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HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY of an ESTUARINE COPEPOD a Thesis Submitted to the Faculty of Sa

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HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY of an ESTUARINE COPEPOD a Thesis Submitted to the Faculty of Sa HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY OF AN ESTUARINE COPEPOD A Thesis submitted to the faculty of San Francisco State University In partial fulfillment of z o l i the requirements for OL the Degree • Hk ^ Master of Science In Biology: Ecology, Evolution, and Conservation Biology by Ann Elisabeth Holmes San Francisco, California Copyright by Ann Elisabeth Holmes 2018 CERTIFICATION OF APPROVAL I certify that I have read High-throughput sequencing reveals unexpected phytoplankton prey of an estuarine copepod by Ann Elisabeth Holmes, and that in my opinion this work meets the criteria for approving a thesis submitted in partial fulfillment of the requirement for the degree Master of Science in Biology: Ecology, Evolution and Conservation Biology at San Francisco State University. Wim Kimmerer, PhD Professor Jopathon Stillman, PhD Professor Andrea Swei, PhD Assistant Professor HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY OF AN ESTUARINE COPEPOD Ann Elisabeth Holmes San Francisco, California 2018 Selective feeding by copepods has important ecological implications such as food web length, nutrient limitation, and control of algal blooms. Traditional methods for investigating copepod feeding in natural waters (e.g. stable isotope and fatty acid tracers or microdissection) have low taxonomic specificity or significant biases. We used high- throughput genetic sequencing (HTS) to identify in situ the phytoplankton prey of Pseudodiaptomus forbesi (Copepoda: Calanoida) in the San Francisco Estuary. Amplicons of the 16s rRNA gene were sequenced on an Illumina MiSeq. Cyanobacteria were the most frequently detected prey taxon, a result not predicted due to expected low nutritional value. In contrast, prey taxa expected to have high nutritional value for copepods (diatoms and cryptophytes) were not detected as frequently as anticipated based on the expectations generated using traditional approaches. Although our data is unable to resolve this unexpected result, the apparent feeding outcome could reflect unexpected feeding patterns, trophic upgrading, or poorly understood artifacts of the method. HTS analysis of copepod predation will become an increasingly valuable method as it is further developed and integrated with traditional approaches. I certify that the Abstract is a correct representation of the content of this thesis. Chair, Thesis Committee Date ACKNOWLEDGEMENTS I thank Wim Kimmerer for giving me this valuable opportunity, for his guidance throughout the project, and for many enlightening discussions of copepod ecology over coffee or IP A. I also appreciate the helpful feedback and support from committee members Andrea Swei and Jonathon Stillman. Thank you to Toni Ignoffo and Anne Slaughter for sharing their expertise in copepod biology and for their unwavering support, and to them and the rest of the Kimmerer Lab (especially Julien Moderan and Michelle Jungbluth) for valuable feedback on this research. Crystal Weaver and I worked through many of challenges of high-throughput sequencing together and I appreciate her insight and comradery. Frank Cipriano, former director of the SFSU Genomics/Transcriptomics Analysis Core (GTAC), was a key resource and guide in molecular methods. Jose de la Torre, Jess Kwan, Virginia Russell, and Betsabel Chicana also provided essential guidance and discussion on high-throughput sequencing methods. Carrie Craig introduced me to genetic studies of copepod feeding ecology. Brian Bergamaschi, Brian Downing, Scott Nagel, Katy O’Donnell, Renee Runyon, and Travis von Dessonneck of USGS made the field collections possible. Matt Settles of UC Davis provided guidance on bioinformatic questions. Comments from Andrea Schreier and Lina Reznicek-Parrado of UC Davis helped to improve this manuscript. This work is dedicated to the memory of my uncle Jacques Losq (1949-2017) whose curious scientific mind and enthusiastic support of my research I will always remember. I thank the State and Federal Contractors Water Agency (SFCWA) for funding this study. I appreciate the additional support from the Estuary & Ocean Science Center (EOS) Bay Scholarship and the San Francisco State Biology Department Instructional Related (IRA) Research Award. v TABLE OF CONTENTS List of Tables.......................................................................................................................... vii List of Figures........................................................................................................................viii List of Appendices...................................................................................................................ix Introduction................................................................................................................................ 1 Methods...................................................................................................................................... 5 Study site and species.................................................................................................. 5 Field samples ...............................................................................................................7 Laboratory studies........................................................................................................9 DNA extraction, library preparation, and sequencing...............................................9 Bioinformatic analysis................................................................................................12 Results...................................................................................................................................... 13 Field samples.............................................................................................................. 13 Laboratory studies.......................................................................................................19 Discussion................................................................................................................................21 Possible explanations for observed feeding patterns...............................................23 Marker choice in predation studies........................................................................... 27 Potential sampling artifacts, contamination risks, and sequence quality control ..29 References................................................................................................................................32 Appendices...............................................................................................................................50 LIST OF TABLES Table Page 1. Common approaches used to study copepod feeding in situ............................3 2. Sampling events (station and date) and environmental data............................8 3. 16S rRNA gene primers (Klindworth et al., 2013)...........................................11 4. Summary of Illumina 16S rRNA sequencing results........................................14 5. Number of distinct OTUs detected in each of six phyla..................................15 vii LIST OF FIGURES Figures Page 1. Study area and sampling events, Cache Slough Complex................................6 2. 16S rRNA sequencing results..............................................................................16 3. Relative abundance of sequences from copepods and seston........................... 17 4. Nonparametric multidimensional scaling plot of copepod and seston............18 5. Differential abundance analysis of copepod and seston samples..................... 20 LIST OF APPENDICES Appendix Page 1. Pilot study to determine eukaryote prey of P. forbesi............................................50 2. Relative abundance by phylum................................................................................53 ix 1 INTRODUCTION Copepods are tiny, abundant crustaceans that make up approximately 50% of zooplankton globally (Longhurst, 1985). They are key to aquatic food webs (Turner, 2004; Beaugrand et al., 2010), the microbial loop (Calbet and Saiz, 2005) and the oceanic carbon cycle (Turner 2002). Copepods are also used as ecological indicators (Bonnet and Frid, 2004; Hoof and Peterson, 2006) and model species in evolution (Lee, 1999), adaptation (Willett, 2010), and ecotoxicology (Raisuddin et al., 2007). In food webs, copepods are the link between fish and microbes. Copepod feeding has broad ecological consequences for primary production (Calbet, 2001) and production in higher trophic levels (Runge, 1988). Identification of copepod prey is important for understanding trophic interactions in aquatic environments, and consequently studies of copepod feeding occupy a central place in ecological analyses of copepod life history (Kiorboe, 2011). A large body of research indicates that copepods feed selectively. Feeding outcome depends on the sequential process of search, detection, pursuit, and capture (Holling, 1966). Prey and predator characteristics both determine the outcome of the feeding process. Copepod feeding may be influenced by prey characteristics such as size (Mullin, 1963; Richman and Rogers, 1969), nutritional value (Cowles et al., 1988; Stoecker and Capuzzo 1990), toxicity (DeMott and Moxter, 1991), digestibility (Brooks and Dodson, 1965), motility (Kiorboe 2011), and chemosensory signals (Poulet and Marsot, 1978), or predator characteristics such as behavior (Kiorboe, 2011) or morphology of feeding appendages (Koehl, 1996; Turner,
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