Royal Netherlands Institute for Sea Research
Royal Netherlands
Institute for Sea Research
Phone number
+31 (0)113 577 485
Senior Scientist

Dr. Tom Ysebaert

Senior Scientist


  • benthic ecology
  • estuarine and delta ecosystems
  • ecological engineering
  • macrobenthos
  • biophysical interactions

Research interest

In my research I focus on benthic ecosystems in estuarine and coastal environments. I study the diversity of benthic macrofauna, and how their distribution is influenced by the environment, but also vice versa, how organisms, as ecosystem engineers, modify their environment. I try to get a fundamental understanding about the mutual interaction between benthic organisms and the physical environmental, for instance how oyster reefs affect hydrodynamics and sediment dynamics, or how stabilizing organisms and destabilizing organisms shape intertidal flats. This fundamental understanding I translate into concepts and guidelines for restoration and nature-based solutions, this is integrating coastal ecosystems into management of our estuaries, deltas and coasts. Monitoring of the effectiveness of restoration projects or nature-based solutions is one of my key interests; this includes for instance the projects in the Oosterschelde related to the sand deficit problem (nourishments of tidal flats, oyster reefs), restoration projects in the Westerschelde, the sand engine along the Dutch coast, ... Finally, I am working on benthic communities and benthic habitats as indicators for ecosystem health, as well as their importance for delivering ecosytem services to society (coastal protection, nutrient cycling, food production, etc.). 

My main focus research area is the Southwest Delta, with the Schelde estuary and the Oosterschelde as my principal research areas, but I also worked in other coastal systems worldwide, including Ems estuary (Netherlands), China (Yangtze, Yellow River), Bangladesh, Denmark (Limfjorden), Finland, Spain (Ria de Vigo), New Zealand, etc.   

Enjoying fieldwork in the Westerschelde during the EMERGO project.

Education and current positions

Tom Ysebaert studied biology at the University of Antwerp (Belgium), where he also received his PhD in 2000, dealing with macrobenthic communities in the Schelde estuary. Since 2001 he is working at NIOZ - Yerseke (former NIOO-CEME), and since 2007 he is also part-time senior researcher at Wageningen Marine Research in Yerseke. Since 2013 he is also lecturer at the University of Antwerp, teaching courses on Ecological Engineering (within the master Technology for Integrated Water Management) and Estuarine and Coastal Systems (within the master Oceans & Lakes). 

Short CV

October 2013 - now

Lecturer (0.05 fte)


University of Antwerp, Department Biology

 November 2007 - now

Senior researcher (0.6 fte)


Wageningen Marine Research, Yerseke, the Netherlands

January 2001 – now

Senior researcher (1.0 fte until nov 2007, 0.4 fte afterwards)


Royal Netherlands Institute for Sea Research – NIOZ, Estuarine & Delta Systems Department, Yerseke, The Netherlands

1992 – December 2000

Scientist / project manager


Institute of Nature Conservation, Ministry of the Flemish Community, Brussels, Belgium

1988 - 1992

Scientific researcher


Ghent University, Laboratory of Ecology, Zoogeography & Nature Conservation, Ghent, Belgium



Linked news

Friday 17 March 2017
Tuinierende wormen en klimaatverandering ondermijnen natuurlijke kustbescherming
Dijken zouden lager kunnen zijn als ze beschermd worden door golvendempende, grassige kwelders. Maar het buitendijkse kweldergras heeft het moeilijk, niet alleen door sterkere golven, maar ook door wormen die de zaden van het gras blijken te…

Linked blogs

Tuesday 02 October 2018
NIOZ@SEA | Ecologisch onderzoek in de Nederlandse delta’s
De ecosystemen in de Oosterschelde, Grevelingen en Haringvliet zijn aan het veranderen door de invloed van onze Deltawerken, maar ook door klimaatverandering. In de Oosterschelde verdrinken de zandplaten langzaam door zandhonger, de bodem in het…
Monday 06 November 2017
NIOZ@SEA DISCLOSE | Protecting vulnerable habitats in the North Sea
The North Sea is home to a diverse range of habitats and species, but at the same time it’s one of the most exploited sea regions in the world. Some of these habitats and species are under threat from this intensive exploitation. DISCLOSE studies how…

NIOZ publications

  • 2019
    Chowdhury, M.S.N.; Walles, B.; Sharifuzzaman, S.M.; Hossain, M.S.; Ysebaert, T.; Smaal, A.C. (2019). Oyster breakwater reefs promote adjacent mudflat stability and salt marsh growth in a monsoon dominated subtropical coast. NPG Scientific Reports 9(1): 12 pp.
    Chowdhury, M.S.N.; Wijsman, J.W.M.; Hossain, M.S.; Ysebaert, T.; Smaal, A.C. (2019). A verified habitat suitability model for the intertidal rock oyster, Saccostrea cucullata. PLoS One 14(6): e0217688.
    Chowdhury, M.S.N.; Wijsman, J.W.M.; Shahadat Hossain, M.; Ysebaert, T.; Smaal, A.C. (2019). Growth potential of rock oyster (Sacosstrea cucullata) exposed to dynamic environmental conditions simulated by a Dynamic Energy Budget model. J. Sea Res. 147: 19-27.
    Cozzoli, F.; Gjoni, V.; Del Pasqua, M.; Hu, Z.; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J. (2019). A process based model of cohesive sediment resuspension under bioturbators' influence. Sci. Total Environ. 670: 18-30.
    Read more
    Fang, X.; Mestdagh, S.; Ysebaert, T.; Moens, T.; Soetaert, K.; Van Colen, C. (2019). Spatio-temporal variation in sediment ecosystem processes and roles of key biota in the Scheldt estuary. Est., Coast. and Shelf Sci. 222: 21-31.
    Meysick, L.; Ysebaert, T.; Jansson, A.; Montserrat, F.; Valanko, S.; Villnäs, A.; Boström, C.; Norkko, J.; Norkko, A. (2019). Context-dependent community facilitation in seagrass meadows along a hydrodynamic stress gradient. J. Sea Res. 150-151: 8-23.
    van der Reijden, K.J.; Koop, L.; O'Flynn, S.; Garcia, S.; Bos, O.; van Sluis, C.; Maaholm, D.J.; Herman, P.M.J.; Simons, D.G.; Olff, H.; Ysebaert, T.; Snellen, M.; Govers, L.L.; Rijnsdorp, A.D.; Aguilar, R. (2019). Discovery of Sabellaria spinulosa reefs in an intensively fished area of the Dutch Continental Shelf, North Sea. J. Sea Res. 144: 85-94.
    van der Werf, J.J.; de Vet, P.L.M.; Boersema, M.P.; Bouma, T.J.; Nolte, A.J.; Schrijvershof, R.A.; Soissons, L.M.; Stronkhorst, J.; van Zanten, E.; Ysebaert, T. (2019). An integral approach to design the Roggenplaat intertidal shoal nourishment. Ocean Coast. Manag. 172: 30-40.
    Yan, J.; Cui, B.; Huang, H.; O'Flynn, S.; Bai, J.; Ysebaert, T. (2019). Functional consumers regulate the effect of availability of subsidy on trophic cascades in the Yellow River Delta, China. Mar. Pollut. Bull. 140: 157-164.
  • 2018
    Chowdhury, M.S.N.; Wijsman, J.W.M.; Hossain, M.S.; Ysebaert, T.; Smaal, A.C. (2018). DEB parameter estimation for Saccostrea cucullata (Born), an intertidal rock oyster in the Northern Bay of Bengal. J. Sea Res. 142: 180-190.
    Cozzoli, F.; Bouma, T.J.; Ottolander, P.; Lluch, M.S.; Ysebaert, T.; Herman, P.M.J. (2018). The combined influence of body size and density on cohesive sediment resuspension by bioturbators. NPG Scientific Reports 8(1): 3831.
    De Vet, P.L.M.; Van Prooijen, B.C.; Schrijvershof, R.A.; van der Werf, J.J.; Ysebaert, T.J.W.; Schrijver, M.C.; Wang, Z.B. (2018). The importance of combined tidal and meteorological forces for the flow and sediment transport on intertidal shoals. Journal of Geophysical Research-Earth Surface 123(10): 2464-2480.
    Ma, Z.; Ysebaert, T.; van der Wal, D.; Herman, P.M.J. (2018). Conditional effects of tides and waves on short-term marsh sedimentation dynamics. Earth Surf. Process. Landforms 43(10): 2243-2255.
    Mestdagh, S.; Bagaço, L.; Braeckman, U.; Ysebaert, T.; De Smet, B.; Moens, T.; van Colen, C.; De Smet, B. (2018). Functional trait responses to sediment deposition reduce macrofauna-mediated ecosystem functioning in an estuarine mudflat. Biogeosciences 15(9): 2587-2599.
    Mestdagh, S.; Fang, X.; Ysebaert, T; Van Colen, C. (2018). Spatio-temporal variation in contribution of biodiversity and environment to benthic ecosystem functioning in the Scheldt estuary, in: Mees, J. et al. (Ed.) Book of abstracts – VLIZ Marine Science Day. Bredene, Belgium, 21 March 2018. VLIZ Special Publication, 81: pp. 21
    Salvador de Paiva, J.N.; Walles, B.; Ysebaert, T.; Bouma, T.J. (2018). Understanding the conditionality of ecosystem services: The effect of tidal flat morphology and oyster reef characteristics on sediment stabilization by oyster reefs. Ecol. Eng. 112: 89-95.
  • 2017
    Cozzoli, F.; Smolders, S.; Eelkema, M.; Ysebaert, T.; Escavarage, V.; Temmerman, S.; Meire, P.; Herman, P.; Bouma, T.J. (2017). A modeling approach to assess coastal management effects on benthic habitat quality: a case study on coastal defense and navigability. Est., Coast. and Shelf Sci. 184: 67-82.
    van der Wal, D.; Lambert, G.I.; Ysebaert, T.; Plancke, Y.; Herman, P.M.J. (2017). Hydrodynamic conditioning of diversity and functional traits in subtidal estuarine macrozoobenthic communities. Est., Coast. and Shelf Sci. 197: 80-92.
    van der Wal, D.; Ysebaert, T.; Herman, P.M.J. (2017). Response of intertidal benthic macrofauna to migrating megaripples and hydrodynamics. Mar. Ecol. Prog. Ser. 585: 17-30.
  • 2016
    Schwarz, C.; Ysebaert, T.; Vandenbruwaene, W.; Temmerman, S.; Zhang, L.; Herman, P. (2016). On the potential of plant species invasion influencing bio-geomorphologic landscape formation in salt marshes. Earth Surf. Process. Landforms 41(14): 2047-2057.
    Soissons, L.M.; Li, B.; Han, Q.; van Katwijk, M.M.; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J. (2016). Understanding seagrass resilience in temperate systems: the importance of timing of the disturbance. Ecol. Indic. 66: 190-198.
    Walles, B.; Fodrie, F.J.; Nieuwhof, S.; Jewell, O.J.W; Herman, P.M.J.; Ysebaert, T. (2016). Guidelines for evaluating performance of oyster habitat restoration should include tidal emersion: reply to Baggett et al. Restor. Ecol. 24(1): 4-7.
    Walles, B.; Smaal, A.C.; Herman, P.M.J.; Ysebaert, T. (2016). Niche dimension differs among life-history stages of Pacific oysters in intertidal environments. Mar. Ecol. Prog. Ser. 562: 113-122.
    Walles, B.; Troost, K.; Van den Ende, D.; Nieuwhof, S.; Smaal, A.C.; Ysebaert, T. (2016). From artificial structures to self-sustaining oyster reefs. J. Sea Res. 108: 1-9
    Ysebaert, T.; Craeymeersch, J.A.M.; van der Wal, D. (2016). De relatie tussen bodemdieren en hydro- en morfodynamiek in het sublitoraal en litoraal van de Westerschelde. IMARES Wageningen Report, C066/16. IMARES Wageningen UR: Yerseke. 84 pp.
    Ysebaert, T.; van der Hoek, D.-J.; Wortelboer, R.; Wijsman, J.W.M.; Tangelder, M.; Nolte, A. (2016). Management options for restoring estuarine dynamics and implications for ecosystems: a quantitative approach for the Southwest Delta in the Netherlands. Ocean Coast. Manag. 121: 33-48.
    Zhu, Z.; Cozzoli, F.; Chu, N.; Salvador, M.; Ysebaert, T.; Zhang, L.; Herman, P.M.J.; Bouma, T.J. (2016). Interactive effects between physical forces and ecosystem engineers on seed burial: a case study using Spartina anglica. Oikos (Kbh.) 125(1): 98-106.
    Zhu, Z.; van Belzen, J.; Hong, T; Kunihiro, T.; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J. (2016). Sprouting as a gardening strategy to obtain superior supplementary food: evidence from a seed-caching marine worm. Ecology 97(12): 3278–3284.
  • 2015
    Schwarz, C.; Bouma, T.J.; Zhang, L.Q.; Temmerman, S.; Ysebaert, T.; Herman, P.M.J. (2015). Interactions between plant traits and sediment characteristics influencing species establishment and scale-dependent feedbacks in salt marsh ecosystems. Geomorphology (Amst.) 250: 298-307.
    van Dalfsen, J.A.; Nolte, A.J.; Deerenberg, C.M.; Escaravage, V.; Brinkman, A.G.; Ysebaert, T.J.W.; de Kluijver, A.; Vergouwen, S.; van Duren, L.A. (2015). Mogelijkheid voor voorspelling van ecologische doelvariabelen uit KRW, KRM en Natura2000 met modellen : Onderdeel KPP B&O Waterkwaliteitsmodelschematisaties 2014. Monitor Taskforce Publication Series, 2015-02. NIOZ: Yerseke. 49 pp.
    van der Werf, J.; Reinders, J.; van Rooijen, A.; Holzhauer, H.; Ysebaert, T. (2015). Evaluation of a tidal flat sediment nourishment as estuarine management measure. Ocean Coast. Manag. 114: 77-87.
    Walles, B.; Mann, R.; Ysebaert, T.; Herman, P.M.J.; Smaal, A.C. (2015). Demography of the ecosystem engineer Crassostrea gigas, related to vertical reef accretion and reef persistence. Est., Coast. and Shelf Sci. 154: 224-233.
    Walles, B.; Salvador de Paiva, J.; Van Prooijen, B.; Ysebaert, T.; Smaal, A.C. (2015). The Ecosystem Engineer Crassostrea gigas Affects Tidal Flat Morphology Beyond the Boundary of Their Reef Structures. Est. Coast. 38(3): 941-950.
  • 2014
    Cozzoli, F.; Eelkema, M.; Bouma, T.J.; Ysebaert, T.; Escaravage, V.; Herman, P.M.J. (2014). A Mixed Modeling Approach to Predict the Effect of Environmental Modification on Species Distributions. PLoS One 9(2): e89131.
    Cozzoli, F.; Eelkema, M.; Bouma, T.J.; Ysebaert, T.; Escaravage, V.; Herman, P.M.J. (2014). A mixed modeling approach to predict the effect of environmental modification on species distributions. Monitor Taskforce Publication Series, 2014-04. NIOZ: Yerseke.
    Ma, Z.; Ysebaert, T.; van der Wal, D.; de Jong, D.J.; Li, X; Herman, P.M.J. (2014). Long-term salt marsh vertical accretion in a tidal bay with reduced sediment supply. Est., Coast. and Shelf Sci. 146: 14-23.
    Schwarz, C.; Ye, Q.H.; van der Wal, D.; Zhang, L.Q.; Bouma, T.; Ysebaert, T.; Herman, P.M.J. (2014). Impacts of salt marsh plants on tidal channel initiation and inheritance. J. Geophys. Res. Earth Surface, 119(2): 385-400.
    Seitz, R.D.; Wennhage, H.; Bergstrom, U.; Lipcius, R.N.; Ysebaert, T. (2014). Ecological value of coastal habitats for commercially and ecologically important species. ICES J. Mar. Sci./J. Cons. int. Explor. Mer 71(3): 648-665.
    Soissons, L.M.; Han, Q.; Li, B.; van Katwijk, M.M.; Ysebaert, T.; Herman, P.M.J.; Bouma, T.J. (2014). Cover versus recovery: Contrasting responses of two indicators in seagrass beds. Mar. Pollut. Bull. 87(1-2): 211–219.
    van der Wal, D.; van Dalen, J.; Wielemaker-van den Dool, A.; Dijkstra, J.T.; Ysebaert, T. (2014). Biophysical control of intertidal benthic macroalgae revealed by high-frequency multispectral camera images. J. Sea Res. 90: 111-120.
    Zhu, Z.; Bouma, T.J.; Ysebaert, T.; Zhang, L.; Herman, P.M.J. (2014). Seed arrival and persistence at the tidal mudflat: identifying key processes for pioneer seedling establishment in salt marshes. Mar. Ecol. Prog. Ser. 513: 97-109.
  • 2013
    Beauchard, O.; Jacobs, S.; Ysebaert, T.; Meire, P. (2013). Avian response to tidal freshwater habitat creation by controlled reduced tide system. Est., Coast. and Shelf Sci. 131: 12-23.
    Beauchard, O.; Jacobs, S.; Ysebaert, T.; Meire, P. (2013). Sediment macroinvertebrate community functioning in impacted and newly-created tidal freshwater habitats. Est., Coast. and Shelf Sci. 120: 21-32.
    Cozzoli, F.; Bouma, T.J.; Ysebaert, T.; Herman, P.M.J. (2013). Application of non-linear quantile regression to macrozoobenthic species distribution modelling: comparing two contrasting basins. Mar. Ecol. Prog. Ser. 475: 119-133.
    Depreiter, D.; Cleveringa, J.; van der Laan, T.; Maris, T.; Ysebaert, T.; Wijnhoven, S. (2013). Samenvatting T2009 rapportage Schelde-estuarium. Monitor Taskforce Publication Series, 2013-11. NIOZ: Yerseke. 21 pp.
    Depreiter, D.; Cleveringa, J.; van der Laan, T.; Maris, T.; Ysebaert, T.; Wijnhoven, S. (2013). Nota evaluatie van de Evaluatiemethodiek. T2009 rapportage Schelde-estuarium. Monitor Taskforce Publication Series, 2013-12. NIOZ: Yerseke. 87 pp.
    Petersen, J.K.; Maar, M.; Ysebaert, T.; Herman, P.M.J. (2013). Near-bed gradients in particles and nutrients above a mussel bed in the Limfjorden: influence of physical mixing and mussel filtration. Mar. Ecol. Prog. Ser. 490: 137-146.
    Temmerman, S.; Meire, P.; Bouma, T.J.; Herman, P.M.J.; Ysebaert, T.; de Vriend, H.J. (2013). Ecosystem-based coastal defence in the face of global change. Nature (Lond.) 504(7478): 79-83.
    Van Colen, C.; Thrush, S.F.; Vincx, M.; Ysebaert, T. (2013). Conditional responses of benthic communities to interference from an intertidal bivalve. PLoS One 8(6): e65861.
    Ysebaert, T.J.W.; De Mesel, I.; Wijnhoven, S.; Kromkamp, J.C. (2013). Flora en fauna. T2009 rapportage Schelde estuarium. Monitor Taskforce Publication Series, 2013-09. NIOZ: Yerseke. 386-497 pp.
    Zettler, M.L.; Proffitt, C.E.; Darr, A.; Degraer, S.; Devriese, L.; Greathead, C.; Kotta, J.; Magni, P.; Martin, G.; Reiss, H.; Speybroeck, J.; Tagliapietra, D.; Van Hoey, G.; Ysebaert, T. (2013). On the myths of indicator species: issues and further consideration in the use of static concepts for ecological applications. PLoS One 8(10): e78219 1-15.
  • 2012
    Van Colen, C.; Rossi, F.; Montserrat, F.; Andersson, M.G.I.; Gribsholt, B.; Herman, P.M.J.; Degraer, S.; Vincx, M.; Ysebaert, T.; Middelburg, J.J,. (2012). Organism-sediment interactions govern post-hypoxia recovery of ecosystem functioning. PLoS One 7(11): e49795.
    Yang, S.L.; Shi, B.W.; Bouma, T.J.; Ysebaert, T.; Luo, X.X. (2012). Wave Attenuation at a Salt Marsh Margin: A Case Study of an Exposed Coast on the Yangtze Estuary. Est. Coast. 35(1): 169-182.
    Zhu, Z.; Zhang, L.; Wang, N.; Schwarz, C.; Ysebaert, T. (2012). Interactions between the range expansion of saltmarsh vegetation and hydrodynamic regimes in the Yangtze Estuary, China. Est., Coast. and Shelf Sci. 96(1): 273-279.
  • 2011
    van der Wal, D.; Forster, R.M.; Rossi, F.; Hummel, H.; Ysebaert, T.; Roose, F.; Herman, P.M.J. (2011). Ecological evaluation of an experimental beneficial use scheme for dredged sediment disposal in shallow tidal waters. Mar. Pollut. Bull. 62(1): 99-108.

Linked projects

STW NatureCoast_Nature-driven nourishment of coastal systems
Tom Ysebaert
Netherlands Organization for Scientific Research
Project duration
1 Dec 2012 - 31 Mar 2017
Smartsediment_Innovative sediment management in the Scheldt Delta
Tom Ysebaert
Interreg Vlaanderen-Nederland
Project duration
1 Sep 2016 - 31 Aug 2019
NWO BwN Emergo Ysebaert
Tom Ysebaert
Netherlands Organization for Scientific Research
Project duration
1 Jan 2013 - 31 Aug 2018