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Open Research Online Oro.Open.Ac.Uk Open Research Online The Open University’s repository of research publications and other research outputs Potential Microbial Processes In An Ancient Martian Environment, An Investigation Into Bio-Signature Production And Community Ecology Thesis How to cite: Curtis-Harper, Elliot (2017). Potential Microbial Processes In An Ancient Martian Environment, An Investigation Into Bio-Signature Production And Community Ecology. PhD thesis The Open University. For guidance on citations see FAQs. c 2017 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.21954/ou.ro.0000cc45 Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk Potential microbial processes in an ancient martian environment, an investigation into bio- signature production and community ecology Elliot Curtis-Harper B.Sc. Natural Sciences (Hons) A Thesis Submitted for the Degree of Doctor of Philosophy Astrobiology April 2017 Department of Physical Sciences The Open University UK i Declaration The research described herein was funded by STFC (Science and Technologies Funding Council) and conducted at The Open University. All of the research carried out in this thesis is my own original research, with the following exceptions: • MiSeq sequencing (Chapters 2 and 3). Conducted by a bioinformatics company (Research and Testing Laboratory, Lubbock, Texas). All subsequent bioinformatic analyses was conducted myself. • XRF analysis (Chapter 3). Samples were prepared myself but operation of the instrument was carried out by John Watson (Open University, UK). • ICP-AES (Chapter 3). Operation of the instrument was carried out by Laboratory Technician Patrick Rafferty (Open University, UK). All subsequent data processing was carried out myself. • XRD (Chapter 3). Sample preparation was carried out by myself but operation of the instrument was carried out by Dr Paul Schofield (Natural History Museum, UK). Subsequent data analysis was carried out by myself. ii Abstract This work investigated whether the River Dee estuary can be considered as an martian environmental analogue and examined the whether an understanding of microbial processes could inform future life detection missions on Mars. The subsurface environment of the River Dee estuary, UK, and its microbial community, was characterised and compared to the palaeolake at Gale Crater, Mars. Similarities were identified in pH, temperature and Total Organic Carbon measurements, as well as potential bioessential element availability (based on comparative mineralogy of the two sites). The microbial community at the River Dee site was also characterised, indicating that a diverse bacterial community thrived there, alongside a single dominant archaeal group. This provided key insight into potential microbial communities on Mars, and associated processes that may inform future Mars research. Since the diversity and attributes of microorganisms is directly linked to their environment, the microbial community of the River Dee estuary was used to investigate potential martian geomicrobiological processes and community dynamics within a simulated martian experimental environment. Concentrations of the bioessential elements Fe, Mg and K were seen to increase in the biological experiments when compared with abiotic controls, leading to, for example, a 143 µmol L-1 difference in the concentration of Fe during the stationary phase. One bacterial group, the Acidobacteria Gp9, dominated the microbial community for 400 hr during the stationary phase, accounting for ~58 % of the microbial community at its peak. For a subsequent experiment, five bacterial species were isolated from the simulated martian environment, and characterised in order to demonstrate their growth optima and tolerance to relevant environmental extremes. Clostridium amygdalinum was iii found to be a model organism for survival within environments like the palaeolake at Gale Crater, and is proposed as a useful biological analogue for future investigations of the potential of life in such environments on Mars. Acknowledgements This thesis is the summation of research carried out under the apt supervision of Dr Karen Olsson-Francis, Dr Victoria Pearson and Dr Susanne Schwenzer. I am extremely grateful for their constant support, knowledge and, of late, patience. Their supervision was excellent and I feel lucky to have had their guidance. Thank you to Dr Stephen Summers, without whom I’d have been defeated by incorrigible PCR reactions and smothered by alien-looking bioinformatics software outputs. You were invaluable to my understanding of molecular biology and to my long-overdue completion of my lab work. To my friend, Thomas Barrett, I also owe thanks. Thank you for all of the gaming nights, Game of Thrones, and the myriad shenanigans in the House of Mirrors. Your brummy-tinged rage and displeasure at the uncompliant NanoSIMS gave me the right dose of schadenfreude to go back to my inept microorganisms and try to convince them to grow. To Rebecca Wolsey, I owe the most. Without you I fear I would not be sitting here writing this gratuitous monologue. When you strolled into the lab in October 2013 you turned my life upside down. Working together in the lab you, without question, handed me solutions to problems you’d spent months solving. You are the source of my happiness and sanity, without which I certainly would not have made it this far. Finally, to my family: your love and support has been invaluable. Thank you. iv Table of contents Declaration ii Abstract iii Acknowledgements iv Table of Contents v Abbreviations and acronyms xi List of tables xiii List of figures xv Chapter 1- Introduction Introduction 1 1.1. The martian environment 2 1.1.1. Past 2 1.1.2. Present 6 1.2. Terrestrial vs martian life 9 1.2.1. Origins of life on Earth 9 1.2.2. Potential origins of life on Mars 10 1.3. Habitability 12 1.3.1. The requirements of life 12 v 1.4. Putative martian life 18 1.4.1. Potential characteristics of martian life 19 1.4.2. Potential analogue microorganisms 20 1.5. Life detection missions 23 1.5.1. Past and present 23 1.5.2. Assumptions of life detection 24 1.5.3. Martian analogues 26 1.6. Biosignatures 29 1.6.1. Inorganic/geochemical 29 1.6.2. Organic 33 1.6.3. The limitations of biosignatures 34 1.7. Ecological processes on Mars 35 1.7.1. Colonisation and succession 35 1.8. Outline of work 39 Chapter 2- The intertidal subsurface microbial community: an analogue for putative martian life 2.1. Introduction 41 2.2. Methods 44 2.2.1. Sample collection 44 2.2.2. Environmental characterisation 46 vi 2.2.3. Microbial community analysis 50 2.3. Results 55 2.3.1. Environmental characterisation 55 2.3.2. Microbial community analysis 67 2.4. Discussion 77 2.4.1. Environmental characterisation 77 2.4.2. Microbial diversity 88 2.4.3. Limitations 92 2.5. Conclusions 94 Chapter 3- The microbial weathering and ecological succession of an intertidal subsurface community under simulated martian conditions 3.1. Introduction 96 3.2. Designing a Mars analogue experimental system 98 3.3. Mars regolith analogue 99 3.3.1. Defining a regolith analogue 100 3.3.2. Production of the regolith analogue 102 3.3.3. Characterisation of the regolith analogue 102 3.4. Optimisation of the Mars analogue system 103 3.5. Methods 106 3.5.1. Anaerobic techniques 106 vii 3.5.2. Enrichment media 108 3.5.3. Minimal medium 109 3.5.4. Final experimental setup 112 3.5.5. Analytical techniques 115 3.6. Results 121 3.6.1. Microbial growth 121 3.6.2. pH 123 3.6.3. ICP-AES 124 3.6.4. Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis 128 3.6.5. Field Electron Gun Scanning Electron Microscopy (FEGSEM) 135 3.6.6. Powder X-Ray Diffraction 142 3.7. Discussion 145 3.7.1. Trends in microbial diversity 145 3.7.2. Microbial weathering, dissolution and secondary mineralisation 155 3.8. Conclusions 160 Chapter 4- Isolation and characterisation of microbial analogues for Mars 4.1. Introduction 162 4.1.1. Summary of previous chapters 162 viii 4.1.2. Putative martian life 163 4.1.3. Potentially habitable martian environments 165 4.1.4. Limits of life 166 4.1.5. Aims of the chapter 167 4.2. Methods 168 4.2.1. Media preparation 168 4.2.2. Isolation 172 4.2.3. DNA sequencing and 16S rRNA contig construction 174 4.2.4. Phenotypic characterisation of isolates 175 4.2.5. Determination of carbon source utilisation by BIOLOG tests 178 4.2.6. Survivability during exposure to environmental stressors 180 4.3. Results 182 4.3.1. Identification of isolates 182 4.3.2. Phenotypic characterisation of isolates 184 4.3.3. Freeze-thaw survival 190 4.3.4. Determination of carbon source utility by BIOLOG tests 192 4.4. Discussion 195 4.4.1. Metabolism 195 4.4.2. Optimum growth conditions 197 4.4.3. Other phenotypes 200 4.4.4. Isolates 202 ix 4.4.5. Sources of life on Mars 206 4.5. Conclusions 208 Chapter 5- Summary and conclusions 5.1. Discussion of findings and limitations 209 5.1.1. Environmental analogue 209 5.1.2. Elemental bioavailability 210 5.1.3. Biological analogue 211 5.1.4. Limitations 214 5.1.5. Biosignatures 216 5.2. Future work to address research aims 218 5.2.1. Further characterisation of the River Dee analogue environment 218 5.2.2. Clarification of microbial weathering processes and biosignature production 218 5.2.3. Further characterisation of isolates 219 5.3.
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