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Bioturbation in Estuarine Sediments: Modelling Macrofauna-Mediated Oxygen Dynamics

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Bioturbation in Estuarine Sediments: Modelling Macrofauna-Mediated Oxygen Dynamics Bioturbation in estuarine sediments: modelling macrofauna-mediated oxygen dynamics Xiaoyu Fang Promoters: Prof. Tom Moens Dr. Carl Van Colen Prof. Karline Soetaert Prof. Antony Knights Academic year 2018-2019 Members of the examination and reading committee Prof. Ann Vanreusel Ghent University (chair) Dr. Ulrike Braeckman Ghent University (secretary) Prof. Jan Vanaverbeke Ghent University Prof. Peter Goethals Ghent University Prof. David Bilton University of Plymouth Dr. Ana Queiros Plymouth Marine Lab Prof. Tom Moens Ghent University (promoter) Dr. Carl Van Colen Ghent University (promoter) Prof. Karline Soetaert Ghent University (promoter) Prof. Antony Knights University of Plymouth (promoter) Acknowledgments The last four years have been the most informative, happiest, thoughtful, altering, moulding, powerful and accepting years of my life. When this PhD journey finally came to an end, I would like to acknowledge the support and encouragement received during my doctoral research. Back then, I was a beginner sailor who can barely handle a ship steering wheel. However, anything is possible when you have the right people to support you. I have been immensely lucky to have a ‘super’ supervisory team who guided me through what started as a daunting sea fog, which eventually turned into a sail of intellectual discovery. I am incredibly grateful for all my supervisors who stood by to support me along the way. Carl, you are the compass. You welcomed me with open arms even though I was lacking the academic background of biology and introduced me those nice and interesting ‘macrobenthos’ buddies. Over the years, you taught me how to adopt a critical view in marine biology research. You cared so much about my work and responded to my questions and queries so promptly. Your door was always open for me to discuss things. You were by my side throughout this PhD journey, in the climate room, field, onboard, from the first day until the very last stage in finalizing this thesis! Tony, you are the motive power. You witnessed my ‘breakdown’ in my toughest time and helped me back on my feet. Thank you for being such a strong and compassionate friend. You helped me to take one step back and see the broad picture when my sail vessel got stuck. Thank you for all the incredible insights into my work and those ‘aha’ moments! Tom, you are the water- and wind- proof jacket. Whenever I was freaking out in the storm, you told me it would be fine, and you have been in the same situation yet got it through. Your excellent eye for science has always motivated me to work harder and aim higher. Thank you for helping me translate the summary to Dutch and backing me up in the last several hours countdown of the finalization! Karline, you wrote the sailing slogan when our ship set sail. The first time we met, you told me we will make it together, since ‘bio-geo-chemistry’ corresponds to expertise of all my supervisors. You taught me to use R in modelling and guided me step by step at every crucial moment! I am still not a skilled sailor, but I learnt how to brave the storms in tough times and enjoy the sea breeze when it is calm. I am confident to compete against my own limits of resilience and brave any challenges in the future. Thank you! My gratitude goes out as well to the reading and examination committee: Prof. Dr. David Bilton, Prof. Dr. Jan Vanaverbeke, Prof. Dr. Peter Goethals, Prof. Ann Vanreusel, Dr. Ana Queiros and Dr. Ulrike Braeckman. Thank you for providing me extensive professional guidance and sharing your expertise and knowledge which have honed my thesis. I also want to thank you for letting my pre-defense be an enjoyable moment. It is the most informed, intelligent and inspiring conversation I had about my PhD study! I am grateful to all of those with whom I have had the pleasure to work with at Ghent University, NIOZ and University of Plymouth. As a marine biologist without great professional skills such as swimming and mud landing, nothing would have been done without all the generous help from my colleagues. Here is an exhaustive list of all the colleagues who helped me out in the field excursions and laboratory work: Sebastiaan Mestdagh, An-Sofie D’Hondt, Tim Tkint, Lisa Mevemkamp, Dirk Van Gansbeke, Bart Beuselinck, Guy Desmet, Mohammed Alsebai, Van Kenhove, Niels Viaene, Elise Toussaint, Emil De Borger, Ninon Mavraki, Ulrike Braeckman, Anna-Maria Vafeiadou, Isolde De Grem, Veerle Rogge, Thomas Kerkhove, Ellen Vlaminck, Lara Macheriotou, the crew of RV Simon Stevin and the students of the IMBRSea programme of UGent. A heartfelt thanks goes to my MARES alumni: Qian Huang, Ee Zin Ong, Valentina Filimonova, Veronica Lo, Sofia Ramalho, Svenja Tidau, Paul Dolder, Cátia Monteiro, Shawn Hinz, Jeffrey Wilson, La Daana Kanhai, who provided support, inspiration, peer pressure, and motivation along this Erasmus Mundus PhD journey. Francesco, I never expected the co-authorship would turn into a sincere friendship. You have been a role model for me since we met at NIOZ four years ago. I am impressed by your enthusiasm and passion for modelling. You taught me a great deal about research and life. Those fun days in your hometown Lecce, the inspiring modelling brainstorm during the custom- tailored city tour, the discussion about collaboration during ice cream breaks and the R scripts writing in the bar, turned out to be one of the most productive periods in my PhD! I would like to extend my sincerest thanks and appreciation to my parents for their unconditional support, love and care to an extent that has exceeded all reasonable expectation (no matter what path I choose). We shared our daily life over these years and geographical distance has never been a problem. I inherited the core values ‘work hard’ and ‘love hard’ from you. From the bottom of my heart, I thank you. 小花大葱我爱你们!你们一直是我最大的骄傲! Benjamin, you are the last piece to solve the Jigsaw puzzle of my life. Eventually, all my ‘mad’ life choices made sense and the complete picture was revealed: I was meant to take this PhD journey to find my best friend, soulmate and life partner. You were with me in all the ups and downs in this journey and had faith in me even when I felt like digging hole and crawling into one due to frustration and self-doubt. We have been through a lot of tears and joyful moments together and strengthened our commitment and determination to each other and to live life to the fullest. There are no words to convey how much I appreciate having you in my life! Dear Mestdagh and de Wilde family, they say you never get to choose your family in-law, but life brought me the best! Thank you for welcoming me warmly into the family and making me experience the sense of belonging in Belgium. I owe special gratitude particularly to Katrien, Karel, Sebastiaan, Rita, Johannes and Nicolas. In those hectic days when the apartment moving, PhD finalization, certificate examination, adaptation to the new job, preparation for the arrival of Chinese family and reception were all scheduled in a few weeks, you were always there supporting Benjamin and me in every possible way and letting us pursue our dreams! In the pre-defence, I was asked if I would re-do my PhD research in the particular manner given a second chance. To wrap up the reflection on my PhD journey by answering this question: PhD work-wise, there are still some aspects which can be improved (please refer to Chapter 6 General discussion of this thesis); but for my four-year PhD journey, no doubt I would duplicate it without changing a tiny bit, to still have all of you in my life! I love you all dearly. I dedicate this thesis to all of you. With much gratitude Xiaoyu Table of contents Chapter 1 General introduction ................................................................................................................ 2 1.1 Macrobenthos in marine soft bottoms ................................................................................................. 2 1.2 Macrobenthos-biogeochemistry ............................................................................................................. 4 Bioturbation ........................................................................................................................................... 4 1.2.1.1 Particle mixing ................................................................................................................................. 5 1.2.1.2 Ventilation patterns ....................................................................................................................... 7 Bioturbation effects on sediment biogeochemistry .............................................................. 8 1.3 The Scheldt estuary ................................................................................................................................... 11 1.4 Using macrobenthos for ecology conservation and estuarine ecosystem management 14 1.5 PhD objectives ............................................................................................................................................. 15 Research gaps..................................................................................................................................... 15 Outline ................................................................................................................................................... 18 Chapter 2 Spatio-temporal variation in sediment ecosystem processes and roles of key biota in the Scheldt estuary .....................................................................................................................
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