QUANTIFYING THE ROLE OF MICROPHYTOBENTHOS IN TEMPERATE INTERTIDAL ECOSYSTEMS USING OPTICAL REMOTE SENSING Tisja Daggers This dissertation has been approved by: Supervisors prof. dr. D. van der Wal prof. dr. P.M.J. Herman Cover design: Job Duim and Tisja Daggers (painting) Printed by: ITC Printing Department Lay-out: Tisja Daggers ISBN: 978-90-365-5124-3 DOI: 10.3990/1.9789036551243 This research was carried out at NIOZ Royal Netherlands Institute for Sea Research and financially supported by the ‘User Support Programme Space Research’ of the Netherlands Organisation for Scientific Research. © 2021 Tisja Dorine Daggers/ NIOZ, The Netherlands. All rights reserved. No parts of this thesis may be reproduced, stored in a retrieval system or transmitted in any form or by any means without permission of the author. Alle rechten voorbehouden. Niets uit deze uitgave mag worden vermenigvuldigd, in enige vorm of op enige wijze, zonder voorafgaande schriftelijke toestemming van de auteur. QUANTIFYING THE ROLE OF MICROPHYTOBENTHOS IN TEMPERATE INTERTIDAL ECOSYSTEMS USING OPTICAL REMOTE SENSING DISSERTATION to obtain the degree of doctor at the Universiteit Twente, on the authority of the rector magnificus, prof. dr. ir. A. Veldkamp, on account of the decision of the Doctorate Board to be publicly defended on Thursday 25 February 2021 at 14.45 hours by Tisja Dorine Daggers born on the 13th of June, 1990 in Leersum, The Netherlands iii Graduation Committee: Chair / secretary: prof.dr. F.D. van der Meer Supervisors: prof.dr. D. van der Wal prof.dr. P.M.J. Herman Committee Members: prof. dr. ir. A. Stein dr. ir. C.M.M. Mannaerts prof. dr. ir. C.J.M. Philippart prof. dr. K. Sabbe dr. V. Meleder-Tard Acknowledgements Many people have contributed to the completion of this PhD. To them I would like to express my sincere gratitude. I would like to thank my promoter prof. dr. Daphne van der Wal for her advice and encouragement. Even though she had a busy schedule, there was always time for constructive discussions. With patience she gave detailed feedback on a large number of manuscripts. I have learnt a great deal from Daphne on all aspects of setting up and conducting scientific research. I would like to thank my co-promotor prof. dr. Peter Herman for his useful feedback on several research set-ups, data analyses and manuscripts, even after he changed jobs. My gratitude also goes to dr. Jacco Kromkamp, advisor in this project, for the pleasant cooperation on Chapter 2, considering the measurement of primary production rates of microphytobenthos. This was the first project I performed and I learnt from Jacco how to deal with knowledge gaps and uncertainties in field and lab measurements. I also would like to thank prof. dr. Tjeerd Bouma, advisor in this project, for providing me the opportunity to join a large field campaign, in which we performed defaunation experiments on several locations (Chapter 4). By combining forces, it was possible to carry out a diverse range of measurements for several Phd and postdoc projects, of which Chapter 4 is one. I would like to thank Tjeerd for his useful feedback on this manuscript. My gratitude also goes to the people of NIOZ-Yerseke. It has been a pleasure to work and study here, and being surrounded by so many inspiring people was invaluable. There are too many people to thank individually, but everyone has in a way contributed to the completion of this work. I would like to especially thank Annette Wielemaker for her contribution to the processing of satellite imagery and valuable discussions on image analyses. Many thanks to Brenda Walles, Dick van Oevelen, Eric Boschker, Laura Soissons, Lodewijk de Vet, Sven Ihnken, Tom Ysebaert, Bas Oteman and Jim van Belzen for valuable discussions and their contributions to papers. I would like to thank Lennart van IJzerloo, Jeroen van Dalen and Daniel Blok for their contributions to several field campaigns. I would also like to acknowledge Anke Engelberts, Angela Dekker, Frank Brouwer and Daniel Blok for their help with the identification of macrofauna and Anke for her help with the identification of macroalgae species. Many thanks to Jan Sinke and Joeri i Minderhoud for chlorophyll-a analyses and Jetta Vlaming for performance of the 14C incubations. Many fellow scientists and students were invaluable by providing field assistance, including Joost Hamoen, Joeri Minderhoud, Roeland van de Vijsel and Clara Cardoso. Also many thanks in particular to all the young scientists I have met during my stay in Yerseke, for all the stimulating discussions we had and who made living in The Keete very pleasant. I would never have completed this PhD without the support and encouragement of my friends and family. Many thanks to my friends from school, university and the rowing club for distracting me from science and sharing many happy moments. Special thanks to Jantien and Marjolein, with whom I could share PhD struggles. I would also like to express my gratitude to my parents and sister, for always having faith in me. And lastly, I would like to express my deepest gratitude to Lars for his support and patience during the final stage of the PhD. ii Table of Contents Acknowledgements ................................................................................ i Chapter 1 Introduction ..................................................................... 1 Chapter 2 A model to assess microphytobenthic primary production in tidal systems using satellite remote sensing ........................................... 13 Chapter 3 Spatial variability in macrofaunal diet composition and grazing pressure on microphytobenthos in intertidal areas .................................. 53 Chapter 4 The influence of macrofauna on biomass and spatial heterogeneity of intertidal microphytobenthos under varying hydrodynamic conditions: an experimental approach ........................................................................ 81 Chapter 5 Seasonal and spatial variability in patchiness of microphytobenthos on intertidal flats from Sentinel-2 satellite imagery ................................ 113 Chapter 6 Synthesis ........................................................................... 137 Supplementary information ................................................................. 147 Bibliography .................................................................................... 179 Summary .................................................................................... 191 Samenvatting .................................................................................... 195 Curriculum Vitae ................................................................................ 199 iii Chapter 1 Introduction 1 Introduction 1.1 Estuaries and tidal flats Estuaries are semi-enclosed coastal water bodies, which are connected to the open sea. Estuaries contain sea water that is measurably diluted with fresh water originating from land drainage (Pritchard, 1967). In most cases, estuaries are situated where rivers flow into the open sea. Estuaries are common in low relief coastal regions such as the east coast of North America, Asia and Europe and are much less common along elevated coastlines, such as the Pacific edge of North and South America (Day, 1990; Murray et al., 2019). Estuaries are often narrow upstream and become wider towards the mouth (Day, 1990). Sediment enters estuaries via rivers and marine sources and may accrete forming tidal flats (Figure 1), depending on local environmental conditions such as tides, waves and fluvial processes (Dalrymple, 1992). Tidal flats are characterized by being submerged by water during high tide and being emerged during low tide. An analysis of over 700,000 satellite images demonstrated that the total surface area of tidal flats (sand, rock and mud flats) worldwide is at least 127,921 km2 (Murray et al., 2019). For a long time, estuaries have been important to mankind as harbors, fishing grounds and locations for towns and cities. Estuaries are highly productive ecosystems and are among the most economically valuable ecosystems worldwide (Costanza et al., 1997; Heip et al., 1995; Schelske and Odum, 1962). However, nowadays, estuaries are heavily exploited and among the most threatened ecosystems globally, mainly due to industrial activities such as dredging for ship navigation and extraction of sand resources (Simonini et al., 2007; Borja et al., 2010) and agricultural activities (Galbraith et al., 2002; Lotze et al., 2006; Worm et al., 2006). As a result, >90% of the species originally living in estuaries have been lost (Lotze et al., 2006). Estuarine intertidal zones are also an important focus of concern with respect to the potential impacts of climate change (Harley et al., 2006). The observed and projected climate trends include changes in air and sea temperature, sea level, tidal range, river discharge and turbidity, wind fields and storm frequency and intensity (Bates et al., 2008). The total area of tidal flats has declined by approximately 16% over the period 1984-2016 (Murray et al., 2019). The combined effects of degradation due to coastal development, reduced sediment input from rivers, increased coastal erosion and sea level rise are expected to lead to a continued decline of tidal flat ecosystems worldwide (Murray et al., 2019). 2 Chapter 1 Oosterschelde Westerschelde Figure 1. The Oosterschelde and Westerschelde estuary, The Netherlands, containing emersed tidal flats. Source image: Copernicus Sentinel-2 MSI, 12 March 2016. 1.2 Abiotic