Large- and Microscale Community Structure and Abundance of Microalgae in the Coorong Lagoons, South Australia Eloise Ann Prime Bachelor of Science in Marine Biology (Hons) Thesis submitted to the School of Biological Sciences, Faculty of Science and Engineering, Flinders University in fulfilment of the requirements for the degree of Doctor of Philosophy September 2016 “Few objects are more beautiful than the minute siliceous cases of the diatomaceæ: were these created that they might be examined and admired under the higher powers of the microscope? The beauty in this latter case, and in many others, is apparently wholly due to symmetry of growth.” - Charles Darwin The Origin of Species (1872) 1 Table of Contents Table of Contents .............................................................................................................. 2 Summary ............................................................................................................................ 7 Declaration ........................................................................................................................ 9 Acknowledgements .......................................................................................................... 10 List of Figures .................................................................................................................... 11 List of Tables ..................................................................................................................... 14 Chapter 1: Introduction ................................................................................................... 15 Microeukaryotes in Aquatic Environments ............................................................. 16 Phytoplankton (Microalgae in the Water Column) ..................................... 16 Microphytobenthos (Microalgae of the Benthos) ....................................... 19 Diatoms ....................................................................................................... 20 Microscale Interactions .......................................................................................... 23 Study Site ................................................................................................................. 24 Microbial Interaction Networks .............................................................................. 25 Aims and Structure of the Thesis ............................................................................ 26 Chapter 2: Phytoplankton Dynamics under Drought Conditions in an Inverse Estuary ............................................................................................................................................. 28 2 Graphical Abstract.................................................................................................. 29 Abstract ................................................................................................................... 30 Introduction............................................................................................................. 31 Methods ................................................................................................................... 33 Study Sites .................................................................................................. 33 Environmental Parameters .......................................................................... 35 Dissolved Nutrient Analysis ....................................................................... 35 Chlorophyll a Analysis ............................................................................... 36 Phytoplankton Sampling and Abundance ................................................... 36 Phytoplankton Diversity ............................................................................. 36 Statistical Analysis ...................................................................................... 37 Results ..................................................................................................................... 38 Environmental Parameters .......................................................................... 38 Dissolved Nutrients ..................................................................................... 42 Chlorophyll a Concentration....................................................................... 45 Phytoplankton Abundance .......................................................................... 46 Phytoplankton Diversity ............................................................................. 50 Correlations Between Communities of the North and South Lagoons ....... 51 Discussion ............................................................................................................... 54 The South Lagoon ....................................................................................... 54 The North Lagoon ....................................................................................... 56 Conclusion .............................................................................................................. 58 Chapter 2 Supplementary Material ........................................................................ 59 3 Chapter 3: Microscale Variation of Microbial Eukaryotic Communities Revealed by 18S Sequencing .................................................................................................................. 62 Abstract ................................................................................................................... 63 Introduction............................................................................................................. 64 Methods ................................................................................................................... 65 Study Site .................................................................................................... 65 Sample Collection ....................................................................................... 67 Bioinformatics and Data Analysis .............................................................. 69 Results ..................................................................................................................... 70 Microscale OTUs ........................................................................................ 70 Correlations with Chlorophyll .................................................................... 72 Species Similarity between Microscale Sites ............................................. 73 Discussion ............................................................................................................... 77 Comparison of Taxonomy and Chlorophyll Concentration ........................ 77 Community Taxonomical Variations at the Microscale ............................. 78 Conclusion .............................................................................................................. 80 Chapter 3 Supplementary Material ........................................................................ 81 Chapter 4: Marine microbial benthic community interactions along a hypersaline microscale transect ........................................................................................................... 120 Abstract ................................................................................................................... 121 Introduction............................................................................................................. 122 4 Results and Discussion ........................................................................................... 124 Chapter 4 Supplementary Material ........................................................................ 134 Chapter 5: Microscale Variation of Diatom Frustule Length in the Microphytobenthos ............................................................................................................................................. 141 Abstract ................................................................................................................... 142 Introduction............................................................................................................. 143 Methods ................................................................................................................... 145 Study Site .................................................................................................... 145 Sample Collection ....................................................................................... 148 Chlorophyll Analysis ................................................................................. 148 Microscopy ................................................................................................. 149 Statistical Analysis ...................................................................................... 149 Descriptive Statistics ....................................................................... 149 Spatial Autocorrelation, Moran’s I ................................................. 150 Spatial Autocorrelation, Geary’s C ................................................. 151 Network Analysis............................................................................ 151 Results ..................................................................................................................... 152 Frustule Length ..........................................................................................