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Impact of Cable Bacteria on the Biogeochemical Cycling in a Seasonally Hypoxic Basin

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Impact of Cable Bacteria on the Biogeochemical Cycling in a Seasonally Hypoxic Basin IMPACT OF CABLE BACTERIA ON THE BIOGEOCHEMICAL CYCLING IN A SEASONALLY HYPOXIC BASIN Dorina Seitaj Promotor: Prof. dr. ir. Filip Meysman Proefschrift ingediend tot het behalen van de graad van Doctor in de Wetenschappen DOCTORAATSJURY Promotor: Prof. dr. ir. Filip Meysman Vrije Universiteit Brussel Overige Prof. dr. Phillipe Claeys Vrije Universiteit Brussel Leden: Prof. dr. Frank Dehairs Vrije Universiteit Brussel Prof. dr. Mark Kochzius Vrije Universiteit Brussel Prof. dr. ir. Eveline Peeters Vrije Universiteit Brussel Prof. dr. ir. Caroline Slomp Universiteit Utrecht Leibniz Institute for Prof. dr. Heide Schulz Baltic Sea Research (IOW) Prof. dr. Nils Risgaard-Petersen Aarhus University The research presented in this thesis was funded by the Darwin Center for Biogeosciences (Netherlands Organization for Scientific Research) and has been primarily conducted in the Department of Ecosystem Studies within the Royal Netherlands Institute for Sea Research in Yerseke. Additional financial support was provided by the European Reseach Council through ERC grant 306933 awarded to my promotor. Cover photo: Silvia Hidalgo-Martinez. Cover design: Flavio Mariani. Copyright © Dorina Seitaj, September 2016. All rights reserved. No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, without written permission of the author. Contents Acknowledgements ......................................................................................................... 4 Summary ......................................................................................................................... 6 Samenvatting .................................................................................................................. 8 Chapter 1 Introduction .................................................................................................................... 11 Chapter 2 Biogeochemical cycling in a seasonally hypoxic coastal basin (Lake Grevelingen, The Netherlands) ................................................................................................................... 29 Chapter 3 Sedimentary oxygen dynamics in a seasonally hypoxic basin ....................................... 57 Chapter 4 Cable bacteria in the sediments of seasonally hypoxic basins: a microbial “firewall” against euxinia................................................................................................................ 93 Chapter 5 Cable Bacteria Control Iron-Phosphorus Dynamics in Sediments of a Coastal Hypoxic Basin ............................................................................................................................ 121 Chapter 6 The paradox of aerobic sulfide oxidation revisited: suboxic zone formation, redox shuttling and cryptic sulfur cycling in marine sediments ............................................. 145 Chapter 7 Discussion .................................................................................................................... 177 Popularizing summary............................................................................................... 192 Popularizerende samenvatting .................................................................................. 194 References ................................................................................................................... 196 Curriculum vitae ........................................................................................................ 216 Acknowledgements I started my PhD expecting to learn about science, and I eventually underestimated how much I would learn also about life and myself, thanks to the people that accompanied me during this journey. Firstly, I thank my supervisor Filip who has guided and supported me during these years. It has been a great pleasure to work with you, and learn from your thorough understanding of biogeochemistry (only as a modeller could do), and your excellent ability to communicate science (not as a typical modeller would do). Yes, my grandmother is beginning to understand my slides. Field data are often ‘intriguing’ (read: the PhD student has no clue what they mean), but I would often leave your office thinking that we had just unravelled one more piece of the puzzle. Our discussions on cables-into-the-wild have been extremely stimulating and interesting, and it has been exciting to be part of this research at such a pioneering stage. I would like to thank Karline Soetaert, who was head of our former department and has been an important example for young female scientist. Caroline Slomp is another example of outstanding female scientist. Caroline, your profound understanding of geochemistry, as well as your determination and enthusiasm are an inspiration. I am grateful to Robert and Josephine Aller for hosting and supporting me during my visit at SoMAS, and for making my stay interesting and pleasant. My field and laboratory work in Long Island Sound was possible only thanks to the help of Robert Aller, Qingzhi Zhu, Jaime Soto-Neira and Christina Heilbrun. Jaime and Carolina, somehow ‘Southern’ people get along, and it took us very little to become friends. Thanks to the Baumann family for welcoming me into their house. I thank all the members of the NIOZ Electro team for sharing the interest and excitement about cable bacteria. Eric, thank you for sharing your knowledge on microbiology and for convincing me that bacteria are capable of unthinkable (until we manage to understand) processes. I would like to thank also the member of the Grevelingen team. Fatimah, ours has been a fruitful collaboration which has also transformed into a friendship. Thank you for the company during the long days and nights in the Luctor, and the sincere and warm conversations. Mathilde, I have never met a modeller that attempts such intense field work and succeeds. I really enjoyed working together during those long 12 sampling campaigns, your rigorous preparation contributed to having an efficient sampling. Thank you for your company during the fish-dinners in the Scharendijke, when we would finally manage to avoid the Chinese food option or…Eros Ramazzotti-pizza. Behind a good scientist, there is an excellent technician. My gratitude goes to Pieter van Rijswijk, the lab-practical-encyclopedia, who is able to quickly find and provide all sorts of lab equipment, even those that no one can remember that existed. Thank you for your prompt help in the lab and during the Grevelingen campaigns, and for never being annoyed by the endless requests of help from us students. I thank the technicians from the Analytical Lab for their help with analytical analysis: J. Sinke, Yvonne, Marco, Jurian, Peter. Anton, thank you for the help in the lab and in the field, I have greatly enjoyed your peaceful and pleasant company. 4 My gratitude goes to all the colleagues from NIOZ-Yerseke for creating such a wonderful working atmosphere. And then there was my Yerseke-family. Diana, my inquisitive, deep- thinker and curious colleague with whom I could share the love for mud and the enthusiasm for science. But not only, you are the friend who helps me push my boundaries, defeat my fears, learn to co-exist with my emotions without being overwhelmed, and face life with a smile and a right dose of silliness. Thank you for your friendship. Francesc, the talented communicator (in science and outside), dedicated to understand ‘everything’ about the world and us humans. Thank you for teaching me that it is not rude to say what I think or want, and for teaching me how to stand my ground. Thanks for dragging me into your world when wondering about places to visit and adventures to live. You have almost convinced me: if I stay true to ourselves, I can become the person I want to be. Sweet Silvia, cheerful and tender from the outside, but tenacious and grounded from the inside. Thank you for your warmth and generous heart, for being there to share happy and more difficult moments, I know I can always count on you. I want to thank the other part of our Yerseke-family, Christine, Jeroen, Michele, Sven, Juliette. Luckily the Benelux is small so I hope we can continue to be part of each other’s life, as a good dysfunctional-family would do. I would like to thank other NIOZ colleagues Eva-Maria, Rebecca, Sebastian, and Lorenz for the nice time spent together. Laurine, thank you for contributing to bridge the gap between me and R! Your sharp mind, generous attitude and enthusiasm for science make you a great scientist. To the other Keete friends: Heiko, Yayu, Alessia, Helene, Roger, Jule, Pierre, Cecile, Francesco, Greg, Sairah, Vanessa for the memorable Keete-time filled with evenings at the beach, dinners, movie nights or just chatting nights. I am greatful to Bart Braun and Laurine for translating to Dutch the abstract of my thesis. Ringrazio i miei genitori per avermi permesso di studiare, e soprattutto per aver deciso di lasciare il vostro paese per buttarvi nell’ignoto. Ora che vivo in Olanda capisco ancora di più cosa probabilmente ha significato per voi, e ve ne sarò sempre grata. Flavio, prima di tutto grazie per avermi seguito qui in Olanda. In questi anni ho alternato periodi di estremo entusismo con periodi di altretanta estrema disperazione. So bene quanto ti sia difficile rapportarti a tali oscillazioni, quindi grazie per essermi stato accanto nonnostante tutto. È sempre molto stimolante cercare di rispondere alle tue domande riguardo a batteri. Il tuo modo di pensare è certamente
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