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Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats

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Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 5-2020 Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats Marley Madsen Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Ecology and Evolutionary Biology Commons Recommended Citation Madsen, Marley, "Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats" (2020). All Graduate Theses and Dissertations. 7750. https://digitalcommons.usu.edu/etd/7750 This Thesis is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. PATTERNS OF MICROBIAL DIVERSITY AND COMMUNITY COMPOSITION IN SLOT CANYONS, ROCK POOLS, AND OTHER EPHEMERAL AND PERENNIAL AQUATIC HABITATS by Marley Madsen A thesis submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE in Ecology Approved: Bonnie Waring, Ph.D. Paul Wolf, Ph.D. Major Professor Committee Member Will Pearse, Ph.D. Richard S. Inouye, Ph.D. Committee Member Vice Provost for Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2020 ii Copyright c Marley Madsen 2020 All Rights Reserved iii Abstract Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats by Marley Madsen, Master of Science Utah State University, 2020 Major Professor: Dr. Bonnie Waring Department: Biology In general, species sorting is the dominant community assembly mechanism for mi- crobes, and this pattern holds true over a diverse range of habitats and spatial scales. However, the relative importance of species sorting and other community assembly mech- anisms, such as dispersal limitation, varies with the habitat being studied. To attempt to understand the conditions that determine dominant community assembly processes, I investigated the diversity and community composition of bacteria in slot canyons and rock pools of the Colorado Plateau, Utah. Though similar to one another, each habitat is actually subject to vastly different environmental conditions and dispersal regimes. The results of my study suggest that species sorting plays the predominant role in struc- turing bacterial communities in both habitats. However, dispersal limitation appears to be more important to slot canyons than to rock pools. I also found that perennial pools within slot canyons have significantly higher alpha diversity than ephemeral open rock pools. In my second study, I used meta-analysis to determine the effect of drying disturbance on microbial diversity in other perennial and ephemeral lentic environments. The results of the meta-analysis support my previous results and indicate that, glob- ally, perennial systems tend to have higher microbial alpha diversity than ephemeral systems. (45 pages) iv Public Abstract Patterns of Microbial Diversity and Community Composition in Slot Canyons, Rock Pools, and Other Ephemeral and Perennial Aquatic Habitats Marley Madsen Microbes are the most diverse life forms on the planet and perform many impor-tant ecological functions. However, despite the abundance, diversity, and ecological importance of microbes they are often overlooked and understudied in many natural systems, including freshwater habitats. This thesis details the first ever investigation of the microbial diversity and community composition within freshwater rock pools and slot canyons of the Colorado Plateau, Utah. The purpose of the study was to determine the relative importance of various microbial community assembly processes. This thesis also includes a meta-analysis of the microbial alpha diversity in other perennial and ephemeral aquatic systems around the globe. The purpose of the meta-analysis was to identify the relationship between microbial alpha diversity and disturbance from drying. Together, these studies complement one another by describing the microbial ecology of a very specific habitat type, rock pools, as well as a diverse group of globally distributed aquatic habitats. (45 pages) v Acknowledgments First, I want to express gratitude to God. It's amazing how much more productive I am after a short prayer. Thank you for guiding me to the right program and helping me finish. Jarom, thank you for being my field crew, my coding tutor, my therapist, my proofreader, my \carrier of things", the best ham sandwich maker, and my absolute favorite human. Thank you also for all your help with Theo. I know there were a lot of sleepless nights, early mornings, and days you were late to work so I could have time to finish my degree. I'm one lucky lady to have you for my husband! Bonnie, Paul, and Will, thank you for being such fantastic advisors. Graduate school was a bit of a shock to the system at first. Thanks for sticking with me. Well...mostly. Being on my committee has the side effect of people getting new jobs thousands of kilometers away from where I live. Bonnie and Will, thanks for having a baby at the same time as me. First of all, she's super cute. Second, it has been tremendously comforting to know that you really \get it" when it comes to all the hurdles of getting things done as a new parent. And Dad, thank you for teaching me to love being outside. It was all the adven- turing we have done together that helped me figure out what I wanted to study. I had a blast turning a regular recreational activity for us into a full blown research project. Marley Madsen vi Contents Page Abstract...................................... iii Public Abstract.................................. iv Acknowledgments................................. v List of Figures................................... vii List of Tables.................................... x 1 Introduction.................................. 1 2 Species Sorting Determines Bacterial Community Composition of Rock Pools and Slot Canyons of the Colorado Plateau, Utah........ 5 2.1 Introduction...................................5 2.2 Methods.....................................7 2.2.1 Experimental Design and Sampling..................7 2.2.2 DNA Extraction and 16s rRNA Gene Sequencing..........8 2.2.3 Analysis of 16s rRNA Gene Sequences................8 2.2.4 Statistical Analysis........................... 10 2.3 Results...................................... 11 2.4 Discussion.................................... 11 2.4.1 Hypothesis 1.............................. 11 2.4.2 Hypotheses 2 and 3.......................... 16 2.4.3 Hypothesis 4.............................. 18 2.5 Conclusion................................... 18 3 A Meta-Analysis of Microbial Alpha Diversity in Perennial and Ephemeral Pool Habitats.................................. 19 3.1 Introduction................................... 19 3.2 Methods..................................... 20 3.2.1 Overall Experimental Design..................... 20 3.2.2 Data Selection............................. 20 3.2.3 Statistical Analysis........................... 21 3.2.4 Results................................. 21 3.3 Discussion.................................... 24 3.4 Conclusion................................... 26 Bibliography.................................... 27 vii List of Figures Figure Page 1.1 Example of a slot canyon rock pool......................2 1.2 Examples of open rock pools..........................2 1.3 Looking into a slot canyon from above. The narrow slit in the center of the photo is the opening to the canyon which is approx. 20m deep. The narrowness of the opening greatly limits the amount of direct sunlight that reaches the rock pools in the canyon bottom. In this particular canyon the average water temperature was 15.9◦C..................3 1.4 A large log jam brought into a slot canyon by a flash flood. Image courtesy of Canyon Collective (Collective 2018).....................3 2.1 Sample Areas - The numbers correspond to (1) Eardley Canyon, (2) Entrajo Canyon, and (3) Fry Canyon. The hatched area is the boundary of the Colorado Plateau. The two photos were taken at the Fry Canyon Area. The top photo is an example of a SCRP. The bottom photo is an example of an ORP. Lake Powell, Utah is visible in the background....9 2.2 NMDS plot of beta diversity - PerMANOVA indicated that bacterial community composition differed significantly by habitat type (F1,90=24.34, 2 2 p<0.001, r =0.179) and sample area (F1,90=6.54, p<0.001, r =0.096), with habitat type explaining more of the variation in community composi- tion than sample area. This can be seen in the NMDS plot (stress=0.076) which shows samples clustering first, by habitat type, and second, by sam- ple area within each habitat cluster. Additionally, ORPs appear to have greater spatial separation than SCRPs. The perMANOVA analyses of environmental parameters showed that bacterial community composition 2 also varied significantly by pH (F1,90=6.67, p<0.001, r =0.049) and max- 2 imum pool volume (F1,90=3.78, p<0.001, r =0.028)............. 12 viii 2.3 Differential Abundance of Phyla - This bar chart shows the top 9 most abundant phyla with all other phyla (60 total) grouped together un- der \Other". ANCOM identified 19 bacterial phyla and 2 archaeal phyla that were differentially abundant by habitat type. Of note is that the phyla Cyanobacteria and
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