Royal Netherlands Institute for Sea Research
Royal Netherlands
Institute for Sea Research
Phone number
+31 (0)113 577 487
Location
Yerseke
Function
Senior Scientist

Prof. Dr. Karline Soetaert

Senior Scientist

Expertise

  • Biogeochemical cycles
  • Sediment-water interactions
  • Environmental modelling
  • Scientific computing
  • Open source software (R)

Research interests

I am interested in the interplay between physics, ecology, and biogeochemistry in the marine environment. I have worked on many topics, including deepsea nematodes, estuarine zooplankton, estuarine biogeochemistry, early diagenesis, benthic and pelagic foodwebs, environmental modelling, software development and differential equations. Usually there is some computational aspect involved in my work -this may be in the form of mechanistic (ecosystem) models, or some other number-crunching procedure that involves computers and programming.  Indeed, my favorite working spot is behind my computer, although the occasional field work definitely has its charm!

Tag cloud of my past workSelfie taken after the Northsea Cruise, June 2017, with the RV Pelagia.

Research statement

I am a firm believer of open, transparent and reusable science, which –in my view- should include documenting the entire chain of research, from data up to the publication. This involves sharing also the raw data and the software and scripts that compute on these data.

Open science starts with open source software, so for more than 10 years, I have contributed to the open source software community, creating around 20 R-packages that are available on CRAN. To make the every-day scientific data analysis or modelling process open and reproducible, I use R with markdown – this creates documents that contain the programming codes and the output they generate (a concept known as literate programming).

Picture taken at the useR conference 2017 in Brussels, where I gave a tutorial on environmental modelling using R.

Short CV

I hold a master degree in Zoology (1983), a master in Computer Sciences (1985) and a PhD in biology (1988), all from Ghent University. I teach environmental modelling at the University of Ghent, for the first-year master “Global Change Biology” and for the first-year master “Oceans and Lakes”.  I am professor in marine ecosystem modelling at the Geosciences department at Utrecht University.

I have written in the order of 200 scientific publications, 20 software packages and 2 books. A list of my scientific output/achievements can be downloaded here.

Miscellaneous

My job is not my only hobby! I play the cello (learnt this as an adult), and used to play the clarinet (as a child). In 2016 I started playing the viola. Bach is my favorite composer, Massive Attack my favorite modern band.

I enjoy my medium-large, wild and natural garden, and like to spend time on my mountain bike – for sports and because it takes me to some wonderful places.

 

 

Linked news

Friday 02 December 2016
Good things come from above for deep-sea coral reefs
Deep-sea coral reefs grow in the oceans at great depths in the dark. They can be found around the peaks of limestone mounds rising from the seafloor up to hundreds of meters. The corals produce these limestone mounds themselves: they consist of dead…

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…
Thursday 26 October 2017
NIOZ@SEA | EXPEDITION NORTH SEA PROJECT SANDBOX
Similar as on land, sunlight is an essential ingredient of life in the seas: it heats up the water and is needed for the tiny algal cells in the water to grow. Sediment particles floating in the water block the light and therefore interfere with…
Tuesday 13 June 2017
NIOZ@Sea: North Sea expedition
Seven PhD students, three senior scientists, two assistants and the 12-headed Pelagia crew will embark on a scientific research cruise to the North Sea in the first two weeks of June.

NIOZ publications

  • 2019
    Braeckman, U.; Pasotti, F.; Vázquez, S.; Zacher, K.; Hoffmann, R.; Elvert, M.; Marchant, H.; Buckner, C.; Quartino, M.L.; Mác Cormack, W.; Soetaert, K.; Wenzhöfer, F.; Vanreusel, A. (2019). Degradation of macroalgal detritus in shallow coastal Antarctic sediments. Limnol. Oceanogr. Early view. https://dx.doi.org/10.1002/lno.11125
    Grenz, C.; Moreno, M.O.; Soetaert, K.; Denis, L.; Douillet, P.; Fichez, R. (2019). Spatio-temporal variability in benthic exchanges at the sediment-water interface of a shallow tropical coastal lagoon (south coast of Gulf of Mexico). Est., Coast. and Shelf Sci. 218: 368-380. https://doi.org/10.1016/j.ecss.2019.01.012
    Vlaminck, E.; Voet, H.; Vanaverbeke, J.; Degraer, S.; Moens, T.; Cattrijsse, A.; Soetaert, K.; Van Colen, C. (2019). Experimental approach towards the understanding of food web interactions in an offshore wind farm environment under different climate and aquaculture scenarios, in: Mees, J. et al. (Ed.) Book of abstracts – VLIZ Marine Science Day. Bredene, Belgium, 13 March 2019. VLIZ Special Publication, 83: pp. 154
  • 2018
    Damveld, J.H.; van der Reijden, K.J.; Cheng, C.; Koop, L.; Haaksma, L.R.; Walsh, C.A.J.; Soetaert, K.; Borsje, B.W.; Govers, L.L; Roos, P.C.; Olff, H.; Hulscher, S.J.M.H. (2018). Video transects reveal that tidal sand waves affect the spatial distribution of benthic organisms and sand ripples. Geophys. Res. Lett. 45(21): 11,837-11,846. https://dx.doi.org/10.1029/2018gl079858
    Husson, B.; Sarrazin, J.; van Oevelen, D.; Sarradin, P.-M.; Soetaert, K.; Menesguen, A. (2018). Modelling the interactions of the hydrothermal mussel Bathymodiolus azoricus with vent fluid. Ecol. Model. 377: 35-50. https://doi.org/10.1016/j.ecolmodel.2018.03.007
    Ivanov, E.; Capet, A.; Barth, A.; Delhez, E.; Soetaert, K.; Grégoire, M. (2018). Application of two way nesting model to upscale sediment processes of the Southern Bight of the North Sea: full model validation, in: Mees, J. et al. (Ed.) Book of abstracts – VLIZ Marine Scientist Day. Bredene, Belgium, 21 March 2018. VLIZ Special Publication, 80: pp. 94
    Lessin, G.; Artioli, Y.; Almroth-Rosell, E.; Blackford, J.C.; Dale, A. W.; Glud, R.N.; Middelburg, J.J.; Pastres, R.; Queirós, A.M.; Rabouille, C.; Regnier, P.; Soetaert, K.; Solidoro, C.; Stephens, N.; Yakushev, E. (2018). Modelling marine sediment biogeochemistry: current knowledge gaps, challenges, and some methodological advice for advancement. Front. Mar. Sci. 5: 19. https://doi.org/10.3389/fmars.2018.00019
    Snelgrove, P.V.R.; Soetaert, K.; Solan, M.; Thrush, S.; Wei, C.L.; Danovaro, R.; Kitazato, H.; Ingole, B.; Norkko, A.; Parkes, R.J.; Volkenborn, N. (2018). Global carbon cycling on a heterogeneous seafloor. Trends Ecol. Evol. 33(2): 96-105. https://doi.org/10.1016/j.tree.2017.11.004
    van Oevelen, D.; Duineveld, G.; Lavaleye, M.S.S.; Kutti, T.; Soetaert, K. (2018). Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition. Mar. Biol. Res. 14(3): 287-306. https://doi.org/10.1080/17451000.2017.1398404
  • 2017
    Cox, T.J.S.; van Beusekom, J.E.E.; Soetaert, K. (2017). Tune in on 11.57 µHz and listen to primary production. Biogeosciences 14(22): 5271-5280. https://dx.doi.org/10.5194/bg-14-5271-2017
    Geerts, L.; Cox, T.J.S.; Maris, T.; Wolfstein, K.; Meire, P.; Soetaert, K. (2017). Substrate origin and morphology differentially determine oxygen dynamics in two major European estuaries, the Elbe and the Schelde. Est., Coast. and Shelf Sci. 191: 157-170. https://dx.doi.org/10.1016/j.ecss.2017.04.009
    Holding, J.M.; Duarte, C.M.; Delgado-Huertas, A.; Soetaert, K.; Vonk, J.E.; Agusti, S.; Wassmann, P.; Middelburg, J. (2017). Autochthonous and allochthonous contributions of organic carbon to microbial food webs in Svalbard fjords. Limnol. Oceanogr. 62(3): 1307-1323. https://dx.doi.org/10.1002/lno.10526
    Ivanov, E.; Capet, A.; Barth, A.; Delhez, E.; Soetaert, K.; Grégoire, M. (2017). Three-dimensional modelling of the Southern Bight of the North Sea: first results and perspectives. Poster at the VLIZ Marine Scientist Day 3 March 2017. University of Liege: Liege. 1 poster pp.
    Le Guitton, M.; Soetaert, K.; Sinninghe Damsté, J.S.; Middelburg, J.J. (2017). A seasonal study of particulate organic matter composition and quality along an offshore transect in the southern North Sea. Est., Coast. and Shelf Sci. 188: 1-11. https://dx.doi.org/10.1016/j.ecss.2017.02.002
    Maugendre, L.; Gattuso, J.-P.; de Kluijver, A.; Soetaert, K.; van Oevelen, D.; Middelburg, J.J.; Gazeau, F. (2017). Carbon-13 labelling shows no effect of ocean acidification on carbon transfer in Mediterranean plankton communities. Est., Coast. and Shelf Sci. 186(Part A): 100-111. dx.doi.org/10.1016/j.ecss.2015.12.018
    Schwarz, C.; Cox, T.; van Engeland, T.; van Oevelen, D.; van Belzen, J.; van de Koppel, J.; Soetaert, K.; Bouma, T.J.; Meire, P.; Temmerman, S. (2017). Field estimates of floc dynamics and settling velocities in a tidal creek with significant along-channel gradients in velocity and SPM. Est., Coast. and Shelf Sci. 197: 221-235. https://dx.doi.org/10.1016/j.ecss.2017.08.041
  • 2016
    Capet, A.; Meysman, Filip; Akoumianaki, I.; Soetaert, K.; Grégoire, M. (2016). Integrating sediment biogeochemistry into 3D oceanic models: a study of benthic-pelagic coupling in the Black Sea. Ocean Modelling 101: 83-100. dx.doi.org/10.1016/j.ocemod.2016.03.006
    De Smet, B.; Braeckman, U.; Soetaert, K.; Vincx, M.; Vanaverbeke, J. (2016). Predator effects on the feeding and bioirrigation activity of ecosystem-engineered Lanice conchilega reefs. J. Exp. Mar. Biol. Ecol. 475: 31-37. hdl.handle.net/10.1016/j.jembe.2015.11.005
    De Smet, B.; van Oevelen, D.; Vincx, M.; Vanaverbeke, J.; Soetaert, K. (2016). Lanice conchilega structures carbon flows in soft-bottom intertidal areas. Mar. Ecol. Prog. Ser. 552: 47-60. hdl.handle.net/10.3354/meps11747
    Soetaert, K.; Mohn, C.; Rengstorf, A.; Grehan, A.; Van Oevelen, D. (2016). Ecosystem engineering creates a direct nutritional link between 600-m deep cold-water coral mounds and surface productivity. NPG Scientific Reports 6(35057 ): 9 pp. hdl.handle.net/10.1038/srep35057
    Ulses, C.; Auger, P.-A.; Soetaert, K.; Marsaleix, P.; Diaz, F.; Coppola, L.; Herrmann, M.J.; Kessouri, F.; Estournel, C. (2016). Budget of organic carbon in the North-Western Mediterranean open sea over the period 2004–2008 using 3-D coupled physical-biogeochemical modeling. JGR: Oceans 121(9): 7026–7055. https://dx.doi.org/10.1002/2016JC011818
    Van Colen, C.; Braeckman, U.; Guilini, K.; Van Gansbeke, D.; Soetaert, K.; Vincx, M.; Vanaverbeke, J. (2016). Context-dependent effects of ocean acidification on soft-sediment biodiversity and ecosystem functioning, in: Degraer, S. et al. (Ed.) North Sea Open Science Conference 7-10/11/2016. Abstract Booklet. pp. 36
    Yevenes, M.A.; Soetaert, K.; Mannaerts, C.M. (2016). Tracing Nitrate-Nitrogen Sources and Modifications in a Stream Impacted by Various Land Uses, South Portugal. Water 8(9): 385. dx.doi.org/10.3390/w8090385
  • 2015
    Braeckman, U.; Provoost, P.; Sabbe, K.; Soetaert, K.; Middelburg, J.J.; Vincx, M.; Vanaverbeke, J. (2015). Temporal dynamics in a shallow coastal benthic food web: Insights from fatty acid biomarkers and their stable isotopes. Mar. Environ. Res. 108: 55-68. hdl.handle.net/10.1016/j.marenvres.2015.04.010
    Cox, T.J.S.; Maris, T.; Soetaert, K.; Kromkamp, J.C.; Meire, P.; Meysman, F.J.R. (2015). Estimating primary production from oxygen time series: A novel approach in the frequency domain. Limnol. Oceanogr., Methods 13(10): 529-552. dx.doi.org/10.1002/lom3.10046
    Le Guitton, M.; Soetaert, K.; Sinninghe Damsté, J.S.; Middelburg, J.J. (2015). Biogeochemical consequences of vertical and lateral transport of particulate organic matter in the southern North Sea: A multiproxy approach. Est., Coast. and Shelf Sci. 165: 117-127. https://dx.doi.org/10.1016/j.ecss.2015.09.010
    Maugendre, L.; Gattuso, J.-P.; Louis, J.; de Kluijver, A.; Marro, S.; Soetaert, K.; Gazeau, F. (2015). Effect of ocean warming and acidification on a plankton community in the NW Mediterranean Sea. ICES J. Mar. Sci./J. Cons. int. Explor. Mer 72(6): 1744-1755. dx.doi.org/10.1093/icesjms/fsu161
    Meire, L.; Sogaard, D.H.; Mortensen, J.; Meysman, F.J.R.; Soetaert, K.; Arendt, K.E.; Juul-Pedersen, T.; Blicher, T.E.; Rysgaard, S. (2015). Glacial meltwater and primary production are drivers of strong CO2 uptake in fjord and coastal waters adjacent to the Greenland Ice Sheet. Biogeosciences 12(8): 2347-2363. https://dx.doi.org/10.5194/bg-12-2347-2015
  • 2014
    Braeckman, U.; Van Colen, C.; Guilini, K.; Van Gansbeke, D.; Soetaert, K.; Vincx, M.; Vanaverbeke, J. (2014). Empirical evidence reveals seasonally dependent reduction in nitrification in coastal sediments subjected to near future ocean acidification. PLoS One 9(10): e108153. dx.doi.org/10.1371/journal.pone.0108153
    Braeckman, U.; Yazdani Foshtomi, M.; Van Gansbeke, D.; Meysman, F.; Soetaert, K.; Vincx, M.; Vanaverbeke, J. (2014). Variable importance of macrofaunal functional biodiversity for biogeochemical cycling in temperate coastal sediments. Ecosystems 17(4): 720-737. dx.doi.org/10.1007/s10021-014-9755-7
    Mohn, C.; Rengstorf, A.; White, M.; Mienis, F.; Soetaert, K.; Grehan, A.; Duineveld, G. (2014). Linking benthic hydrodynamics and cold-water coral occurrences: A high-resolution model study at three cold-water coral provinces in the NE Atlantic. Prog. Oceanogr. 122: 92-104. dx.doi.org/10.1016/j.pocean.2013.12.003
    Moneta, A.; Veuger, B.; van Rijswijk, P.; Meysman, F; Soetaert, K.; Middelburg, J.J. (2014). Dissolved inorganic and organic nitrogen uptake in the coastal North Sea: a seasonal study. Est., Coast. and Shelf Sci. 147: 78-86. dx.doi.org/10.1016/j.ecss.2014.05.022. hdl.handle.net/10.1016/j.ecss.2014.05.022
  • 2013
    Adams Krumins, J.; van Oevelen, D.; Bezemer, T.M.; de Deyn, G.B.; Hol, W.H.G.; van Donk, E.; de Boer, W.; de Ruiter, P.C.; Middelburg, J.J.; Monroy, F.; Soetaert, K.; Thébault, E.; van de Koppel, J.; van Veen, J.A.; Viketoft, M.; van der Putten, W.H. (2013). Soil and Freshwater and Marine Sediment Food Webs: Their Structure and Function. BioScience 63(1): 35-42. dx.doi.org/10.1525/bio.2013.63.1.8
    Braeckman, U.; Vanaverbeke, J.; Vincx, M.; van Oevelen, D.; Soetaert, K. (2013). Meiofauna metabolism in suboxic sediments: currently overestimated. PLoS One 8(3): e59289. hdl.handle.net/10.1371/journal.pone.0059289
    de Kluijver, A.; Soetaert, K.; Czerny, J.; Schulz, K.G.; Boxhammer, T.; Riebesell, U.; Middelburg, J.J. (2013). A 13C labelling study on carbon fluxes in Arctic plankton communities under elevated CO2 levels. Biogeosciences 10(3): 1425-1440. dx.doi.org/10.5194/bg-10-1425-2013
    Koho, K.A.; Nierop, K.G.J.; Moodley, L.; Middelburg, J.J.; Pozzato, L.; Soetaert, K.; van der Plicht, J.; Reichart, G.J. (2013). Microbial bioavailability regulates organic matter preservation in marine sediments. Biogeosciences 10(2): 1131-1141. dx.doi.org/10.5194/bg-10-1131-2013
    Meire, L.; Soetaert, K.; Meysman, F.J.R. (2013). Impact of global change on coastal oxygen dynamics and risk of hypoxia. Biogeosciences 10(4): 2633-2653. https://dx.doi.org/10.5194/bg-10-2633-2013
    Morris, E.P.; Peralta, G.; Van Engeland, T.; Bouma, T.J.; Brun, F.G.; Lara, M.; Hendriks, I.E.; Benavente, J.; Soetaert, K.; Middelburg, J.J.; Perez-Llorens, J.L. (2013). The role of hydrodynamics in structuring in situ ammonium uptake within a submerged macrophyte community. Limnol. Oceanogr. 3: 210-224. hdl.handle.net/10.1215/21573689-2397024
    Pape, E.; van Oevelen, D.; Moodley, L.; Soetaert, K.; Vanreusel, A. (2013). Nematode feeding strategies and the fate of dissolved organic matter carbon in different deep-sea sedimentary environments. Deep-Sea Res., Part 1, Oceanogr. Res. Pap. 80: 94-110. hdl.handle.net/10.1016/j.dsr.2013.05.018
    Pozzato, L.; van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J.J (2013). Sink or link? The bacterial role in benthic carbon cycling in the Arabian Sea's oxygen minimum zone. Biogeosciences 10: 6879-6891. hdl.handle.net/10.5194/bg-10-6879-2013
    Pozzato, L.; van Oevelen, D.; Moodley, L.; Soetaert, K.; Middelburg, J.J. (2013). Carbon processing at the deep-sea floor of the Arabian Sea oxygen minimum zone: A tracer approach. J. Sea Res. 78: 45-58. dx.doi.org/10.1016/j.seares.2013.01.002
    Provoost, P.; Braeckman, U.; Van Gansbeke, D.; Moodley, L.; Soetaert, K.; Middelburg, J.J.; Vanaverbeke, J. (2013). Modelling benthic oxygen consumption and benthic-pelagic coupling at a shallow station in the southern North Sea. Est., Coast. and Shelf Sci. 120: 1-11. hdl.handle.net/10.1016/j.ecss.2013.01.008
    Tecchio, S.; van Oevelen, D.; Soetaert, K.; Navarro, J.; Ramírez-Llodra, E. (2013). Trophic Dynamics of Deep-Sea Megabenthos Are Mediated by Surface Productivity. PLoS One 8(5). dx.doi.org/10.1371/journal.pone.0063796
    Van Engeland, T.; Bouma, T.J.; Morris, E.P.; Brun, F.G.; Peralta, G.; Lara, M.; Hendriks, I.E.; van Rijswijk, P.; Veuger, B.; Soetaert, K.; Middelburg, J.J. (2013). Dissolved organic matter uptake in a temperate seagrass ecosystem. Mar. Ecol. Prog. Ser. 478: 87-100. dx.doi.org/10.3354/meps10183
  • 2012
    Braeckman, U.; Provoost, P.; Sabbe, K.; Soetaert, K.; Middelburg, J.J.; Vincx, M.; Vanaverbeke, J. (2012). Temporal dynamics in the diet of two marine polychaetes as inferred from fatty acid biomarkers. J. Sea Res. 68: 6-19. dx.doi.org/10.1016/j.seares.2011.11.003
    Dähnke, K.; Moneta, A.; Veuger, B.; Soetaert, K.; Middelburg, J.J. (2012). Balance of assimilative and dissimilative nitrogen processes in a diatom-rich tidal flat sediment. Biogeosciences 9(10): 4059-4070. hdl.handle.net/10.5194/bg-9-4059-2012
    Evrard, V.; Huettel, M.; Cook, P.L.M.; Soetaert, K.; Heip, C.H.R.; Middelburg, J.J. (2012). Importance of phytodetritus and microphytobenthos for heterotrophs in a shallow subtidal sandy sediment. Mar. Ecol. Prog. Ser. 455: 13-31. dx.doi.org/10.3354/meps09676
    Mazzia, F.; Cash, J.R.; Soetaert, K. (2012). A Test Set for stiff Initial Value Problem Solvers in the open source software R: Package deTestSet. Journal of Computational and Applied Mathematics 236(16): 4119-4131. dx.doi.org/10.1016/j.cam.2012.03.014
    Soetaert, K; van Oevelen, D.; Sommer, S. (2012). Modelling the impact of Siboglinids on the biogeochemistry of the Captain Arutyunov mud volcano (Gulf of Cadiz). Biogeosciences 9(12): 5341-5352. dx.doi.org/10.5194/bg-9-5341-2012
    Soetaert, K. (2012). Solving differential equations in R. Springer: London; Berlin. ISBN 9783642280702. 1-248 pp.
    Soetaert, K.; Meysman, F. (2012). Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R. Environ. Model. Softw. 32: 49-60. dx.doi.org/10.1016/j.envsoft.2011.08.011
    van Oevelen, D.; Soetaert, K.; Heip, C. (2012). Carbon flows in the benthic food web of the Porcupine Abyssal Plain: The(un)importance of labile detritus in supporting microbial and faunal carbon demands. Limnol. Oceanogr. 57(2): 645-664. dx.doi.org/10.4319/lo.2012.57.2.0645
  • 2011
    van Oevelen, D.; Soetaert, K.; Garcia, R.; de Stigter, H.C.; Cunha, M.R.; Pusceddu, A.; Danovaro, R.; Garcia, R. (2011). Canyon conditions impact carbon flows in food webs of three sections of the Nazare canyon. Deep-Sea Res., Part 2, Top. Stud. Oceanogr. 58(23-24): 2461-2476. dx.doi.org/10.1016/j.dsr2.2011.04.009

Linked projects

NWO SANDBOX_Smart and sustainable design for offshore operations in a sandy seabed
Supervisor
Karline Soetaert
Funder
Netherlands Organization for Scientific Research
Project duration
28 May 2015 - 31 Aug 2019
EMODnet_The European Marine Observation and Data Network - part biology
Supervisor
Karline Soetaert
Funder
European Community
Project duration
19 Apr 2017 - 18 May 2019
PULS_Impact Assessment of Pulstrawl Fishery (IAPF)
Supervisor
Karline Soetaert
Funder
Wageningen Marine Research
Project duration
1 Jan 2016 - 31 Dec 2019