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Interactions with Heterotrophic Bacteria in the Microcystis Phycosphere

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Interactions with Heterotrophic Bacteria in the Microcystis Phycosphere James Madison University JMU Scholarly Commons Masters Theses, 2010-2019 The Graduate School 5-2-2019 The Microcystis microbiome: Interactions with heterotrophic bacteria in the Microcystis phycosphere Alexa Hoke Follow this and additional works at: https://commons.lib.jmu.edu/master201019 Recommended Citation Hoke, Alexa, "The Microcystis microbiome: Interactions with heterotrophic bacteria in the Microcystis phycosphere" (2019). Masters Theses, 2010-2019. 637. https://commons.lib.jmu.edu/master201019/637 This Thesis is brought to you for free and open access by the The Graduate School at JMU Scholarly Commons. It has been accepted for inclusion in Masters Theses, 2010-2019 by an authorized administrator of JMU Scholarly Commons. For more information, please contact [email protected]. The Microcystis microbiome: Interactions with heterotrophic bacteria in the Microcystis phycosphere Alexa Hoke A thesis submitted to the Graduate Faculty of JAMES MADISON UNIVERSITY In Partial Fulfillment of the Requirements for the degree of Master of Science Department of Biology August 2019 FACULTY COMMITTEE: Committee Chair: Dr. Morgan Steffen Committee Members/ Readers: Dr. Louie Wurch Dr. Raymond Enke Table of Contents List of Tables ................................................................................................................................. iv List of Figures ................................................................................................................................. v Abstract .......................................................................................................................................... vi Chapter I. Literature Review ........................................................................................................ 1 1. Introduction ........................................................................................................................... 2 2. Cyanobacterial Harmful Algal Blooms ................................................................................. 2 2.1 Ecological Impact .............................................................................................................. 3 2.2 Economic and Public Health Impact.................................................................................. 4 2.3 Geographic Distribution of Cyanobacterial Harmful Algal Blooms ................................. 5 3. Microcystis ............................................................................................................................ 6 3.1 Genomics of Microcystis ................................................................................................ 7 4. Drivers of Cyanobacterial Harmful Algal Blooms ................................................................ 8 4.1 Nutrients .......................................................................................................................... 8 4.2 Climate Change ............................................................................................................... 9 5. Microbial Interactions in Bloom Communities ................................................................... 11 5.1 Nutrient Exchange in the Phycosphere ......................................................................... 12 6. Works Cited ......................................................................................................................... 14 Chapter II. The heterotrophic bacterial community of a western Lake Erie Microcystis bloom and impacts of co-culture ..................................................................... 19 Abstract ...................................................................................................................................... 20 1. Introduction ......................................................................................................................... 21 2. Methods ............................................................................................................................... 22 2.1 Sample Collection ............................................................................................................ 22 2.2 Culturable Microbiome .................................................................................................... 23 2.3 Bacterial Growth Curves ................................................................................................. 25 2.4 Co-Culture Conditions ..................................................................................................... 26 2.5 Metagenomics .................................................................................................................. 27 3. Results and Discussion ........................................................................................................ 27 3.1 Culturable Microbiome .................................................................................................... 27 3.2 Response to Co-culture .................................................................................................... 37 3.3 Response to Filtrate ......................................................................................................... 44 4. Metagenomics ..................................................................................................................... 52 5. Conclusions ......................................................................................................................... 55 ii 6. Works Cited ......................................................................................................................... 56 Chapter III. Comparative genomics of heterotrophic bacteria isolated from a Lake Erie Microcystis bloom ............................................................................................................ 58 1. Abstract ............................................................................................................................... 59 2. Introduction ......................................................................................................................... 60 3. Methods ............................................................................................................................... 61 3.1 DNA Extraction and Sequencing ..................................................................................... 61 3.2 Genome Assembly and Annotation ................................................................................. 62 4. Results and Discussion ........................................................................................................ 62 4.1 Sequencing Output, Assembly, and Annotation ............................................................ 62 4.2 Nitrogen ......................................................................................................................... 63 4.3 Carbon Utilization/Carbohydrates ................................................................................. 69 4.4 Iron ................................................................................................................................ 70 4.5 Heavy Metal and Antibiotic Resistance ........................................................................ 72 4.6 Secondary Metabolites .................................................................................................. 72 4.7 Quorum Sensing and Signaling ..................................................................................... 73 4.8 Other Genes ................................................................................................................... 73 5. Conclusions ......................................................................................................................... 74 6. Works Cited ......................................................................................................................... 75 7. Chapter IV. Conclusions ................................................................................................... 79 iii List of Tables Chapter II Table 1. Characterization of heterotrophic bacteria chosen to be grown with axenic Microcystis Table 2. Description of co-culture treatments Table 3. Identification of the 55 isolates that were cultured based on 16S sequencing Table 4. Comparison of the Fv/Fm of Microcystis in co-culture at three different growth phases Table 5. Comparison of the Fv/Fm of Microcystis in filtrate at three different growth phases Chapter III Table 1. DNA concentration and quality from sequenced heterotrophic bacteria and the number of raw and corrected reads obtained from sequencing Table 2. Characteristics of genome assemblies Table 3. Number of coding sequences obtained from RAST Table 4. Nitrogen genes called by RAST iv List of Figures Chapter II Figure 1. Phylogenetic tree of organisms in the Exiguobacterium genus Figure 2. Phylogenetic tree of organisms in the Enterobacter genus Figure 3. Phylogenetic tree of organisms in the Deinococcus genus Figure 4. Phylogenetic tree of organisms in the Paenibacillus genus Figure 5. Phylogenetic tree of organisms in the Acidovorax genus Figure 6. Fluorescence of Microcystis grown with different concentrations of bacterial cells Figure 7. Direct cell counts of Microcystis grown with different concentrations of bacterial cells Figure 8. Fv/Fm of Microcystis grown with different concentrations of bacterial cells Figure 9. Fluorescence of Microcystis grown in different bacterial filtrate
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