ORGANIC CARBON SOURCES AND THEIR TRANSFER IN A GULF OF MEXICO CORAL REEF ECOSYSTEM By © Laura Carreón-Palau (B.Sc., M.Sc.) A thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science Department of Biology Memorial University of Newfoundland June, 2015 St. John’s Newfoundland, Canada ABSTRACT Coral reefs face unprecedented threats throughout most of their range. Poorly planned coastal development has contributed increased nutrients and sewage contamination to coastal waters, smothering some corals and contributing to overgrowth by macroalgae. My approach to assessing the degree to which coral reef ecosystems have been influenced by terrestrial and anthropogenic organic carbon inputs is through the use of carbon (C) and nitrogen (N) stable isotopes and lipid biomarkers in a marine protected area, the Coral Reef System of Veracruz: Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) in the southwest Gulf of Mexico. Firstly, I used a C and N stable isotope mixing model and a calculated fatty acid (FA) retention factor to reveal the primary producer sources that fuel the coral reef food web. Secondly, I used lipid classes, FA and sterol biomarkers to determine production of terrestrial and marine biogenic material of nutritional quality to pelagic and benthic organisms. Finally, I used coprostanol to determine pollutant loading from sewage in the suspended particulate matter. Results indicate that phytoplankton is the major source of essential metabolite FA for marine fish and that dietary energy from terrestrial sources such as mangroves are transferred to juvenile fish, while seagrass non-essential FA are transferred to the entire food web mainly in the rainy season. Sea urchins may be the main consumers of brown macroalgae, especially in the dry season, while surgeon fish prefer red algae in both dry and rainy seasons. C and N isotopic values and the ratio C:N suggest that fertilizer is the principal source of nitrogen to macroalgae. Thus nitrogen supply also favored phytoplankton and seagrass growth leading to a better nutritional condition and high retention of organic ii carbon in the food web members during the rainy season when river influence increases. However, the great star coral Montastrea cavernosa nutritional condition decreased significantly in the rainy season. The nearest river to the PNSAV was polluted in the dry season; however, a dilution effect was detected in the rainy season, when some coral reefs were contaminated. In 2013, a new treatment plant started working in the area. I would suggest monitoring δ15N and the C: N ratio in macroalgae as indicators of the nitrogen input and coprostanol as an indicator of human feces pollution in order to verify the efficiency of the new treatment plant as part of the management program of the PNSAV. iii ACKNOWLEDGEMENTS I am grateful to my supervisor, Dr. Christopher C. Parrish, for accepting to help me and for sharing his knowledge of tracing organic carbon in cold waters and showing me how to apply it to coral reefs; thanks for his patience, support, good advice, and generosity. I am thankful to my supervisory committee for their support, to Horacio Pérez España for inviting me to participate in the project ‘Fuentes orgánicas de carbono y nitrógeno y su función sobre la estructura trófica en el Sistema Arrecifal Veracruzano Fomix-Veracruz 37567 ’ [Organic sources of carbon and nitrogen and their function on the trophic structure of the Coral Reef System of Veracruz], his support in the field work and good advice. Thanks go to Dr. Annie Mercier for her conscientious revisions and good advice. Also I want to thank the other members of the Project, especially Jorge Arturo Del Angel- Rodriguez and Sergio Aguiñiga-García for their support in the first chapter. To all the bachelor students that worked in the project from Instituto Tecnológico de Boca del Río, Veracruz, their help in the collection and labelling of samples was fundamental. The Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico, and the Veracruz state government co-financed the field and lab work. Analytical work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC). Thanks go to the Ph.D. fellowships from CONACYT (grant number 117304) and from the School of Graduate Studies, Memorial University of Newfoundland I appreciate the support of my work place the Centro de Investigaciones Biologicas del Noroeste in La Paz, Baja California Sur, Mexico. Dr. Sergio Hernández-Vázquez, Dr. Illie Racotta-Dimitrov, Dr. Bertha Olivia Arredondo-Vega, Dr. Pedro Cruz-Hernández iv and Dr. Daniel Lluch-Cota provided access to all the administrative facilities to complete my thesis. Also Dr. Arredondo-Vega generously provided me the lab facilities to be more efficient in the biochemical analysis. The Departments of Biology and Ocean Sciences at Memorial University were great places to work, thanks to Jeanette Wells and Linda Windsor, I really appreciated their expertise. Thanks to the friendship of Wally Martin, Zhao Sun, Stefanie Hixson, Giseli Swerts-Rocha, Jean Tucker, Lindsey Hemphill, Khalil Eslamloo, Neus Campanya and all the shuttle community. The people from the Society of Spanish at MUN made me enjoy this thesis with the Latino dancing breaks. The warm people from St. John’s, Elizabeth and Caroline Watton, Cameron and Holly Dunn, Ted and Margarita Miller, and Dr. Parrish’s family: Leslie, Nicholas, and Kathleen all shared their generosity and friendship with us and made my son happy. I can´t express how much I appreciate that. To my friends Lourdes Castillo, Oscar Meruvia, Soledad Porta and Alejandro Buren for all the talks and fun that we had together. Thanks go to my mother Angela Palau Betancourt for her visits to St. John’s and my sisters Martha, Silvia and Alicia and my brothers Carlos and Miguel, they gave me the love and confidence to face any challenge. I dedicate this thesis to the memory of my father Miguel Carreón-Lopez and our first land lord in St. John’s Maxwell Watton; they taught me to face the dark side of life with love, hope, and humor. Finally, I feel deeply thankful to my husband Jorge A. Del Angel- Rodríguez and my son Aarón Sinhué Del Angel-Carreón, my partners in this adventure for their love and enthusiasm to learn and discover. v Table of Contents ABSTRACT ........................................................................................................................ ii ACKNOWLEDGEMENTS ............................................................................................... iv List of Tables ................................................................................................................ xii List of Figures ............................................................................................................. xvii List of Symbols, Nomenclature or Abbreviations ......................................................... xx List of Appendices ....................................................................................................... xxv I General Introduction and Overview ................................................................................. 1 I.1 Importance of marine protected areas for coral reefs ................................................. 1 I.2 The organic carbon cycle ............................................................................................ 5 I.3 Use of biomarkers to trace organic carbon sources through the ecosystem ............... 8 I.3.1 Primary producers ................................................................................................ 8 I.3.2 Urban sewage .................................................................................................... 10 I.4 Organic carbon trophic transfer ................................................................................ 10 I.5 Thesis overview ........................................................................................................ 13 I.6 Thesis objectives ....................................................................................................... 15 I.7 Bibliography ............................................................................................................. 16 II Co-authorship statements .............................................................................................. 26 III Research Chapters ........................................................................................................ 28 vi Chapter 1 Revealing Organic Carbon Sources Fueling a Coral Reef Food Web in the Gulf of Mexico Using Stable Isotopes and Fatty Acids ............................................................ 29 1.1 Abstract .................................................................................................................... 29 1.2 Introduccion ............................................................................................................. 30 1.3 Material and methods ............................................................................................... 34 1.3.1 Study area .......................................................................................................... 34 1.3.2 Selection of food web members ........................................................................ 35 1.3.3 Sampling methods ............................................................................................. 35 1.3.4 Stable