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Investigation of Microbial Interactions and Ecosystem

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Investigation of Microbial Interactions and Ecosystem INVESTIGATION OF MICROBIAL INTERACTIONS AND ECOSYSTEM DYNAMICS IN A LOW O2 CYANOBACTERIAL MAT by Alexander A. Voorhies A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Earth and Environmental Sciences) in The University of Michigan 2014 Doctoral Committee: Assistant Professor Gregory J. Dick, Chair Associate Professor Matthew R. Chapman Assistant Professor Vincent J. Denef Professor Daniel C. Fisher Associate Professor Nathan D. Sheldon © Alexander A. Voorhies 2014 DEDICATION To my wife Hannah ii ACKNOWLEDGEMENTS Funding for the research presented here was provided by the National Science Foundation, the University of Michigan CCMB Pilot Grant, and a Scott Turner research award from the University of Michigan Earth and Environmental Sciences Department. I am grateful for the opportunities to explore my scientific interests this funding has made possible. I would like to acknowledge my co-authors and collaborators, who offered advice, guidance and immeasurable assistance throughout this process. Gregory J. Dick, Bopi Biddanda, Scott T. Kendall, Sunit Jain, Daniel N. Marcus, Stephen C. Nold and Nathan D. Sheldon are co- authors on CHAPTER II, which was published in Geobiology in 2012; Gregory J. Dick was a co-author on CHAPTER III, which is in preparation for publication; and Gregory J. Dick, Sarah D. Eisenlord, Daniel N. Marcus, Melissa B. Duhaime, Bopaiah A. Biddanda and James D Cavalcoli are co-authors on Chapter IV, which is in preparation for publication. I thank my committee members: Matt Chapman, Nathan Sheldon, Vincent Denef and Dan Fisher. Their input and guidance throughout my graduate studies has kept me on track and made significant enhancements to this dissertation. Specifically I would like to thank my advisor and chair, Greg Dick. I first met Greg working on tangential projects at UC Berkeley, and came to the University of Michigan specifically to work with him. He has given me enough support and guidance to succeed in my graduate studies, but also enough room to grow as a scientist and follow my own scientific interests. I will be forever grateful for his understanding, patience and mentorship. iii I would like to thank the National Oceanic and Atmospheric Administration’s Thunder Bay National Marine Sanctuary for logistical and sampling assistance. Specifically I wish to thank Jeff Grey, Russ Green, Wayne Lusardi, Joe Hoyt and Tane Casserly, and the many crews of the R/V Storm for their sampling assistance, observations of the Middle Island Sinkhole and the great deal of care and effort they put into assisting us. This research would not have been possible without their assistance. Thank you to my lab mates and fellow graduate students who were always available to help sort out issues that arose or commiserate upon the life of a graduate student. Specifically I would like to thank Sunit Jain for extensive assistance with script writing and DNA assembly theory. Thank you to Melissa Duhaime for help with viral identification and excellent advice. Thank you to Jim Cavalcoli for de novo genome assembly assistance, and Ryan Lesniewski for metagenome assembly assistance. Thank you to Sarah Eisenlord for statistical analysis, editing, and company on long runs that helped to keep me sane through this process. I wish to thank my family and friends who have supported me financially and emotionally during my years at UM. Thank you to my parents Dave and Laurie for the nudge to do something different with my life that came at just the right time, and their support throughout this process. Thank you to my Mother-Outlaw Jean for the bags of coffee, chocolate and editing assistance on multiple occasions. Finally, thank you to my Wife Hannah, for following me into the cold Midwest, and her tireless support and love. iv Table of Contents DEDICATION............................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................ iii LIST OF FIGURES ..................................................................................................................... ix LIST OF TABLES ....................................................................................................................... xi ABSTRACT ................................................................................................................................. xii CHAPTER I Introduction ............................................................................................................ 1 1.1 Microbial mediation of geochemical cycles ......................................................................... 1 1.2 Cyanobacteria and the oxygenation of the Earth .................................................................. 2 1.3 The Middle Island Sinkhole .................................................................................................. 4 1.4 Microbial genomics and the age of the genome ................................................................... 5 1.5 Organization of the dissertation ............................................................................................ 8 1.6 References ............................................................................................................................. 9 CHAPTER II Cyanobacterial life at low O2: Community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat ... 14 2.1 Introduction ......................................................................................................................... 15 2.2 Methods............................................................................................................................... 20 Field work and sampling ..................................................................................................................... 20 Microscopic studies of mat structure and composition ....................................................................... 21 Autotrophic process measurements by 14C bicarbonate uptake .......................................................... 23 Stable Isotope Analyses ...................................................................................................................... 24 X-ray Diffraction (XRD) .................................................................................................................... 25 DNA extraction, Genome Sequencing Annotation, and Phylogenetic Analyses ................................ 25 v 2.3 Results and Discussion ....................................................................................................... 26 Mat structure and microscopy ............................................................................................................. 26 Carbon metabolism and respiration .................................................................................................... 29 Identification of minerals associated with mats and underlying sediments ........................................ 33 Metagenomic sequencing, assembly, and binning .............................................................................. 37 Putative genes for anoxygenic photosynthesis .................................................................................... 38 Evidence for a complete genome of Phormidium sp. MIS-Ph1 .......................................................... 42 Carbon acquisition and metabolism .................................................................................................... 44 Oxygen sensing, regulation, and respiratory metabolism ................................................................... 45 Hopanoid biosynthesis ........................................................................................................................ 46 Genomic insights into interactions of MIS-Ph1 with the mat community .......................................... 46 Environmental sensing, regulation, and nutrient acquisition .............................................................. 47 2.4 Conclusions ......................................................................................................................... 48 2.5 Appendix A ......................................................................................................................... 50 CHAPTER II Supplemental Material ................................................................................................. 50 2.6 References ........................................................................................................................... 57 CHAPTER III Metabolic function and microbial mediation of geochemical cycling revealed by community genomic analysis and gene expression of a low-O2 cyanobacterial mat .......................................................................................................... 65 3.1 Introduction ......................................................................................................................... 66 3.2 Materials and Methods ........................................................................................................ 69 Sample collection and sequencing ...................................................................................................... 69 Assembly and genomic analysis ........................................................................................................
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