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Transcript of Uncovering the role of biomineralisation in otolith trace ... (endoskeletons), protection...

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    Uncovering the role of biomineralisation in otolith trace element uptake by

    microstructural and microchemical analysis

    Thesis submitted in fulfilment of Masters of

    Philosophy (Chemistry)

    Aoife McFadden

    Department of Chemistry,

    School of Physical Sciences

    The University of Adelaide

    November 2016

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    Table of Contents

    List of Abbreviations .................................................................................................................... vi

    Abstract ....................................................................................................................................... vii

    Declaration ................................................................................................................................... ix

    Acknowledgments ......................................................................................................................... x

    Chapter 1 ..................................................................................................................................... 13

    Introduction to otolith biomineralisation and trace element uptake ......................................... 13

    Biomineralisation .................................................................................................................... 13

    Otolith Biomineralisation ........................................................................................................ 14

    Calcium Carbonate .................................................................................................................. 16

    Otolith Trace Element Chemistry ............................................................................................ 17

    Implications ............................................................................................................................. 19

    Analytical Approach ................................................................................................................ 20

    Scanning Electron Microscopy (SEM) .................................................................................. 21

    Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) .................... 21

    Electron Probe Microanalysis (EPMA)................................................................................. 23

    Electron Backscatter Diffraction (EBSD) .............................................................................. 25

    Raman Microspectroscopy .................................................................................................. 27

    Powder X-ray Diffraction (XRD) ........................................................................................... 28

    Objective/Aims ........................................................................................................................ 29

    Chapter 2 ..................................................................................................................................... 33

    Investigation of the orientation and alignment of otolith aragonite with the organic matrix

    provides insight into the mechanism of otolith growth .............................................................. 33

    Abstract ................................................................................................................................... 33

    Introduction ............................................................................................................................ 33

    Biomineralisation ................................................................................................................ 33

    Otolith Organic Matrices ..................................................................................................... 35

    Aragonite Crystal Structure ................................................................................................. 35

    Twinning .............................................................................................................................. 36

    Otolith Aragonite Growth ................................................................................................... 37

    Otolith Aragonite Orientation ............................................................................................. 38

    Otolith Organic Matrix Orientation ..................................................................................... 39

    Methods .................................................................................................................................. 40

    Sample Preparation ............................................................................................................. 40

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    Powder X-Ray Diffraction .................................................................................................... 40

    Scanning Electron Microscopy and Image Analysis ............................................................ 40

    Electron Backscatter Diffraction ......................................................................................... 41

    Raman Microspectrometry ................................................................................................. 41

    Results ..................................................................................................................................... 43

    Powder X-Ray Diffraction .................................................................................................... 43

    Scanning Electron Microscopy Imaging .............................................................................. 43

    Electron Backscatter Diffraction ......................................................................................... 47

    Raman Microspectroscopy .................................................................................................. 50

    Discussion ................................................................................................................................ 52

    Otolith Mineral Polymorph ................................................................................................. 52

    Otolith Growth and Habit ................................................................................................... 52

    Otolith Growth Orientation ................................................................................................ 53

    Implications for Otolith Applications .................................................................................. 55

    Conclusion ............................................................................................................................... 55

    Chapter 3 ..................................................................................................................................... 57

    Quantitative electron microprobe mapping of otoliths suggests elemental incorporation is

    influenced by organic matrices: implications for the interpretation of otolith chemistry .......... 57

    Abstract ................................................................................................................................... 57

    Introduction ............................................................................................................................ 58

    Methods .................................................................................................................................. 60

    Sample Preparation ............................................................................................................. 60

    Scanning Electron Microscopy (SEM) .................................................................................. 61

    Electron Probe Microanalysis (EPMA)................................................................................. 61

    EPMA Wavelength Dispersive Spectrometer Signal Aggregation ....................................... 62

    EPMA Repeated Spot Measurements ................................................................................. 63

    EPMA Mean Atomic Number Backgrounds ........................................................................ 64

    Laser Ablation – Inductively Coupled Plasma Mass Spectrometry ..................................... 64

    Results ..................................................................................................................................... 65

    Effect of Wavelength Dispersive Spectrometer Signal Aggregation in EPMA .................... 65

    Effect of Repeated Measurements in EPMA ....................................................................... 67

    Effect of Mean Atomic Number Backgrounds in EPMA ...................................................... 68

    Otolith Growth Patterns and Microstructure ..................................................................... 69

    Otolith Elemental Distribution by EPMA ............................................................................. 70

    Detection limits and Limits of Quantification by EPMA ...................................................... 74

    Otolith Elemental Distribution by LAICPMS ........................................................................ 74

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    Discussion ...............