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Paracoccus Denitrificans and Its Effects on Porous Media

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Paracoccus Denitrificans and Its Effects on Porous Media X-RAY CT-TECHNOLOGY REVEALING THE EFFECTS OF DENITRIFYING BACTERIA ON POROUS LIMESTONE Laurenz Schröer Student number: 01202662 Promotor: Prof. Dr. Veerle Cnudde Copromotor: Dr. Tim De Kock Jury: Prof. Dr. Ir. Nico Boon, Dr. Jan Dewanckele Master’s dissertation submitted in partial fulfilment of the requirements for the degree of Master of Science in Geology Academic year: 2016 - 2017 ACKNOWLEDGMENTS I would like to express my gratitude for all the people who helped me to bring this thesis to a good end. First of all I would like to thank my promoters Tim De Kock and Professor Veerle Cnudde. Their input and expertise in µCT and porous media combined with their extreme creativity, were essential to bring this thesis to a higher level. Thank you to let me join to the Interpore conference and an extra very big thank you for Tim as you always were willing to help, when needed, to answer my many questions and to learn me to use the µCT scanner. A lot of gratitude goes actually to everyone of Progress. Although Tim was my supervisor, I could ask everything to each one of you, and everybody was ready to help me: Jeroen Van Stappen with my setups, Géraldine Fiers with the microscopy, Maxim Deprez with mercury intrusion porosimetry, Redouane Meftah with the computer programs,… Thank you Stefanie Van Offenwert to share a desk together and to listen to all my thesis struggles and to motivate me afterwards. As I almost did not know anything about bacteria, I would be literally completely lost with this thesis subject. Thank you Professor Nico Boon to guide me through the world of microbiology explaining it with normal terms and with your creativity, solving complex looking problems very easily. I also thank Jana De Bodt to help me in the laboratories of CMET and to prepare the bacteria for my experiments. This was certainly not an easy task as I was completely unfamiliar with all the techniques at CMET. I thank furthermore Amelie De Muynck, Ivan Josipovic and all the people of UGCT from the Physics department to help me with the scanner and with the more fundamental questions about the scanner and radiation. Besides all the professional help that I got, the thesis would also not have been possible without my great classmates, we had an amazing five years together. Although our university adventures has ended, it is certainly not a goodbye and we will stay always in touch. To all my non-geological friends, thank you to let me forget my thesis now and then and to listen to all my geology facts. Hannes and Ilias thank you for letting me relax sometimes, to explain biology in detail and to travel together. It really refreshed my mind and let me work at my studies and thesis more efficiently. Also an extra thank you to Olav to explain statistics to me and motivate me constantly. Most gratitude goes however to my parents and my grandparents, who supported me all the time. Thank you for preparing food, when I came home very lately, thank you to be silent and be capable to handle my grumpy mood, especially during exam periods and the last weeks of my thesis. But especially thank you for being there. Table of Contents 1. INTRODUCTION ................................................................................................................................................... 1 1.1. State of Art ................................................................................................................................................... 1 1.2. Objectives ..................................................................................................................................................... 2 2. BACTERIA WITHIN POROUS ROCKS: OCCURRENCE, INFLUENCE AND IMAGING ................................................ 3 2.1. Bacteria in the subsurface ............................................................................................................................ 3 2.1.1. Microbial life and the geosphere .......................................................................................................... 3 2.1.2. Microscopic life within saturated porous media and its relationship to the pore distribution ............ 4 2.2. Bacterial colonization and its effects on porous rocks ................................................................................. 7 2.2.1. Bacterial adhesion and attachment ...................................................................................................... 7 2.2.2. Bacterial growth within porous media and their direct effects on the hydraulic conductivity ............ 9 2.2.3. Metabolites of Paracoccus denitrificans and its effects on porous media ......................................... 10 2.3. Imaging the biosphere on a microscale ..................................................................................................... 12 2.3.1. Bacteria and biofilms........................................................................................................................... 12 2.3.2. Bacterial influence on a microscale – MICP, biodegradation and biogenic gas .................................. 14 3. MATERIALS ........................................................................................................................................................ 16 3.1. Savonnières limestone ............................................................................................................................... 16 3.2. Tabaire stone.............................................................................................................................................. 18 3.3. Paracoccus denitrificans ............................................................................................................................. 19 3.3.1. Basic characteristics ............................................................................................................................ 19 3.3.2. Denitrification ..................................................................................................................................... 20 4. METHODS .......................................................................................................................................................... 22 4.1. General overview about some of the most sophisticated used techniques .............................................. 22 4.1.1. Mercury intrusion porosimetry (MIP) ................................................................................................. 22 4.1.2. Flow cytometry ................................................................................................................................... 22 4.1.3. High resolution X-ray computed tomography (HRXCT) or micro-CT (µCT) ......................................... 23 4.2. Experimental setups and procedures......................................................................................................... 24 4.2.1. Characterization of the rocks .............................................................................................................. 24 4.2.2. Flow experiments – Estimation of bacterial adhesion within the porous rocks ................................. 25 4.2.3. Radiation experiments ........................................................................................................................ 26 4.2.4. Growth experiments ........................................................................................................................... 26 4.3. Applied µCT reconstruction and data analysis protocol ............................................................................ 28 4.3.1. Reconstruction .................................................................................................................................... 28 4.3.2. Data analysis ....................................................................................................................................... 28 4.3.3. Dataviewer and VGStudio ................................................................................................................... 29 5. RESULTS ............................................................................................................................................................. 31 5.1. Characterization of the micro-environment – Porosity ............................................................................. 31 5.2. Flow experiments – Bacterial adhesion within porous limestone ............................................................. 34 5.3. Radiation experiments ............................................................................................................................... 35 5.4. Growth experiments .................................................................................................................................. 36 5.4.1. Biological activity during the different cycles – Chemical analyses .................................................... 36 5.4.2. Reaction products – Gas ..................................................................................................................... 37 5.4.3. Reaction products – Microbially induced calcite precipitation ........................................................... 47 6. DISCUSSION ....................................................................................................................................................... 50 6.1 Characterization of the micro-environment – Porosity .............................................................................
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