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Open Thesis 17May2011.Pdf The Pennsylvania State University The Graduate School Department of Geosciences BIOGEOCHEMISTRY OF ISOPRENOID PRODUCTION AND ANAEROBIC HYDROCARBON BIODEGRADATION A Dissertation in Geosciences by Katherine S. Dawson © 2011 Katherine S. Dawson Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2011 The dissertation of Katherine S. Dawson was reviewed and approved* by the following: Jennifer L. Macalady Assistant Professor of Geosciences Dissertation Co-Advisor Co-Chair of Committee Katherine H. Freeman Professor of Geosciences Dissertation Co-Advisor Co-Chair of Committee Christopher H. House Associate Professor of Geosciences John M. Regan Associate Professor of Environmental Engineering Chris J. Marone Professor of Geosciences Associate Head for Graduate Programs and Research in Geosciences *Signatures are on file in the Graduate School iii ABSTRACT This dissertation is an exploration of microbial isoprenoid production and destruction by anaerobic hydrocarbon biodegradation. Isoprenoids are methyl-branched hydrocarbons, and include biomarkers from all three domains of life such as archaeal lipids, hopanoids, and sterols. Isoprenoid production was examined through variation in the molecular structure of archaeal lipids across a hypersaline gradient (Chapter 5). This study identified unsaturated analogues of archaeol in four halophilic archaeal strains and revealed an increase in the percentage of unsaturated lipids with increasing salinity. Anaerobic isoprenoid biodegradation was examined through the enrichment of bacteria under anaerobic conditions utilizing pristane as a carbon source (Chapter 2). Further analysis of anaerobic degradation utilized 13C-labelled phytane as a stable isotope tracer (Chapter 3). In both cases, a microbial community dominated by denitrifying Beta- and Gammaproteobacteria was responsible for the degradation of pristane and phytane. Environmental anaerobic hydrocarbon degradation was examined through the analysis of in situ microbial communities associated with the transformation of coal to methane (Chapter 4). Through FISH and 16S rRNA tag pyrosequencing a coal transformation pathway ending in acetoclastic/methylotrophic methanogenesis was identified in the Cook Inlet Basin, Alaska. These studies demonstrate the microbial impact on hydrocarbon production and alteration, which influences the transition over geologic time scales from biomolecules to biomarkers in the sedimentary record. iv TABLE OF CONTENTS LIST OF FIGURES vii LIST OF TABLES x ACKNOWLEDGEMENTS xi CHAPTER 1: INTRODUCTION 1.1 Isoprenoids 1 1.2 Microbial Hydrocarbon Degradation 2 1.3 Archaeal Membrane Lipids 5 1.4 Biogenic Coal Bed Methane 6 1.5 Organization Of The Thesis 8 1.6 Anticipated Publications From This Work 8 1.7 Figures 10 1.8 References 19 CHAPTER 2: ANAEROBIC BIODEGRADATION OF ISOPRENOID BIOMARKERS BY A DENITRIFYING MICROCOSM 2.1 Abstract 26 2.2 Introduction 26 2.3 Materials and Methods 28 2.4 Results 32 2.5 Discussion 36 v 2.6 Acknowledgements 39 2.7 Figures and Tables 40 2.8 References 47 CHAPTER 3: STABLE ISOTOPE TRACING OF ANAEROBIC ISOPRENOID BIODEGRADATION WITH 13C LABELLED PHYTANE 3.1 Abstract 52 3.2 Introduction 52 3.3 Experimental Procedures 54 3.4 Results 59 3.5 Discussion 62 3.6 Conclusions 65 3.7 Acknowledgements 66 3.8 Figures and Tables 67 3.9 References 78 CHAPTER 4: QUANTITATIVE FISH ANALYSIS OF MICROBIAL CONSORTIA FROM A BIOGENIC GAS FIELD IN THE COOK INLET BASIN, ALASKA 4.1 Abstract 83 4.2 Introduction 83 4.3 Materials and Methods 85 4.4 Results 88 vi 4.5 Discussion 92 4.6 Conclusions 94 4.7 Figures and Table 96 4.8 References 103 CHAPTER 5: MOLECULAR CHARACTERIZATION OF ARCHAEAL LIPIDS ACROSS A HYPERSALINE GRADIENT 5.1 Abstract 107 5.2 Introduction 107 5.3 Methods 109 5.4 Results 111 5.5 Discussion 113 5.6 Conclusions 115 5.7 Acknowledgements 116 5.8 Figures and Tables 117 5.9 References 123 CHAPTER 6: CONCULSIONS AND FUTURE DIRECTIONS 6.1 Anaerobic isoprenoid degradation 128 6.2 Coal bed methane biogeochemistry 129 6.3 Halophilic archaeal lipids 130 6.4 References 131 vii LIST OF FIGURES Figure 1-1: Examples of isoprenoid biopolymers that may serve as biomarkers 10 Figure 1-2: Proposed mechanisms for anaerobic hydrocarbon degradation 11 Figure 1-3: Membrane glycerolipid structures in the three domains of life 12 Figure 1-4: Structures of archaeal glycerol diphytanyl glycerol tetraethers (GDGT’s) and diphytanyl glycerol diethers (DGD’s) 13 Figure 1-5: Isotopic values of methane showing the differences between thermogenic and biogenic methane generated from different pathways 14 Figure 1-6: Phylogenetic tree of 16s rDNA sequences of Firmicutes, Bacteroidetes, Planctomycetes, Spirochaetes, and other bacterial lineages associated with coal bed methane 15 Figure 1-7: Phylogenetic tree of 16s rDNA sequences of Betaproteobacteria and Gammaproteobacteria associated with CBM 16 Figure 1-8: Phylogenetic tree of 16s rDNA sequences of Alphaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria associated with CBM 17 Figure 1-9: Phylogenetic tree of 16s rDNA sequences of methanogenic archaea associated with CBM 18 Figure 2-1: FISH micrographs of cells in the denitrifying, pristane-degrading enrichment culture 40 Figure 2-2: Neighbor-joining phylogenetic tree showing betaproteobacteria from pristane degrading enrichments 41 Figure 2-3: Neighbor-joining phylogenetic tree showing gammaproteobacteria from pristane degrading enrichments 42 viii Figure 2-4: Fraction of bacterial cells hybridizing to specific oligonucleotide probes in pristane degrading cultures 43 Figure 2-5: Anaerobic consumption of nitrate, and the production of nitrite and bicarbonate in a denitrifying, pristane degrading enrichment culture 44 Figure 2-6: Anaerobic consumption of nitrate in denitrifying enrichments with pristane, DGD and GDGT core lipids 45 Figure 3-1: Preparation scheme for 13C-labeled phytane 67 Figure 3-2: Gas chromatogram and mass spectra of saponified 13C-labeled diphytanyl glycerol diether from Haloferax sulfurifontis SD1 68 Figure 3-3: Gas chromatograms and mass spectra of 13C-phytane before and after SPE purification 69 Figure 3-4: Loss of nitrate and production of nitrite and bicarbonate in incubation grown with 13C-labeled phytane as a carbon source 70 13 13 Figure 3-5: Values of δ C for the CO2 produced during incubations on C-labeled phytane, unlabeled phytane and with no added carbon 71 13 13 Figure 3-6: Keeling plot of C for CO2 produced during incubation on C-labeled - phytane versus 1/[HCO3 ] 72 Figure 3-7: Percentage of cells hybridizing to specific oligonucleotide probes in phytane degrading incubations 73 Figure 3-8: FISH micrographs of cells in the denitrifying, phytane-degrading enrichment culture 74 Figure 3-9: Neighbor-joining phylogenetic tree showing gammaproteobacteria clones in 13C-phytane and pristane degrading enrichments 75 ix Figure 3-9: Neighbor-joining phylogenetic tree showing betaproteobacteria clones in 13C- labeled phytane and pristane degrading enrichments 76 Figure 4-1: FISH micrographs depicting major bacterial and archaeal lineages observed in production water samples from the Cook Inlet Basin 97 Figure 4-2: Microbial communities of the Cook Inlet gas field expressed as a percentage of DAPI stained cells 98 Figure 4-3: Comparison of the microbial communities of the Cook Inlet gas field determined by FISH and 16S rRNA tag pyrosequencing 99 Figure 4-4: Carbon and hydrogen isotopic classification of methane of the Cook Inlet sample sites 100 Figure 4-5: PCA of Cook Inlet basin microbial population data with geochemical data projected onto the ordination using the ‘envfit’ function 101 Figure 4-6: PCA of microbial population data from five sedimentary basins with geochemical data projected onto the ordination using the ‘envfit’ function 102 Figure 5-1: Structures of archaeal diphytanyl glycerol diether (DGD) with various chain lengths, cyclization, unsaturation and hydroxyl substitutions 118 Figure 5-2: Total ion chromatograms of saturated C20-20 and C25-20 DGD 119 Figure 5-3: Partial GC-MS chromatograms of polar lipid extracts of halophilic archaea showing C20-20 and C25-20 DGDs 120 Figure 5-4: Plot of total unsaturated archaeal C20-20 and C25-20 DGD lipids for four halophilic archaeal strains 121 Figure 5-5: Average fraction of unsaturated DGDs versus optimal % NaCl (w/v) for four halophilic archaeal strains 122 x LIST OF TABLES Table 2-1: Ratios of isoprenoid peak areas in GC-MS chromatograms 46 Table 2-2: Oligonucleotide probes used in the study of denitrifying, pristane degrading enrichments 46 Table 3-1: Oligonucleotide probes used in the study of denitrifying, phytane degrading incubations 77 Table 4-1: Oligonucleotide probes used in the study of coal bed methane production water 96 Table 5-1: Presence of absence of C20-20 and C25-20 DGDs in halophilic archaea from various genera 117 xi ACKNOWLEDGEMENTS First I would like to thank my advisors Jenn Macalady and Kate Freeman. As mentors your support has made this possible. Thank you both for turning a chemist into a geomicrobiologist and organic geochemist. Chris House, you have been generous with your time and guidance, which has helped me to develop the ideas behind these projects. Thanks also to Jay Regan whose advice has helped to improve this thesis. I’ve learned analytical techniques from many people. Many members of the Macalady, Freeman and House labs have helped scientific discussions and experimental trouble-shooting. Irene Schaperdoth taught me most of the molecular biology
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