University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 8-21-2014 Karst Estuaries: A newly described ecosystem governed by aquifer hydrology Damian M. Menning University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Cell Biology Commons, and the Microbiology Commons Scholar Commons Citation Menning, Damian M., "Karst Estuaries: A newly described ecosystem governed by aquifer hydrology" (2014). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5382 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Karst Estuaries: A newly described ecosystem governed by aquifer hydrology by Damian M. Menning A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology, and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: James R. Garey, Ph.D. Kathleen M. Scott, Ph.D. Jonathan G. Wynn, Ph.D. James T. Riordan, Ph.D. Date of Approval: August 21, 2014 Keywords: anchialine, aquifer, microbial, hydrology, geochemistry Copyright © 2014, Damian M. Menning DEDICATION I dedicate this work to my wife and my parents without whose love, support, and encouragement this would not have been possible. TABLE OF CONTENTS LIST OF TABLES ......................................................................................................................... iii LIST OF FIGURES ....................................................................................................................... vi ABSTRACT ................................................................................................................................. viii CHAPTER ONE: INTRODUCTION ..............................................................................................1 Site Description ........................................................................................................6 Geological and Hydrological Background ...............................................................6 CHAPTER TWO: HYDROLOGY AND GEOCHEMISTRY ......................................................10 Materials and Methods ...........................................................................................10 Sample Collection ......................................................................................10 Water Sample Analysis ..............................................................................11 Statistical Analyses ....................................................................................13 Results ....................................................................................................................13 Double Keyhole Spring Profile ..................................................................13 Double Keyhole Spring ‘Deep Room’ Profile ...........................................13 Rainfall Patterns .........................................................................................14 Tidal Fluctuations and Flow Reversals ......................................................15 Aquifer Hydraulic Head Measurements ....................................................18 Aquifer Discharge ......................................................................................18 Strontium Concentration and δ18O Values.................................................19 Water Quality Along the Estuarine Transect .............................................20 Discussion ..............................................................................................................21 Double Keyhole Spring Profile ..................................................................21 Double Keyhole ‘Deep Room’ Profile ......................................................22 Tidal Fluctuations ......................................................................................27 Rainfall Patterns .........................................................................................29 Aquifer Hydraulic Head Measurements ....................................................30 Aquifer Discharge ......................................................................................31 Water Quality Along the Estuarine Transect .............................................34 CHAPTER THREE: MICROBIAL AND MACROFAUNAL COMMUNITIES ........................37 Material and Methods ............................................................................................37 Sample Collection ......................................................................................37 Sample Preparation ....................................................................................37 Quantitative Polymerase Chain Reaction ..................................................38 Length Heterogeneity Polymerase Chain Reaction ...................................39 Macrofauna ................................................................................................41 i Statistical Analyses ....................................................................................41 Results ....................................................................................................................42 Testing q-PCR Methods Using Known DNA ............................................42 Estimated Abundance ................................................................................42 Species Richness ........................................................................................43 Macrofauna ................................................................................................43 Multi-Dimensional Scaling Plots ...............................................................43 Statistical Analyses ....................................................................................49 Discussion ..............................................................................................................51 Testing q-PCR Methods Using Known DNA ............................................53 Estimated Abundance ................................................................................54 Species Richness ........................................................................................63 Macrofauna ................................................................................................65 Multi-Dimensional Scaling Plots ...............................................................66 CHAPTER FOUR: CONCLUSIONS............................................................................................71 REFERENCES ..............................................................................................................................77 ii LIST OF TABLES Table 2-1: Discharge data of Double Keyhole Spring from fall 2011 through winter 2013 ............................................................................................................17 Table 2-2: Correlations of rainfall, Double Keyhole Spring discharge, and aquifer hydraulic head............................................................................................19 Table 2-3: Strontium concentrations and δ18O values at all sites from fall 2011 through fall 2013 ....................................................................................................20 Table 2-4: Correlations of rainfall, Double Keyhole Spring discharge, and aquifer hydraulic head to studied geochemical parameters at the marine site ..............................................................................................................25 Table 2-5: Correlations of rainfall, Double Keyhole Spring discharge, and aquifer hydraulic head to studied geochemical parameters at the estuary site .............................................................................................................25 Table 2-6: Correlations of rainfall, Double Keyhole Spring discharge, and aquifer hydraulic head to studied geochemical parameters at the Double Keyhole Pond site .....................................................................................26 Table 2-7: Correlations of rainfall, Double Keyhole Spring discharge, and aquifer hydraulic head to studied geochemical parameters at the Double Keyhole Spring site ...................................................................................26 Table 2-8: Correlations of total daily rainfall, average daily discharge, and maximum daily discharge at Double Keyhole Spring with a six week delay .............................................................................................................34 Table 3-1: List of primers used for LH-PCR and q-PCR with associated data .......................38 Table 3-2: List of organisms used for q-PCR validation experiment, standard curves produced for each organism and associated r2 values ................................39 Table 3-3: Estimated amount of DNA determined from the standard curves when using 10ng of DNA ......................................................................................40 Table 3-4: Prokaryotic DNA concentrations when using three different molar ratios .......................................................................................................................40