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Geothermal Soil Ecology in Yellowstone National Park

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Geothermal Soil Ecology in Yellowstone National Park GEOTHERMAL SOIL ECOLOGY IN YELLOWSTONE NATIONAL PARK by James Francis Meadow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Land Resources and Environmental Sciences MONTANA STATE UNIVERSITY Bozeman, Montana April 2012 ©COPYRIGHT by James Francis Meadow 2012 All Rights Reserved ii APPROVAL of a dissertation submitted by James Francis Meadow This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to The Graduate School. Dr. Catherine A. Zabinski Approved for the Department of Land Resources and Environmental Sciences Dr. Tracy M. Sterling Approved for the The Graduate School Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with \fair use" as prescribed in the U. S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted \the exclusive right to reproduce and distribute my dissertation in and from microform along with the non-exclusive right to reproduce and distribute my abstract in any format in whole or in part." James Francis Meadow April 2012 iv ACKNOWLEDGEMENTS Funding was provided by a GK-12 Graduate Fellowship from the NSF and the Big Sky Institute, a Boyd Evison Graduate Fellowship from the Grand Teton Association, a dissertation fellowship from the Institute on Ecosystems, and also from a USDA NRICG to Dr. Zabinski. I would like to thank Rosie Wallander, Galena Ackerman, John Dore, Christian Klatt, Dana Skorupa, Scott Klingenpeel, Jake Beam and Mark Kozubal for endless help with sample processing, analysis, supplies, and dumb ques- tions. Thanks to Dr. Ylva Lekberg for helping me to step into the world I am now in, and for introducing me to molecular biology. Thanks to the incredibly patient YNP Permitting Staff. Thanks to my graduate committee, Dr. Tim McDermott, Dr. David Roberts, Dr. Cathy Cripps, Dr. Tom Deluca, Dr. Billie Kerans and Dr. Rick Engel for support throughout the process. I especially have my major advisor, Dr. Cathy Zabinski, to thank for helping me maintain balance and perspective during my five years at MSU, and for being a terrific example of quiet stability in academia. Thanks to my lab mates for well-timed discussions on everything but science, and to my great friend, Adam Sigler, who will often drop everything when we both need to have good time. Most of all, thanks to my amazing wife, Kelly Meadow, for working with me through all of the challenges of graduate school and for her constant support. v TABLE OF CONTENTS 1. INTRODUCTION ............................................................... 1 Geothermal Soils ............................................................. 2 Arbuscular Mycorrhizal Fungi .............................................. 5 Biological Soil Crusts ........................................................ 6 High-Throughput DNA Sequencing of Soil Microbial Communities...... 8 Overview of Dissertation .................................................... 12 2. LINKING SYMBIONT COMMUNITY STRUCTURES IN A MODEL ARBUSCULAR MYCORRHIZAL SYSTEM .............................. 15 Contribution of Author and Co-Author ........................................ 15 Manuscript Information Page ................................................... 16 Summary.......................................................................... 18 Introduction ...................................................................... 19 Materials and Methods .......................................................... 24 Plant and Soil Collection .................................................... 24 DNA Extraction, PCR ...................................................... 25 Phylogeny .................................................................... 27 Statistical Analysis........................................................... 29 Results ............................................................................ 30 Soil Analysis.................................................................. 30 Molecular Identification and Phylogeny .................................... 31 Diversity and Community Composition .................................... 39 Cluster and Discriminant Analysis ......................................... 42 Discussion......................................................................... 44 Acknowledgments ................................................................ 49 3. SPATIAL HETEROGENEITY OF EUKARYOTIC MICROBIAL COM- MUNITIES IN AN UNSTUDIED GEOTHERMAL DIATOMA- CEOUS BIOLOGICAL SOIL CRUST: YELLOWSTONE NA- TIONAL PARK, WY, USA ................................................. 50 Abstract........................................................................... 50 Introduction ...................................................................... 51 Experimental Procedures ........................................................ 57 Sample Collection and DNA Extraction. ................................... 57 Bar-coded Pyrosequencing................................................... 59 Sequence Processing. ........................................................ 59 Statistical Analysis. .......................................................... 60 Results ............................................................................ 62 vi TABLE OF CONTENTS (cont.) Sequence Processing ......................................................... 62 Sample Dissimilarity ......................................................... 64 Subsample Clustering........................................................ 65 Eukaryotic Combined Samples .............................................. 68 Diatoms....................................................................... 71 Spatial Heterogeneity ........................................................ 73 Discussion......................................................................... 74 4. PROKARYOTIC COMMUNITIES DIFFER ALONG A GEOTHER- MAL SOIL PHOTIC GRADIENT.......................................... 81 Contribution of Author and Co-Author ........................................ 81 Manuscript Information Page ................................................... 82 Abstract........................................................................... 84 Introduction ...................................................................... 85 Methods........................................................................... 86 Site Description and Sample Collection .................................... 86 DNA Extraction ............................................................. 89 Bar-coded Pyrosequencing................................................... 89 Sequence Processing. ........................................................ 90 Phylogeny and Statistical Analysis ......................................... 91 Results ............................................................................ 92 Sequence Processing ......................................................... 92 Ordination and Discriminant Analysis ..................................... 93 Phylum-Level Comparisons ................................................. 95 Discussion......................................................................... 101 Acknowledgements ............................................................... 104 5. CONCLUSIONS.................................................................. 105 LITERATURE CITED .............................................................. 112 APPENDICES ........................................................................ 129 APPENDIX A: Sample Total Standardization Equations..................... 130 APPENDIX B: Influence of Rarefaction on β-Diversity....................... 132 APPENDIX C: Combined 18S and 16S Ordination ........................... 140 vii LIST OF TABLES Table Page 2.1. Mean Soil Parameter Values ............................................... 34 2.2. Mean Soil Parameter Values (cont.)....................................... 35 2.3. Operational Taxonomic Unit Metadata ................................... 37 2.4. Operational Taxonomic Unit Metadata (cont.)........................... 38 3.1. Chemical characterization of geothermal water........................... 63 3.2. Chemical characterization of geothermal water (cont.) .................. 63 3.3. Results from Analysis of Similarities (ANOSIM)......................... 71 3.4. BLAST Identification of Diatoms ......................................... 74 3.5. Results from quadratic model ............................................. 75 4.1. FSO model results .......................................................... 96 4.2. Permutational MANOVA results .......................................... 98 4.3. Multiple comparisons of three ecologically relevant phyla ............... 100 B.1. Rarefaction comparisons for 16S data ..................................... 135 C.1. Normalization of combined datasets....................................... 142 C.2.
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