South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2019 Shrimp Production Environment and the Gut Microbiome: Effects of Aquaculture Practices and Selective Breeding on the Gut Microbiome of Pacific Whiteleg Shrimp, Litopenaeus vannamei Angela Landsman South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Aquaculture and Fisheries Commons, Environmental Microbiology and Microbial Ecology Commons, Marine Biology Commons, and the Microbial Physiology Commons Recommended Citation Landsman, Angela, "Shrimp Production Environment and the Gut Microbiome: Effects of Aquaculture Practices and Selective Breeding on the Gut Microbiome of Pacific Whiteleg Shrimp, Litopenaeus vannamei" (2019). Electronic Theses and Dissertations. 3360. https://openprairie.sdstate.edu/etd/3360 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. SHRIMP PRODUCTION ENVIRONMENT AND THE GUT MICROBIOME: EFFECTS OF AQUACULTURE PRACTICES AND SELECTIVE BREEDING ON THE GUT MICROBIOME OF PACIFIC WHITELEG SHRIMP, LITOPENAEUS VANNAMEI BY ANGELA LANDSMAN A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2019 iii This thesis is in dedication to: My parents: Steven & Vicki Hansen who impressed upon me the value of education, setting goals and to never stop learning My loving husband: Heath Landsman my best friend who continually offered his support and encouragement with a good dose of reality My two curious boys: Devin & Kaden who inspire me daily to seek not only answers but also new questions My brother: Nicholas Hansen who taught me so many things about optimism, persistence and overcoming preconceived ideas and obstacles My sister: Tonja Cantú, Ph.D. who instilled a love of learning in me at a young age and never stopped learning herself iv ACKNOWLEDGEMENTS I am immensely thankful to a number of employees at The trū Shrimp Company for their technical assistance and continued support, particularly to Michael Ziebell for encouragement and guidance. I thank Bruce Paterson for countless stories all leading to a lesson or a break from the stresses of everyday work, for allowing time in the day for “school-work” and just the right amount of pressure when needed. My co-workers Tim Gross and Misael Rosales for imparting on me just a small piece of their knowledge of engineering and shrimp aquaculture, animal health and so, so much more. Dahee Kim for her astute skills in statistical analysis and Lisa Broderius, Melissa Friedrichs and Brittany Loosbrock for sharing numerous hours of gut pulls and DNA extraction. Finally the Innovation Center and Reef staff for their dedication to a job well done and attention to detail. Additional gratitude for the educational and support staff at South Dakota State University, particularly to Benoit St-Pierre for his patience and tolerance while instructing on the methods of data analysis and countless revisions to manuscripts for publication, William Gibbons and Michael Brown for exceptional guidance and constructive criticisms, and the staff of the office of graduate studies for promptly answering all of my questions and guiding me down the winding path to graduation. v CONTENTS LIST OF FIGURES ......................................................................................................... viii LIST OF TABLES .............................................................................................................. x ABSTRACT ..................................................................................................................... xiii INTRODUCTION .............................................................................................................. 1 LITERATURE REVIEW ................................................................................................... 4 1. Industry Overview ....................................................................................................... 4 2. Wild Caught Shrimp.................................................................................................... 6 2.1 History of Wild Harvest of Shrimp ....................................................................... 6 2.2 Methods of Wild Harvest of Shrimp ..................................................................... 7 2.3 Adverse Effects of Wild Harvest of Shrimp .......................................................... 8 2.4 Regulations on and Improvements to Wild Harvest Methods ............................... 9 3. Aquaculture Production of Shrimp ........................................................................... 11 3.1 History of Aquaculture Production...................................................................... 11 3.2 Methods of Aquaculture Production.................................................................... 14 3.3 Advantages of Aquaculture Production ............................................................... 17 3.4 Disadvantages of Aquaculture Production .......................................................... 19 4. Microbiome ............................................................................................................... 20 4.1 Introduction ......................................................................................................... 20 4.2 Methods to Study the Microbiome ...................................................................... 22 4.3 The Shrimp Microbiome ..................................................................................... 23 vi 4.4 Effects of Age and Physiological Development on the Gut Microbiome ........... 25 4.5 Effects of Nutrition on the Gut Microbiome ....................................................... 26 4.6. Effects of Environment and Water Quality on the Gut Microbiome ................. 27 4.7 Shrimp Health and Disease as Influenced by the Gut Microbiome .................... 27 CHAPTER ONE ............................................................................................................... 29 Impact of Aquaculture Practices on Intestinal Bacterial Profiles of Pacific Whiteleg Shrimp Litopenaeus vannamei ...................................................................................... 29 1. Abstract .................................................................................................................. 29 2. Introduction ........................................................................................................... 30 3. Materials and Methods .......................................................................................... 34 4. Results ................................................................................................................... 41 5. Discussion .............................................................................................................. 48 CHAPTER TWO .............................................................................................................. 54 Host genetics is an important determinant of gut bacterial community composition in aquaculture-raised Pacific Whiteleg shrimp Litopenaeus vannamei ............................ 54 1. Abstract .................................................................................................................. 54 2. Introduction ........................................................................................................... 55 3. Materials and Methods .......................................................................................... 59 4. Results ................................................................................................................... 68 5. Discussion .............................................................................................................. 77 CONCLUSIONS............................................................................................................... 82 vii APPENDIX ....................................................................................................................... 87 LITERATURE CITED ..................................................................................................... 96 viii LIST OF FIGURES Introduction Figure 1. Dredge ..............................................................................................................................7 Figure 2. Trawler .............................................................................................................................8 Chapter 1 Figure 1. Venn diagram showing the number of shared and unique OTUs from the intestine of indoor-raised, pond-reared and wild caught white leg shrimp. Also shown is the proportion of sequence reads for each category. .............................................................42 Figure 2. Comparison of intestinal bacterial communities from whiteleg shrimp using Principle Coordinate Analysis (PCoA). A) Comparative analysis between shrimps raised under two different production