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Characterizing the Molecular Mechanisms for the Bacterial Transformation of Recalcitrant Organic Matter in Coastal Salt Marshes

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Characterizing the Molecular Mechanisms for the Bacterial Transformation of Recalcitrant Organic Matter in Coastal Salt Marshes University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2018 CHARACTERIZING THE MOLECULAR MECHANISMS FOR THE BACTERIAL TRANSFORMATION OF RECALCITRANT ORGANIC MATTER IN COASTAL SALT MARSHES Lauren Nicole Quigley University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Quigley, Lauren Nicole, "CHARACTERIZING THE MOLECULAR MECHANISMS FOR THE BACTERIAL TRANSFORMATION OF RECALCITRANT ORGANIC MATTER IN COASTAL SALT MARSHES. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/5051 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 Lauren Nicole Quigley entitled "CHARACTERIZING THE MOLECULAR MECHANISMS FOR THE BACTERIAL TRANSFORMATION OF RECALCITRANT ORGANIC MATTER IN COASTAL SALT MARSHES." 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. Alison Buchan, Major Professor We have read this dissertation and recommend its acceptance: Sarah L. Lebeis, Andrew D. Steen, Erik R. Zinser 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.) CHARACTERIZING THE MOLECULAR MECHANISMS FOR THE BACTERIAL TRANSFORMATION OF RECALCITRANT ORGANIC MATTER IN COASTAL SALT MARSHES A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Lauren Nicole Mach Quigley August 2018 Copyright © 2018 by Lauren Nicole Mach Quigley All rights reserved. ii ACKNOWLEDGEMENTS I would like to thank my friends and family who have supported me throughout my life and in particular during the past five and a half years of graduate school. I’d especially like to thank my parents Tim and Kim who have supported me both emotionally and financially for the past 28 years. They have been in my corner every step of the way even if they don’t totally understand exactly what it is I’ve been doing for the past five years. I’d also like to thank my sisters Marla and Noelle who have been very supportive and are my biggest cheerleaders. Additionally, I have made some of the most incredible friends in graduate school who have been so helpful every step of the way as they went through the same trials and tribulations of graduate school. They have gone above and beyond to be supportive even driving the 500 miles to South Bend, IN (in December no less) to celebrate my wedding. I would be remiss if I did not thank my wonderful husband, Kevin, who has gracefully and calmly dealt with me coming home frustrated from long days in the lab (looking at you, RNA extractions and respirometer). His impulse is always to identify the problem and troubleshoot to find a solution as quickly as possible even if it is something he’s unfamiliar with. In addition to being a calming influence Kevin has done everything imaginable to help me through graduate school including but not limited to making 95% of our meals, only being slightly repulsed when I would bring plates home to count while watching TV, and formatting the table of contents in this document. Without his love and support I would not be where I am today. I would also like to thank Drew Steen for making me use R. When I started my rotation project in Alison’s lab Drew insisted that all of the data be visualized in R. At the time I was convinced that I was not capable and never would be of programming after struggling immensely in a biostatistics course my senior year at Notre Dame, a large component of which was running analyses in R. Drew worked with me, was very patient, and refused to iii accept for one second that I was not capable. Thanks in large part to Drew’s efforts every figure in this dissertation was generated in R. Lastly, I need to thank my advisor Alison Buchan who had been incredibly supportive over the past five years. Alison’s positive attitude and encouragement have been instrumental in my success in graduate school. Additionally, Alison has been exceedingly patient with me has I learned what it means to be scientist, and always gave me the benefit of the doubt when lab work was not going to plan. This gave me the space and independence to develop into the best scientist I could be for which I am exceedingly thankful. iv ABSTRACT Terrestrially-derived dissolved organic matter (t-DOM) is one of the largest reservoirs of reduced carbon on the planet with approximately 2.5x1014 g-C entering the global coastal oceans annually. This carbon pool is largely derived from the products of vascular plant degradation, such as humic and fulvic acids, which are recalcitrant due to their enrichment in aromatic moieties. As t-DOM travels through riverine systems to the coastal oceans it becomes increasingly refractory as riverine microbial communities preferentially oxidize the most bioavailable components. However, most chemical tracers diagnostic of t-DOM (e.g. lignin-derived phenols) are removed before reaching the open oceans, suggesting that this material is transformed in the coastal margins. Microbial transformations are expected to contribute to the disappearance of t-DOM in these systems, but the mediating factors and mechanisms are presently unknown. The work described in this dissertation aims to understand how coastal microbial communities degrade t-DOM. Within, I show that a concept well studied in soil systems, the priming effect (PE), may help explain the disappearance of t-DOM in these systems. PE occurs when the presence of a labile carbon source and/or nutrients stimulates the degradation of a recalcitrant carbon source. I focused my studies on coastal margins of the Southeastern United States. These systems represent a transition zone between riverine systems, carrying recalcitrant t-DOM, and marsh systems, which are sites of new production and contain small yet labile carbon pools. As such, they are ideal study sites in which to investigate whether coastal microbial communities can indeed be primed. A first study employed a mesocosm experiment to demonstrate that PE could be invoked in a natural coastal microbial community. A second study demonstrates that concentration and type of labile carbon influence the magnitude, timing and sign of PE in a species-specific manner. Finally, metatranscriptome-based field studies provide evidence that coastal marsh microbial communities are actively catabolizing aromatics and carbohydrates common to the systems. Collectively, these studies enhance our understanding of the mechanisms through which estuarine communities transform t-DOM and provide insights and future directions for continued study in the field. v TABLE OF CONTENTS CHAPTER ONE - INTRODUCTION ............................................................................. 1 I. TERRESTRIALLY-DERIVED, DISSOLVED ORGANIC MATTER ................ 2 t-DOM in global carbon (C) cycling ........................................................................ 2 Composition of t-DOM ........................................................................................... 3 Ecological importance of t-DOM ............................................................................. 5 II. PRIMING EFFECT ............................................................................................. 6 Mechanisms of PE ................................................................................................... 7 Factors influencing PE............................................................................................. 9 Aquatic PE ............................................................................................................ 10 III. COASTAL SALT MARSHES OF THE SOUTHEASTERN UNITED STATES.................................................................................................................... 11 Biogeochemical characteristics .............................................................................. 12 Microbial ecology of salt marshes ......................................................................... 13 The Roseobacter clade ........................................................................................... 15 IV. OBJECTIVES ............................................................................................... 16 V. REFERENCES .................................................................................................. 18 VI. APPENDIX: FIGURES ................................................................................. 31 CHAPTER TWO - EVIDENCE FOR THE PRIMING EFFECT IN A PLANKTONIC ESTUARINE MICROBIAL COMMUNITY ................................................................ 32 I. ABSTRACT .......................................................................................................... 34 II. INTRODUCTION ................................................................................................ 35 III. MATERIALS AND METHODS ......................................................................... 36 Generation of 14C-labeled
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