-Romero Anonymous reviewer of published chapter 2, the Associate Editor, Basil Gomez, Murray Hicks and two anonymous reviewers of published chapter 3 and the Submission Editor and two anonymous reviewers of accepted chapter 4. ii Co-authorship in chapters for peer-reviewed publication This thesis includes some collaborative work. Whilst undertaking this collaboration I was responsible for project conceptualisation, field study design and data collection, laboratory and data analysis and synthesis of results into a publishable format. Stephen Lewis, Scott Smithers, Jon Brodie, Scott Wilkinson, Petra Kuhnert, Grant Douglas (Chapter 4), Stephen Hillier (Chapter 4), Eric Wolanski (Chapter 2), Jorge Álvarez- Romero (Chapter 2) and Brent Henderson (Chapter 3) all provided a range of editorial advice, technical instruction and contributed to publications associated with this thesis. Specifically, in Chapter 2 I undertook field sampling with assistance from SL and SS, I prepared the samples for and took the microphotograph images, analysed the samples for particle size, interpreted the data, conceptualised and constructed the figures and tables and wrote the chapter. EW, JB and SL contributed to study design, provided technical instruction and editorial comments. JA-R provided editorial comments, ran the ocean colour algorithm and created Fig 2.3 (Eduardo Teixeira da Silva is acknowledged for processing the raw satellite imagery for this figure). Pia Harkness assisted with map production (Fig 2.1). In chapter 3 I designed the field study and undertook the sampling with assistance from SL (and others mentioned in acknowledgements), I co-ordinated and trained the grazier volunteer network, analysed selected samples for particle size, processed the raw data, constructed the annual sediment budget and other figures, interpreted and wrote the chapter. PK and BH developed the LRE model (Kuhnert et al. 2012), with Burdekin catchment-specific process understanding provided by myself and SL. SL, SS and JB contributed to study design and provided editorial assistance. Adella Edwards assisted with the final production quality versions of Figures 3.1 and 3.3. Chapter 4 utilises field data collected in Chapter 3. In this chapter I recovered the <10 µm sediment fraction of stored water samples, prepared them for X-ray diffraction, interpreted the raw diffraction data with technical assistance from SH and Raphael Wust, further analysed the particle-size specific catchment budget of Chapter 3, interpreted the data, designed and constructed the figures and tables, and wrote the chapter. All co-authors contributed to various aspects of study design or final data interpretation, and provided editorial comments. iii Every reasonable effort has been made to gain permission from and acknowledge the owners of copyright material. I would be pleased to hear from any copyright owner who has been omitted or incorrectly acknowledged. iv Acknowledgements I am indebted to my supervisory team, for your invaluable wisdom and guidance along this journey. A very special thank you to my principal and co-supervisors Scott Smithers and Stephen Lewis – for your endless support, patience, friendship and editing, and your invaluable instruction in undertaking and publishing clear science. Jon Brodie, my mentor, thank you for all you have taught me since I volunteered to work for ACTFR on a tiny Burdekin project all those years ago, and for encouraging me to undertake this PhD. I am immensely grateful for the additional support received by my CSIRO supervisors Scott Wilkinson and Petra Kuhnert part-way through the thesis – I have learnt so much from you both, and you have helped to shape and strengthen this thesis in many ways. I am also grateful to Rebecca Bartley, Grant Douglas, Eric Wolanski and Steve Hillier, from whom I have been fortunate to receive additional guidance and scientific inspiration during the course of this PhD. A huge thank you to Damien Burrows and Susan Lesley, and TropWater more generally, for administrative, financial and emotional support throughout my PhD. I am also appreciative of the academic and administrative support provided by the School of Earth and Environmental Sciences (now CMES), especially Adella Edwards, Clive Grant, Paul Givney, Glenn Connolly, Bec Steele, Melissa Crawford and Beth Moore, as well as Jodie Wilson and the Graduate Research School team. I am grateful to the CSIRO’s Ian Watson, Di Popham, Keith Bristow and Jim Wallace for their support and guidance through this endeavour. Finally I am extremely grateful to Scott Crawford, Di O’Donnell, Ian Dight and Paul Duncanson of NQDT for believing in the community volunteer project and finding ways for me to continue the network between funding cycles. I am grateful to a number of people for their contributions to this thesis including Raphael Wust for generous assistance with initial clay mineral interpretation discussions; Michelle Tink, Pat Cunningham and Brett Baker and the TropWATER laboratory for all their assistance and for making long days in the lab much more enjoyable; Brendan Jones for XRD analytical support; the Queensland Government’s DSITIA Loads Monitoring Program (Ryan Turner) for providing additional water samples and Reef Policy Project (RP65G) for providing the Old Reef sediment sample; v Morgain Sinclair, Geoff Pocock and Phil Kerr of the DNRM for providing streamflow gauging station data, and collection of water samples at Inkerman in 2011; Brett Baker and Peter Lawn for plume sampling assistance; and a number of TropWATER and Qld Government staff for field support including Alan Mitchell, David Reid, Michelle Cooper, Peter Verwey, Shane Ross, Sarah Thornton, Tom Coughlin, and to Katrina Cullen for starting the grazier network. Finally I am forever indebted to the network of graziers across the Burdekin who embraced this project and whose collection efforts were invaluable in capturing real time suspended sediment in transport across this large, episodic catchment: John & Lindy, Nevil & Stacey, Chris & Kathy, Bill & Milly, Keith & Alma, Pat & Colleen, Jim & Kim, John, Trevor & Selina, Cath, David & Di, Robyn & Richard, Mick & Amanda, Tim & Alison, Shane & Trish, Elsie & Jack, Chris & Jenny, Kath & Dan, John & Janet, Jamie & Gail, Glen & Kellie, Tony & Dominie. To the additional volunteers in the Haughton and Don River catchments (data reported in outputs associated with this thesis) my gratitude is also extended to Steve and Kristine, Owen & Marjorie, Jenny & Graham, and Russell Todd from Bowen State High School. Tony Bailey and Gary Caddies of Sunwater are also acknowledged for their dedicated daily wet season sampling of the Burdekin Falls Dam spillway. Thank you to my GBR water quality colleagues for support throughout this PhD, especially Jane Waterhouse, Joanne Burton, Bronwyn Masters, Louise Hateley, Amelia Wenger, Michelle Devlin, Caroline Petus, Britta Schaffelke, Colette Thomas, Dom O’Brien, John Bennett and Nyssa Henry, many of whom were involved in a MTSRF conference dance floor discussion that kicked-off my PhD enrolment! I am forever indebted to my regular field companions, Steve Lewis and Aaron Davis, for all those long days travelling and sampling across the Burdekin, and your encouragement in completing this thesis. To my friends outside the science world, thank you for your continued support and comic relief as needed. Finally, and most importantly, I wish to thank my family for all the support, patience and encouragement you have shown throughout this journey. A special mention to Will’s wonderful Grandmas who travelled the distance of this country multiple times over the past year to support me in this