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UNIVERSITY of CALIFORNIA, MERCED the Utility of Marine UNIVERSITY OF CALIFORNIA, MERCED The utility of marine neogastropod Californiconus californicus as a model system for investigation of the venom microbiome A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Quantitative and Systems Biology by Sabah Ul-Hasan Committee in Charge Professor J Michael Beman, Chair Professor Suzanne Sindi Professor Eric W Schmidt Professor Thomas F Duda Professor Tanja Woyke Professor Clarissa J Nobile Chapter 2 © Ul-Hasan, Bowers, Figueroa-Montiel, Licea-Navarro, Beman, Woyke, and Nobile 2019 Chapter 4.1 © Cheng, Dove, Mena, Perez, and Ul-Hasan 2018 Chapter 4.3 © Jones, Shipley and Ul-Hasan 2017 All other chapters © Sabah Ul-Hasan, 2019 All Rights Reserved The dissertation of Sabah Ul-Hasan is approved: Faculty Advisors _______________________________ Tanja Woyke, Ph.D. _______________________________ Clarissa J Nobile, Ph.D. Committee _______________________________ J. Michael Beman, Ph.D. _______________________________ Suzanne Sindi, Ph.D. _______________________________ Eric W Schmidt, Ph.D. _______________________________ Thomas F Duda, Ph.D. University of California, Merced 2019 iii Table of Contents List of Tables .............................................................................................................................. viii List of Figures ............................................................................................................................... ix Acknowledgements ...................................................................................................................... xi Curriculum Vitae ........................................................................................................................ xii Abstract of dissertation ............................................................................................................. xvi 1 Bergmann’s Rule across the Pleistocene, Holocene, and Anthropocene in an Eastern Pacific gastropod, Californiconus californicus (Reeve, 1844) (Gastropoda: Conidae) ...........1 1.1 Abstract ..................................................................................................................................1 1.2 Introduction ............................................................................................................................2 1.3 Methods and Materials ...........................................................................................................3 1.3.1 Sample Selection .............................................................................................................3 1.3.2 Shell Measurements.........................................................................................................4 1.3.3 Epoch Designations, Geographic Range, and Data Bins ................................................6 1.3.4 Sea Surface Temperatures and Urbanization Impact as Human Population Density and MPAs ........................................................................................................................................7 1.3.5 Statistical Analyses ..........................................................................................................7 1.4 Results ....................................................................................................................................8 1.4.1 Distribution of Adult C. californicus Shells ...................................................................8 1.4.2 Latitude and Sea Surface Temperature (SST) ................................................................9 1.4.3 Adult C. californicus Shell Size and Bergmann’s Rule ................................................13 1.4.4 Adult C. californicus Shell Shape and Bergmann’s Rule .............................................13 1.4.5 Adult C. californicus Shell Size and Shape by Marine Ecoregion ................................14 1.4.6 Adult C. californicus Shell Shape and Size by Coastal Proximity (islands vs. mainland coastline) ................................................................................................................................14 1.4.7 Adult C. californicus Shell Shape and Size by Coastal Urbanization & Human Population Density .................................................................................................................17 1.5 Discussion ............................................................................................................................19 1.5.1 Distribution and Range of Adult C. californicus ..........................................................19 1.5.2 Californiconus californicus Shell Size and Shape within Bergmann’s Rule ..........20 1.5.3 Shell Shape and Size by Marine Ecoregion and Coastal Proximity (islands vs. mainland coastline) ...........................................................................................................20 1.5.4 Dispersal Ability and Larval Development as Confounding Factors .......................21 1.6 Conclusion ............................................................................................................................22 1.7 References ............................................................................................................................22 iv 2 Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California ..........................................................28 2.1 Abstract ................................................................................................................................28 2.2 Introduction ..........................................................................................................................29 2.3 Methods and Materials .........................................................................................................30 2.3.1 Study Area and Sampling ..............................................................................................30 2.3.2 DNA Extraction, PCR Amplification for Validation and Illumina Amplicon Sequencing ............................................................................................................................32 2.3.3 Sequence Processing .....................................................................................................33 2.3.4 Data Analyses and Statistics ..........................................................................................34 2.4 Results ..................................................................................................................................35 2.4.1 Coastal Puerto Nuevo sample site metadata .................................................................35 2.4.2 Microbial community diversity richness and abundance .............................................35 2.4.3 Microbial community composition ..............................................................................36 2.5 Discussion ............................................................................................................................42 2.6 Conclusions ..........................................................................................................................44 2.7 References ............................................................................................................................45 3 Marine gastropod species Californiconus californicus possesses a core microbiome specific to its venom with Streptomyces as a prospective contributor to conotoxin integrity ........................................................................................................................................................51 3.1 Abstract ................................................................................................................................51 3.2 Introduction ..........................................................................................................................52 3.3 Methods and Materials .........................................................................................................54 3.3.1 Sample Sites and Collection ...........................................................................................54 3.3.2 DNA Extraction, PCR Amplification for Validation, and Illumina Amplicon Sequencing ................................................................................................................................56 3.3.3 Post-Processing Data Analyses and Statistics ................................................................57 3.4 Results ..................................................................................................................................58 3.4.1 Post-Processing Amplicon Sequence Data Results .......................................................58 3.4.2 The Venom Microbiome Across Space and Time ........................................................58 3.4.3 The Venom Microbiome is Localized Across the Gland, With Variation by Treatment ........................................................................................................................................................62 3.5 Discussion ............................................................................................................................64 v 3.5.1 Venom as a Microenvironment .....................................................................................64 3.5.2 Microbial Eukaryote
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