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I CHARACTERIZING the EFFECTS of ANTHROPOGENIC CHARACTERIZING THE EFFECTS OF ANTHROPOGENIC DISTURBANCE ON DEEP-SEA CORALS OF THE GULF OF MEXICO A Dissertation Submitted to the Temple University Graduate Board In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY by Danielle M. DeLeo December 2016 Examining Committee Members: Erik E. Cordes, Advisory Chair, Biology Robert W. Sanders, Biology Rob J. Kulathinal, Biology Santiago Herrera, External Member, Lehigh University i © Copyright 2016 by Danielle M. DeLeo All Rights Reserved ii ABSTRACT Cold-water corals are an important component of deep-sea ecosystems as they establish structurally complex habitats that support benthic biodiversity. These communities face imminent threats from increasing anthropogenic influences in the deep sea. Following the 2010 Deepwater Horizon blowout, several spill-impacted coral communities were discovered in the deep Gulf of Mexico, and subsequent mesophotic regions, although the exact source and extent of this impact is still under investigation, as is the recovery potential of these organisms. At a minimum, impacted octocorals were exposed to flocculant material containing oil and dispersant components, and were visibly stressed. Here the impacts of oil and dispersant exposure are assessed for the octocoral genus Paramuricea. A de novo reference assembly was created to perform gene expression analyses from high-throughput sequencing data. Robust assessments of these data for P. biscaya colonies revealed the underlying expression-level effects resulting from in situ floc exposure. Short-term toxicity studies, exposing the cold-water octocorals Paramuricea type B3 and Callogorgia delta to various fractions and concentrations of oil, dispersant and oil/dispersant mixtures, were also conducted to determine overall toxicity and tease apart the various components of the synergistic exposure effects. Finally, alterations in Paramuricea B3 gene expression profiles were inspected to characterize genome-wide changes induced by each treatment and putative genes under differential regulation. The experimental results provide evidence for a relatively high toxicity of chemical dispersants as compared to oil additions alone, elucidating the implications of applying oil dispersants to future oil spills. My findings iii revealed signatures of cellular stress in floc-exposed corals associated with xenobiotic metabolism, immune and inflammatory responses as well as transcriptional suppression of vital cellular components like ribosomal proteins. The data also suggests poor recovery potential in our coral samples exposed to floc. In addition, promising biomarker candidates were identified from the differential expression data for use in future spill- impact monitoring. iv DEDICATION To my husband for inspiring me to be curious and pursue our mutual love of science, and my mother for her adoration and encouragement. v ACKNOWLEDGMENTS I first and foremost need to thank my advisor and mentor Erik Cordes for his support and guidance while pursuing my doctorate degree. I thank him for having unyielding confidence in me and my abilities as a scientist, and for the amazing travel opportunities I never expected to have- both near and far, and to the bottom of the ocean! I am so grateful our paths crossed and I can only hope to follow in his footsteps as a successful marine scientist. I have confidence that our friendship and collaborations will not end here. Additional heartfelt thanks to my dissertation committee, Robert Sanders and Rob Kulathinal who have been great mentors over the years, and to Santiago Herrera whose recent guidance has been invaluable. Equally important, I need to thank my husband and my best friend for over a decade, Nicholas, for venturing into a career of science alongside me and supporting my ambitions with sincere enthusiasm. His curiosity and appetite for knowledge inspires me every day. His fascination with science also emboldened me to pursue a career researching what I love- the ocean. Without his love and support, I would not have gotten through this chapter of my life and for that I am forever grateful. I am thankful for my mother Donna, for her never-ending support and for instilling in me the strength to overcome any obstacle, the drive to follow my dreams and the gall to stand up for what I believe in. I am also thankful to my family, who each support me in their own way, including my grandmother Betti, my aunt Karan, Bill, and my beautiful niece Ariana- who inspires me to be a better person every day. Additional thanks to my in-laws, Ed and Sheila- who have supported me like one of their own for vi over a decade now. And to Gabby, Mike and Eddy for showing me the meaning of true sibling camaraderie. Words cannot describe my gratitude and adoration towards the graduate students in the Cordes lab whom I’ve had the pleasure of working alongside over the past few years. I am extremely thankful for Jay Lunden and Andrea Quattrini who helped train me when I first started graduate school and quickly became a much-needed support system. Jay and Andrea were more than just cherished mentors; they became lifelong friends and valued colleagues. Additional thanks to Samuel Georgian for being a great friend and travel buddy, and for our port (mis)adventures. I am forever thankful for my friends, Alexis Weinnig, Sarah DeVaul Princiotta and Elizabeth Reilly for their encouragement and for empowering me as a woman and as a scientist. And to the best friend I lost too early in life, Lee Ann, who loved life and learning and inspired me to follow suit. I am also thankful for the friends who have supported and encouraged me over the years in college and in graduate school including Alanna Durkin, Carmela Romeo, Coady and Laura Knowles, Kim Reuter, Katherine Papacostas, Carlos Gomez, Steven Auscavitch, Nichole Rigby, Craig Stanley Jr. and Janne Pfeiffenberger. Aspects of my dissertation research, as well as ongoing projects not presented here, would not have been possible without the assiduous efforts of several undergraduate students at Temple University, including Conall McNicholl, Melissa Kurman, Alexandria Barkman, Samuel Nguyen, Kari Strouse, Jessica Hart and Lyanna Kessler. Likewise, I am thankful for Charles Fisher, Amanda Demopoulos, Iliana Baums, Fanny Girard, Veronica Radice, Helen White and Rachel Simister for sharing their vii knowledge, resources and passion for science with me. I also need to thank several people for their laborious assistance at sea, including Dannise Ruiz-Ramos, Rich Dannenberg and Danielle McKean. Various facets of my graduate research relied on technical support from a number of people. I am grateful to the ship crews aboard the R/V Falkor, E/V Nautilus, R/V Atlantis and vehicle crews of the ROV Global Explorer, ROV Hercules and the DSV Alvin, for their assistance with sample collections. Additionally, I would like to thank the faculty and staff at Temple University who have supported me in many ways including Richard Waring, Allen Nicholson, Toni Matthews, Derrick Love, Tania Stephens, Evelyn Vleck, Daniel Spaeth and Sheryl Love. I am extremely grateful for the funding that supported my dissertation research from the Gulf of Mexico Research Initiative’s “Ecosystem Impacts of Oil and Gas Inputs to the Gulf” (ECOGIG) program. The data fall under GRIIDC accession numbers R1 x 132.136.0004 and R1 x 132.136.0005. Funding was also provided through Temple University in the form of teaching and research assistantships and travel grants to attend workshops and conferences. Additionally, the in situ impacted corals were collected during the AT18-3 cruise on the R/V Atlantis with the Alvin submersible and AUV Sentry, with support to EEC from NSF RAPID grant OCE-1045079. A final thanks to my Fox for brightening my life and lastly, to the city of Philadelphia, my hometown and touchstone. Thank you for providing me with great food, libations, music and friends. Till we meet again. viii TABLE OF CONTENTS Page ABSTRACT ....................................................................................................................... iii DEDICATION .....................................................................................................................v ACKNOWLEDGMENTS ................................................................................................. vi LIST OF TABLES ........................................................................................................... xiv LIST OF FIGURES ...........................................................................................................xv LIST OF ILLUSTRATIONS .......................................................................................... xvi CHAPTER 1. INTRODUCTION ........................................................................................................1 1.1 The deep sea ......................................................................................................1 1.2 Coral fauna ........................................................................................................2 1.2.1 Cold-water corals ...................................................................5 1.2.2 Octocorals ..............................................................................7 1.2.3 Genus Paramuricea ...............................................................8 1.3 Anthropogenic threats to cold-water corals ......................................................9 1.3.1 Deep-water trawling and fisheries .........................................9
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