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Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon

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Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon Western Washington University Western CEDAR WWU Graduate School Collection WWU Graduate and Undergraduate Scholarship Summer 2020 Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon Amanda Stromecki [email protected] Follow this and additional works at: https://cedar.wwu.edu/wwuet Part of the Biology Commons Recommended Citation Stromecki, Amanda, "Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon" (2020). WWU Graduate School Collection. 969. https://cedar.wwu.edu/wwuet/969 This Masters Thesis is brought to you for free and open access by the WWU Graduate and Undergraduate Scholarship at Western CEDAR. It has been accepted for inclusion in WWU Graduate School Collection by an authorized administrator of Western CEDAR. For more information, please contact [email protected]. Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon By Amanda Stromecki Accepted in Partial Completion of the Requirements for the Degree Master of Science ADVISORY COMMITTEE Dr. Craig Moyer, Chair Dr. Shawn Arellano Dr. Dietmar Schwarz GRADUATE SCHOOL David L. Patrick, Dean Master’s Thesis In presenting this thesis in partial fulfillment of the requirements for a master’s degree at Western Washington University, I grant to Western Washington University the non- exclusive royalty-free right to archive, reproduce, distribute, and display the thesis in any and all forms, including electronic format, via any digital library mechanisms maintained by WWU. I represent and warrant this is my original work, and does not infringe or violate any rights of others. I warrant that I have obtained written permissions from the owner of any third party copyrighted material included in these files. I acknowledge that I retain ownership rights to the copyright of this work, including but not limited to the right to use all or part of this work in future works, such as articles or books. Library users are granted permission for individual, research and non-commercial reproduction of this work for educational purposes only. Any further digital posting of this document requires specific permission from the author. Any copying or publication of this thesis for commercial purposes, or for financial gain, is not allowed without my written permission. Amanda Stromecki August 1, 2020 Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake, Oregon A Thesis Presented to The Faculty of Western Washington University In Partial Fulfillment Of the Requirements for the Degree Master of Science by Amanda Stromecki August 2020 Abstract Crater Lake, Oregon is an oligotrophic freshwater caldera lake fed by thermally and chemically- enriched hydrothermal springs. These vents distinguish Crater Lake from other freshwater systems and provide a unique ecosystem for study. This study examines the microbial community structure of hydrothermal mat communities found in the bottom of Crater Lake. Small subunit rRNA gene amplicon sequencing from eight microbial mats was used to assess community structure. These findings revealed a relatively homogeneous, yet diverse bacterial community. High alpha diversity and low beta diversity indicates that these communities that are likely fueled by homogeneous and consistent hydrothermal fluids. An examination of autotrophic taxa abundance revealed the potential importance of reduced iron and sulfur inputs to the primary productivity of these mats. Chemoautotrophic potential within the mats was dominated by iron oxidation from Gallionella and Mariprofundus and by sulfur oxidation from Sulfuricurvum and Thiobacillus with an additional contribution of nitrite oxidation from Nitrospira. These data link the importance of the detected autotrophic metabolisms driven by fluids derived from benthic hydrothermal springs to Crater Lake’s entire lentic ecosystem. iv Acknowledgments I am very grateful for those who have contributed to and supported my graduate education during the past three years. First, I would like to thank my advisor, Dr. Craig Moyer, for the opportunity to conduct research in his lab and for sharing his insight, ideas, and positive attitude. I would like to extend thanks to my graduate committee, Dr. Shawn Arellano and Dr. Dietmar Schwarz, for their contributions and counsel. I would also like to thank Dr. Marion Brodhagen and Dr. Adam Moles for their support and mentorship in both teaching and microbiology research. Dr. Benjamin Miner and Dr. Merrill Peterson have also been incredibly helpful throughout my graduate career at Western, and I am very grateful to them. I would like to express my gratitude to Kendra Bradford and Joe Somera who I worked closely with for several years. I am very thankful for my funding, provided by WWU’s Office of Research and Sponsored Programs, biology department, and the Fraser Family Endowment. It has been a privilege to be a part of the biology department, and I am extremely grateful to all the faculty and staff. I could not have completed my thesis without the friendship and support of my graduate cohort: Nolan Exe, Britta Fast, Holly Flann, Jake Lawlor, Katie Mills-Orcutt, Caitlin O’Brien, Samantha Ness Ernest, and Weston Staubus. I am also extremely grateful to my fellow Moyer lab members: Lindsey Benedict, Jaykish Patel, Lilja Strang, and Christina Turner, among others, who have shared their expertise and entertainment. I would lastly like to thank my friends and family for believing in me and keeping me motivated: you know who you are and I will always be grateful for you. A final thanks to Western Washington University and all of the privileges and opportunities I have had to be able to grow myself in this meaningful way. v Table of Contents Abstract .............................................................................................................................. iv Acknowledgements ..............................................................................................................v List of Tables .................................................................................................................... vii List of Figures ................................................................................................................... vii Introduction ..........................................................................................................................1 Materials and Methods .........................................................................................................5 Results ..................................................................................................................................9 Discussion ..........................................................................................................................13 Tables and Figures .............................................................................................................21 References ..........................................................................................................................30 Supplementary Materials ...................................................................................................34 vi List of Tables Table 1. Description of sample locations. Data from Collier et al., 1991. Table 2. Geochemical profiles of mats and pool fluids. Data from Collier et al., 1991. Table 3. Zetaproteobacteria phylotype and relative abundance for all samples representing the total Crater Lake microbial community. All Zetaproteobacteria sequences used represent greater than 10 reads per the total Crater Lake community. Zetaproteobacteria phylotype determined by ZetaHunter. Table 4. Sequencing information and diversity metrics. Supplementary Table 1. Taxonomy and metabolic potential for abundant OTUs representing > 1% total reads per sample in at least one sample. Supplementary Table 2. Taxonomy and metabolic potential for abundant OTUs representing > 2% total reads per sample in at least one sample. Supplementary Table 3. Diversity metrics of Lō‘ihi Seamount and Mariana Arc and back-arc. Adapted from Duchinski et al., 2019. vii List of Figures Figure 1. Shaded relief of surrounds and bathymetric map of the floor of Crater Lake, Oregon. Surrounding terrain from USGS 10 m digital elevation model (DEM). DEM illuminated from 225° azimuth, 45° elevation. Colored region is the lake floor (±1 m resolution) whereas the gray region is the surrounding land. The distance across the width of the lake is approximately 9 km (5.6 miles). The reds and yellows show the shallower depths of the lake, whereas the greens and blues show the deeper depths. Adapted from Bacon et al., 2002. Figure 2. Representative photos of mat collection sites: (A) “Brain mat” bacterial growth west of Llao’s Bath within the Llao’s Bath/Brain Mat complex. Field of view is approximately three meters across; (B) Elongated bacterial mat in the Palisades Point area; (C) A rill within the Palisades Point area. This channel or rill flow downhill from its origin under the boulder (upper part of the photo). Images courtesy of Collier et al., 1991. Figure 3. Community structure of eight benthic microbial mats from hydrothermal springs in Crater Lake, Oregon, at various taxonomic levels: (A) Community structure of abundant taxa representing > 1% total reads/sample in at least one sample at the phylum level. Phyla < 1% included as separate taxon; (B) Community structure of abundant taxa representing > 2% total reads/sample in
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