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Nutrient Availability and Changes in Microbial Communities in Flooded Rice Production in South Florida

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Nutrient Availability and Changes in Microbial Communities in Flooded Rice Production in South Florida NUTRIENT AVAILABILITY AND CHANGES IN MICROBIAL COMMUNITIES IN FLOODED RICE PRODUCTION IN SOUTH FLORIDA By RACHELLE BERGER A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2020 © 2020 Rachelle Berger To my family and children ACKNOWLEDGMENTS I would like to give my give the biggest thank you to my advisors, Dr. Samira Daroub and Dr. Willm Martens-Habbena, your patience, understanding, caring disposition, and continuous support have allowed me to complete this thesis. I would like to thank all my Dr. Mabry McCray and Dr. Sarah Strauss (committee members) for their guidance and consistent support. I would like to thank everyone at the UF Everglades Research and Education Center (EREC), UF Fort Lauderdale Research and Education Center (FLREC), and Gainesville for contributing to my research, education, and career path. I would also like to thank the UF Soil and Water Sciences Department for the incredible opportunities, professors, ad staff. The past three years in graduate school have been some of the best memories of my life. Thank you, Johnny Mosley for helping me navigate through the EAA, you have been a great human compass and soil sampler! Thank you, Tim, for your help with maps and experimental design. Thank you Viviana, Maryory, and Irina for your help and support in the EREC lab. I would like to thank all the farmers in the EAA that made this research possible and allowing us to sample on your land. Thank you to the Rice Council of the EAA for your financial support. Thank you, Argonne National Laboratory in Chicago, for sequencing my samples. Thank you to Mike Sisk who has encouraged me and made sure I made every deadline since my undergraduate degree. Thank you to the entire Soil and Water Graduate Student Association and all graduate school association I have had the pleasure of working with. Thank you, Dr. Allan Bacon, for encouraging me to learn more about soil classification and pedology. It was a pleasure to serve at the Vice President of Distance Education for Soil and Water Science Graduate students as well as President of the Everglades Research and Education Center Student Association. It 4 was so moving to be able to enhance our centers community growth and support, especially during COVID19. Thank you to Seemanti, Claire, Andy, and Kelly at the UF FLREC, you all have been so helpful and amazing to work with at your laboratory. Thank you to everyone in Gainesville. Thank you to all my professors in the Soil and Water Sciences Department! Thank you to anyone and everyone who has supported me in any way. Additionally, thank you to my entire family, without which I would not have the support needed to achieve my goals. Thank you to my beautiful children (Ava and Isaac),sister (Alyssa) , and my amazing friends especially, Tiffany, Alyssa T., Chelsea, and Mike. Thank you to my incredible grandparents who have survived the Holocaust. Your willingness to survive, never give up has given me a better outlook on life and a passion to become the best version of myself. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 8 LIST OF FIGURES .......................................................................................................... 9 ABSTRACT ................................................................................................................... 11 CHAPTER 1 INTRODUCTION .................................................................................................... 13 The Everglades Agricultural Area (EAA) ................................................................. 13 Histosols in the EAA ............................................................................................... 14 Subsidence of the Organic Soils in the EAA ..................................................... 15 Best management practices (BMPs) ................................................................ 16 Phosphorus Runoff and Water Quality Issues .................................................. 17 Flooded Rice Cultivation Benefits in the EAA ................................................... 18 Soil Chemistry of Flooded Soils ........................................................................ 19 Microbial Communities in Flooded Soils ................................................................. 21 Project Hypothesis .................................................................................................. 23 Project Statement and Objectives ........................................................................... 23 Methods and Materials............................................................................................ 24 2 SOIL NUTRIENT AVAILABILITY FOLLOWING FLOODED RICE PRODUCTION IN SOUTH FLORIDA ..................................................................... 31 Introduction of Chapter 2 ........................................................................................ 31 Subsidence of Histosols ................................................................................... 31 Flooded Rice Production .................................................................................. 32 Nutrients and Rice Production in Histosols ............................................................. 34 Hypothesis and Objectives ..................................................................................... 38 Methods and Materials............................................................................................ 38 Soil Sampling and Analysis .............................................................................. 38 Nutrient Analyses ............................................................................................. 40 Statistical Analysis .................................................................................................. 40 Results and Discussion........................................................................................... 41 Soil Properties .................................................................................................. 41 Total C and N ................................................................................................... 42 Nutrients ................................................................................................................. 43 Macronutrients and Si ...................................................................................... 43 Micronutrients ................................................................................................... 45 Soil Properties ........................................................................................................ 46 Macronutrients ........................................................................................................ 47 6 Micronutrients ......................................................................................................... 50 Conclusions ............................................................................................................ 55 3 IMPACT OF THE CULTIVATION OF FLOODED RICE ON SOIL MICROBIAL COMMUNITIES ...................................................................................................... 69 Introduction of Chapter 3 ........................................................................................ 69 Denitrification .................................................................................................... 73 Fermenting Bacteria ......................................................................................... 75 Hypotheses and Objectives .................................................................................... 76 Methods .................................................................................................................. 77 Soil Sampling and Analysis .............................................................................. 77 DNA Extractions ............................................................................................... 78 Statistical analyses ........................................................................................... 80 Results and Discussion........................................................................................... 80 Comparative analysis of selected metabolic groups of microbes ..................... 81 Sulfate reducing bacteria (SRB) ....................................................................... 84 Methanogens .................................................................................................... 84 Ammonia-oxidizing Thaumarchaeota ............................................................... 89 Conclusion .............................................................................................................. 90 APPENDIX: FARM REGIONS AND MICROBIAL GROUPS ......................................... 96 LIST OF REFERENCES ............................................................................................... 97 BIOGRAPHICAL SKETCH .......................................................................................... 107 7 LIST OF TABLES Table page 1-1 Histosol soil series found in the Everglades Agricultural Area. ........................... 26 2-1 Location
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