BENTHIC COMMUNITY STRUCTURE AND RESPONSES TO ENVIRONMENTAL DRIVERS IN THE FLORIDA KEYS A Thesis Presented to The Faculty of the College of Arts and Sciences Florida Gulf Coast University In Partial Fulfillment Of the Requirement for the Degree of Master of Science By Ashley Lauren Brandt 2016 ii APPROVAL SHEET This thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science _________________________________ Ashley Lauren Brandt Approved: May 1, 2016 _________________________________ Michael L. Parsons, Ph.D. Committee Chair/Advisor _________________________________ James G. Douglass, Ph.D. _________________________________ Tyler B. Smith, Ph.D. The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline. iii Acknowledgements This project would not have been possible without all of the help I received from God, my family and friends, and the many faculty and students involved. First and foremost, I would like to thank Jesus Christ for giving me the daily strength and perseverance that enabled me to see this project through to completion. I also want to thank my parents for all their love and support throughout my entire college career and my friends for their support as well. The most notable credit goes to my primary advisor, Dr. Michael Parsons. I was only able to pursue this research project as a result of his hard work as an active research scientist as well as an engaging professor. Funding for this research was primarily provided through his NOAA ECOHAB funded project, CiguaHAB. I am so thankful that he gave me the opportunity to be a part of the CiguaHAB project and for the resulting field and professional experience it has given me. Dr. Parsons has challenged me to take advantage of multiple professional opportunities that I would not have been able to accomplish without his endless help and encouragement, primarily the work involving this thesis. I would also like to thank my other committee members, Drs. James Douglass and Tyler Smith, for their helpful feedback and multiple edits involved in writing my thesis. There are many other students at FGCU that contributed immensely to this project. I have to thank Alexander Leynse specifically for all his help in the field and for sharing nutrient data. Amanda Ellsworth and Lacey Rains were helpful in that the monthly trips to the field would not have been possible without them. I would also like to iv thank all the other students involved in CiguaHAB for their help as well: Jessica Schroeder, Adam Catasus, Jeff Zingre, Rebecca May, Kevin Tyre, and Elena Stanca. Finally, I want to show my gratitude to Florida Gulf Coast University as a whole for my college career. Additional funds for this research were provided in the form of undergraduate research grants from the Office of Research and Graduate Studies (ORGS) at FGCU. I would like to show my gratitude for the many opportunities I had through receiving financial assistance from FGCU ORGS and the Whitaker Center for STEM Education. Lastly, I am so grateful for all of the great professors that have contributed to my dynamic through sharing their knowledge and time with me. All of your efforts have been greatly appreciated. v Abstract As the frequency and intensity of disturbances threatening coastal ecosystems increase, there is a greater need to determine which factors are actually driving the changes in these environments. This three-year study investigated the possible influences of stressors alongside changes in community ecology of three disparate marine habitats within the Florida Keys. The approach used in this study was purposefully large-scale, involving high-resolution monthly sampling of the benthic community structure and environmental data in order to capture associated relationships between stressors and benthic taxa. The need for this novel approach has been proposed in the scientific literature, as there has been greater recognition towards the influence of multiple stressors and the possibility of synergistic effects. Specifically within the Florida Keys, declining water quality and recent extreme temperature anomalies have caused changes in the dynamics of these habitats. Results of this study showed the most influential factors appear to be waves, nutrients, and temperatures within the three sites examined in this study. Waves appeared to have a regional effect, being influential at all three sites, while nutrients and temperatures showed local effects, only being influential at some sites. High and low extremes of these factors appeared to drive the dynamics seen in the top taxa present at these sites, consisting mostly of macrophytes, with some relationships being supported by correlations. In addition, effects from other stressors appeared to be important once combined with the influential factors at some sites, showing evidence of synergistic effects. While all possible stressors were not addressed within this study, there is evidence that there is further need to use this ecosystem-scale approach in order to determine any and all effects of multiple stressors. This will allow for better vi understanding of integrated effects and provide insight into marine management efforts in terms of anthropogenic and natural stressors or local (manageable) or regional (less controllable) influences. vii Table of Contents Acknowledgements iii Abstract v List of Tables viii List of Figures ix Chapter 1: Introduction and background information 1 Chapter 2: Methods 16 Chapter 3: Site characterization. 37 Chapter 4: Influence of environmental factors on community structure 67 Chapter 5: Discussion and Conclusions 87 Appendices 104 Appendix A: List of CPCe4.0 codefile subcategories with classifications. References 110 viii List of Tables Table Page Chapter 2: 2.1 List of major category and sub-category taxa groupings 28 2.2 Local and regional environmental factor classifications and hypotheses 33 2.3 List of hypotheses tested by each statistical test 36 Chapter 3: 3.1 Community composition of each site 38 3.2 Results of SIMPER analyses of community composition 48 3.3 Environmental characteristics of each site (ranges) 61 3.4 Environmental characteristics of each site (mean and SD) 62 3.5 Results of SIMPER analyses of environmental characteristics 66 Chapter 4: 4.1 Results of DistLM tests 69 4.2 Results of SIMPER analyses of taxon and environmental factors 78 ix List of Figures Figure Page Chapter 1: 1.1 Diagram from Connell et al. (2013) 11 Chapter 2: 2.1 Site locations 17 2.2 Hypothetical diagram of local versus regional influences 19 2.3 Visual aid depicting benthic photoquadrats 22 2.4 Computer screenshot of CPCe 4.0 25 2.5 Graphs of Coefficient of Variance analysis 26 Chapter 3: 3.1 Pie charts displaying top taxa within HGB 39 3.2 Pie charts displaying top taxa within LKH 41 3.3 Pie charts displaying top taxa within TRL 43 3.4 Dendrogram graph showing results of cluster analysis 45 3.5 Results of nMDS analysis of all three sites’ composition 47 3.6 Results of nMDS analyses of HGB 50 3.7 SigmaPlot graph of Thalassia spp. at HGB 52 3.8 Results of nMDS analyses of LKH 54 3.9 SigmaPlot graphs of Laurencia spp. and Halimeda spp. at LKH 55 3.10 Results of nMDS analyses of TRL 57 3.11 SigmaPlot graph of Dictyota spp. at TRL 58 3.12 Results of nMDS analysis of all three sites’ environmental data 64 Chapter 4: 4.1 Time series graph of monthly temperature 72 x 4.2 Time series graph of monthly wave data 74 4.3 Time series graph of monthly nitrate concentrations 76 4.4 Time series graphs of taxa and environmental factors at HGB 79 4.5 Time series graphs of taxa and environmental factors at LKH 82 4.6 Time series graphs of taxa and environmental factors at TRL 85 1 Chapter 1: Introduction and background information Global threats to marine environments As anthropogenic activities threaten coastal ecosystems, there is a need to ascertain the specific mechanisms influencing these environmental perturbations. Humans have not only impacted ecosystems directly through the exploitation of goods, but also indirectly by interrupting species competition, recovery, and dispersal mechanisms (O’Neill 2001; Lirman & Biber 2000; Jompa & McCook 2002). Because marine habitats are important to surrounding coastal communities, and to global biodiversity and ecosystem functions, it is vital to understand the stability of these ecosystems in order to effectively protect them and their assets. The stability of a marine ecosystem is related to its resilience, or its ability to return to its original community composition after a disturbance (Hughes et al. 2007). This stability is usually achieved via negative feedback loops (i.e., ecological processes such as competition, herbivory, etc.; see Norström et al. 2009) that cause the community proportions within the reef to remain stable relative to original structure, therein practicing resilience despite perturbations (Beisner et al. 2003; Graham et al. 2013; Hughes et al. 2010). The Intermediate Disturbance Hypothesis (IDH; Connell 1978) has long been accepted to explain how ecosystems appear able to maintain a steady equilibrium of high diversity. The IDH states that an intermediate amount of natural disturbances allow these highly diverse ecosystems, like coral reefs, to maintain relatively stable states by preventing competitive exclusion (i.e., dominance of one or few biota; Connell 1978). However, anthropogenic influences have disrupted ecosystem 2 stability indirectly by affecting how and when species can respond to perturbations, which essentially is caused by an increase in frequency of these disturbances (O’Neill 2001). Increasing frequency and/or intensity (e.g., storm activity, temperature stress, etc.) as well as an increasing variety of disturbances (e.g., natural and anthropogenic) requires a greater need for effective as well as time-efficient responses from species within the ecosystem (Connell 1978; O’Neill 2001).