University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 5-19-2008 Patch Reefs in Biscayne National Park, FL: Sediments, Foraminiferal Distributions, and a Comparison of Three Biotic Indicators of Reef Health Alexa Ramirez University of South Florida Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the American Studies Commons Scholar Commons Citation Ramirez, Alexa, "Patch Reefs in Biscayne National Park, FL: Sediments, Foraminiferal Distributions, and a Comparison of Three Biotic Indicators of Reef Health" (2008). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/465 This Thesis 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]. Patch Reefs in Biscayne National Park, FL: Sediments, Foraminiferal Distributions, and a Comparison of Three Biotic Indicators of Reef Health by Alexa Ramirez A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science University of South Florida Major Professor: Pamela Hallock Muller, Ph.D. David Mann, Ph.D. Benjamin Flower, Ph.D. Date of Approval: May 19, 2008 Keywords: bioindicator, SEDCON, FORAM, carbonate, coral © Copyright 2008, Alexa Ramirez ACKNOWLEDGEMENTS I am very thankful for the help and support I have received from my major professor, Dr. Pamela Hallock Muller. Her dedication to helping me formulate and carry out this project makes her an outstanding advisor for whom I am glad to have had the pleasure to work with. I would also like to thank the rest of my committee, David Mann and Ben Flower, for their advice and input during the critical points of creation and revision of my thesis. Special thanks go to the staff at Biscayne National Park in Homestead, FL who made my sample collection a fast and painless process (BNP permit number BISC-2007- SCI-0023). Sample collection and processing was funded by NOAA through the Florida Hurricane Alliance and by the U.S. Environmental Protection Agency Gulf Ecology Division Grant No. X7-96465607-0. Acknowledgment of funding does not imply endorsement of results by any of the funding or permitting agencies. Thank you to the Von Rosenstiels and the Sanibel-Captiva Shell Club for their financial support to the College of Marine Science and myself, making it possible for me to concentrate on my degree and finish quickly. Thanks also to the members of the Reef Indicators Lab, especially Bryan McCloskey and Heidi Souder, for their foraminiferal identification expertise. Melanie Peters and James Locasio accompanied me on my sampling trip and helped make the trip run smoothly and on time. The end of my thesis would never have been reached without the support of my family and friends. Thank you to everyone who listened over the past two years. TABLE OF CONTENTS LIST OF TABLES iii LIST OF FIGURES v ABSTRACT vii INTRODUCTION 1 Reef Decline in the Florida Keys 1 Patch Reefs in Biscayne National Park 4 Foraminifera 6 Biotic Indicators 7 PROJECT OBJECTIVES 13 METHODS 14 Field Area 14 Sampling Methods 16 Sample Processing 16 SEDCON and FORAM Indices 16 Live Symbiont-bearing Foraminifera (LSF) 18 Data Analysis 18 Statistical Analysis 18 Index Calculations 19 Pattern Analysis 23 RESULTS 25 Grain Size Analysis 25 Environmental Data 27 Foraminiferal Assemblages 29 FORAM Index 45 Sediment Constituent Analysis 48 SEDCON Index 55 Live Symbiont-bearing Foraminifera (LSF) 58 Photic Index 60 FORAM Index v SEDCON Index 62 i DISCUSSION 66 Limitations of Study 66 The Offshore Environment 67 Foraminiferal Assemblages 67 Sediment Constituent Assemblages 74 An Index Comparison 76 Live Symbiont-Bearing Foraminifera (LSF) 80 Patch Reef Health 83 Islands v Inlet: Sources of Stress or Security? 86 CONCLUSIONS 89 REFERENCES 91 APENDICES 97 Appendix I Results of grain-size analysis. 98 Appendix II-a List of foraminiferal genera found within the patch reefs of Biscayne National Park 101 Appendix II-b Raw counts of foraminiferal genera in patch reefs of Biscayne National Park. 102 Appendix III SIMPER results for dissimilarity between groups based on foraminiferal assemblages. 118 Appendix IV Moran’s I values and plots for both the FORAM Index and the SEDCON Index. 124 Appendix V-a Raw counts of sediment constituents. 129 Appendix V-b Visual identification aid for major sediment constituents 134 Appendix VI SIMPER results for dissimilarity between groups based on LSF assemblages 135 Appendix VII Results of bleaching surveyed in live specimens of Amphistegina gibbosa and density of live symbiont- bearing foraminifera 136 Appendix VIII Environmental data and comments from divers and boat captain 137 ii LIST OF TABLES Table 1 Calculation of the FORAM Index 21 Table 2 Division of grains for sediment constituent analysis. 22 Table 3 Calculation of the SEDCON Index 22 Table 4 Visualization of the Photic Index 23 Table 5 List of common abbreviations used in summarizing results 24 Table 6 Size classifications of sediments and summary of median grain size. 25 Table 7 Pearson’s correlation matrix of environmental data 29 Table 8 Within-group similarity of the SIMPER defined groups for the foraminiferal assemblage 31 Table 9 Means for diversity, density, and environmental data for foraminiferal assemblage SIMPER groups. 35 Table 10 Correlation matrix of foraminiferal taxa 39 Table 11 Correlation matrix of foraminiferal taxa and environmental data 43 Table 12 Results of BIO-ENV test of correlation between environmental variables and the foraminiferal assemblage. 45 Table 13 Correlation matrix for FORAM Index functional groups with environmental variables 48 Table 14 Within-group similarity of the two main SIMPER defined groups for the sediment constituents. 51 Table 15 Means for environmental data for sediment constituent SIMPER groups 51 Table 16 Dissimilarity between the two main groups defined by the SIMPER analysis of sediment constituents 52 iii Table 17 Correlation matrix for sediment constituents 54 Table 18 Correlation matrix for sediment constituents and environmental variables 54 Table 19 Results of BIO-ENV test of correlation between environmental variables and the sediment constituents 55 Table 20 Correlation matrix for SEDCON Index functional groups with environmental variables 56 Table 21 Within group similarity of SIMPER defined groups for the live symbiont-bearing foraminiferal assemblage 59 Table 22 Means for density, diversity, and environmental data for LSF assemblage SIMPER groups 60 Table 23 Correlation matrix for foraminiferal taxa and sediment constituents 63 Table 24 One Way ANOVAs for a) SEDCON Index replicates and b) FORAM Index replicates 66 Table 25 Summary table for percent contribution of foraminiferal taxa to each SIMPER group 69 Table 26 Comparison of three different methods of calculating the FORAM Index 73 Table 27 Summary of data presented in this report as rankings 88 iv LIST OF FIGURES Figure 1 Ozone anomaly at 45°N 4 Figure 2 South Florida, Biscayne National Park 5 Figure 3 Sampling sites in Biscayne National Park 15 Figure 4 Percent mud in sediments from patch reefs of Biscayne National Park 26 Figure 5 Contours of a) salinity and b) temperature data collected during sampling 28 Figure 6 MDS plot of reefs represented by their SIMPER groups defined by similarity of foraminiferal assemblages 30 Figure 7 Sample sites with more than 50 forams represented by their foraminiferal assemblage SIMPER groups 35 Figure 8 Contours of FORAM Index values 47 Figure 9 Percentages of sediment constituents for sites with highest and lowest percentages of unidentifiable grains 49 Figure 10 MDS plot of reefs represented by their SIMPER groups defined by similarity of sediment constituents 50 Figure 11 Contours of SEDCON Index values 57 Figure 12 MDS plot of reefs represented by their SIMPER groups defined by similarity of live symbiont-bearing foraminiferal assemblage 58 Figure 13 Sites represented by their Photic Index relative value 61 Figure 14 FORAM Index values plotted against median grain size represented by Phi values. 72 Figure 15 FORAM Index values plotted against adjusted SEDCON Index values 79 v Figure 16 Schematic of “Goldilocks” scenario reefs now face 81 Figure 17 Densities of Amphistegina gibbosa plotted against depth 83 vi PATCH REEFS IN BISCAYNE NATIONAL PARK, FL: SEDIMENTS, FORAMINIFERAL DISTRIBUTIONS AND A COMPARISON OF THREE BIOTIC INDICATORS OF REEF HEALTH Alexa Ramirez ABSTRACT Coral cover remains highest on patch reefs at the northern end of the Florida reef tract. The reasons for this trend are not well understood, but may be related to the protection from extreme variations in water quality parameters provided by the near constant presence of islands at the north extent of the Florida Keys. Three indices have been developed based on Foraminifera and sediment constituents. Two of the indices, the FORAM Index and the SEDCON Index, were developed to indicate the suitability of a reef environment for continued reef accretion. The third index, the Photic Index, is an assessment of photic stress on reefs based on incidence of bleaching in a species of Foraminifera, Amphistegina gibbosa , which is known to experience loss of algal endosymbionts similar to bleaching in corals. Patch reefs were sampled in Biscayne National Park, FL to assess sediment characteristics and foraminiferal assemblages, as well as to examine trends in the three indices. Sediments associated with a majority (59%) of reefs were coarse sands; muddy sediments were restricted to a few inner patch reefs that were isolated from the influence of Caesar’s Creek, which flushes water from inside Biscayne Bay onto the open shelf. Unidentifiable grains predominated in the sediment constituents, along with calcareous vii algae and molluskan debris. Shells from 82 genera of Foraminifera were identified in the sediments. Quinqueloculina was the most consistently common genus. Percent mud was the single most influential measured variable on the distribution of both sediment constituents and foraminiferal assemblages.