Publications
2023
Scholarly publications
Stuart-Lee, A. E., Mortensen, J., Juul-Pedersen, T., Middelburg, J. J., Soetaert, K., Hopwood, M. J., Engel, A., & Meire, L. (2023). Influence of glacier type on bloom phenology in two Southwest Greenland fjords. Estuarine, Coastal and Shelf Science, 284, [108271]. https://doi.org/10.1016/j.ecss.2023.108271
2022
Scholarly publications
Kaaden, A-S. V. D., Mohn, C., Gerkema, T., Maier, S. R., de Froe, E., van de Koppel, J., Rietkerk, M., Soetaert, K., & van Oevelen, D. (2022). Corrigendum to “Feedbacks between hydrodynamics and cold-water coral mound development” [Deep-Sea Res. 178 (2021) 103641]. Deep-Sea Research Part I: Oceanographic Research Papers, 184, [103743]. https://doi.org/10.1016/j.dsr.2022.103743
de Froe, E., Maier, S. R., Horn, H. G., Wolff, G. A., Blackbird, S., Mohn, C., Schultz, M., van der Kaaden, A-S., Cheng, C. H., Wubben, E., van Haastregt, B., Moller, E. F., Lavaleye, M., Soetaert, K., Reichart, G. J., & van Oevelen, D. (2022). Hydrography and food distribution during a tidal cycle above a cold-water coral mound. Deep-Sea Research Part I: Oceanographic Research Papers, 189, [103854]. https://doi.org/10.1016/j.dsr.2022.103854
2021
Scholarly publications
Webb, A. E., De Bakker, D. M., Soetaert, K., Da Costa, T., Van Heuven, S. M. A. C., Van Duyl, F. C., Reichart, G. J., & De Nooijer, L. J. (2021). Quantifying functional consequences of habitat degradation on a Caribbean coral reef. Biogeosciences, 18(24), 6501-6516. https://doi.org/10.5194/bg-18-6501-2021
Stratmann, T., Soetaert, K., Kersken, D., & van Oevelen, D. (2021). Polymetallic nodules are essential for food‑web integrity of a prospective deep‑seabed mining area in Pacific abyssal plains. Scientific Reports, 11(1), 1-11. [12238]. https://doi.org/10.1038/s41598-021-91703-4
de Kluijver, A., Bart, M. C., van Oevelen, D., de Goeij, J. M., Leys, S. P., Maier, S. R., Maldonado, M., Soetaert, K., Verbiest, S., & Middelburg, J. J. (2021). An Integrative Model of Carbon and Nitrogen Metabolism in a Common Deep-Sea Sponge (Geodia barretti). Frontiers in Marine Science, 7, 1-18. [596251]. https://doi.org/10.3389/fmars.2020.596251
Seepma, S., Ruiz Hernandez, S., Nehrke, G., Soetaert, K., Philipse, A. P., Kuipers, B. W. M., & Wolthers, M. (2021). Controlling CaCO3 particle size with {Ca2+}:{CO32-} ratios in aqueous environments. Crystal Growth & Design, 21(3), 1576-1590. https://doi.org/10.1021/acs.cgd.0c01403
2020
Scholarly publications
van der Kaaden, A-S., van Oevelen, D., Rietkerk, M., Soetaert, K., & van de Koppel, J. (2020). Spatial Self-Organization as a New Perspective on Cold-Water Coral Mound Development. Frontiers in Marine Science, 7, [631]. https://doi.org/10.3389/fmars.2020.00631
Stratmann, T., Lins, L., Vanreusel, A., Purser, A., Marcon, Y., Rodrigues, C. F., Ravara, A., Esquete, P., Cunha, M. R., Simon-Lledó, E., van Breugel, P., Sweetman, A. K., Soetaert, K., van Oevelen, D., & de Jonge, D. S. W. (2020). Abyssal food-web model indicates faunal carbon flow recovery and impaired microbial loop 26 years after a sediment disturbance experiment. Progress in Oceanography, 189, 1-24. [102446]. https://doi.org/10.1016/j.pocean.2020.102446
Middelburg, J. J., Soetaert, K., & Hagens, M. (2020). Ocean Alkalinity, Buffering and Biogeochemical Processes: Review Article. Reviews of Geophysics, 58(3), [e2019RG000681]. https://doi.org/10.1029/2019RG000681
Stratmann, T., van Oevelen, D., Martínez Arbizu, P., Wei, C-L., Liao, J-X., Cusson, M., Scrosati, R. A., Archambault, P., Snelgrove, P. V. R., Ramey-Balci, P. A., Burd, B. J., Kenchington, E., Gilkinson, K., Belley, R., & Soetaert, K. E. R. (2020). The BenBioDen database, a global database for meio-, macro- and megabenthic biomass and densities. Scientific data, 7, [206]. https://doi.org/10.1038/s41597-020-0551-2
2019
Scholarly publications
Stratmann, T., Soetaert, K. E. R., Wei, C-L., Lin, Y-S., & van Oevelen, D. (2019). The SCOC database: a large, open, and global database with sediment community oxygen consumption rates. Scientific data, 6, [242]. https://doi.org/10.1038/s41597-019-0259-3
https://dspace.library.uu.nl/bitstream/handle/1874/387012/Stratmann_et_al._2019_The_SCOC_database_a_large_open_and_global_database_._.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/387012/Stratmann_et_al._2019_The_SCOC_database_a_large_open_and_global_database_._.pdf?sequence=1
2018
Scholarly publications
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., & Yakushev, E. (2018). Modelling marine sediment biogeochemistry: current knowledge gaps, challenges and some methodological advice for advancement. Frontiers in Marine Science, 5, [19]. https://doi.org/10.3389/fmars.2018.00019
2017
Scholarly publications
Holding, J. M., Duarte, C. M., Delgado-Huertas, A., Soetaert, K., Vonk, J. E., Agusti, S., Wassmann, P., & Middelburg, J. J. (2017). Autochthonous and allochthonous contributions of organic carbon to microbial food webs in Svalbard fjords. Limnology and Oceanography, 62(3), 1307-1323. https://doi.org/10.1002/lno.10526
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. Estuarine, Coastal and Shelf Science, 188, 1-11. https://doi.org/10.1016/j.ecss.2017.02.002
Maugendre, L., J.-P., G., 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. Estuarine, Coastal and Shelf Science, 186(Part A), 100-111. https://doi.org/10.1016/j.ecss.2015.12.018
Other output
Gattuso, J-P. (Author), Epitalon, J-M. (Author), Lavigne, H. (Author), Orr, J. C. (Author), Gentili, B. (Author), Hagens, M. (Author), Hofmann, A. (Author), Proye, A. (Author), Soetaert, K. (Author), & Rae, J. (Author). (2017). Package 'seacarb': Seawater Carbonate Chemistry. Software https://cran.r-project.org/package=seacarb
2016
Other output
Hofmann, A. (Author), Soetaert, K. (Author), Meysman, F. J. R. (Author), & Hagens, M. (Author). (2016). Package 'AquaEnv': Integrated Development Toolbox for Aquatic Chemical Model Generation. Software https://cran.r-project.org/package=AquaEnv
2015
Scholarly publications
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. Estuarine, Coastal and Shelf Science, 165, 117-127. https://doi.org/10.1016/j.ecss.2015.09.010
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. Marine Environmental Research, 108, 55. https://doi.org/10.1016/j.marenvres.2015.04.010
2014
Scholarly publications
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. Estuarine, Coastal and Shelf Science, 147, 78-86. https://doi.org/10.1016/j.ecss.2014.05.022
2013
Scholarly publications
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. Journal of Sea Research, 78, 45-58. https://doi.org/10.1016/j.seares.2013.01.002
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. https://doi.org/10.5194/bg-10-1425-2013
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. Marine Ecology Progress Series, 478, 87-100. https://doi.org/10.3354/meps10183
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. https://doi.org/10.5194/bg-10-6879-2013
Koho, K. A., Nierop, K. G. J., Moodley, L., Middelburg, J. J., Pozzato, L., Soetaert, K., & Reichart, G-J. (2013). Microbial bioavailability regulates organic matter preservation in marine sediments. Biogeosciences, 10(2), 1131-1141. https://doi.org/10.5194/bg-10-1131-2013
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. Limnology and Oceanography: Fluids and Environments, 3, 210-224. https://doi.org/10.1215/21573689-2397024
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. Estuarine, Coastal and Shelf Science, 120, 1-11. https://doi.org/10.1016/j.ecss.2013.01.008
2012
Scholarly publications
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. Marine Ecology Progress Series, 455, 13-31. https://doi.org/10.3354/meps09676
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. Journal of Sea Research, 68, 6-19. https://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, 4059-4070. https://doi.org/10.5194/bg-9-4059-2012
2011
Scholarly publications
Braeckman, U., Provoost, P., Moens, T., Soetaert, K., Middelburg, J. J., Vincx, M., & Vanaverbeke, J. (2011). Biological vs. physical mixing effects on benthic food web dynamics. PLoS One, 6(3), e18078. https://doi.org/10.1371/journal.pone.0018078
Van Engeland, T., Bouma, T. J., Morris, E. P., Brun, F. G., Peralta, G., Lara, M., Hendriks, I. E., Soetaert, K., & Middelburg, J. J. (2011). Potential uptake of dissolved organic matter by seagrasses and macroalgae. Marine Ecology Progress Series, 427, 71-81. https://doi.org/10.3354/meps09054
Moodley, L., Nigam, R., Ingole, B., Prakash Babu, C., Panchang, R., Nanajkar, M., Sivadas, S., van Breugel, P., van IJzerloo, L., Rutgers, R., Heip, C. H. R., Soetaert, K., & Middelburg, J. J. (2011). Oxygen minimum seafloor ecological (mal) functioning. Journal of Experimental Marine Biology and Ecology, 398(1-2), 91-100. https://doi.org/10.1016/j.jembe.2010.12.015
Van den Meersche, K., Soetaert, K., & Middelburg, J. J. (2011). Plankton dynamics in an estuarine plume: a mesocosm 13C and 15N tracer study. Marine Ecology Progress Series, 429, 29-43. https://doi.org/10.3354/meps09097
2010
Scholarly publications
Van Frausum, J., Middelburg, J. J., Soetaert, K., & Meysman, F. J. R. (2010). Different proxies for the reactivity of aquatic sediments towards oxygen: A model assessment. Ecological Modelling, 221, 2054-2067.
Van Engeland, T., Soetaert, K., Knuijt, A., Laane, R. W. P. M., & Middelburg, J. J. (2010). Dissolved organic nitrogen dynamics in the North Sea: A time series analysis (1995 - 2005). Estuarine, Coastal and Shelf Science, 89, 31-42.
De Laender, F., van Oevelen, D., Soetaert, K., & Middelburg, J. J. (2010). Carbon transfer in herbivore- and microbial loop-dominated pelagic food webs in the southern Barents Sea during spring and summer. Marine Ecology Progress Series, 398, 93-107, doi: 10.3354/meps08335.
Hofmann, A. F., Soetaert, K., Middelburg, J. J., & Meysman, F. J. R. (2010). AquaEnv: An Aquatic Acid–Base Modelling Environment in R. Aquatic Geochemistry, 16(4), 507-546, doi: 10.1007/s10498-009-9084-1.
Guilini, K., van Oevelen, D., Soetaert, K., Middelburg, J. J., & Vanreusel, A. (2010). Nutritional importance of benthic bacteria for deep-sea nematodes from the Arctic ice margin: Results of an isotope tracer experiment. Limnology and Oceanography, 55(5), 1977-1989.
van Oevelen, D., Van den Meersche, K., Meysman, F. J. R., Soetaert, K., Middelburg, J. J., & Vézina, A. F. (2010). Quantifying food web flows using linear inverse models. Ecosystems, 13(1), 32-45. https://doi.org/10.1007/s10021-009-9297-6
Evrard, V., Soetaert, K., Heip, C. H. R., Huettel, M., Xenopoulos, M. A., & Middelburg, J. J. (2010). Carbon and nitrogen flows through the benthic food web of a photic subtidal sandy sediment. Marine Ecology Progress Series, 416, 1-16.
De Laender, F., van Oevelen, D., Frantzen, S., Middelburg, J. J., & Soetaert, K. (2010). Seasonal PCB bioaccumulation in an arctic marine ecosystem: A model analysis incorporating lipid dynamics, food-web productivity and migration. Environmental Science and Technology, 44(1), 356-361.
Provoost, P., van Heuven, S., Soetaert, K., Laane, R. W. P. M., & Middelburg, J. J. (2010). Seasonal and long-term changes in pH in the Dutch coastal zone. Biogeosciences, 7, 3869-3878.
Braeckman, U., Provoost, P., Gribsholt, B., Van Gansbeke, D., Middelburg, J. J., Soetaert, K., Vincx, M., & Vanaverbeke, J. (2010). Role of macrofauna functional traits and density in biogeochemical fluxes and bioturbation. Marine Ecology Progress Series, 399, 173-186.
De Laender, F., van Oevelen, D., Middelburg, J. J., & Soetaert, K. (2010). Uncertainties in ecological, chemical and physiological parameters of a bioaccumulation model: Implications for internal concentrations and tissue based risk quotients. Ecotoxicology and Environmental Safety, 73, 240-246.
De Laender, F., Soetaert, K., De Schamphelaere, K. A. C., Middelburg, J. J., & Janssen, C. R. (2010). Ecological significance of hazardous concentrations in a planktonic food web. Ecotoxicology and Environmental Safety, 73(3), 247-253.
De Laender, F., Soetaert, K., & Middelburg, J. J. (2010). Inferring chemical effects on carbon flows in aquatic food webs: Methodology and case study. Environmental Pollution, 158, 1775-1782.
de Kluijver, A., Soetaert, K., Schulz, K. G., Riebesell, U., Bellerby, R. G. J., & Middelburg, J. J. (2010). Phytoplankton-bacteria coupling under elevated CO2 levels: a stable isotope labelling study. Biogeosciences, 7, 3783-3797, doi:10.5194/bg-7-3783-2010.
Hofmann, A. F., Middelburg, J. J., Soetaert, K., Wolf-Gladrow, D. A., & Meysman, F. J. R. (2010). Proton cycling, buffering, and reaction stoichiometry in natural waters. Marine Chemistry, 121, 246-255.
2009
Scholarly publications
Cook, P. L. M., van Oevelen, D., Soetaert, K., & Middelburg, J. J. (2009). Carbon and nitrogen cycling on intertidal mudflats of a temperate Australian estuary. IV. Inverse model analysis and synthesis. Marine Ecology Progress Series, 394, 35-48.
Hofmann, A. F., Middelburg, J. J., Soetaert, K., & Meysman, F. J. R. (2009). pH modelling in aquatic systems with time-variable acid-base dissociation constants applied to the turbid, tidal Scheldt estuary. Biogeosciences, 6, 1539-1561. http://www.biogeosciences.net/6/1539/2009/bg-6-1539-2009.html
Vandewiele, S., Cowie, G., Soetaert, K., & Middelburg, J. J. (2009). Amino acid biogeochemistry and organic matter degradation state accross the Pakistan Margin Oxygen minimum zone. Deep-Sea Research. Part II: topical studies in oceanography, 56(6-7), 376-392.
Cox, T. J. S., Maris, T., Soetaert, K., Conley, D. J., van Damme, S., Meire, P., Middelburg, J. J., Vos, M., & Struyf, E. (2009). A macro-tidal freshwater ecosystem recovering from hypereutrophication: the Schelde case study. Biogeosciences, 6, 2935-2948.
2008
Scholarly publications
Hofmann, A., Soetaert, K., & Middelburg, J. J. (2008). Present nitrogen and carbon dynamics in the Scheldt estuary using a novel1-D model. Biogeosciences, 5(4), 981-1006.
Andersson, J. H., Woulds, C., Schwarz, M., Cowie, G. L., Levin, L. A., Soetaert, K., & Middelburg, J. J. (2008). Short-term fate of phytodetritus in sediments across the Arabian Sea Oxygen Minimum Zone. Biogeosciences, 5(1), 43-53.
Hofmann, A. F., Meysman, F. J. R., Soetaert, K., & Middelburg, J. J. (2008). A step-by-step procedure for pH model construction in aquatic systems. Biogeosciences, 5(1), 227-251.
2007
Scholarly publications
Soetaert, K., Hoffman, A., Middelburg, J. J., Meysman, F. J. R., & Greenwood, J. (2007). The effect of biogeochemical processes on pH. Marine Chemistry, 105, 30-51.
2006
Scholarly publications
Andersson, J. H., Middelburg, J. J., & Soetaert, K. (2006). Identifiability and uncertainty analysis of bio-irrigation. Journal of Marine Research, 64(3), 407-429.
2005
Scholarly publications
Moodley, L., Middelburg, J. J., Herman, P. M. J., Soetaert, K., & de Lange, G. J. (2005). Oxygenation and organic-matter preservation in marine sediments: Direct experimental evidence from ancient organic carbon-rich deposits. Geology, 33(11), 889-892.
2004
Scholarly publications
Andersson, J. H., Wijsman, J. W. M., Herman, P. M. J., Middelburg, J. J., Soetaert, K., & Heip, C. H. R. (2004). Respiration patterns in the deep ocean. Geophysical Research Letters, 31.