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Thermal and Microbial Effects on Brown Macroalgae: Heat The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library Winter 11-19-2018 Thermal and Microbial Effects on Brown Macroalgae: Heat Acclimation and the Biodiversity of the Microbiome Charlotte TC Quigley University of Maine, [email protected] Follow this and additional works at: https://digitalcommons.library.umaine.edu/etd Part of the Bacteriology Commons, Bioinformatics Commons, Computational Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Genetics Commons, Marine Biology Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation Quigley, Charlotte TC, "Thermal and Microbial Effects on Brown Macroalgae: Heat Acclimation and the Biodiversity of the Microbiome" (2018). Electronic Theses and Dissertations. 2933. https://digitalcommons.library.umaine.edu/etd/2933 This Open-Access Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. THERMAL AND MICROBIAL EFFECTS ON BROWN MACROALGAE: HEAT ACCLIMATION AND THE BIODIVERSITY OF THE MICROBIOME By Charlotte Terry Carrigan Quigley B.A. Colby College, 2009 A DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctorate of Philosophy (in Marine Biology) The Graduate School The University of Maine December 2018 Advisory Committee: Susan Brawley, Professor of Marine Sciences, Advisor Nick Brown, Former Director of Center for Cooperative Aquaculture Research Bill Halteman, Professor Emeritus of Mathematics and Statistics Vicki Hertzberg, Professor of Biostatistics and Bioinformatics Benildo de los Reyes, Professor of Plant Genomics John Singer, Professor of Microbiology THERMAL AND MICROBIAL EFFECTS ON BROWN MACROALGAE: HEAT ACCLIMATION AND THE BIODIVERSITY OF THE MICROBIOME By Charlotte Terry Carrigan Quigley Dissertation Advisor: Dr. Susan H. Brawley An Abstract of the Dissertation Presented in Partial Fulfillment of the Requirements for the Degree of Doctorate of Philosophy (in Marine Biology) December 2018 This dissertation examines effects of stress on brown algal biology from a macroscopic scale by examining whole aquaculture crops, to a microscopic level by examining the macroalgal microbiome across the vertical stress gradient of the intertidal zone and across their latitudinal biogeographic ranges. Thermal stress negatively affected seedstock gametophytes of the kelp Alaria esculenta isolated from northern and southern locations in Maine. However, prior thermal stress had a positive effect on growth of the next-generation sporophytes. Alaria esculenta has potential as a kelp crop in Maine’s sea vegetable aquaculture sector and implementing this protocol may allow the sea vegetable industry to increase crop yields. Studies found that stress gradients that influence distributions of brown macroalgae, specifically Fucus spp., can affect the microbial composition of the macroalgal microbiome. Various methods of describing macroalgal microbiomes were examined with a common garden approach using a lab-cultured strain of Porphyra umbilicalis. Methods examined included different preservation techniques, differences between algal tissue types, variability across the algal thallus, and type of analytical pipeline (e.g. mothur versus MED) used. Results were applied to in situ studies of the natural microbiome of Fucus spp.: each host species of the high, mid-, and low intertidal zones had a different microbiome. Manipulative transplants of mid-zone F. vesiculosus into the high zone assessed algal-associated bacterial tolerance to stress. Trans-Atlantic surveys of microbial diversity of F. vesiculosus found a biogeographic break in microbial community structure that correlated with sea surface temperatures and environmental stress across latitudes. These studies expand current knowledge of the direct and indirect effects of stress on phaeophytes across multiple scales. ACKNOWLEDGEMENTS This degree would not have been possible without the help and support of a huge list of people. Firstly, I would like to thank my family for their constant love and encouragement during these years of my graduate education. Above all, I thank my husband, Bryan, for his role as field recorder, lab assistant, travel companion, and cheerleader. I thank my parents for believing in me and telling me to always believe in myself, and not to worry too much because even null data tell a story. I thank my grandparents-in-law for their positive outlook on life that helped keep me grounded. I thank my advisor, Susan Brawley, for all of the opportunities that she has given me. I have learned so much about so many subjects due to her vast knowledge of science and her advisement; I am especially grateful for her help in improving my scientific writing. I appreciate the financial support of my research and field work from her research grants. I thank my committee members, Drs. Nick Brown, Bill Halteman, Vicki Hertzberg, Benildo de los Reyes, and John Singer for their support and advice through coursework and conversation. Special thanks to Drs. Halteman and Hertzberg for help with statistical analyses and coding as well as Dr. de los Reyes for hosting me during a research trip to his lab at Texas Tech. ii Without the significant contributions from my co-authors and collaborators, these projects would not be possible. Thanks to Dr. Hillary Morrison of the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, for her major contributions to the analyses of microbial communities of macroalgae, and her design of peptide nucleic acid clamps that are of incredible value to the scientific community; her support and advice were crucial to my degree. Thanks to Emma White and Aleksey Morozov also of MBL. Thanks to Dr. Ladd Johnson of Laval University in Quebec, Canada, for advisement and assistance in field experimental design in transplant projects. Thanks to my collaborators and co-authors from along the east coast and in Europe: Drs. Galice Hoarau, Yaccine Badis, Juliet Brodie, Ester Serrão, Catarina Mota, Ricardo Bermejo, Wayne Littaker, Patricia Tester, Joseph Scudlark, Leigh Sterns, and Gordon Hamilton. Special thanks to Drs. Badis, Brodie, and Tester who went above and beyond to help me complete my field work, and support me while abroad. Thanks to all of the undergraduate members of the Brawley lab that I have had the pleasure of mentoring and working with: Inara Mendonça, Chad Flinkstrom, Ian Jones, Ashley Serra, Olivia Barberi, and Riley Cummings. Special thanks to Ellie McCarthy, Alie Pergerson, Kit Buda, and Maggie Aydlett who have significantly contributed to my work. Thanks to senior lab members that have collaborated with me on projects, offered advice, and supported me, both in and out of lab: Geneva York, M.S., Charlotte Royer, M.S., Dr. Rémy Luthringer, and Kyle Capistrant-Fossa (M.S. student). And thanks to my iii SEANET graduate student cohort for their support, especially Emma Taccardi, Molly Miller, and Gretchen Grebe. Lastly, thanks to Steve Eddy and Luz Kogson Hurtado at the Center for Cooperative Aquaculture Research (CCAR) in Franklin, Maine, for assistance with aquaculture nursery facilities and to Sarah Redmond of Springtide Seaweed, LLC. for use of her sea farm and for assistance with grow-out experiments. Thanks to the sea vegetable farming community for supporting and working with the me and the scientific community to ensure aquaculture is a success in Maine. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................... ii LIST OF TABLES ............................................................................................................. x LIST OF FIGURES ......................................................................................................... xii Chapter 1. INTRODUCTION ................................................................................................. 1 Phaeophyceae: Brown Macroalgae ............................................................ 1 Local and Global Environmental Stressors ................................................ 3 Brown Algae in Aquaculture ..................................................................... 5 Goals and Specific Objectives: From Macro to Micro .............................. 7 2. TEMPERATURE TOLERANCE OF MAINE STRAINS OF THE KELP ALARIA ESCULENTA AND ITS SUITABILITY FOR AQUACULTURE IN THE GULF OF MAINE ................................................................................... 9 Introduction ................................................................................................ 9 Methods .................................................................................................... 16 Study Organism ........................................................................... 16 Study Site ..................................................................................... 17 Reproductive Phenology .............................................................. 19 Gametophyte Thermal Acclimation ............................................. 20 Sporophyte Grow-Out .................................................................. 23 v Results ...................................................................................................... 25 Reproductive
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