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Nixon2014.Pdf This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Microbial iron reduction on Earth and Mars Sophie Louise Nixon Doctor of Philosophy – The University of Edinburgh – 2014 Contents Declaration .............................................................................................................. i Acknowledgements ............................................................................................... ii Abstract ..................................................................................................................iv Lay Summary .........................................................................................................vi Chapter 1: Introduction ......................................................................................... 1 1.1 Thesis scope and objectives .................................................................... 1 1.2 Thesis outline ............................................................................................ 2 Chapter 2: Literature review.................................................................................. 4 2.1 Microbial iron reduction ............................................................................ 4 2.1.1 Electron donors and acceptors known to support MIR ..................................... 10 2.1.2 Biogeography and growth parameters of MIR on Earth .................................... 18 2.2 Habitable Mars? ........................................................................................20 2.3 The feasibility of MIR on Mars .................................................................24 2.3.1 Sources of electron donors on Mars ................................................................. 24 2.3.2 Sources of terminal electron acceptors ............................................................. 29 2.4 Relevant other work .................................................................................31 2.5 The knowledge gap ..................................................................................33 Chapter 3: General methodology.........................................................................35 3.1 Preparation of anaerobic growth medium ..............................................35 3.2 Anaerobic techniques ..............................................................................35 3.3 Determination of iron concentration .......................................................36 3.4 Preparation of 2-line ferrihydrite .............................................................36 3.5 Cell enumerations ....................................................................................37 3.6 DNA extraction .........................................................................................38 3.7 16S rRNA sequencing and data analysis methodology ........................39 3.8 PCR amplification .....................................................................................40 Chapter 4: MIR in Mars-relevant environments on Earth ...................................42 4.1 Introduction ..............................................................................................42 4.2 Field sites ..................................................................................................43 4.2.1 Iceland ............................................................................................................... 45 4.2.2 Namib Desert ..................................................................................................... 46 4.2.3 Río Tinto ............................................................................................................ 47 4.2.4 Subglacial sediments ......................................................................................... 48 4.3 Materials and methods .............................................................................51 4.3.1 Initiation of enrichments ..................................................................................... 51 4.3.2 Incubation and determination of MIR ................................................................ 52 4.3.3 DNA extraction .................................................................................................. 52 4.3.4 Geobacteraceae-specific PCR .......................................................................... 52 4.3.5 Bacterial 16S rRNA sequencing ........................................................................ 53 4.3.6 Denaturing Gradient Gel Electrophoresis (DGGE) ........................................... 53 4.4 Results ......................................................................................................54 4.4.1 Detection and rates of MIR ................................................................................ 54 4.4.2 Presence of Geoacteraceae .............................................................................. 61 4.4.3 Phylogenetic diversity ........................................................................................ 62 4.5 Discussion ................................................................................................69 4.5.1 Occurrence of MIR ............................................................................................ 69 4.5.2 Rates of MIR ...................................................................................................... 69 4.5.3 MIR at different temperatures ............................................................................ 70 4.5.4 Phylogenetic diversity of MIR ............................................................................ 71 4.5.5 Factors controlling MIR ...................................................................................... 74 4.5.6 Implications for the biogeography of terrestrial MIR .......................................... 77 4.5.7 Implications for MIR on Mars ............................................................................. 77 4.5.8 Limitations.......................................................................................................... 78 4.6 Conclusions ..............................................................................................79 Chapter 5: Does recalcitrant carbonaceous material in the terrestrial subsurface serve as a source of electron donors for MIR? ...............................81 5.1 Introduction ..............................................................................................81 5.2 Materials and methods .............................................................................83 5.2.1 Shale samples ................................................................................................... 83 5.2.2 Kerogen samples ............................................................................................... 84 5.2.3 Microorganisms and growth conditions ............................................................. 87 5.2.4 Experimental setup ............................................................................................ 87 5.2.5 Analytical methods ............................................................................................ 89 5.3 Results ......................................................................................................90 5.3.1 Shales ................................................................................................................ 90 5.3.2 Kerogens ........................................................................................................... 92 5.4 Discussion ................................................................................................98 5.4.1 Use of bulk carbonaceous material as a source of electron donors for MIR .... 98 5.4.2 Inhibition of MIR in the presence of bulk carbonaceous material .................... 100 5.4.3 Implications for MIR on Earth .......................................................................... 101 5.4.4 Implications for MIR on Mars ........................................................................... 101 5.4.5 Limitations........................................................................................................ 102 5.5 Conclusions ............................................................................................ 103 Chapter 6: Do extraterrestrial non-proteinogenic amino acids serve as electron donors for MIR? ................................................................................... 104 6.1 Introduction ............................................................................................ 104 6.2 Materials and methods ........................................................................... 105 6.2.1 Microorganisms ..............................................................................................
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