WATER QUALITY DYNAMICS IN A LOWLAND TROPICAL CATCHMENT: THE KINABATANGAN RIVER, SABAH, MALAYSIA By SAHANA HARUN A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Geography, Earth and Environmental Sciences College of Life and Environmental Sciences The University of Birmingham February 2013 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Spatial and temporal trends of dissolved organic matter (DOM) were investigated in the Lower Kinabatangan River, Sabah, Malaysia over the period 2008-2012. The objectives were to: i. quantify DOM in areas of the catchment dominated by oil palm plantations; ii. characterise DOM quantity and quality in waters draining three contrasting land use types (oil palm plantations, secondary forests and coastal swamps); iii. characterise and interpret DOM quantity and quality in the main stem of the Kinabatangan river according to depth; and iv. infer differences in water movement through the catchment. Optical parameters, including fluorescence excitation-emission matrices (EEMs) and ultraviolet absorbance spectroscopy (UV-vis); and Parallel Factor Analysis were used throughout the investigation. The research comprised a preliminary catchment-wide study (225 samples) and concentrated fieldwork campaigns (510 samples). The results indicated the dominance of peaks C and M in waters from the oil palm plantations and coastal swamps respectively. The relative loss of terrestrial derived peaks could indicate progressive DOM degradation from the upper reaches towards the estuary. Results also showed DOM was transported back to the main river, as dominated by fluorescence index peak A/peak C, particularly in the coastal swamps. DOM characterisation with depth in the river, showed the dominance of peaks C and M (relative to terrestrial and microbial and/or photo-degradation processes) in waters near the riverbed. Untuk Mak dan Abah, Aishah Pandak Ismail & Harun Saad To my parents, Aishah Pandak Ismail & Harun Saad ACKNOWLEDGEMENTS Bagaimana sahaya ta’ikat, Could I ever fail to bind, Kait-kait d!ngan duri-nya. Lawyer-vine’s full of thorny wood? Bagaimana sahaya ta’ingat, Could I fail to call to mind, Orang baik d!ngan budi-nya. Persons who are kind and good.1 First and foremost, my gratitude goes to my supervisors Dr. Chris Bradley, Prof. Andy Baker and Prof. Gilles Pinay; for their endless support, enthusiasm for the project and kindness that had kept me going. My appreciation also goes to staff at the School of Geography, Earth and Environmental Sciences (GEES), the Director and colleagues at the Institute for Tropical Biology and Conservation (ITBC), UMS and the organising committees of Chemometrics for Environmental Course II (especially Dr. Colin Stedmon and Dr. Nikoline Juul Nielsen), University of Copenhagen, Denmark for their guidance and help. Thanks to Mr. Zainal Abidin Jaafar, who had helped me throughout a series of fieldwork. I am grateful to Ms. Asnih Etin and Mr. Baharudin Resake too! I would like to thank my amazing friends who had supported me all the way: Liz, Zahran, Shahad, Kina, Hana, Eti, Sarah, Renee, Kalsum, Ina, Newati and Sureena. To Diha, Almeezan and Masyhad, I am filled with gratitude for your optimism, support and wonderful friendship for all these years. I am forever indebted to my family, parents and siblings (Kak Ti, Yang, Amam and Haziq), for their boundless support and always being there for me. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 1 Pantun (pantoum) is a Malay traditional poem equivalent to Japanese Haiku, widely recognised in the Malay Archipelago as one of the classical ways to express feelings courteously. It is characterised by quatrains, often with pleasing assonance; using simple language, nevertheless with deep meaning. The aforementioned pantun was translated by: Hamilton, A. W. 1941. Malay Pantuns: Pantun M!layu. Australasian Publishing Co. Pty. Ltd. I am also thankful to the following institutions and agencies for providing funds and data support: Ministry of Higher Education Malaysia (MoHE), Universiti Malaysia Sabah (UMS), Borneo Marine Research Institute (BMRI), Department of Environment Malaysia (DoE), Sabah Forestry Department (SFD), Sabah Wildlife Department (SWD) and Sabah Biodiversity Centre (SBC). And finally, to those who had helped me directly or indirectly in this journey: T!rima kaseh. Thank you. TABLE OF CONTENTS 1. INTRODUCTION ............................................................................................ 1 1.1 BACKGROUND ......................................................................................... 1 1.2 SIGNIFICANCE OF STUDY ...................................................................... 4 1.3 SCOPE OF STUDY ................................................................................... 8 1.4 THESIS STRUCTURE ............................................................................. 13 2. ORGANIC MATTER IN TROPICAL FRESHWATER ECOSYSTEMS .......... 15 2.1 INTRODUCTION ..................................................................................... 15 2.2 SOURCE, UPTAKE AND LOSS OF DOM WITHIN STREAM SYSTEMS .......................................................................................................................... 20 2.3 DOM IN AQUATIC ECOSYSTEMS ......................................................... 27 2.4 SPATIAL AND TEMPORAL TRENDS: DOM QUALITY .......................... 36 2.5 DOM BIOGEOCHEMISTRY IN LARGE TROPICAL RIVERS ................. 40 2.6 EFFECTS OF LAND USE CHANGE ON DOM IN TROPICAL REGIONS .......................................................................................................................... 47 2.7 CONCLUSION ......................................................................................... 54 3. MATERIALS, METHODS AND ANALYTICAL PROCEDURES ................... 56 3.1 INTRODUCTION ...................................................................................... 56 3.1.1 Preliminary Survey ............................................................................ 61 3.1.2 Concentrated Sampling Programme ................................................. 63 3.1.3 Sampling Locations ........................................................................... 68 3.2 FLUORESCENCE SPECTROSCOPY ..................................................... 77 3.3 LABORATORY METHODS ...................................................................... 85 ! 3.3.1 Excitation-Emission Spectroscopy (EEMs) ....................................... 85 3.3.2 Dissolved Organic Carbon (DOC) ..................................................... 87 3.3.3 Stable Isotopes ................................................................................. 87 3.4 DATA PRE-PROCESSING ...................................................................... 88 3.5 DATA POST-PROCESSING .................................................................... 88 3.5.1 Parallel Factor Analysis (PARAFAC) ................................................ 88 3.5.2 Discriminant Analysis (DA) ................................................................ 92 3.6 CONCLUSION ......................................................................................... 93 4. CHARACTERISATION OF DISSOLVED ORGANIC MATTER IN THE LOWER KINABATANGAN RIVER CATCHMENT, SABAH, MALAYSIA ........... 95 4.1 INTRODUCTION ...................................................................................... 96 4.2 RESULTS ............................................................................................... 100 4.2.1 Stable Isotope Analyses ................................................................. 100 4.2.2 DOM Characteristics ....................................................................... 105 4.2.3 Parallel Factor Analysis (PARAFAC) Modelling .............................. 116 4.3 DISCUSSION AND CONCLUSIONS ..................................................... 124 5. SEASONAL VARIATION OF DISSOLVED ORGANIC MATTER COMPOSITION IN A TROPICAL CATCHMENT: LOWER KINABATANGAN RIVER, SABAH, MALAYSIA ............................................................................ 127 5.1 INTRODUCTION .................................................................................... 128 5.2 RESULTS AND DISCUSSION ............................................................... 131 5.2.1 Characterisation of PARAFAC Components .................................. 131 5.2.2 DOM Characterisation .................................................................... 138 5.2.3 Seasonal and Land Use Variations ................................................ 141 ! 5.3 CONCLUSIONS ..................................................................................... 144 6. SPATIAL AND TEMPORAL VARIATIONS IN THE COMPOSITION OF DISSOLVED ORGANIC MATTER IN A TROPICAL RIVER: THE LOWER KINABATANGAN RIVER, SABAH, MALAYSIA ............................................. 146 6.1 INTRODUCTION ...................................................................................