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A Comparison of Intertidal Metazoan Biodiversity Between Previously Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School March 2021 A Comparison of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared and Intact Marsh Margins and Between Multiple Salinity Zones in the Coastal Marshes of Louisiana Patrick M. Rayle Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Biodiversity Commons, Bioinformatics Commons, Biology Commons, Environmental Microbiology and Microbial Ecology Commons, and the Molecular Biology Commons Recommended Citation Rayle, Patrick M., "A Comparison of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared and Intact Marsh Margins and Between Multiple Salinity Zones in the Coastal Marshes of Louisiana" (2021). LSU Master's Theses. 5287. https://digitalcommons.lsu.edu/gradschool_theses/5287 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. A COMPARISON OF INTERTIDAL METAZOAN BIODIVERSITY BETWEEN PREVIOUSLY OILED SHEARED AND INTACT MARSH MARGINS AND BETWEEN MULTIPLE SALINITY ZONES IN THE COASTAL MARSHES OF LOUISIANA A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfilment of the requirements for the degree of Master of Science in The Department of Entomology by Patrick Michael Rayle B.S., Louisiana State University, 2015 May 2021 Acknowledgements This research was made possible through grants from the Gulf of Mexico Research Initiative. I would like to extend my thanks to Dr. Lane Foil, my major professor, for his help in the experimental design and writing of this thesis. I would also like to extend my thanks to my committee members Dr. Claudia Husseneder for her assistance in the bioinformatics methods of this thesis, and Dr. Brant Faircloth for many helpful insights. I would also like to acknowledge many members of the Foil Lab, both past and present: Dr. Mike Becker, Erin Stevens, Darius Davis, Julian Lucero, and Igor Sokolov for their field and logistical support, Ben Aker, for his statistical expertise, and Colleen Walsh, Amy Mitchell, Fallon Ross, and Dakota Mengel for their assistance with lab work. I acknowledge the ecological expertise of Dr. Michael Kaller, who gave important insights on how to handle the intersection of bioinformatics and ecology. Many thanks go to the team behind the World Register of Marine Species (WoRMS Editorial Board 2020, marinespecies.org) for keeping detailed, consistent, and expert-reviewed records of taxonomic strings and other data for marine species online and freely available. I also acknowledge Dr. W. Kelley Thomas, Jeffrey Hall, Joseph Sevigny, Devin Thomas, Krystalynne Morris, and the other team members at the Hubbard Center for Genome Studies at the University of New Hampshire for handling our sequencing and computing needs and for their continued support. Lastly, I would like to thank Michael, Joanne, Christopher and Stephen Rayle for their constant love and support, and Brandi Wozniak for her unending love and patience during my time in graduate school. ii Table of Contents Acknowledgements ..........................................................................................................................ii List of Tables .................................................................................................................................... v List of Figures ................................................................................................................................ viii Abstract .......................................................................................................................................... xii Introduction .................................................................................................................................... 1 Chapter 1. Literature Review .......................................................................................................... 3 1.1. Tidal Marshes .................................................................................................................... 3 1.2. Marsh Ecosystem Services ................................................................................................ 3 1.3. Natural and Anthropogenic Threats to Salt Marshes ....................................................... 4 1.4. Proposed solutions to combat global salt marsh losses .................................................. 8 1.5. Louisiana specific issues ................................................................................................... 9 1.6. Proposed solutions to Louisiana issues ............................................................................ 9 1.7. Meiofauna as a measure of marsh health and recovery................................................ 11 1.8. DNA metabarcoding and associated analyses ................................................................ 11 Chapter 2. A Comparison of Intertidal Metazoan Infauna Biodiversity between Previously Oiled Sheared and Intact Marsh Margins in Bay Jimmy, Louisiana, Using DNA Extraction of Whole Sediments ..................................................................................................................................... 14 2.1. Introduction .................................................................................................................... 14 2.2. Materials and Methods .................................................................................................. 16 2.3. Results ............................................................................................................................. 25 2.4. Discussion ....................................................................................................................... 81 Chapter 3. A Comparison of Intertidal Metazoan Meiofauna Biodiversity between Previously Oiled Sheared and Intact Marsh Margins in Bay Jimmy, Louisiana, Using DNA Extraction of the Organic Portion of Sediments .................................................................................................................... 94 3.1. Introduction .................................................................................................................... 94 3.2. Materials and methods .................................................................................................. 97 iii 3.3. Results ........................................................................................................................... 103 3.4. Discussion ..................................................................................................................... 152 Chapter 4. A Comparison of Intertidal Metazoan Biodiversity among Three Different Salinity Zones and Two Different Bays in the Marshes of Louisiana ................................................................. 164 4.1. Introduction .................................................................................................................. 164 4.2. Materials and Methods ................................................................................................ 166 4.3. Results ........................................................................................................................... 173 4.4. Discussion ..................................................................................................................... 237 Summary and Conclusions .......................................................................................................... 250 Glossary ....................................................................................................................................... 252 Literature Cited ........................................................................................................................... 254 Vita .............................................................................................................................................. 280 iv List of Tables Table 2.1. Mean and standard deviation values for soil chemistry analyses, 1 ......................................... 27 Table 2.2. Mean and standard deviation values for soil chemistry analyses, 2. ........................................ 27 Table 2.3. Mean and standard deviation values for soil chemistry analyses, 3 ......................................... 28 Table 2.4. ANOVA results for Carbon (%) ................................................................................................... 29 Table 2.5. ANOVA results for Nitrogen (%) ................................................................................................. 29 Table 2.6. ANOVA results for Percent Organic Matter ............................................................................... 30 Table 2.7. ANOVA results for C/N ratios .................................................................................................... 30 Table 2.8. Sub-Domain level taxonomy assignments for the full 18S sequence dataset ........................... 32 Table 2.9. OTU diversity profile .................................................................................................................. 40 Table 2.10. Shared and total number
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