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Hyperspectral Studies of New South Wales Seagrasses with Particular HYPERSPECTRAL STUDIES OF NEW SOUTH WALES SEAGRASSES WITH PARTICULAR EMPHASIS ON THE DETECTION OF LIGHT STRESS IN EELGRASS Zostera capricorni A thesis submitted in fulfilment of the requirements for the award of the degree DOCTOR OF PHILOSOPHY from UNIVERSITY OF WOLLONGONG by Suzanne Kay Fyfe, B.Sc. (hons) SCHOOL OF EARTH AND ENVIRONMENTAL SCIENCES / SCHOOL OF BIOLOGICAL SCIENCES 2004 “There is some truth to the notion that much very unexciting groundwork must be laid before remote sensing can be used to support really exciting science.” D.S. Schimel, 1993. New technologies for physiological ecology, pp. 359-365, In, Ehleringer, J.R., and C.B. Field (eds), Scaling physiological processes: Leaf to globe, Academic Press, Sydney. ii CERTIFICATION I, Suzanne Kay Fyfe, declare that this thesis, submitted in partial fulfilment of the requirements for the award of Doctor of Philosophy, in the School of Earth and Environmental Sciences / Department of Biological Sciences, University of Wollongong, is wholly my own work unless otherwise referenced or acknowledged. The document has not been submitted for qualifications at any other academic institution. Suzanne Kay Fyfe 31 May 2004 iii PUBLICATIONS ARISING FROM THIS THESIS The results of Chapter 4, Part A: Spectral reflectance of seagrass leaves, were published in the following conference paper and peer-reviewed journal article: Fyfe, S.K., and A.G. Dekker, 2001. Seagrass species: are they spectrally distinct?, Proceedings of the IEEE International Geosciences and Remote Sensing Symposium, Sydney, July 2001, Vol VI: 2740-2742. Fyfe, S.K., 2003. Spatial and temporal variation in spectral reflectance: are seagrass species spectrally distinct?, Limnology and Oceanography, Coastal Optics Special Issue, 48(1part2):464-479. Aspects of the thesis, in particular the literature review (Chapter 1), were incorporated into the following book chapter: Dekker, A., V. Brando, J. Anstee, S. Fyfe, T. Malthus, and E. Karpouzli, 2005. Chapter 15. Remote sensing of seagrass ecosystems: use of spaceborne and airborne sensors, 26 pp., In, Larkum, A.W.D., R.J. Orth and C.M. Duarte (eds), Seagrasses: Biology, Ecology and Conservation, Springer, Berlin. The field and laboratory datasets which form the basis for Chapters 4 and 5 were subsequently reanalysed and published in the following conference papers and peer- reviewed journal article: Ressom, H., S. Fyfe, P. Natarajan, and S. Sriranganam, 2003. Monitoring seagrass health using neural networks, Proceedings of the International Joint Conference on Neural Networks (IJCNN), Portland, USA, July 20-24 2003, CD Edition, pp. 1019-1024. Ressom,H., S. K. Fyfe, S. Sriranganam, M.T. Musavi, and P. Natarajan, 2004. Estimation of photosynthetic efficiency for monitoring seagrass health using neural networks, Proceedings of IASTED International Conference on Neural Networks and Computational Intelligence (NCI 2004), Grindelwald, Switzerland, Feb. 23-25 2004, pp. 232-237. Ressom, H., S.K. Fyfe, S. Sriranganam, M.T. Musavi and P. Natarajan, in press. Neural network-based estimation of photosynthetic efficiency for monitoring seagrass health, IEEE Transactions on Systems, Man and Cybernetics: Part C. iv TABLE OF CONTENTS LIST OF TABLES xiii LIST OF FIGURES xvii LIST OF PLATES xxiii LIST OF SYMBOLS AND ABBREVIATIONS xxiv ABSTRACT xxvii ACKNOWLEDGEMENTS xxxi CHAPTER 1: INTRODUCTION 1.1 Introduction 1 1.2 Threats to seagrass meadows 1 1.3 Seagrass management 5 1.4 Mapping and monitoring of seagrass meadows 5 1.4.1 Regional scale: seagrass resource mapping 13 1.4.2 Local scale: seagrass habitat mapping and change detection 16 Fine scale mapping 17 Change detection 24 1.4.3 Meadow scale: monitoring seagrass health 25 Monitoring seagrass canopy parameters 26 Monitoring the physiological status of seagrasses 28 1.5 Image processing and the application of spectral libraries 31 1.6 Aims and objectives 32 CHAPTER 2: SEAGRASSES OF NEW SOUTH WALES 2.1 Seagrasses 36 2.2 Seagrass species of south eastern NSW 38 2.2.1 Eelgrass Zostera capricorni Aschers. 39 2.2.2 Strapweed Posidonia australis Hook. f. 41 v 2.2.3 Paddleweed Halophila ovalis (R. Br.) Hook. f. 42 2.2.4 Minor species 43 2.3 Seagrass structure and morphology 44 2.4 Photosynthesis in seagrasses 49 2.4.1 Photosynthetic pigments 50 2.4.2 The light reactions of photosynthesis 51 2.4.3 Limitations on photosynthesis 53 CHAPTER 3: DATA COLLECTION METHODS 3.1 Field experiments 55 3.1.1 Study sites 55 3.2 Manipulative laboratory experiments 59 3.2.1 Preliminary laboratory experiment 60 3.2.2 Collecting and transplanting seagrass 60 3.2.3 Laboratory setup and maintenance 62 Benches 62 Lighting 62 Temperature and salinity 64 Nutrients 65 Aeration and stirring 65 Cleaning 66 3.2.4 Experimental treatments 67 3.3 Sampling procedures 68 3.3.1 Spectroradiometry 70 Background 70 Timing of spectral reflectance sampling 71 Field spectroradiometry methods 72 Laboratory spectroradiometry methods 73 Correction of spectra 74 3.3.2 Chlorophyll fluorescence 75 Background 75 Methods 77 3.3.3 High Performance Liquid Chromatography 78 vi Background 78 Methods 79 Water content of seagrass leaves 80 3.3.4 Spectrophotometry 81 Background 81 Methods 82 3.3.5 Elemental analysis of C, N content 83 Background 83 Methods 83 CHAPTER 4: SPATIAL AND TEMPORAL VARIATION IN THE SPECTRAL REFLECTANCE AND FOLIAR CHEMISTRY OF SEAGRASSES 4.1 Introduction 85 4.1.1 Spectral reflectance of plant leaves and canopies 86 4.1.2 Spectral reflectance discrimination of plant species 88 4.1.3 Aims 91 4.2 Methods 93 4.2.1 Field sampling of spectral reflectance 93 4.2.2 Analysis of spectral data 94 4.2.3 Field sampling of pigment content 97 4.2.4 Percent water content of seagrass leaves 98 4.2.5 Analysis of pigment data 99 4.2.6 Influence of epibionts on leaf pigment content 101 4.3 Results A. – Spectral reflectance of seagrass leaves 102 4.3.1 Spectral reflectance differences between seagrass species 102 4.3.2 Spectral reflectance differences within seagrass species: spatial and temporal effects 105 Zostera capricorni 105 Posidonia australis 109 Halophila ovalis 109 4.3.3 Wavelength selection for remote sensing of seagrass species 112 4.4 Results B. – Biochemistry of seagrass leaves 113 vii 4.4.1 Percent water content of seagrass leaves 113 4.4.2 Chlorophyll and carotenoid content of seagrass leaves 117 4.4.3 Pigment differences between seagrass species 119 4.4.4 Pigment differences within seagrass species: spatial and temporal effects 124 Zostera capricorni 124 Posidonia australis 126 Halophila ovalis 127 Pigments contributing to within species differences 129 4.4.5 Anthocyanin content of seagrass leaves 130 4.4.6 Species differences in the anthocyanin content of seagrass leaves 132 4.4.7 Within-species differences in anthocyanin content: spatial and temporal effects 132 Zostera capricorni 132 Posidonia australis 135 Halophila ovalis 136 4.4.8 Influence of epibionts on leaf pigment content 139 Chlorophylls and carotenoids 139 Anthocyanins 142 4.5 Discussion 143 4.5.1 Spectral reflectance discrimination of seagrass species 143 4.5.2 Advantages of PMSC correction 144 4.5.3 Determinants of reflectance 145 Seagrass leaf morphology 145 Seagrass leaf pigment content 148 Influence of epibionts 153 4.5.4 Intraspecific variability in reflectance 156 4.5.5 Waveband selection and application 160 CHAPTER 5: SPECTRAL AND PHYSIOLOGICAL RESPONSE OF EELGRASS Zostera capricorni TO LIGHT STRESS 5.1 Introduction 163 viii 5.1.1 Stress and acclimation in seagrasses 163 5.1.2 Light and photosynthetic rate 166 5.1.3 Photodamage, photoinhibition and photoprotection 169 5.1.4 Response of seagrasses to light stress 172 Low light stress 172 High light stress 177 5.15 Spectral reflectance shifts associated with stress in plants 182 5.16 Aims 186 5.2 Methods 188 5.2.1 Field sampling of photosynthetic efficiency 188 5.2.2 Diurnal cycle in the field 188 5.2.3 Estimating photosynthetic parameters of laboratory-grown Z. capricorni 189 5.2.4 Manipulative laboratory experiments 190 Low light stress 190 High light stress 192 Data analysis 193 5.3 Results A. – Photosynthetic parameters of Zostera capricorni 194 5.3.1 Photosynthetic efficiency in the field 194 5.3.2 Diurnal cycle of photosynthetic efficiency in the field 194 5.3.3 Photosynthetic parameters of laboratory grown Z. capricorni 196 5.4 Results B. – Manipulative laboratory experiments 198 5.4.1 Response of Z. capricorni to low light stress 198 5.4.2 Response of Z. capricorni to high light stress 207 5.5 Discussion 214 5.5.1 Summary of results 214 Laboratory experiments 214 Patterns in combined laboratory and field data 217 5.5.2 P-I curves and evidence for photoacclimation in Z. capricorni 220 5.5.3 Response of Z. capricorni to low light stress 223 Effects of low light stress on health and growth 223 Effects of low light stress on pigment content 228 ix 5.5.4 Response of Z. capricorni to high light stress 231 Effects of high light stress on health and growth 231 Effects of high light stress on pigment content 234 5.5.5 Evidence for chromatic acclimation in Z. capricorni 241 5.5.6 Sun-adapted or shade-adapted? 245 5.5.7 Effects of light stress on the spectral reflectance of Z. capricorni 248 Low light stress 248 High light stress 251 5.5.8 Conclusions and application to remote sensing 255 CHAPTER 6: SPECTRAL REFLECTANCE INDICES FOR THE PREDICTION OF LIGHT STRESS IN SEAGRASSES 6.1 Introduction 258 6.1.1 Vegetation indices 258 6.1.2 Narrow band vegetation indices 259 6.1.3 Vegetation indices utilizing only visible wavelengths 264 6.1.4 Aims 277 6.2 Methods
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