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Publications Ecosysteem Studies

2013
  1. Braeckman, U., J. Vanaverbeke, M. Vincx, D. van Oevelen, and K. Soetaert. 2013. Meiofauna metabolism in suboxic sediments: currently overestimated. Plos One 8:e59289-e59289.
    http://dx.doi.org/doi:10.1371/journal.pone.0059289
  2. Koho, K. A., Nierop, K. G. J., Moodley, L., Middelburg, J. J., Pozzato, L., Soetaert, K., van der Plicht, J., and Reichart, G-J.: Microbial bioavailability regulates organic matter preservation in marine sediments, Biogeosciences, 10, 1131-1141, doi:10.5194/bg-10-1131-2013, 2013.
    http://dx.doi.org/10.5194/bg-10-1131-2013
  3. Krumins, J. A., D. van Oevelen, T. M. Bezemer, G. B. De Deyn, W. H. G. Hol, E. van Donk, W. de Boer, P. C. de Ruiter, J. J. Middelburg, F. Monroy, K. Soetaert, E. Thebault, J. van de Koppel, J. A. van Veen, M. Viketoft, and W. H. van der Putten. 2013. Soil and Freshwater and Marine Sediment Food Webs: Their Structure and Function. BioScience 63:35-42.
    http://dx.doi.org/10.1525/bio.2013.63.1.8
  4. Larsson, A. I., T. Lundalv, and D. van Oevelen. 2013a. Skeletal growth, respiration rate and fatty acid composition in the cold-water coral Lophelia pertusa under varying food conditions. Marine Ecology Progress Series 483:169-184.
    http://www.int-res.com/abstracts/meps/v483/p169-184/
  5. Larsson, A. I., D. van Oevelen, A. Purser, and L. Thomsen. 2013b. Tolerance to long-term exposure of suspended benthic sediments and drill cuttings in the cold-water coral Lophelia pertusa. Marine Pollution Bulletin 70:176-188.
    http://dx.doi.org/10.1016/j.marpolbul.2013.02.033
  6. Meire, L., Soetaert, K. E. R., and Meysman, F. J. R. Impact of global change on coastal oxygen dynamics and risk of hypoxia, Biogeosciences, 10, 2633-2653, doi:10.5194/bg-10-2633-2013, 2013.
    http://dx.doi.org/10.5194/bg-10-2633-2013
  7. Mueller, C. E., T. Lundalv, J. J. Middelburg, and D. van Oevelen. 2013. The symbiosis between Lophelia pertusa and Eunice norvegica stimulates coral calcification and worm assimilation. Plos One 8:e58660-e58660.
    http://dx.doi.org/10.1371/journal.pone.0058660
  8. Pozzato, L., D. van Oevelen, L. Moodley, K. Soetaert, and J. J. Middelburg. 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.
    http://dx.doi.org/10.1016/j.seares.2013.01.002
  9. Pozzato, L., Van Oevelen, D., Moodley, L., Soetaert, K., and Middelburg, J. J.: Sink or link? The bacterial role in benthic carbon cycling in the Arabian sea oxygen minimum zone, Biogeosciences Discuss., 10, 10399-10428, doi:10.5194/bgd-10-10399-2013, 2013.
    http://dx.doi.org/10.5194/bgd-10-10399-2013
  10. Regnier P., Friedlingstein P., Ciais P., Mackenzie F.T., Gruber N., Janssens I.A., Laruelle G.G., Lauerwald R., Luyssaert S., Andersson A.J., Arndt S., Arnosti C., Borges A.V., Dale A.W., Gallego-Sala A., Goddéris Y., Goossens N., Hartmann J., Heinze C., Ilyina T., Joos F., LaRowe D.E., Leifeld J., Meysman F.J.R., Munhoven G., Raymond P.A., Spahni R., Suntharalingam P., Thullner M. (2013) Anthropogenic perturbation of the carbon fluxes from land to ocean. Nature Geoscience(2013).
    http://dx.doi.org/10.1038/ngeo1830 
  11. Rossi F, Gribsholt B, Gazeau F, Di Santo V, Middelburg JJ (2013) Complex Effects of Ecosystem Engineer Loss on Benthic Ecosystem Response to Detrital Macroalgae. PLoS ONE 8(6): e66650. doi:10.1371/journal.pone.0066650
    http://dx.doi.org/10.1371/journal.pone.0066650
  12. Takasu H., T. Kunihiro, S. Nakano (2013) Estimation of carbon biomass and community structure of planktonic bacteria in Lake Biwa using respiratory quinone analysis. Limnology. in press.
    http://dx.doi.org/10.1007/s10201-013-0402-3
  13. Tecchio, S., D. van Oevelen, K. Soetaert, J. Navarro, and E. Ramirez-Llodra. 2013. Trophic dynamics of deep-sea megabenthos are mediated by surface productivity. Plos One 8:e63796-e63796.
    http://dx.doi.org/10.1371/journal.pone.0063796
  14. Van Engeland, T., T. J. Bouma, E. P. Morris, F. G. Brun, G. Peralta, M. Lara, I. E. Hendriks, P. van Rijswijk, B. Veuger, K. Soetaert, J. J. Middelburg. 2013. Dissolved organic matter uptake in a temperate seagrass ecosystem. Marine Ecology Progress Series 478:87-100
    http://www.int-res.com/abstracts/meps/v478/p87-100/
2012
  1. Braeckman, U., P. Provoost, K. Sabbe, K. Soetaert, J. J. Middelburg, M. Vincx, and J. Vanaverbeke. 2012. Temporal dynamics in the diet of two marine polychaetes as inferred from fatty acid biomarkers. Journal of Sea Research 68:6-19.
  2. Dähnke, K., A. Moneta, B. Veuger, K. Soetaert, and J. J. Middelburg. 2012. Balance of assimilative and dissimilative nitrogen processes in a diatom-rich tidal flat sediment. Biogeosciences 9:4059-4070.
  3. de Kluijver, A., J. L. Yu, M. Houtekamer, J. J. Middelburg, and Z. W. Liu. 2012. Cyanobacteria as a carbon source for zooplankton in eutrophic Lake Taihu, China, measured by C-13 labeling and fatty acid biomarkers. Limnology and Oceanography 57:1245-1254.
  4. Downing, J. A., J. J. Cole, C. M. Duarte, J. J. Middelburg, J. M. Melack, Y. T. Prairie, P. Kortelainen, R. G. Striegl, W. H. McDowell, and L. J. Tranvik. 2012. Global abundance and size distribution of streams and rivers. Inland Waters 2:229-236.
  5. Evrard, V., M. Huettel, P. L. M. Cook, K. Soetaert, C. H. R. Heip, and J. J. Middelburg. 2012. Importance of phytodetritus and microphytobenthos for heterotrophs in a shallow subtidal sandy sediment. Marine Ecology-Progress Series 455:13-31.
  6. Faber, P. A., A. J. Kessler, J. K. Bull, I. D. McKelvie, F. J. R. Meysman, and P. L. M. Cook. 2012. The role of alkalinity generation in controlling the fluxes of CO2 during exposure and inundation on tidal flats. Biogeosciences 9:4087-4097.
  7. Hunter, W. R., B. Veuger, and U. Witte. 2012. Macrofauna regulate heterotrophic bacterial carbon and nitrogen incorporation in low-oxygen sediments. Isme Journal 6:2140-2151.
  8. Kürten, B., Frutos, I., Struck, U., Painting, S.J., Polunin, N.V.C., Middelburg, J.J. Trophodynamics and functional feeding groups of North Sea fauna: a combined stable isotope and fatty acid approach. Biogeochemistry. DOI 10.1007/s10533-012-9701-8
  9. Mazzia, F., J. R. Cash, and K. Soetaert. 2012. A Test Set for stiff Initial Value Problem Solvers in the open source software R: Package deTestSet. Journal of Computational and Applied Mathematics 236:4119-4131.
  10. Oakes, J. M., B. D. Eyre, and J. J. Middelburg. 2012. Transformation and fate of microphytobenthos carbon in subtropical shallow subtidal sands: A 13C-labeling study. Limnology and Oceanography 57:1846-1856.
  11. Pedrotti, M. L., S. Fiorini, M. E. Kerros, J. J. Middelburg, and J. P. Gattuso. 2012. Variable production of transparent exopolymeric particles by haploid and diploid life stages of coccolithophores grown under different CO2 concentrations. Journal of Plankton Research 34:388-398.
  12. Polsenaere, P., E. Lamaud, V. Lafon, J. M. Bonnefond, P. Bretel, B. Delille, J. Deborde, D. Loustau, and G. Abril. 2012. Spatial and temporal CO2 exchanges measured by Eddy Covariance over a temperate intertidal flat and their relationships to net ecosystem production. Biogeosciences 9:249-268.
  13. Rao, A. M. F., L. Polerecky, D. Ionescu, F. J. R. Meysman, and D. de Beer. 2012. The influence of physically-induced pore-water advection, benthic photosynthesis, and respiration on calcium carbonate dynamics in reef sands. Limnology and Oceanography 57:809-825.
  14. Rao, A. and M. A. Charette. 2012. Benthic nitrogen fixation in an eutrophic estuary impacted by groundwater discharge. Journal of Coastal Research 28(2) : 477-485.
  15. Scholes, R. J., M. Walters, E. Turak, H. Saarenmaa, C. H. R. Heip, E. O. Tuama, D. P. Faith, H. A. Mooney, S. Ferrier, R. H. G. Jongman, I. J. Harrison, T. Yahara, H. M. Pereira, A. Larigauderie, and G. Geller. 2012. Building a global observing system for biodiversity. Current Opinion in Environmental Sustainability 4:139-146.
  16. Soetaert, K. and F. Meysman. 2012a. Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R. Environmental Modelling & Software 32:49-60.
  17. Soetaert, K. and F. Meysman. 2012b. Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software R (vol 32, pg 49, 2012). Environmental Modelling & Software 35:194-194.
  18. Soetaert, K., van Oevelen, D., and Sommer, S.: Modelling the impact of Siboglinids on the biogeochemistry of the Captain Arutyunov mud volcano (Gulf of Cadiz), Biogeosciences, 9, 5341-5352, doi:10.5194/bg-9-5341-2012, 2012.
  19. Tamooh, F., K. Van den Meersche, F. Meysman, T. R. Marwick, A. V. Borges, R. Merckx, F. Dehairs, S. Schmidt, J. Nyunja, and S. Bouillon. 2012. Distribution and origin of suspended matter and organic carbon pools in the Tana River Basin, Kenya. Biogeosciences 9:2905-2920.
  20. Trinh, A. D., F. Meysman, E. Rochelle-Newall, and M. P. Bonnet. 2012. Quantification of sediment-water interactions in a polluted tropical river through biogeochemical modeling. Global Biogeochemical Cycles 26.
  21. Van Colen, C., F. Rossi, F. Montserrat, M. G. Andersson, B. Gribsholt, P. M. Herman, S. Degraer, M. Vincx, T. Ysebaert, and J. J. Middelburg. 2012. Organism-sediment interactions govern post-hypoxia recovery of ecosystem functioning. Plos One 7:e49795.
  22. van Oevelen, D., K. Soetaert, and C. Heip. 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. Limnology and Oceanography 57:645-664.
  23. Veuger, B., D. van Oevelen, and J. J. Middelburg. 2012. Fate of microbial nitrogen, carbon, hydrolysable amino acids, monosaccharides, and fatty acids in sediment. Geochimica Et Cosmochimica Acta 83:217-233.
  24. Woulds, C., J. J. Middelburg, and G. L. Cowie. 2012. Alteration of organic matter during infaunal polychaete gut passage and links to sediment organic geochemistry. Part I: Amino acids. Geochimica Et Cosmochimica Acta 77:396-414.
  25. Zetsche, E. M. and F. J. R. Meysman. 2012. Dead or alive? Viability assessment of micro- and mesoplankton. Journal of Plankton Research 34:493-509. 

PhD theses

  1. De Kluijver, A. Carbon flows in natural plankton communities in the Anthropocene. Utrecht University, 156 pp. 
  2. Pozzato, L. Prokaryotic, protozoan and metazoan processing of organic matter in sediments: a tracer approach. Utrecht University, 154 pp.
2011
  1. 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): 1-12. http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0018078
  2. Soetaert, K., Gregoire, M.L., 2011. Data assimilation of the carbonate pH system – a kalman filter tested. Ecol. Modelling 222, 1929-1942. 
  3. Van den Meersche, K., Soetaert, K, J.J. Middelburg, 2011. Plankton dynamics in an estuarine plume” a 13C and 15N tracer study. Marine Ecology Progress Series 429, 29-43.
  4. Pastor, L, Cathalot, C., Deflandre, B., Soetaert, K., Meysman, F., Ulses, C., Metzger, E., Viollier, E., Rabouille, C., 2011. Modeling biogeochemical processes in sediments from the Rhône River prodelta area (NW Mediterranean Sea). Biogeosciences 8, 1351-1366. 
  5. 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. 
  6. van Oevelen, D., Bergmann, M., Soetaert, K., Bauerfeind, E., Hasemann, C., Klages, M., Schewe, I., Soltwedel, T. & Budaeva, N. E., 2011. Carbon flows in the benthic food web at the deep-sea observatory HAUSGARTEN (Fram Strait). Deep-Sea Research Part I-Oceanographic Research Papers 58, 1069-1083.
  7. Gontikaki, E., van Oevelen, D.; Soetaert, K., Witte, U., 2011. Food web flows through a sub-arctic deep-sea benthic community. Progress in Oceanography. vol 91, pp. 245-259.
    http://dx.doi.org/10.1016/j.pocean.2010.12.014 
  8. De Laender, F, Hammer, J, Hendriks, J, Soetaert, K, Janssen, C, 2011. Combining Monitoring Data and Modeling Identifies PAHs as Emerging Contaminants in the Arctic. Environmental Science & Technology 45 (20), pp 9024–9029
  9. van Oevelen, D., Soetaert, K., García, R., Stigter, H.C. De, Cunha, M. da, Pusceddu, A., Danovaro, R. 2011. Canyon conditions impact carbon flows in food webs of three sections of the Nazare canyon. Deep-Sea Research Part II-Topical Studies in Oceanography 58, 2461,2476.
  10. Braeckman, U., Van Colen, C., Soetaert, K., Vincx, M., Vanaverbeke. J., 2011. Contrasting macrobenthic activities differentially affect nematode density and diversity in a shallow subtidal marine sediment. Marine Ecology Progress Series 422:179-191. 
  11. Danovaro, R., Corinaldesi, C., Dell'Anno, A., Fuhrman, J., Middelburg, J., Noble, R. , Suttle, C, 2011. Marine viruses and global climate change. FEMS Microbiology Reviews.
    http://dx.doi.org/10.1111/j.1574-6976.2010.00258.x 
  12. Guilini, K., Soltwedel, T., van Oevelen, D, Vanreusel, A., 2011. Deep-sea Nematodes Actively Colonise Sediments, Irrespective of the Presence of a Pulse of Organic Matter: Results from an In- Situ Experiment. PLoS One 6(4): e18912.
    http://hdl.handle.net/10.1371/journal.pone.0018912
  13. Joassin, P., B. Delille, K. Soetaert, J. Harley, A. V. Borges, L. Chou, U. Riebesell, K. Suykens, and M. Gregoire, 2011. Carbon and nitrogen flows during a bloom of the coccolithophore Emiliania huxleyi: modelling a mesocosm experiment.Journal of Marine Systems 85: 71-85. 
  14. Koopmans, M., van Rijswijk, P., Martens, D., Egorova-Zachernyuk, T. A., Middelburg, J. J. and R. H. Wijffels. 2011. Carbon conversion and metabolic rate in two marine sponges Mar Biol 158:9-20
  15. 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., Soetaert, K., Middelburg, J., 2011. Oxygen minimum seafloor ecological (mal)functioning.Journal of Experimental Marine Biology and Ecology 398:91-100. 
  16. Rossi, F., Middelburg, J. J., 2011. Intraspecific diet shift of Macoma balthica during community reassembly in an estuarine intertidal flat. Estuarine Coastal and Shelf Science 92: 496-501. 
  17. Teuchies, J., L. Bervoets, T. J. S. Cox, P. Meire, De Deckere, E., 2011. The effect of waste water treatment on river metal concentrations: removal or enrichment? Journal of Soils and Sediments 11:364-372. 
  18. van Duyl, F.C., Moodley, L., Nieuwland, G., van Ijzerloo, L., van Soest, R.W.M. Houtekamer, M., Meesters, E.H.W.G., Middelburg, J.J., 2011. Coral cavity sponges depend on reef-derived food resources: stable isotope and fatty acid constraints. Marine BiologyMarine Biology 158, 1653 - 1666. 
  19. Vandenbruwaene, W., Maris, T., Cox, T. J. S., Cahoon, D. R., Meire, P., Temmerman, S., 2011. Sedimentation and response to sea-level rise of a restored marsh with reduced tidal exchange: comparison with a natural tidal marsh. Geomorphology 130(3-4): 115-126.
    http://dx.doi.org/10.1016/j.geomorph.2011.03.004 
  20. Veuger, B., Van Oevelen, D. , 2011. Long-term pigment dynamics and diatom survival in dark sediment. Limnology and Oceanography 56, 3: 1065-1074.
  21. Hardison, A.K., Anderson, I.C., Canuel, E.A., Tobias, C.R., Veuger, B., 2011. Carbon and nitrogen dynamics in shallow photic systems: Interactions between macroalgae, microalgae, and bacteria. Limnology and Oceanography56:1489-1503.
  22. Thuróczy, C.-E., Gerringa, L. J. A., Klunder, M., Laan, P., Le Guitton, M., de Baar, H. J. W., 2011. Distinct trends in the speciation of iron between the shallow shelf seas and the deep basins of the Arctic Ocean. Journal of Geophysical Research 116, C10009. doi: 10.1029/2010JC006835.

Book chapters

  1. Niquil, N., K. Soetaert, G. A. Johnson, D. Van Oevelen, C. Bacher, B. Saint-Béat, and A. F. Vézina, 2011. Inverse modelling in modern ecology and application to coastal ecosystems. in Treatise on Estuarine and Coastal Science, Vol.9, 115-133, DOI: 10.1016/B978-0-12-374711-2.00906-2.

PhD theses

  1. Braeckman, Ulrike. Macrobenthos structuring the sea floor: Importance of its functional biodiversity for the benthic ecosystem. Ghent University (239 pag.).
2010
  1. Bahlmann, E., S. M. Bernasconi, S. Bouillon, M. Houtekamer, M. Korntheuer, F. Langenberg, C. Mayr, M. Metzke, J. J. Middelburg, B. Nagel, U. Struck, M. Voß, and K. C. Emeis. 2010 Performance evaluation of nitrogen isotope ratio determination in marine and lacustrine sediments: An inter-laboratory comparison. Organic Geochemistry 41:3-12.
  2. Boudreau, B. P., J. J. Middelburg, A. F. Hofmann, and F. J. R. Meysman. 2010 Ongoing transients in carbonate compensation. Global  Biogeochemical Cycles 24:13 p. 
  3. Boudreau, B. P., J. J. Middelburg, and F. J. R. Meysman. 2010 Carbonate compensation dynamics.Geophysical Research Letters 37:L03603. 
  4. Braeckman, U., P. Provoost, B. Gribsholt, D. Van Gansbeke, J. J. Middelburg, K. Soetaert, M. Vincx, and J. Vanaverbeke. 2010 Role of macrofauna functional traits and density in biogeochemical fluxes and bioturbation.Marine Ecology Progress Series 399:173-186.
  5. Cathalot, C., Rabouille, C., Pastor, L, Deflandre, B., Viollier, E., Buscail, R., Grémare, A., Treignier, C. & Pruski, A. (2010). Temporal variability of carbon recycling in coastal sediments influenced by rivers: assessing the impact of flood inputs in the Rhone River prodelta. Biogeosciences, 7, 1187-1207.
  6. Cox, T., K. Soetaert, J. P. Vanderborght, J. Kromkamp, and P. Meire. 2010 Modelling photosynthesis-irradiance curves: effects of temperature, dissolved silica depletion and changing community assemblage on community photosynthesis.Limnology and Oceanography Methods 8:424-440.
  7. De Kluijver, A., K. Soetaert, K. G. Schulz, U. Riebesell, R. G. J. Bellerby, and J. J. Middelburg. 2010 Phytoplankton-bacteria coupling under elevated CO2 levels: a stable isotope labelling study.Biogeosciences 7:3783-3797.
  8. De Laender, F., K. Soetaert, K. A. C. De Schamphelaere, J. J. Middelburg, and C. R. Jansen. 2010 Ecological significance of hazardous concentrations in a planktonic food web.Ecotoxicology and Environmental Safety 73:247-253. 
  9. De Laender, F., K. Soetaert, and J. J. Middelburg. 2010 Inferring chemical effects on carbon flows in aquatic food webs: Methodology and case study.Environmental Pollution 158:1775-1782. 
  10. De Laender, F., D. Van Oevelen, S. Frantzen, J. J. Middelburg, and K. Soetaert. 2010 Seasonal PCB bioaccumulation in an Arctic marine ecosystem: a model analysis incorporating lipid dynamics, food-web productivity and migration.Environmental Science & Technology 44:356-361.
  11. De Laender, F., D. Van Oevelen, J. J. Middelburg, and K. Soetaert. 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.
  12. De Laender, F., D. Van Oevelen, K. Soetaert, and J. J. Middelburg. 2010 Carbon transfer in a herbivore- and microbial loop-dominated pelagic food webs in the southern Barents Sea during spring and summer.Marine Ecology Progress Series 398:93-107. 
  13. Eid, E. M., K. H. Shaltout, Y. M. Al-Sodany, K. Soetaert, and K. Jensen. 2010 Modeling growth, carbon allocation and nutrient budgets of Phragmites australis in Lake Burullus, Egypt.Wetlands 30:240-251.
  14. Evrard, V., K. Soetaert, C. H. R. Heip, M. Huettel, M. A. Xenopoulos, and J. J. Middelburg. 2010 Carbon and nitrogen flows through the benthic food web of a photic subtidal sandy sediment.Marine Ecology Progress Series 416:1-16. 
  15. Fiorini, S., J.-P. Gattuso, P. Van Rijswijk, and J. J. Jack Middelburg. 2010 Coccolithophores lipid and carbon isotope composition and their variability related to changes in seawater carbonate chemistry.Journal of Experimental Marine Biology and Ecology 394:74-85.    
  16. Franco, M. A., J. Vanaverbeke, D. Van Oevelen, K. Soetaert, M. Costa, M. Vincx, and T. Moens. 2010 Respiration partitioning in contrasting subtidal sediments: seasonality and response to a spring phytoplankton deposition.Marine Ecology - An Evolutionary Perspective 31:276 - 290. 
  17. Garcia, R., H. C. De Stigter, K. Soetaert, E. Epping, L. Koning, L. Thomsen, and P. A. De Jesus Mendes. 2010 Sediment bioavailable organic matter, deposition rates and mixing intensity in the Setubal-Lisbon canyon and adjacent slope (Western Iberian Margin).Deep-Sea Research Part I: Oceanographic Research Papers 57:1012-1026.
  18. Gazeau, F., J.-P. Gattuso, C. Dawber, A. E. Pronker, F. Peene, J. Peene, C. H. R. Heip, and J. J. Middelburg. 2010 Effect of ocean acidification on the early life stages of the blue mussel Mytilus edulis.Biogeosciences 7:2051-2060.
  19. Grégoire, M., and K. Soetaert. 2010 Carbon, nitrogen, oxygen and sulfide budgets in the Black Sea : a biogeochemical model of the whole water column coupling the oxic and anoxic parts.Ecological Modelling 221:2287-2301.  
  20. Guilini, K., D. Van Oevelen, K. Soetaert, J. J. Middelburg, and A. Vanreusel. 2010 Nutritional importance of benthic bacteria for deep-sea nematodes from the Arctic ice margin: results of an isotope tracer experiment.Limnology and Oceanography 55:1977-1989. 
  21. Hardison, A. K., E. A. Canuel, I. C. Anderson, and B. Veuger. 2010 Fate of macroalgae in benthic systems: Carbon and nitrogen cycling within the microbial community. Marine Ecology Progress Series 414:41-55.
  22. Hofmann, A. F., J. J. Middelburg, K. Soetaert, D. A. Wolf-Gladrow, and F. J. R. Meysman. 2010 Proton cycling, buffering, and reaction stoichiometry in natural waters.Marine Chemistry 121:246-255. 
  23. Hofmann, A. F., K. Soetaert, J. J. Middelburg, and F. J. R. Meysman. 2010 AquaEnv: an aquatic acid–base modelling environment in R  Aquatic Geochemistry 16:507-546. 
  24. Kennedy, H., J. Beggins, C. M. Duarte, J. W. Fourqurean, M. Holmer, N. Marbà, and J. J. Middelburg. 2010 Seagrass sediments as a global carbon sink: isotope constraints.Global Biogeochemical Cycles 24:8
  25. Kromkamp, J.C. & van Engeland, T. (2010). Changes in phytoplankton biomass in the Western Scheldt estuary during the period 1978-2006. Estuaries and Coasts, 33(2), 270-285.
  26. Koopmans, M., P. Van Rijswijk, D. Martens, T. A. Egorova-Zachernyuk, J. J. Middelburg, and R. H. Wijffels. 2010 Carbon conversion and metabolic rate in two marine sponges.Marine Biology 158:9-20. 
  27. Lecroart, P., O. Maire, S. Schmidt, A. Grémare, P. Anschutz, and F. J. R. Meysman. 2010 Bioturbation, short-lived radioisotopes, and the tracer-dependence of biodiffusion coefficients.Geochimica et Cosmochimica Acta 74:6049-6063.
  28. Liefferinge, C. van, Simoens, I., Vogt, C., Cox, T.J.S., Breine, J., Ercken, D., Goethals, P., Belpaire, C. & Meire, P. (2010). Impact of habitat diversity on the sampling effort required for the assessment of river fish communities and IBI. Hydrobiologia, 644: 169-183.
  29. Meysman, F. J. R., and S. Bruers. 2010 Ecosystem functioning and maximum entropy production: a quantitative test of hypothes.Philosophical Transactions of the Royal Society B: Biological Sciences 365:1405-1416. 
  30. Meysman, F. J. R., O. S. Galaktionov, R. N. Glud, and J. J. Middelburg. 2010 Oxygen penetration around burrows and roots in aquatic sediments.Journal of Marine Research 68:309-336. 
  31. Nisumaa, A.-M., S. Pesant, R. G. J. Bellerby, B. Delille, J. J. Middelburg, J. C. Orr, U. Riebesell, T. Tyrrell, D. Wolf-Gladrow, and J.-P. Gattuso. 2010 EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data 2:167-175. 
  32. Oakes, J. M., B. D. Eyre, J. J. Middelburg, and H. T. S. Boschker. 2010 Composition, production, and loss of carbohydrates in subtropical shallow subtidal sandy sediments: Rapid processing and long-term retention revealed by 13C-labeling. Limnology and Oceanography 55:2126-2138. 
  33. Provoost, P., S. Van Heuven, K. Soetaert, R. W. P. M. Laane, and J. J. Middelburg. 2010 Seasonal and long-term changes in pH in the Dutch coastal zone. Biogeosciences 7:3869–3878. 
  34. Purser, A., A. I. Larsson, L. Thomsen, and D. Van Oevelen. 2010 The influence of flow velocity and food concentration on Lophelia pertusa (Scleractinia) zooplankton capture rates.Journal of Experimental Marine Biology and Ecology 395:55-62. 
  35. Schouten, S., J. J. Middelburg, E. C. Hopmans, and J. S. Sinninghe  Damsté. 2010 Fossilization and degradation of intact polar lipids in deep subsurface sediments: A theoretical approach. Geochimica et Cosmochimica Acta 74:3806-3814.
  36. Soetaert, K., and T. Petzoldt. 2010 Inverse modelling, sensitivity and Monte Carlo analysis in R using package FME.Journal of Statistical Software 33:1-28.
  37. Soetaert, K., T. Petzoldt, and R. W. Setzer. 2010 Solving Differential Equations in R: Package deSolve.Journal of Statistical Software 33:1-25.
  38. Sweetman, A. K., J. J. Middelburg, A. M. Berle, A. F. Bernardino, C. Schander, A. W. J. Demopoulos, and C. R. Smith. 2010 Impacts of exotic mangrove forests and mangrove deforestation on carbon remineralization and ecosystem functioning in marine sediments.Biogeosciences 7:2129-2145.
  39. Van Engeland, T., K. Soetaert, A. Knuijt, R. W. P. M. Laane, and J. J. Middelburg. 2010 Dissolved organic nitrogen dynamics in the North Sea: A time series analysis (1995-2005).Estuarine, Coastal and Shelf Science 89:31-42.
  40. Van Frausum, J., J. J. Middelburg, K. Soetaert, and F. J. R. Meysman. 2010 Different proxies for the reactivity of aquatic sediments towards oxygen: a model assessment. Ecological Modelling 221:2054-2067. 
  41. Van Oevelen, D., K. Van den Meersche, F. J. R. Meysman, K. Soetaert, J. J. Middelburg, and A. F. Vézina. 2010 Quantifying food web flows using linear inverse models. Ecosystems 13:32-45. 
  42. Vandepitte, L., B. Vanhoorne, A. Kraberg, N. Anisimova, C. Antoniadou, R. Araújo, I. Bartsch, B. Beker, L. Benedetti-Cecchi, I. Bertocci, S. Cochrane, K. Cooper, J. Craeymeersch, E. Christou, D. J. Crisp, S. Dahle, M. De Boissier, M. De Kluijver, S. Denisenko, D. De Vito, G. Duineveld, V. Escaravage, D. Fleischer, S. Fraschetti, A. Giangrande, C. Heip, H. Hummel, U. Janas, R. Karez, M. Kedra, P. Kingston, R. Kuhlenkamp, M. Libes, P. Martens, J. Mees, N. Mieszkowska, S. Mudrak, I. Munda, S. Orfanidis, M. Orlando-Bonaca, R. Palerud, E. Rachor, K. Reichert, H. Rumohr, D. Schiedek, P. Schubert, W. C. H. Sistermans, I. S. Sousa Pinto, A. J. Southward, A. Terlizzi, E. Tsiaga, J. E. E. Van Beusekom, E. Vanden Berghe, J. Warzocha, N. Wasmund, J. M. Weslawski, C. Widdicombe, M. Wlodarska-Kowalczuk, and M. L. Zettler. 2010 Data integration for European marine biodiversity research: creating a database on benthos and plankton to study large-scale patterns and long-term changes. Hydrobiologia 644:1-13. 
  43. Woulds, C., G. Cowie, and J. J. Middelburg. 2010 A method for the quantitative detection of 13C labelled amino acids and aldoses in marine sediments and fauna. Organic Geochemistry 41:13-21.
  44. Zhang, J., D. Gilbert, A. J. Gooday, L. Levin, S. W. A. Naqvi, J. J. Middelburg, M. Scranton, W. Ekau, A. Pena, B. Dewitte, T. Oguz, P. M. S. Monteiro, E. Urban, N. N. Rabalais, V. Ittekkot, W. M. Kemp, O. Ulloa, R. Elmgren, E. Escobar-Briones, and A. K. Van der Plas. 2010 Natural and human-induced hypoxia and consequences for coastal areas: synthesis and future development. Biogeosciences 7:1443-1467 
  45. Zhang, L., K. Li, Z. Liu, and J. J. Middelburg. 2010 Sedimented cyanobacterial detritus as a source of nutrient for submerged macrophytes (Vallisneria spiralis and Elodea nuttallii): An isotope labeling experiment using 15N.Limnology and Oceanography 55:1912-1917. 
  46. Zonneveld, K. A. F., G. J. M. Versteegh, S. Kasten, T. I. Eglinton, K.-C. Emeis, C. Huguet, B. P. Koch, G. J. De Lange, J. W. De Leeuw, J. J. Middelburg, G. Mollenhauer, F. G. Prahl, J. Rethemeyer, and S. G. Wakeham. 2010 Selective preservation of organic matter in marine environments; processes and impact on the sedimentary record. Biogeosciences 7:483-511. 

Book chapters

  1. Heip, C., Hummel, H., van Avesaath, P., Appeltans, W., Arvanitidis, C., Aspden, R., Austen, M., Boero, F., Bouma, TJ., Boxshall, G., Buchholz, F., Crowe, T., Delaney, A., Deprez, T., Emblow, C., Feral, JP.,Gasol, JM., Gooday, A., Harder, J., Ianora, A., Kraberg, A., Mackenzie, B., Ojaveer, H., Paterson, D.,Rumohr, H., Schiedek, D., Sokolowski, A., Somerfield, P., Sousa Pinto, I., Vincx, M., Węsławski, JM., Nash, R. (2009). Marine Biodiversity and Ecosystem Functioning. Printbase, Dublin, Ireland ISSN 2009-2539

PhD theses

  1. van Engeland, T.. Dissolved Organic Nitrogen dynamics in coastal ecosystems. Utrecht University.

Open source Software packages

  1. Frederik De Laender and Karline Soetaert (2010). ToxLim: Incorporating Ecological Data and Associated Uncertainty in Bioaccumulation Modeling . R package 1.0
    http://cran.r-project.org/web/packages/ToxLim/index.html
2009
  1. Almroth, E., A. Tengberg, J. H. Andersson, S. Pakhomova, and P. O. J. Hall. 2009 Effects of resuspension on benthic fluxes of oxygen, nutrients, dissolved inorganic carbon, iron and manganese in the Gulf of Finland, Baltic Sea. Continental Shelf Research 29:807-818.
  2. Arvanitidis, C., P. J. Somerfield, H. Rumohr, S. Faulwetter, V. Valavanis, A. Vasileiadou, G. Chatzigeorgiou, E. Vanden Berghe, J. Vanaverbeke, C. Labrune, A. Grémare, M. L. Zettler, M. Kedra, M. Wlodarska-Kowalczuk, I. F. Aleffi, J. M. Amouroux, N. Anisimova, G. Bachelet, M. Büntzow, S. J. Cochrane, M. J. Costello, J. Craeymeersch, S. Dahle, S. Degraer, S. Denisenko, C. Dounas, G. Duineveld, C. Emblow, V. Escavarage, M. C. Fabri, D. Fleischer, J. S. Gray, C. H. R. Heip, M. Herrmann, H. Hummel, U. Janas, I. Karakassis, M. A. Kendall, P. Kingston, L. Kotwicki, J. Laudien, A. S. Y. Mackie, E. L. Nevrova, A. Occhipinti-Ambrogi, P. G. Oliver, F. Olsgard, R. Palerud, A. Petrov, E. Rachor, N. K. Revkov, A. Rose, R. Sardá, W. C. H. Sistermans, J. Speybroeck, G. Van Hoey, M. Vincx, P. Whomersley, W. Willems, and A. Zenetos. 2009 Biological geography of the European seas: results from the MacroBen database. Marine Ecology Progress Series 382:265-278. 
  3. Bouillon, S., G. Abril, A. V. Borges, F. Dehairs, G. Govers, H. Hughes, R. Merckx, F. J. R. Meysman, J. Nyunja, C. Osburn, and J. J. Middelburg. 2009 Distribution, origin and cycling of carbon in the Tana River (Kenya): a dry season basin-scale survey from headwaters to the delta. Biogeosciences 6:2475-2493. 
  4. Cook, P. L. M., D. van Oevelen, K. Soetaert, and J. J. Middelburg. 2009 Carbon and nitrogen cycling on intertidal mudflats in a temperate Australian estuary. IV. An inverse model analysis and synthesis. Marine Ecology Progress Series 394:35-48. 
  5. Cox, T. J. S., T. Maris, K. Soetaert, D. J. Conley, S. Van Damme, P. Meire, J. J. Middelburg, M. Vos, and E. Struyf. 2009 A macro-tidal freshwater ecosystem recovering from hypereutrophication: the Schelde case study. Biogeosciences 6:2935-2948. 
  6. De Laender, F., C. R. Janssen, and K. A. C. De Schamphelaere. 2009 Non-simultaneous ecotoxicity testing of single chemicals and their mixture results in erroneous conclusions about the joint action of the mixture. Chemosphere 76:428-432. 
  7. De Laender, F., D. Van Oevelen, J. J. Middelburg, and K. Soetaert. 2009 Incorporating ecological data and associated uncertainty in bioaccumulation modelling: methodology development and case study. Environmental Science & Technology 43:2620-2626.
  8. Dijkman, N. A., H. T. S. Boschker, J. J. Middelburg, and J. C. Kromkamp. 2009 Group-specific primary production based on stable-isotope labeling of phospholipid-derived fatty acids. Limnology and Oceanography Methods 7:612-625. 
  9. Escaravage, V., P. M. J. Herman, B. Merckx, M. W. Bodarska-Kowalczuk, J.-M. Amouroux, S. Degraer, A. Grémare, C. H. R. Heip, H. Hummel, I. Karakassis, C. Labrune, and W. Willems. 2009 Distribution patterns of macrofaunal species diversity in subtidal soft sediments: biodiversity-productivity relationships from the MacroBen database. Marine Ecology Progress Series 382:253-264.
  10. Gooday, A. J., F. Jorissen, L. A. Levin, J. J. Middelburg, S. W. A. Naqvi, N. N. Rabalais, M. Scranton, and J. Zhang. 2009 Historical records of coastal eutrophication-induced hypoxia. Biogeosciences 6:1707-1745. 
  11. Grémare, A., C. Labrune, E. Vanden Berghe, J. M. Amouroux, G. Bachelet, M. L. Zettler, J. Vanaverbeke, D. Fleischer, L. Bigot, O. Maire, B. Deflandre, J. Craeymeersch, S. Degraer, C. Dounas, G. Duineveld, C. Heip, M. Herrmann, H. Hummel, I. Karakassis, M. Kedra, M. Kendall, P. Kingston, J. Laudien, A. Occhipinti-Ambrogi, E. Rachor, R. Sardá, J. Speybroeck, G. Van Hoey, M. Vincx, P. Whomersley, W. Willems, M. Wlodarska-Kowalczuk, and A. Zenetose. 2009 Comparison of the performances of two biotic indices based on the MacroBen database. Marine Ecology Progress Series 382:297-311.
  12. Gribsholt, B., B. Veuger, A. Tramper, J. J. Middelburg, and H. T. S. Boschker. 2009 Long-term 15N-nitrogen retention in tidal freshwater marsh sediment: Elucidating the microbial contribution. Limnology and Oceanography 54:13-22. 
  13. Hofmann, A. F., J. J. Middelburg, K. Soetaert, and F. J. R. Meysman. 2009 pH modelling in aquatic systems with time-variable acid-base dissociation constants applied to the turbid, tidal Scheldt estuary. Biogeosciences 6:1539-1561. 
  14. Jacobs, S., O. Beauchard, E. Struyf, T. Cox, T. Maris, and P. Meire. 2009 Restoration of tidal freshwater vegetation using controlled reduced tide (CRT) along the Schelde Estuary (Belgium). Estuarine Coastal and Shelf Science 85:368-376. 
  15. Kones, J. K., K. Soetaert, D. van Oevelen, and J. Owino. 2009 Are network indices robust indicators of food web functioning ? A Monte Carlo approach. Ecological Modelling 220:370-382. 
  16. Konn, C., J. L. Charlou, J. P. Donval, N. G. Holm, F. Dehairs, and S. Bouillon. 2009 Hydrocarbons and oxidized organic compounds in hydrothermal fluids from Rainbow and Lost City ultramafic-hosted vents. Chemical Geology 258:299-314.
  17. Levin, L. A., W. Ekau, A. J. Gooday, F. Jorissen, J. J. Middelburg, W. Naqvi, C. Neira, N. N. Rabalais, and J. Zhang. 2009 Effects of natural and human-induced hypoxia on coastal benthos. Biogeosciences 6:2063-2098. 
  18. Lorrain, A., B. Graham, F. Ménard, B. Popp, S. Bouillon, P. van Breugel, and Y. Cherel. 2009 Nitrogen and carbon isotope values of individual amino acids: a tool to study foraging ecology of penguins in the Southern Ocean. Marine Ecology Progress Series 391:293-306. 
  19. Middelburg, J. J., and L. A. Levin. 2009 Coastal hypoxia and sediment biogeochemistry. Biogeosciences 6:1273-1293.   
  20. Montserrat, F., C. Van Colen, P. Provoost, M. Milla, M. Ponti, K. Van den Meersche, T. Ysebaert, and P. M. J. Herman. 2009 Sediment segregation by biodiffusing bivalves. Estuarine Coastal and Shelf Science 83:379-391.   
  21. Nyunja, J., M. Ntiba, J. Onyari, K. Mavuti, K. Soetaert, and S. Bouillon. 2009 Carbon sources supporting a diverse fish community in a tropical coastal ecosystem (Gazi Bay, Kenya). Estuarine Coastal and Shelf Science 83:333-341.   
  22. Obade, P., N. Koedam, K. Soetaert, G. Neukermans, J. Bogaert, E. Nyssen, F. van Nedervelde, U. Berger, and F. Dahdouh-Guebas. 2009 Impact of anthropogenic disturbance on a mangrove forest assessed by a 1D-cellular automaton model using Lotka-Volterra type competition. International Journal of Design & Nature and Ecodynamics 3:1-25  .
  23. Rossi, F., M. Vos, and J. J. Middelburg. 2009 Species identity, diversity and microbial carbon flow in reassembling macrobenthic communities. Oikos 118:503-512.   
  24. Soetaert, K., M. Franco, N. Lampadariou, A. Muthumbi, M. Steyaert, L. Vandepitte, E. Vanden Berghe, and J. Vanaverbeke. 2009 Factors affecting nematode biomass, length and width from the shelf to the deep sea. Marine Ecology Progress Series 392:123-132.   
  25. Soetaert, K., and J. J. Middelburg. 2009 Modeling eutrophication and oligotrophication of shallow-water marine systems: the importance of sediments under stratified and well-mixed conditions. Hydrobiologia 629:239-254. 
  26. Soetaert, K., and D. Van Oevelen. 2009 Modeling food web interactions in benthic deep-sea ecosystems. A practical guide. Oceanography 22:128-143. 
  27. Somerfield, P. J., C. Arvanitidis, S. Faulwetter, G. Chatzigeorgiou, A. Vasileiadou, J. M. Amouroux, N. Anisimova, S. J. Cochrane, J. Craeymeersch, S. Dahle, S. Denisenko, K. Dounas, G. Duineveld, A. Grémare, C. H. R. Heip, M. Herrmann, I. Karakassis, M. Kedra, M. A. Kendall, P. Kingston, L. Kotwicki, C. Labrune, J. Laudien, H. Nevrova, A. Nicolaidou, A. Occhipinti-Ambrogi, R. Palerud, A. Petrov, E. Rachor, N. Revkov, H. Rumohr, R. Sardá, U. Janas, E. Vanden Berghe, and M. Wlodarska-Kowalczuk. 2009 Assessing evidence for random assembly of marine benthic communities from regional species pools. Marine Ecology Progress Series 382:279-286.   
  28. Somerfield, P. J., C. Arvanitidis, E. Vanden Berghe, P. Van Avesaath, H. Hummel, and C. H. R. Heip. 2009 MarBEF, databases, and the legacy of John Gray. Marine Ecology Progress Series 382:221-224
  29. Van Damme, S., F. Dehairs, M. Tackx, O. Beauchard, E. Struyf, B. Gribsholt, O. Van Cleemput, and P. Meire. 2009 Tidal exchange between a freshwater tidal marsh and an impacted estuary: the Scheldt estuary, Belgium. Estuarine Coastal and Shelf Science 85:197-207.   
  30. Van den Meersche, K., K. Soetaert, and D. Van Oevelen. 2009 xsample(): An R function for sampling linear inverse problems. Journal of Statistical Software 30: [1-15]. 
  31. Van den Meersche, K., P. van Rijswijk, K. Soetaert, and J. J. Middelburg. 2009 Autochthonous and allochthonous contributions to mesozooplankton diet in a tidal river and estuary:  Integrating carbon isotope and fatty acid constraints. Limnology and Oceanography 54:62-74.   
  32. Van Gaever, S., L. Moodley, F. Pasotti, M. Houtekamer, J. J. Middelburg, R. Danovaro, and A. Vanreusel. 2009 Trophic specialisation of metazoan meiofauna at the Håkon Mosby Mud Volcano: fatty acid biomarker isotope evidence. Marine Biology 156:1289-1296.   
  33. Van Nugteren, P., P. M. J. Herman, L. Moodley, J. J. Middelburg, M. Vos, and C. H. R. Heip. 2009 Spatial distribution of detrital resources determines the outcome of competition between bacteria and a facultative detritivorous worm. Limnology and Oceanography 54:413-1419.   
  34. Van Nugteren, P., L. Moodley, G. J. Brummer, C. H. R. Heip, P. M. J. Herman, and J. J. Middelburg. 2009 Seafloor ecosystem functioning: the importance of organic matter priming. Marine Biology 156:2277-2287.  
  35. Van Oevelen, D., G. Duineveld, M. Lavaleye, F. Mienis, K. Soetaert, and C. H. R. Heip. 2009 The cold-water coral community as a hot spot of carbon cycling on continental margins: a food-web analysis from Rockall Bank (northeast Atlantic). Limnology and Oceanography 54:1829-1844.   
  36. Van Oevelen, D., K. Soetaert, M. A. Franco, L. Moodley, L. van IJzerloo, M. Vincx, and J. Vanaverbeke. 2009 Organic matter input and processing in two contrasting North Sea sediments: insights from stable isotope and biomass data. Marine Ecology Progress Series 380:19-32.    
  37. Vanden Berghe, E., S. Claus, W. Appeltans, S. Faulwetter, C. Arvanitidis, P. J. Somerfield, I. F. Aleffi, J. M. Amouroux, N. Anisimova, G. Bachelet, S. J. Cochrane, M. J. Costello, J. Craeymeersch, S. Dahle, S. Degraer, S. Denisenko, C. Dounas, G. Duineveld, C. Emblow, V. Escaravage, M. C. Fabri, D. Fleischer, A. Grémare, M. Herrmann, H. Hummel, I. Karakassis, M. Kedra, M. A. Kendall, P. Kingston, L. Kotwicki, C. Labrune, J. Laudien, E. L. Nevrova, A. Occhipinti-Ambrogi, F. Olsgard, R. Palerud, A. Petrov, E. Rachor, N. Revkov, H. Rumohr, R. Sardá, W. C. H. Sistermans, J. Speybroeck, U. Janas, G. Van Hoey, M. Vincx, P. Whomersley, W. Willems, M. Wlodarska-Kowalczuk, A. Zenetos, M. L. Zettler, and C. H. R. Heip. 2009 MacroBen integrated database on benthic invertebrates of European continental shelves: a tool for large-scale analysis across Europe. Marine Ecology Progress Series 382:225-238. 
  38. Vandewiele, S., G. Cowie, K. Soetaert, and J. J. Middelburg. 2009 Amino acid biogeochemistry and organic matter degradation state across the Pakistan margin oxygen minimum zone. Deep-Sea Research Part II-Topical Studies in Oceanography 56:376-392.   
  39. Woulds, C., J. H. Andersson, G. L. Cowie, J. J. Middelburg, and L. A. Levin. 2009 The short-term fate of organic carbon in marine sediments: Comparing the Pakistan margin to other regions. Deep-Sea Research Part II-Topical Studies in Oceanography 56:393-402.   

Book chapters

  1. Bouillon, S., and R. Connolly. 2009.  Carbon exchange among tropical coastal ecosystems. In: I. Nagelkerken, editor. Ecological Linkages Across Tropical Coastal Ecosystems. Pp. 45-70, Springer.
  2. Kroeze, C., J. J. Middelburg, R. Leemans, E. Escobar-Briones, W. Fennel, M. Glaser, A. Harashima, K. K. Kee Liu, and M. Meybeck. 2009. Integrating tools to assess changes in semi-enclosed marine systems. Pages 77-96 in J. Urban, E.R., B. Sundby, P. Malanotte-Rizzoli, and J. M. Melillo, editors. Watersheds, bays and bounded seas: The science and management of semi-enclosed marine systems. Island Press, Chicago. 4395

Books

  1. Soetaert, K., and P. M. J. Herman. 2009. A Practical Guide to Ecological Modelling. Using R as a Simulation Platform. Springer, 372 pp. 

PhD theses

  1. Andreas Hofmann, Utrecht University. Quantifying the influence of biogeochemical processes on pH of natural waters.
  2. Karel van den Meersche, Ghent University. Carbon flows in the planktonic food web of temperate estuaries: a combined approach using stable isotopes, biomarkers and modeling.

Open source Software packages

  1. Karline Soetaert and Peter MJ Herman, 2009. ecolMod: "A practical guide to ecological modelling - using R as a simulation platform". The scripts to make the figures in the book. R package version 1.2.
    http://cran.r-project.org/web/packages/ecolMod/index.html
  2. Karline Soetaert, Jeff Cash and Francesca Mazzia (2009). bvpSolve:  Solvers for boundary value problems of ordinary differential  equations. R package version 1.1.
    http://cran.r-project.org/web/packages/bvpSolve/index.html
  3. Karline Soetaert, Thomas Petzoldt and Filip Meysman (2009).  marelac: Tools for Aquatic Sciences. R package version 1.0. 
    http://cran.r-project.org/web/packages/marelac/index.html
  4. Karline Soetaert and Filip Meysman (2009). ReacTran: Reactive  transport modelling in 1D, 2D and 3D. R package version 1.1.
    http://cran.r-project.org/web/packages/ReacTran/index.html
  5. Karline Soetaert and Thomas Petzoldt (2009). FME: A Flexible Modelling Environment for inverse modelling, sensitivity, identifiability, Monte Carlo analysis.. R package version 1.1.
    http://cran.r-project.org/web/packages/FME/index.html
  6. Andreas F. Hofmann, Karline Soetaert, Jack J. Middelburg and Filip J. R. Meysman. AquaEnv –  an integrated development toolbox for aquatic chemical model generation.
    http://cran.r-project.org/web/packages/AquaEnv/index.html
2008
  1. Andersson, J., C. Woulds, M. Schwartz, G. L. Cowie, L. A. Levin, K. Soetaert, and J. J. Middelburg. 2008. Short-term fate of phytodetritus across the Arabian Sea Oxygen Minimum Zone. Biogeosciences 5:43-53. 
  2. Bernard, O., A. Sciandra, and S. Madani. 2008
    Multimodel analysis of the response of the coccolithophore Emiliania huxleyi to an elevation of  under pCO(2) nitrate limitation. Ecological Modelling 211:324-338   
  3. Boschker, H. T. S., T. C. W. Moerdijk-Poortvliet, P. van Breugel, M. Houtekamer, and J. J. Middelburg. 2008 A versatile method for stable carbon isotope analysis of carbohydrates by high-performance liquid chromatography/isotope ratio mass spectrometry. Rapid Communications in Mass Spectrometry 22:3902-3908.   
  4. Bouillon, S., A. V. Borges, E. Castañeda-Moya, K. Diele, T. Dittmar, N. C. Duke, E. Kristensen, S. Y. Lee, C. Marchand, J. J. Middelburg, V. H. Rivera-Monroy, T. Smith III, and R. R. Twilley. 2008 Mangrove production and carbon sinks: a revision of global budget estimates. Global Biogeochemical Cycles 22 GB2013 [2011-2012].   
  5. Bouillon, S., R. Connolly, and S. Y. Lee. 2008 Organic matter exchange and cycling in mangrove ecosystems: Recent insights from stable isotope studies. Journal of Sea Research 59:44-58.   
  6. Brion, N., M. G. I. Andersson, M. Elskens, C. Diaconu, W. Baeyens, F. Dehairs, and J. J. Middelburg. 2008 Nitrogen cycling, retention and export in a eutrophic temperate macrotidal estuary. Marine Ecology Progress Series 357:87-99.  
  7. De Goeij, J. M., L. Moodley, M. Houtekamer, N. M. Carballeira, and F. C. van Duyl. 2008 Tracing 13C-enriched dissolved and particulate organic carbon in the bacteria-containing coral reef sponge Halisarca caerulea: evidence for DOM feeding. Limnology and Oceanography 53:1376-1386.   
  8. Downing, J. A., J. J. Cole, J. J. Middelburg, R. G. Striegl, C. M. Duarte, P. Kortelainen, Y. T. Prairie, and K. A. Laube. 2008 Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century. Global Biogeochemical Cycles 22:GB1018 [1011-1010].   
  9. Duce, R. A., J. LaRoche, K. Altieri, K. R. Arrigo, A. R. Baker, D. G. Capone, S. Cornell, F. Dentener, J. Galloway, R. S. Ganeshram, R. J. Geider, T. Jickells, M. M. Kuypers, R. Langlois, P. S. Liss, S. M. Liu, J. J. Middelburg, C. M. Moore, S. Nickovic, A. Oschlies, T. Pedersen, J. Prospero, R. Schlitzer, S. Seitzinger, L. L. Sorensen, M. Uematsu, O. Ulloa, M. Voss, B. Ward, and L. Zamora. 2008 Impacts of atmospheric anthropogenic nitrogen on the open ocean. Science 320:893-897.   
  10. Evrard, V., P. L. M. Cook, B. Veuger, M. Huettel, and J. J. Middelburg. 2008 Tracing carbon and nitrogen incorporation and pathways in the microbial community of a photic subtidal sand. Aquatic Microbial Ecology 53:257-269. 
  11. Franco, M. A., K. Soetaert, M. J. Costa, M. Vincx, and J. Vanaverbeke. 2008 Uptake of phytodetritus by meiobenthos using 13C labelled diatoms and Phaeocystis in two contrasting sediments from the North Sea. Journal of Experimental Marine Biology and Ecology 362:1-8.   
  12. Franco, M. A., K. Soetaert, D. Van Oevelen, D. Van Gansbeke, M. J. Costa, M. Vincx, and J. Vanaverbeke. 2008 Density, vertical distribution and trophic responses of metazoan meiobenthos to phytoplankton deposition in contrasting sediment types. Marine Ecology Progress Series 358:51-62.   
  13. García, R., D. van Oevelen, K. Soetaert, L. Thomsen, H. C. De Stigter, and E. Epping. 2008 Deposition rates, mixing intensity and organic content in two contrasting submarine canyons. Progress in Oceanography 76:192-215   
  14. Greenwood, J. E., and K. Soetaert. 2008 Interannual variability in the seasonal cycle of chlorophyll in the Leeuwin Current off the southwest Western Australian coast. Journal of Marine Research 66:373-390.    
  15. Grégoire, M., C. Raick, and K. Soetaert. 2008 Numerical modeling of the central Black Sea ecosystem functioning during the eutrophication phase. Progress in Oceanography 76:286-333. 
  16. Gypens, N., C. Lancelot, and K. Soetaert. 2008 Simple parameterisations for describing N and P diagenetic processes: Application in the North Sea. Progress in Oceanography 76:89-110.   
  17. Hofmann, A. F., F. J. R. Meysman, K. Soetaert, and J. J. Middelburg. 2008 A step-by-step procedure for pH model construction in aquatic systems. Biogeosciences 5:227-251.   
  18. Hofmann, A. F., K. Soetaert, and J. J. Middelburg. 2008 Present nitrogen and carbon dynamics in the Scheldt estuary using a novel 1-D model. Biogeosciences 5:981-1006.   
  19. Huguet, C., G. J. de Lange, Ö. Gustafsson, J. J. Middelburg, J. S. Sinninghe Damsté, and S. Schouten. 2008 Selective preservation of soil organic matter in oxidized marine sediments (Madeira Abyssal Plain). Geochimica et Cosmochimica Acta 72:6061-6068.  
  20. Kristensen, E., S. Bouillon, T. Dittmar, and C. Marchand. 2008 Organic carbon dynamics in mangrove ecosystems: a review. Aquatic Botany 89:201-219.  
  21. Kristensen, E., M. R. Flindt, S. Ulomi, A. V. Borges, G. Abril, and S. Bouillon. 2008 Emission of CO2 and CH4 to the atmosphere by sediments and open waters in two Tanzanian mangrove forests. Marine Ecology Progress Series 370:53-67.   
  22. Meysman, F. J. R., V. S. Malyuga, B. P. Boudreau, and J. J. Middelburg. 2008 Quantifying particle dispersal in aquatic sediments at short time scales: model selection. Aquatic Biology 2:239-254.   
  23. Meysman, F. J. R., V. S. Malyuga, B. P. Boudreau, and J. J. Middelburg. 2008 A generalized stochastic approach to particle dispersal in soils and sediments. Geochimica et Cosmochimica Acta 72:3460-3478.   
  24. Meysman, F. J. R., and J. J. Middelburg. 2008 Bioturbation from square millimeter to global scales. EOS, Transactions American Geophysical Union 89:473. 
  25. Moodley, L., M. Steyaert, E. Epping, J. J. Middelburg, M. Vincx, P. van Avesaath, T. Moens, and K. Soetaert. 2008 Biomass-specific respiration rates of benthic meiofauna: Demonstrating a novel oxygen micro-respiration system. Journal of Experimental Marine Biology and Ecology 357:41-47.
  26. Na, T., B. Gribsholt, O. S. Galaktionov, T. Lee, and F. J. R. Meysman. 2008 Influence of advective bio-irrigation on carbon and nitrogen cycling in sandy sediments. Journal of Marine Research 66:691-722.   
  27. Nagelkerken, I., S. J. M. Blaber, S. Bouillon, P. Green, M. Haywood, L. G. Kirton, J.-O. Meynecke, J. Pawlik, H. M. Penrose, A. Sasekumar, and P. J. Somerfield. 2008 The habitat function of mangroves for terrestrial and marine fauna : A review. Aquatic Botany 89:155-185.   
  28. Ralison, O., A. V. Borges, F. Dehairs, J. J. Middelburg, and S. Bouillon. 2008 Carbon biogeochemistry in the Betsiboka estuary (northwestern Madagascar). Organic Geochemistry 39:1649-1658.   
  29. Riou, V., S. Halary, S. Duperron, S. Bouillon, M. Elskens, R. Bettencourt, R. Santos, F. Dehairs, and A. Colaço. 2008 Influence of CH4 and H2S availability on symbiont distribution, carbon assimilation and transfer in the dual symbiotic vent mussel Bathymodiolus azoricus. Biogeosciences 5:1681-1691.   
  30. Rossi, F., B. Gribsholt, J. J. Middelburg, and C. H. R. Heip. 2008 Context-dependent effects of suspension feeding on intertidal ecosystem functioning. Marine Ecology Progress Series 354:47-57. 
  31. Teugels, B., S. Bouillon, B. Veuger, J. J. Middelburg, and N. Koedam. 2008 Kleptoplasts mediate nitrogen acquisition in the sea slug Elysia viridis. Aquatic Biology 4:15-21. 
  32. Ulses, C., C. Estournel, X. Durrieu de Madron, and A. Palanques. 2008 Suspended sediment transport in the Gulf of Lions (NW Mediterranean): Impact of extreme storms and floods. Continental Shelf Research 28:2048-2070.   
  33. Ulses, C., C. Estournel, P. Puig, X. Durrieu de Madron, and P. Marsaleix. 2008 Dense shelf water cascading in the northwestern Mediterranean during the cold winter 2005: Quantification of the export through the Gulf of Lion and the Catalan margin. Geophysical Research Letters 35:L07610.
  34. Van den Meersche, K., J. J. Middelburg, and K. Soetaert. 2008 A Bayesian compositional estimator for microbial taxonomy based on biomarkers. Limnology and Oceanography Methods 6:190-199.   
  35. Van der Stap, I., M. Vos, R. Tollrian, and W. M. Mooij. 2008 Inducible defenses, competition and shared predation in planktonic food chains. Oecologia 157:697-705.   
  36. Vonk, J. A., J. J. Middelburg, J. Stapel, and T. J. Bouma. 2008 Dissolved organic nitrogen uptake by seagrasses. Limnology and Oceanography 53:542-548.   
  37. Warwick, R., J. Field, C. Heip, and S. Stebbing. 2008 Prof. John Stuart Gray (1941-2007): Marine ecology: A tribute to the life and work of John S. Gray. Journal of Experimental Marine Biology and Ecology 366:1-5
  38. Warwick, R., J. Field, C. Heip, and T. Stebbing. 2008 In Memoriam John Stuart Gray. Marine Ecology Progress Series 354:1.   

Book chapters

  1. Gazeau, F. 2008.  Impact of ocean acidification on marine shellfish. Pages 81-89 in F. Briand, editor. Impact of Acidification on Biological, Chemical and Physical Systems in the Mediterranean and Black Seas. Menton 1 - 4 October 2008. CIESM, Monaco. 4593
  2. Vanaverbeke, J., M. Franco, D. van Oevelen, L. Moodley, P. Provoost, M. Steyaert, K. Soetaert, and M. Vincx. 2008.  Benthic responses to sedimentation of phytoplankton on the Belgian Continental Shelf. Pages 73-90 in V. Rousseau, C. Lancelot, and D. Cox, editors. Current Status of Eutrophication in the Belgian Coastal Zone. Universite Libré de Bruxelles, Bruxelles. 4445

Open source Software packages

  1. Karline Soetaert, Thomas Petzoldt and R. Woodrow Setzer, 2008. deSolve: General solvers for ordinary differential equations (ODE) and for differential algebraic equations (DAE). R package version 1.0.
    http://cran.r-project.org/web/packages/deSolve/index.html
  2. Karline Soetaert, 2008. rootSolve: Nonlinear root finding, equilibrium and steady-state analysis of ordinary differential equations. R package version 1.1.
    http://cran.r-project.org/web/packages/rootSolve/index.html
  3. Karline Soetaert, Karel Van den Meersche and Dick van Oevelen, 2008. limSolve:Solving linear inverse models. R package version 1.
    http://cran.r-project.org/web/packages/limSolve/index.html
  4. Karline Soetaert and Dick van Oevelen, 2008. LIM: Linear Inverse Model examples and solution methods. R package version 1.1.
    http://cran.r-project.org/web/packages/LIM/index.html
  5. Karline Soetaert and Julius K Kones, 2008. NetIndices: a package of network indices. R package version 1.0.
    http://cran.r-project.org/web/packages/NetIndices/index.html
  6. Karline Soetaert, 2008. shape: Functions for plotting graphical shapes, colors. R package version 1.1.
    http://cran.r-project.org/web/packages/shape/index.html
  7. Karline Soetaert, 2008. diagram: Functions for visualising simple graphs (networks), plotting flow diagrams. R package version 1.1.
    http://cran.r-project.org/web/packages/diagram/index.html
  8. Karel Van den Meersche and Karline Soetaert 2008. BCE: Bayesian composition estimator: estimating sample (taxonomic) composition from biomarker data. R package version 1.
    http://cran.r-project.org/web/packages/BCE/index.html
2007
  1. Bouillon, S., F. Dehairs, B. Velimirov, G. Abril, and A. V. Borges. 2007. Dynamics of organic and inorganic carbon across contiguous mangrove and seagrass systems (Gazi Bay, Kenya). Journal of Geophysical Research 112:G02018.   
  2. Bouillon, S., J. J. Middelburg, F. Dehairs, A. V. Borges, G. Abril, M. R. Flindt, S. Ulomi, and E. Kristensen. 2007. Importance of intertidal sediment processes and porewater exchange on the water column biogeochemistry in a pristine mangrove creek (Ras Dege, Tanzania). Biogeosciences 4:311-322.   
  3. Cole, J., Y. T. Prairie, N. Caraco, W. H. McDowell, L. Tranvil, R. G. Striegl, C. M. Duarte, P. Kortelainen, J. A. Downing, J. J. Middelburg, and J. Melack. 2007.Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget. Ecosystems 10:172-185. 
  4. Cook, P., B. Veuger, S. Böer, and J. J. Middelburg. 2007. Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment. Aquatic Microbial Ecology 49:165-180.   
  5. Dedieu, K., C. Rabouille, F. Gilbert, K. Soetaert, E. Metzger, C. Simonucci, D. Jézéquel, F. Prévot, P. Anschutz, S. Hulth, S. Ogier, and V. Mesnage. 2007. Coupling of carbon, nitrogen and oxygen cycles in sediments from a Mediterranean lagoon: a seasonal perspective. Marine Ecology Progress Series 346:45-59.   
  6. Delmotte, S., F. J. R. Meysman, A. Ciutat, A. Boudou, S. Sauvage, and M. Gerino. 2007. Cadmium transport in sediments by tubificid bioturbation: an assessment of model complexity. Geochimica et Cosmochimica Acta 71:844-862.  
  7. Franco, M. A., I. De Mesel, M. Demba Diallo, K. Van der Gucht, D. Van Gansbeke, P. Van Rijswijk, M. J. Costa, M. Vincx, and J. Vanaverbeke. 2007 Effect of phytoplankton bloom deposition on benthic bacterial communities in two contrasting sediments in the southern North Sea. Aquatic Microbial Ecology 48:241-254.   
  8. Gazeau, F., J. J. Middelburg, M. Loijens, J. P. Vanderborght, M. D. Pizay, and J.-P. Gattuso. 2007 Planktonic primary production in estuaries: a comparison of the 14C, O2 and 18O methods. Aquatic Microbial Ecology 46:96-106. 
  9. Gazeau, F., C. Quiblier, J. M. Jansen, J.-P. Gattuso, J. J. Middelburg, and C. H. R. Heip. 2007 Impact of elevated CO2 on shellfish calcification. Geophysical Research Letters 34:L07603.   
  10. Gillikin, D. P., and S. Bouillon. 2007 Determination of δ18O of water and  δ13C of dissolved inorganic carbon using a simple modification of an elemental analyzer-isotope ratio mass spectrometer an evaluation. Rapid Communications in Mass Spectrometry 21:1475-1478.   
  11. Gribsholt, B., E. Struyf, A. Tramper, L. De Brabandere, N. Brion, S. van Damme, P. Meire, F. Dehairs, J. J. Middelburg, and H. T. S. Boschker. 2007 Nitrogen assimilation and short term retention in a nutrient-rich tidal freshwater marsh - a whole ecosystem 15N enrichment study. Biogeosciences 4:11-26.   
  12. Huettel, M., P. Cook, F. Janssen, G. Lavik, and J. Middelburg. 2007 Transport and degradation of a dinoflagellate bloom in permeable sublittoral sediment. Marine Ecology Progress Series 340:139-153.   
  13. Khalil, K., C. Rabouille, M. Gallinari, K. Soetaert, D. J. DeMaster, and O. Ragueneau. 2007 Constraining biogenic silica dissolution in marine sediments: a comparison between diagenetic models and experimental dissolution rates. Marine Chemistry 106:223-238.   
  14. Kratina, P., M. Vos, and B. R. Anholt. 2007 Species diversity modulates predation. Ecology 88:1917-1923.   
  15. Kube, S., A. Sokolowski, J. M. Jansen, and D. Schiedek. 2007 Seasonal variability of free amino acids in two marine bivalves, Macoma balthica and Mytilus spp., in relation to environmental and physiological factors. Comparative Biochemistry and Physiology A-Molecular and Integrative Physiology 147:1015-1027.   
  16. Lenartz, F., C. Raick, K. Soetaert, and M. Grégoire. 2007 Application of an Ensemble Kalman filter to a 1-D coupled hydrodynamic-ecosystem model of the Ligurian Sea. Journal of Marine Systems 68:327-348.  
  17. Maire, O., J. C. Duchêne, A. Grémare, V. Malyuga, and F. Meysman. 2007 A comparison of sediment reworking rates by the surface deposit-feeding bivalve Abra ovata during summertime and wintertime, with a comparison between two models of sediment reworking. Journal of Experimental Marine Biology and Ecology 343:21-36.  
  18. Meysman, F. J. R., and S. Bruers. 2007 A thermodynamic perspective on food webs: Quantifying entropy production within detrital-based ecosystems. Journal of Theoretical Biology 249:124-139.   
  19. Meysman, F. J. R., O. S. Galaktionov, P. L. M. Cook, F. Janssen, M. Huettel, and J. J. Middelburg. 2007 Quantifying biologically and physically induced flow and tracer dynamics in permeable sediments. Biogeosciences 4:627-646.   
  20. Meysman, F. J. R., V. S. Malyuga, B. P. Boudreau, and J. J. Middelburg. 2007 The influence of porosity gradients on mixing coefficients in sediments. Geochimica et Cosmochimica Acta 71: 961-973.  
  21. Middelburg, J. J., and P. M. J. Herman. 2007 Organic matter processing in tidal  estuaries. Marine Chemistry 106:127-147.   
  22. Middelburg, J. J., and F. J. R. Meysman. 2007 Burial at sea. Science 316:1294-1295   
  23. Moriceau, B., M. Gallinari, K. Soetaert, and O. Ragueneau. 2007 Importance of particle formation to reconstructed water column biogenic silica fluxes. Global Biogeochemical Cycles 21:GB 3012.   
  24. Pace, M. L., S. R. Carpenter, J. J. Cole, J. J. Coloso, J. F. Kitchell, J. R. Hodgson, J. J. Middelburg, N. D. Preston, C. T. Solomon, and B. C. Weidel. 2007 Does terrestrial organic carbon subsidize the planktonic food web in a clear-water lake? Limnology and Oceanography 52:2177-2189.   
  25. Raick, C., A. Alvera-Azcarate, A. Barth, J.-M. Brankart, K. Soetaert, and M. Grégoire. 2007 Application of a SEEK filter to a 1D biogeochemical model of the Ligurian Sea: Twin experiments and real data assimilation. Journal of Marine Systems 65:561-583.   
  26. Rochelle-Newall, E. J., C. Winter, C. Barrón, A. V. Borges, C. M. Duarte, M. Elliott, M. Frankignoulle, F. Gazeau, J. J. Middelburg, M.-D. Pizay, J. Thioulouse, and J. P. Gattuso. 2007 Artificial neural network analysis of factors controlling ecosystem metabolism in coastal systems. Ecological Applications 17:S185-S196.   
  27. Rossi, F. 2007 Recycle of buried -macro-algal detritus in sediments: use of dual-labeling experiments in the field. Marine Biology 150:1073-1081.   
  28. Rossi, F., R. M. Forster, F. Montserrat, M. Ponti, A. Terlizzi, T. Ysebaert, and J. J. Middelburg. 2007 Human trampling as short-term disturbance on intertidal mudflats: effects on macrofauna biodiversity and population dynamics of bivalves. Marine Biology 151:2077-2090.   
  29. Soetaert, K., A. Hofmann, J. J. Middelburg, F. J. R. Meysman, and J. Greenwood. 2007 The effect of biogeochemical processes on pH. Marine Chemistry 105:30-51.   
  30. Steyaert, M., L. Moodley, T. Nadong, T. Moens, K. Soetaert, and M. Vincx. 2007 Responses of intertidal nematodes to short-term anoxic events. Journal of Experimental Marine Biology and Ecology 345:175-184.  
  31. Struyf, E., S. Van Damme, B. Gribsholt, K. Bal, O. Beauchard, J. J. Middelburg, and P. Meire. 2007 Phragmites australis and silica cycling in tidal wetlands. Aquatic Botany 87:134-140.   
  32. Van der Stap, I., M. Vos, and W. M. Mooij. 2007 Inducible defenses and rotifer food chain dynamics. Hydrobiologia 593:103-110.   
  33. Van der Stap, I., M. Vos, A. M. Verschoor, N. R. Helmsing, and W. M. Mooij. 2007 Induced defenses in herbivores and plants differentially modulate a trophic cascade. Ecology 88:2474-2481.
  34. Veuger, B., B. D. Eyre, D. Maher, and J. J. Middelburg. 2007 Nitrogen incorporation and retention by bacteria, algae, and fauna in a subtropical, intertidal sediment: An in situ 15N-labeling study. Limnology and Oceanography 52:1930-1942.   
  35. Veuger, B., and J. J. Middelburg. 2007 Incorporation of nitrogen from amino acids and urea by benthic microbes: role of bacteria versus algae and coupled incorporation of carbon. Aquatic Microbial Ecology 48:35-46. 
  36. Veuger, B., J. J. Middelburg, H. T. S. Boschker, and M. Houtekamer. 2007 UPDATE of Analysis of 15N incorporation into D-alanine: A new method for tracing nitrogen uptake by bacteria (Veuger et al. 2005, Limnology and Oceanography Methods 3: 230-240). Limnology and Oceanography Methods 5:192-194.    
  37. Woulds, C., G. L. Cowie, L. A. Levin, J. H. Andersson, J. J. Middelburg, S. Vandewiele, P. A. Lamont, K. E. Larkin, A. J. Gooday, S. Schumacher, C. Whitcraft, R. M. Jeffreys, and M. Schwartz. 2007 Oxygen as a control on sea floor biological communities and their roles in sedimentary carbon cycling. Limnology and Oceanography 52:1698-1709. 

Book chapters

  1. Heip , C.H.R., 2007. Marine biodiversity - What is it and what are the problems? Pages 23-26 in W. Cieslikiewicz, e. al.], editors. Proceedings of the EurOCEAN 2004: European Conference on Marine Science & Ocean Technology: Celebrating European Marine Science; building the European research area; communicating marine science, Galway, Ireland, 10-13 May 2004.
  2. DeAngelis, D.L., M. Vos, W.M. Mooij, P.A. Abrams. 2007.Feedback effects between the food chain and induced defense strategies. Pages 213-236 in N. Rooney, K. McCann, D. Noakes, editors. From Energetics to Ecosystems: The Dynamics and Structure of Ecological Systems. Springer, Heidelberg.

PhD theses

  1. Maria Andersson, N cycling and metabolic balance of the Scheldt Estuary, Utrecht University.
  2. Henrik Andersson, Biogeochemical processes in sediments along ocean margin, Utrecht University.
  3. Victor Evrard, Stable isotope constraints on benthic ecology and biogeochemistry, Utrecht University.
2006
  1. Andersson, J.H., J.J. Middelburg, K. Soetaert. 2006. Identifiability and uncertainty analysis of bio-irrigation rates. Journal of Marine Research 64:407-429.
  2. Andersson, M.G.I., N. Brion, J.J. Middelburg. 2006.Comparison of nitrifier activity versus growth in the scheldt estuary - a turbid, tidal estuary in northern Europe. Aquatic Microbial Ecology 42:149-158.
  3. Andersson, M.G.I., P. van Rijswijk, J.J. Middelburg. 2006. Uptake of dissolved inorganic nitrogen, urea and amino acids in the Scheldt estuary: comparison of organic carbon and nitrogen uptake. Aquatic Microbial Ecology 44:303-315.
  4. Barron, C., J.J. Middelburg, C.M. Duarte. 2006.Phytoplankton trapped within seagrass (Posidonia oceanica) sediments are a nutrient source: An in situ isotope labeling experiment. Limnology and Oceanography 51:1648-1653.
  5. Borges, A.V., L.-S. Schiettecatte, G. Abril, B. Delille, F. Gazeau. 2006. Carbon dioxide in European coastal waters. Estuarine, Coastal and Shelf Science 70:375-387.
  6. Bos, O.G., I.E. Hendriks, M. Strasser, P. Dolmer, P. Kamermans. 2006. Estimation of food limitation of bivalve larvae in coastal waters of north-western Europe. Journal of Sea Research 55:191-206.
  7. Boudreau, B.P., F.J.R. Meysman. 2006. Predicted tortuosity of muds. Geology 34:693-696. 
  8. Buhring, S.I., S. Ehrenhauss, A. Kamp, L. Moodley, U. Witte. 2006. Enhanced benthic activity in sandy sublittoral sediments: Evidence from 13C tracer experiments. Marine Biology Research 2:120-129.
  9. Buhring, S.L., N. Lampadariou, L. Moodley, A. Tselepides, U. Witte. 2006. Benthic microbial and whole-community responses to different amounts of 13C-enriched algae: in situ experiments in the deep Cretan Sea (Eastern Mediterranean). Limnology and Oceanography 51:157-165.
  10. Como, S., F. Rossi, C. Lardicci. 2006.
    Caging experiment: relationship between mesh size and artifacts. Journal of Experimental Marine Biology and Ecology 335:157-166. 
  11. Cook, P.L.M., F. Wenzhöfer, S. Rysgaard, O.S. Galaktionov, F.J.R. Meysman, B.D. Eyre, J. Cornwell, M. Huettel, R.N. Glud. 2006.
    Quantification of denitrification in permeable sediments: Insights from a two-dimensional simulation analysis and experimental data. Limnology and Oceanography Methods 4:294-307.
  12. Cox, T., T. Maris, P. De Vleeschauwer, T. De Mulder, K. Soetaert, P. Meire. 2006.
    Flood control areas as an opportunity to restore estuarine habitat. Ecological Engineering 28:55-63.
  13. Dekker, T., G.D. Greve, T.L. Ter Laak, M.E.Y. Boivin, B. Veuger, G. Gortzak, S. Dumfries, S.M.G. Lücker, M.H.S. Kraak, W. Admiraal, H.G. Van der Geest. 2006. Development and application of a sediment toxicity test using the benthic cladoceran Chydorus sphaericus. Environmental Pollution 140:231-238.
  14. Downing, J.A., Y.T. Prairie, J.J. Cole, C.M. Duarte, L.J. Tranvik, R.G. Striegl, W.H. McDowell, P. Kortelainen, N.F. Caraco, J.M. Melack, J.J. Middelburg. 2006. The global abundance and size distribution of lakes, ponds, and impoundments. Limnology and Oceanography 51:2388-2397.
  15. Fernandes, S., F.J.R. Meysman, P. Sobral. 2006. The influence of Cu contamination on Nereis diversicolor bioturbation. Marine Chemistry 102:148-158.
  16. Friedrichs, M., G. Graf, L.A. van Duren. 2006. Preface : Bio-fluid-dynamics: Exchange processes at the sediment-water interface. Journal of Sea Research 55:1-2.
  17. Gattuso, J.P., B. Gentili, C.M. Duarte, J.A. Kleypas, J.J. Middelburg, D. Antoine. 2006. Light availability in the coastal ocean: impact on the distribution of benthic photosynthesic organisms and their contribution to primary production. Biogeosciences 3:489-513.
  18. Gribsholt, B., E. Struyf, A. Tramper, M.G.I. Andersson, N. Brion, L. De Brabandere, S. Van Damme, P. Meire, J.J. Middelburg, F. Dehairs, H.T.S. Boschker. 2006. Ammonium transformation in a nitrogen-rich tidal freshwater marsh. Biogeochemistry 80:289-298.
  19. Hendriks, I.E., C.M. Duarte, C.H.R. Heip. 2006.
    Biodiversity research still grounded. Science 312:1715.
  20. Hendriks, I.E., L.A. Van Duren, P.M.J. Herman. 2006. Turbulence levels in a flume compared to the field: Implications for larval settlement studies. Journal of Sea Research 55:15-29.
  21. Jonsson, P.R., L.A. Van Duren, M. Amielh, R. Asmus, R.J. Aspden, D. Daunys, M. Friedrichs, P.L. Friend, F. Olivier, N. Pope, E. Precht, P.-G. Sauriau, E. Schaaff. 2006.Making water flow: a comparison of the hydrodynamic characteristics of 12 different benthic biological flumes. Aquatic Ecology 40:409-438.
  22. Kones, J.K., K. Soetaert, D. van Oevelen, J.O. Owino, K. Mavuti. 2006.Gaining insight into food webs reconstructed by the inverse method. Journal of Marine Systems 60:153-166.
  23. Kube, S., A. Gerber, J.M. Jansen, D. Schiedek. 2006. Patterns of organic osmolytes in two marine bivalves, Macoma balthica, and Mytilus spp., along their European distribution. Marine Biology 149:1387-1396.
  24. Loreau, M., A. Oteng-Yeboah, M.T.K. Arroyo, D. Babin, R. Barbault, M. Donoghue, M. Gadgil, C. Häuser, C. Heip, A. Larigauderie, K. Ma, G. Mace, H.A. Mooney, C. Perrings, P. Raven, J. Sarukhan, P. Schei, R.J. Scholes, R.T. Watson. 2006.Diversity without representation. Nature 442:245-246.
  25. Meysman, F.J.R., O.S. Galaktionov, B. Gribsholt, J.J. Middelburg. 2006. Bioirrigation in permeable sediments: Advective pore water transport induced by burrow ventilation. Limnology and Oceanography 51:142-156.
  26. Meysman, F.J.R., O.S. Galaktionov, B. Gribsholt, J.J. Middelburg. 2006. Bio-irrigation in permeable sediments: An assessment of model complexity. Journal of Marine Research 64:589-627.
  27. Meysman, F.J.R., J.J. Middelburg, C.H.R. Heip. 2006. Bioturbation: a fresh look at Darwin's last idea. Trends in Ecology & Evolution 21:688-695.
  28. Rabouille, S., M. Staal, L.J. Stal, K. Soetaert. 2006. Modeling the dynamic regulation of nitrogen fixation in the cyanobacterium Trichodesmium sp. Applied and Environmental Microbiology 72:3217-3227.
  29. Raick, C., B. J.-M., K. Soetaert, M. Grégoire. 2006. Can principal component analysis be used to predict the dynamics of a strongly non-linear marine biogeochemical model? Ecological Modelling 196:345-364.
  30. Raick, C., K. Soetaert, M. Grégoire. 2006. Model complexity and performance: how far can we simplify? Progress in Oceanography 70:27-57.
  31. Reed, D.C., K. Huang, B.P. Boudreau, F.J.R. Meysman. 2006. Steady-state tracer dynamics in a lattice-automaton model of bioturbation. Geochimica et Cosmochimica Acta 70:5855-5867.
  32. Rossi, F. 2006. Small-scale burial of macroalgal detritus in marine sediments: effects of Ulva spp. on the spatial distribution of macrofauna assemblages. Journal of Experimental Marine Biology and Ecology 332:84-95.
  33. Rossi, F., A. Castelli, C. Lardicci. 2006. Distribution of macrobenthic assemblages along a marine gradient in Mediterranean eutrophic coastal lagoons. Marine Ecology 27:66-75.
  34. Schiettecatte, L.-S., F. Gazeau, C. van der Zee, N. Brion, A.V. Borges. 2006. Time series of the partial pressure of carbon dioxide (2001-2004) and preliminary inorganic carbon budget in the Scheldt plume (Belgian coastal waters). Geochemistry Geophysics Geosystems 7:Q06009 (pp. 06001-06016).
  35. Soetaert, K., J.J. Middelburg, C. Heip, P. Meire, S. Van Damme, T. Maris. 2006. Long-term change in dissolved inorganic nutrients in the heterotrophic Scheldt estuary (Belgium, The Netherlands). Limnology and Oceanography 51:409-423.
  36. Struyf, E., A. Dausse, S. Van Damme, K. Bal, B. Gribsholt, H.T.S. Boschker, P. Meire. 2006. Tidal marshes and biogenic silica recycling at the land-sea interface. Limnology and Oceanography 51:838-846.
  37. Tengberg, A., J. Hovdenes, H.J. Andersson, O. Brocandel, R. Diaz, D. Hebert, T. Arnerich, C. Huber, A. Körtzinger, A. Khripounoff, F. Rey, C. Rönning, J. Schimanski, S. Sommer, A. Stangelmayer. 2006. Evaluation of a lifetime-based optode to measure oxygen in aquatic systems. Limnology and Oceanography Methods 4:7-17.
  38. Van der Stap, I., M. Vos, W.M. Mooij. 2006. Linking herbivore-induced defenses to population dynamics. Freshwater Biology 51:424-434.
  39. Van Duren, L.A., P.M.J. Herman, A.J.J. Sandee, C.H.R. Heip. 2006. Effects of mussel filtering activity on boundary layer structure. Journal of Sea Research 55:3-14.
  40. Van Duren, L.A., P.R. Jonsson. 2006. Preface [by Volme 40 Aquatic Ecology]. Aquatic Ecology 40:407-408.
  41. Van Gaever, S., L. Moodley, D. de Beer, A. Vanreusel. 2006. Meiobenthos at the Arctic Håkon Mosby Mud Volcano with a parental caring nematode thriving in sulphide-rich sediments. Marine Ecology Progress Series 321:143-155.
  42. Van Oevelen, D., J.J. Middelburg, K. Soetaert, L. Moodley. 2006. The fate of bacterial carbon in an intertidal sediment: Modeling an in situ isotope tracer experiment. Limnology and Oceanography 51:1302–1314.
  43. Van Oevelen, D., L. Moodley, K. Soetaert, J.J. Middelburg. 2006. The trophic significance of bacterial carbon in a marine intertidal sediment: Results of an in situ stable isotope labeling study. Limnology and Oceanography 51:2349-2359.
  44. Van Oevelen, D., K. Soetaert, J.J. Middelburg, P.M.J. Herman, L. Moodley, I. Hamels, T. Moens, C.H.R. Heip. 2006. Carbon flows through a benthic food web: Integrating biomass, isotope and tracer data. Journal of Marine Research 64:453-482.
  45. Veuger, B., D. Van Oevelen, H.T.S. Boschker, J.J. Middelburg. 2006. Fate of peptidoglycan in an intertidal sediment: an in situ 13C-labeling study. Limnology & Oceanography 51:1572-1580.
  46. Vijverberg, J., M. Vos. 2006. Predator-released compounds, ambient temperature and competitive exclusion among differently sized Daphnia species. Freshwater Biology 51:756-767.
  47. Vos, M., L.E.M. Vet, F.L. Wäckers, J.J. Middelburg, W.H. Van der Putten, W.M. Mooij, C.H.R. Heip, E. Van Donk. 2006.
    Infochemicals structure marine, terrestrial and freshwater food webs: implications for ecological informatics. Ecological Informatics 1:23-32.
  48. Wuchter, C., B. Abbas, M. Coolen, L. Herfort, J. van Bleijswijk, P. Timmers, M. Strous, E. Teira, G. Herndl, J.J. Middelburg, S. Schouten, J.S. Sinninghe Damsté. 2006. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences of the United States of America 103:12317-12322.

Book chapters

  1. Van Tussenbroek, B., J.A. Vonk, J. Stapel, P.L.A. Erftemeijer, J.J. Middelburg, J.C. Zieman. 2006. The Biology of Thalassia:  Paradigms and Recent Advances in Research. Pages 409-439 in A.W.D. Larkum, R.J. Orth, C.M. Duarte, editors. Seagrasses: Biology, Ecology and Conservation. Springer, Dordrecht.

PhD theses

  1. Veuger, B.. A new method for tracing flows of nitrogen and carbon through bacteria and algae in aquatic microbial communities: Analysis of 15N- and 13C-incorporation into D-alanine and other hydrolysable amino acids. University Utrecht.
  2. Van Oevelen D. (2006) PhD thesis “The structure of marine benthic food webs:  Combining stable isotope techniques and inverse modelling”. PhD thesis. University of Groningen. The Netherlands
2005
  1. Barranguet, C., B. Veuger, S.A.M. van Beusekom, P. Marvan, J.J. Sinke, W. Admiraal, 2005. Divergent composition of algal-bacterial biofilms developing under various external factors. European Journal of Phycology 39:1-8.
  2. Boschker, H.T.S., J.C. Kromkamp, J.J. Middelburg, 2005. Biomarker and carbon isotopic constraints on bacterial and algal community structure and functioning in a turbid, tidal estuary. Limnology and Oceanography 50:70-80.
  3. Duarte, C.M., J.J. Middelburg, N. Caraco, 2005. Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences 1:173-180.
  4. Evrard, V., W. Kiswara, T.J. Bouma, J.J. Middelburg, 2005. Nutrient dynamics of seagrass ecosystems: 15N evidence for the importance of particulate organic matter and root systems. Marine Ecology Progress Series 295:49-55.
  5. Forster R.M., Martin-Jézéquel V. (2005). Photophysiological variability of microphytobenthic diatoms after growth in different types of culture conditions. Phycologia 44: 393-402.
  6. Gattuso, J.P., N.A. Dawson, C.M. Duarte, J.J. Middelburg, 2005. Patterns of publication effort in coastal biogeochemistry: a bibliometric survey (1971 to 2003). Marine Ecology Progress Series 294:9-22.
  7. Gazeau, F., J.-P. Gattuso, J.J. Middelburg, N. Brion, L.-S. Schiettecatte, M. Frankignoulle, A.V. Borges, 2005. Planktonic and whole system metabolism in a nutrient-rich estuary (The Scheldt Estuary). Estuaries 28:868-883.
  8. Gazeau, F., A.V. Borges, C. Barrón, C.M. Duarte, N. Iversen, J.J. Middelburg, B. Delille, M.-D. Pizay , M. Frankignoulle, J.-P. Gattuso, 2005. Net ecosystem metabolism in a micro-tidal estuary (Randers Fjord, Denmark): evaluation of methods. Marine Ecology Progress Series 301:23-41.
  9. Greenwood, J.E., V.W. Truesdale, A.R. Rendell, 2005. Toward an understanding of biogenic-silica dissolution in seawater – An initial rate approach applied between 40 and 90°C. Aquatic Geochemistry 11:1-20.
  10. Gribsholt, B., H.T.S. Boschker, E. Struyf, M. Andersson, A. Tramper, L. De Brabandere, S. Van Damme, N. Brion, P. Meire, F. Dehairs, J.J. Middelburg, C. Heip, 2005. Nitrogen processing in a tidal freshwater marsh: a whole ecosystem 15N labeling study. Limnology and Oceanography 50:1945-1959.
  11. Hendriks, I.E., L.A. Van Duren, P.M.J. Herman, 2005. Image analysis techniques: A tool for the identification of bivalve larvae? Journal of Sea Research 54:151-164.
  12. Maes, J., M. Tackx, K. Soetaert, 2005. The predation impact of juvenile herring Clupea harengus and sprat Sprattus sprattus on estuarine zooplankton. Hydrobiologia 540:225-235.
  13. Malyuga, V.S., 2005. Viscous eddies in a circular cone. Journal of Fluid Mechanics 522:101-116.
  14. Meysman, F.J.R., B.P. Boudreau, J.J. Middelburg, 2005. Modeling reactive transport in sediments subject to bioturbation and compaction. Geochimica et Cosmochimica Acta 69:3601-3617.
  15. Meysman, F.J.R., J.J. Middelburg, 2005. Acid volatile sulfide (AVS)- a comment. Marine Chemistry 97:206-212. Publication 3680
  16. Meysman, F., O. Galaktionov, J. Middelburg, 2005. Irrigation patterns in permeable sediments induced by burrow ventilation: a case study of Arenicola marina. Marine Ecology Progress Series 303:195-212.
  17. Moodley, L., J.J. Middelburg, P.M.J. Herman, K. Soetaert, G.J. de Lange, 2005. Oxygenation and organic matter preservation in marine sediments: direct experimental evidence from ancient carbon-rich deposits. Geology 33:889-892.
  18. Moodley, L., J.J. Middelburg, K. Soetaert, H.T.S. Boschker, P.M.J. Herman, C.H.R. Heip, 2005. Similar rapid response to phytodetritus deposition in shallow and deep-sea sediments. Journal of Marine Research 63:457-469.
  19. Raick, C., E.J.M. Delhez, K. Soetaert, M. Grégoire, 2005. Study of the seasonal cycle of the biogeochemical processes in the Ligurian Sea using a 1D interdisciplinary model. Journal of Marine Systems 55:177-203.
  20. Steyaert, M., L. Moodley, J. Vanaverbeke, S. Vandewiele, M. Vincx, 2005. Laboratory experiments on the infaunal activity of intertidal nematodes. Hydrobiologia 540:217-233.
  21. Struyf, E., S. Van Damme, B. Gribsholt, P. Meire, 2005. Freshwater marshes as dissolved silica recyclers in an estuarine environment (Schelde estuary, Belgium). Hydrobiologia 540:69-77.
  22. Struyf, E., S. Van Damme, B. Gribsholt, J.J. Middelburg, P. Meire, 2005. Biogenic silica in tidal freshwater marsh sediments and vegetation (Schelde estuary, Belgium). Marine Ecology Progress Series 303:51-60.
  23. Tackx, M., F. Azémar, S. Boulêtreau, N. De Pauw, K. Bakker, B. Sautour, S. Gasparini, K. Soetaert, S. Van Damme, P. Meire, 2005. Zooplankton in the Schelde estuary, Belgium and the Netherlands: long-term trends in spring populations. Hydrobiologia 540:275-278.
  24. Truesdale, V.W., J.E. Greenwood, A. Rendell, 2005. The Rate-equation for Biogenic Silica Dissolution in Seawater – New Hypotheses. Aquatic Geochemistry 11:319-343.
  25. Truesdale, V.W., J.E. Greenwood, A.R. Rendell, 2005. In vitro, batch-dissolution of biogenic silica in seawater – the application of recent modelling to real data. Progress in Oceanography 66:1-24.
  26. Van Damme, S., E. Struyf, T. Maris, T. Ysebaert, F. Dehairs, M. Tackx, C. Heip, P. Meire, 2005. Spatial and temporal patterns of water quality along the estuarine salinity gradient of the Scheldt estuary (Belgium and The Netherlands): results of an integrated monitoring approach. Hydrobiologia 540:29-45.
  27. Veuger, B., J.J. Middelburg, H.T.S. Boschker, M. Houtekamer, 2005. Analysis of 15N incorporation into D-alanine: a new method for tracing nitrogen uptake by bacteria. Limnology and Oceanography Methods 3:230-240.

Book chapters

  1. Arístegui, J., S. Agustí, J.J. Middelburg, C.M. Duarte, 2005. Respiration in the mesopelagic and bathypelagic zones of the oceans. Pages 181-205 in P.A. del Giorgio, P.J.l.B. Williams, editors. Respiration in Aquatic Ecosystems. Oxford University Press, Oxford.
  2. Herman, P.M.J., Ysebaert, C.H.R. Heip, 2005. Land-ocean fluxes and coastal ecosystems - a guided tour of ELOISE results. Pages 21-85 in J. Vermaat, L. Bouwer, K. Turner, W. Salomons, editors. Managing European Coasts : Past, Present and Future. Springer, Berlin.