UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Anchialine Cave Environments: a novel chemosynthetic ecosystem and its ecology Permalink https://escholarship.org/uc/item/5989g049 Author Pakes, Michal Joey Publication Date 2013 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Anchialine Cave Environments: a novel chemosynthetic ecosystem and its ecology By Michal Joey Pakes Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Roy L. Caldwell, Co-Chair Professor David R. Lindberg, Co-Chair Professor Steven R. Beissinger Fall 2013 Abstract Anchialine Cave Environments: a novel chemosynthetic ecosystem and its ecology by Michal Joey Pakes Doctor of Philosophy in Integrative Biology University of California, Berkeley Professor Roy L. Caldwell, Co-Chair Professor David R. Lindberg, Co-Chair It was long thought that dark, nutrient depleted environments, such as the deep sea and subterranean caves, were largely devoid of life and supported low-density assemblages of endemic fauna. The discovery of hydrothermal vents in the 1970s and their subsequent study have revolutionized ecological thinking about lightless, low oxygen ecosystems. Symbiosis between chemosynthetic microbes and their eukaryote hosts has since been demonstrated to fuel a variety of marine foodwebs in extreme environments. We also now know these systems to be highly productive, exhibiting greater macrofaunal biomass than areas devoid of chemosynthetic influx. This dissertation research has revealed chemosynthetic bacteria and crustaceans symbionts that drive another extreme ecosystem - underwater anchialine caves - in which a landlocked, discrete marine layer rests beneath one or more isolated layers of brackish or freshwater. Most anchialine caves contain low invertebrate abundances, yet some have inexplicably large biomasses of shrimp and remipedes, a rare crustacean class endemic to caves. Since only anecdotal evidence of remipede feeding in the field has been published and little ecological information about anchialine organisms is known, in situ studies are crucial to understanding whether there are direct or indirect links between chemosynthetic input into anchialine foodwebs and remipede abundance. This dissertation research integrates studies of geochemistry, microbiology, invertebrate food web dynamics, and behavior in these extreme ecosystems. Findings include the following: 1) highly stratified anchialine caves support communities of freeliving chemosynthetic bacteria, 2) Typhlatya pearsi, an anchialine shrimp, harbors chemosynthetic endosymbiotic bacteria, 3) the remipede, S. tulumensis, may also harbor chemosynthetic symbionts ectobiotically 4) food webs in the cave are complex and vary spatially, driving community structure changes 5) remipedes likely use chemical gradients and specialized chemosensory receptors to navigate in their lightless environment. This combined body of research provides the first systematic study into anchialine ecology and has found them to be rich in taxa for comparative study with other chemosynthetic systems. For example, the finding of the first chemosynthetic 1 endosymbiosis in a crustacean, T. pearsi, and the first chemosynthetic epibiosis in a remipede, S. tulumensis, allows for a variety of comparative coevolutionary studies. Typhlatya, a genus of troglobytic shrimp, are found in anchialine systems across the Caribbean and Bermuda and likely all contain chemoendosymbiotic bacteria. As such this discovery provides a springboard for comparative research into the transmission and evolution of chemosynthetic symbiotic associatons. The most interesting outcomes, however, may result from comparing ecological and ecosystem function patterns described in caves to those known for deepwater as well as molluscan and annelid systems. Furthermore, anchialine systems, a primary source for agricultural, domestic, and industrial water use, are especially susceptible to climate change. Therefore, not only are studies of ecosystem function such as this imperative to conserving endemic cave fauna and their suitable habitat, but they may also help in the preservation of clean water caches for future generations. 2 TABLE OF CONTENTS Dedication iii Acknowledgements iv Chapter 1: Anchialine cave geomicrobiology: a multilayered perspective Introduction 1 Materials and Methods 3 Results 6 Discussion 7 Acknowledgements 9 References 10 Table Captions 13 Tables 13 Figure Captions 14 Figures 16 Appendices 24 Chapter 2: An unusual symbiosis in discovered in anchialine shrimp, Typhlatya pearsei Introduction 25 Materials and Methods 26 Results 27 Discussion 28 Acknowledgements 30 References 31 Figure Captions 33 Figures 35 Appendices 39 Chapter 3: Chemosynthetic ectosymbiosis in Speleonectes tulumensis (Remipedia) Introduction 49 Materials and Methods 50 Results 51 Discussion 52 Acknowledgements 54 References 54 Figure Captions 56 Figures 57 Chapter 4: Concurrent triple-isotope approach reveals chemosynthetic base to anchialine food web and intraspecific diet variation Introduction 59 Materials and Methods 61 Results 63 Discussion 64 Acknowledgements 66 i References 67 Table Captions 69 Tables 69 Figure Captions 70 Figures 71 Appendices 78 Chapter 5: Behavior of the remipede, Speleonectes tulumensis: swimming in the dark Introduction 81 Materials and Methods 82 Results 85 Discussion 86 Acknowledgements 88 References 88 Figure Captions 90 Figures 92 Appendices 98 Conclusions: Changing caves: Shifting focus to the dynamic anchialine environment Review 100 References 104 ii DEDICATION I dedicate this work to three mentors from whom I have been fortunate to learn and take inspiration. C. Cavanaugh • T. Thomsen • J. Yager iii ACKNOWLEDGEMENTS A dissertation is in many ways a study in learning with the student as the central experiment. Throughout my time at UC Berkeley, people at the university and beyond have carefully observed my progression, making adjustments where needed and providing the materials and support necessary for this experiment to succeed. There are many institutions, agencies, mentors, and peers without whom this project would not have progressed. Their generosity can not only be seen through the written words and figures that follow, but also in the way that I now view teaching and learning. I have trouble finding words to thank my co-advisors, Roy Caldwell and David Lindberg. Together they have made me an academic in a way I didn’t realize I could be. They have allowed me to test, fail, and succeed with help and on my own. Early on, they allowed me to gamble on a largely unknown system and fostered my questioning with both interest and realism. I could not have wished for better academic family. The way that Roy has drawn from his knowledge and experiences to advise me over the past 7 years has shaped this dissertation research. While some would say that Roy’s academic love is stomatopods, I would counter that it is his students. He is always willing to meet with us, whether at his desk or while photographing a new Pseudosquilla egg clutch. During this time, he prepared me for fieldwork in a complicated underwater system, and with teams of researchers. He advised me to plan carefully, all the while telling me about his own difficulties in the field (lots of sharks, lots of decompression). He similarly could joke with me while expecting my rigor in experimental design and focus in writing style. Most importantly, he has asked me questions that are so relevant about my system that have changed the way that I look at it. I frequently ask myself: When I leave here, how will I know what I have left out? Thank you Roy for all of your guidance. Dave Lindberg has instilled in me an evolutionary and deep time perspective that was only burgeoning when I arrived at Berkeley. “Things Change” may be a mantra of the lab, but we will always (past and future) benefit from your encouragement that we think outside of our organism, outside of our system, and outside of our timescale. This depth of perspective has affected me in my research, in my mentorship, in my teaching, in my outreach, and in my general worldview. In these ways, Dave has expanded the toolbox I will use to tackle academic, interpersonal or canine problems. For this, I will always be grateful. Several other mentors have generously advised me throughout my time at Berkeley. Steve Biessinger was a fantastic outside dissertation committee member, aiding me with data interpretation and improving my writing immensely. His integrative work inspires me to both broaden my reaches and to focus my questions. C. Marshall has been an informal mentor, taking time from his directorship to provide writing, research, public presentation, and career advice. His words have brought me both encouragement and warnings– sometimes at once, reminding me that “success begets success.” I have also carried with me the advice granted from- R. Woollacott, C. Cavanaugh and G. Giribet and have returned to Cambridge to get tune ups on occasion. iv I would additionally like to thank my qualifying exam committee. J. Coates, T. Dawson, M. Power, and J. Lipps have mentored me into a new field through multiple conversations leading up to my exam and after it. There are few times when I have felt more lucky or stretched than during my qualifying exam. Their support