University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2018 Microbial Communities and Biogeochemistry in Marine Sediments of the Baltic Sea and the High Arctic, Svalbard Joy Buongiorno University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Buongiorno, Joy, "Microbial Communities and Biogeochemistry in Marine Sediments of the Baltic Sea and the High Arctic, Svalbard. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/5268 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Joy Buongiorno entitled "Microbial Communities and Biogeochemistry in Marine Sediments of the Baltic Sea and the High Arctic, Svalbard." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Karen Lloyd, Major Professor We have read this dissertation and recommend its acceptance: Alison Buchan, Terry Hazen, Jill Mickuki, Andrew Steen Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Microbial Communities and Biogeochemistry in Marine Sediments of the Baltic Sea and the High Arctic, Svalbard A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Joy Buongiorno December 2018 Copyright © 2018 by Joy Buongiorno Altom All rights reserved ii Dedication To my beloved husband Michael Patrick Altom my dogs Barney and Nyla and my cats Muffin, Oby, Oscar, and Phantom iii Acknowledgements My deepest gratitude belongs to my major advisor, Dr. Karen Lloyd, who intentionally cultivated a work culture of patience and encouragement that allowed me to flourish as an independent researcher and find the confidence that this path requires. I am forever indebted to the people who served as both mentors and friends to me along the way: Dr. Linda Kah, Ashley R. Manning-Berg, Sarah Sheffield, Jordan Bird, and Mallory Ladd. I would like to thank my committee for challenging me and believing that I was up to that challenge. Dr. Jill Mikucki, for inspiring me to find a deeper, more impactful purpose while on this path and Dr. Heidi Goodrich-Blair for ensuring that I had the means to achieve those purpose-driven milestones. The Ladies of the Lloyd lab for being sentinels of support and encouragement. My collaborators at The Center for Geomicrobiology at Aarhus University in Denmark, The University of Vienna, and Stony Brook University for insightful discussions. The C-DEBI family for contributing to my personal growth as an academic and for providing invaluable resources that made much of this work possible. The Simons Foundation, Explorer’s Club, Geological Society of America, Society for Sedimentary Geology, Sandra White, and The Graduate School for providing significant or supplemental funding for this research. And finally, my loving husband, Michael Altom, for the daily sacrifices that this long journey required of him, which he always bore with patience and humility. iv Abstract Marine sediments contain more microorganisms than all of the world’s oceans, with current of estimates of 1×1029 microorganisms. Despite marine sediments being replete with microbial cells, the majority of these microorganisms remain uncultured in the laboratory. At present, it is estimated that over 99% of all microorganisms have evaded culture, although truer estimates likely depend upon environment. Factors responsible for the intractability of these microorganisms include very slow doubling times, predicted to be on the orders of years to centuries, as well as special physiological needs of extremophiles. Unsuccessful laboratory growth of these microorganisms requires us to rely on culture-independent tools, including molecular techniques, metagenomics, and bioinformatic tools to glean insight into their ecological structure and function. This dissertation combines molecular and bioinformatic techniques to evaluate the biosphere within deeply buried sediments of the Baltic Sea and shallow sediments in Arctic fjords. Quantification of microbial biomass within marine sediments lays the groundwork for questions related to organic carbon and element cycling. Although essential, reliable and reproducible estimates of microbial biomass within deeply buried sediments has proved challenging. Here we present an interlaboratory comparison of quantification results from International Ocean Discovery Program Exp. 347 sediments that allowed us to define best practices that lead to meaningful quantification estimates. We then transferred these best practices to marine sediments in a Svalbard fjord (Van Keulenfjorden) to understand how glacial proximity influences microbial communities. Through 16S rRNA gene libraries, organic geochemistry, and genome reconstruction, we illustrate that cross-fjord trends in organic matter influence community structure in the sediment. In addition, we argue that biological iron and v sulfur cycling facilitates rapid recycling of electron acceptors crucial for carbon oxidation. We delved deeper into their metabolic pathways with metagenomic sequencing and contig binning. We reconstructed several genomes of the Woeseiaceae clade that can act both as a sink and a source of carbon. Ultimately, our work provides a framework for understanding how glacial proximity influences microbial community composition and metabolic function, which is important and timely with ongoing climate change and a strong threat of severe glacial retreat in this region. vi Table of Contents Chapter 1: Introduction ............................................................................................................... 1 Tools for Estimating Abundance of Subsurface Microorganisms .............................................. 2 Metagenomics and Genome Reconstruction ............................................................................... 4 ‘Omics for Understanding the Roles of Microorganisms in Climate Feedbacks ........................ 5 References ................................................................................................................................... 7 Chapter 2: Inter-laboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Exp. 347) ........................................................................... 14 Abstract ..................................................................................................................................... 15 Introduction ............................................................................................................................... 17 Methods ..................................................................................................................................... 19 Sample collection .................................................................................................................. 19 Total cell counts and CARD-FISH ........................................................................................ 20 DNA extraction and qPCR analyses ...................................................................................... 22 DNA-HCR ............................................................................................................................. 24 Results ....................................................................................................................................... 25 Total cell counts..................................................................................................................... 25 CARD-FISH .......................................................................................................................... 26 qPCR ...................................................................................................................................... 28 DNA-HCR ............................................................................................................................. 31 Discussion ................................................................................................................................. 31 Conclusion ................................................................................................................................. 37 References ................................................................................................................................. 39 Appendix I: Tables and Figures ................................................................................................ 46 Chapter 3: Methanogen genome from Antarctic permafrost reveals cold adaptation and multiple pathways of methane formation ................................................................................. 64 Abstract ..................................................................................................................................... 65 Introduction ..............................................................................................................................