Ongoing and recently completed work

1. Exploring new proxies. In the context of NESSC, the Netherlands Earth System Science Center, we (i.e. together with my PhD students Anne Roepert and Shaun Akse and UU colleague Lubos Polerecky) explore coccolith and diatom skeleton chemistry for novel proxies using the nanoSIMS facility at Utrecht.
2. Exploit modern biogeochemical knowledge to better read the paleorecord, largely supported by NESSC. Together with UU colleague Appy Sluijs and his team we aim to better understand PETM and MECO phenomena. Cooperations with Bernie Boudreau and Jerry Dickens have been initiated to study methane hydrate dynamics during these periods. A new project with PhD student Matthias Kuderer aims to advance understanding of bioturbation and its consequences for the paleorecord (with Andy Ridgwell).
3. Develop global biogeochemical-river models. Together with colleague Lex Bouwman, associate scientists Jose Mogollon and Arthur Beusen and PhD students Joep Langeveld and Wim-Joost van Hoek, we are developing global scale river biogeochemistry models.
4. High-school teacher Nicole Geerlings is performing PhD research on the impact of cable bacteria on mineral formation under guidance of Filip Meysman and me.
5. My former PhD student Mathilde Hagens has developed novel, generic theory to deal with ocean acidification issues.
6. Coral reefs and sponges are biogeochemical hotspots. Postdoc Anna de Kluijver studies deep-sea sponges within the project SponGES.
7. Carbon flows in lakes (Netherlands, China, USA, Switzerland) have been studied using stable isotope as deliberate tracers by former PhD students Anna de Kluijver and Marieke Lammers and post-doc Regina Flores.

Past research

1. Introduction of reactive continuum concept to organic matter decomposition in marine systems. The concept and model were presented in Middelburg (1989) and in subsequent organic geochemical work I have developed a quantitative continuous measure of organic matter ‘quality’ (Dauwe and Middelburg, 1998; Dauwe et al., 1999). This concept is covered in multiple textbooks (Sarmiento & Gruber, Burdige, Hedges & Emerson), has been adopted by oceanographers, limnologist, engineers and deep biosphere scientists and its implications are still being discussed (article, new and views, comment and rebuttal in Science, 2007).
• Middelburg, J.J. (1989). A simple rate model for organic matter decomposition in marine sediments. Geochim. Cosmochim. Acta, 53, 1577-1581.
• Dauwe, B. and Middelburg J.J. (1998) Amino acids and hexosamines as indicators of organic matter degradation state in North Sea sediments. Limnol. Oceanogr. 43: 782-798.
• Dauwe, B. Middelburg, J.J., Herman, P.M.J., Heip, C.H.R. (1999) Particulate organic matter degradation in the ocean: changes in biochemical composition and reactivity are linked. Limnol. Oceanogr. 44: 1809-1814.
• Middelburg, J.J. and F.J.R. Meysman (2007). Burial at sea. Science 317: 1294-1295

2. Pioneered the development of generic sediment biogeochemical models that accurate reproduce observations, that allow global estimates of benthic processes to be made and that can be linked to water-column biogeochemical models (Soetaert et al., 1996). We have made the first global marine assessment of sediment denitrification and how it depends on bottom-water composition and carbon fluxes (Middelburg et al., 1996). These generic sediment biogeochemical models are now common tools in many labs.
• Middelburg, J.J., Soetaert K., Herman P.M.J. and Heip C.H.R. (1996) Marine sedimentary denitrification: a model study. Global Biogeochemical Cycles 10, 661-673.
• Soetaert, K, Herman P.M.J. and  Middelburg, J.J. (1996).  A model of early diagenetic processes from the shelf to abyssal depths. Geochimica Cosmochimica Acta  60: 1019-1040.
• Soetaert, K, Herman P.M.J. and  Middelburg J.J., (1996). Dynamic response of deep-sea sediments to seasonal variation: a model. Limnol. Ocean. 41(8): 1651-1668.

3. Elucidation of the role of benthic animals in sediment biogeochemistry. We have developed and explored new approaches to quantitatively describe animal induced mixing processes (Meysman et al., 2003, 2005, 2008). In Meysman et al. (2006) we identified benthic animals as ecosystem engineers andhave linked the Cambrian explosion of metazoan life to the ecosystem engineering activities of benthic fauna.
• Meysman FJR, Boudreau BP and Middelburg JJ (2003) Relations between local,  non-local, discrete and continous models of bioturbation. J. Mar. Res. 61, 391-410.
• Meysman FJR, Boudreau BP and Middelburg JJ (2005) Modeling reactive transport in sediment subject to bioturbation and compaction. Geochim. Cosmochim. Acta 69: 3601-3617.
• Meysman FJR, Middelburg JJ, Heip CHR (2006)  New insights into Darwin’s last idea: bioturbation. Trends Ecol. Evol 21, 688-695.
• Meysman FJR, Malyuga VS, Boudreau BP, Middelburg JJ (2008) A generalized stochastic approach to particle dispersal in soils and sediments Geochim. Cosmochim. Acta 72, 3460-3478.

4. Pioneered the use of stable isotopes as deliberate tracer in combination with compound specific isotope analysis of biomarkers to study carbon and/or nitrogen flows through entire food webs and ecosystems and to link activity and identity of microbes.  Middelburg et al. (2000) first used this approach and elucidated the pivotal role of benthic microalgae in moderating carbon flows in estuarine systems. This approach has since been used by many scientists and in many ecosystems (lakes, tidal marshes, mangroves, intertidal flats, continental shelf sediments, slope, margin and deep-sea sediments, tropical and cold-water corals) and stable isotopes addition experiments are now common tools within ecology. Using this approach we discovered the sponge loop in coral reef ecosystems (de Goeij et al., 2013), identified bacteria as sinks rather than links in benthic food webs (van Oevelen et al., 2006), elucidated the prominent role of benthic foraminifera in deep-sea and low-oxygen sediments (Moodley et al., 2002; Woulds et al., 2007), advanced understanding on the competition between benthic animals and bacteria (van Nugteren et al., 2009) and studied the role of external subsidies in lakes (Pace et al., 2007).
• Middelburg, J.J., Barranguet, C, Boschker H.T.S., Herman, P.M.J., Moens, T. and Heip C.H.R. (2000) The fate of intertidal microphytobenthos carbon: an in situ ¹³C labelling study. Limnol. Oceanogr. 45: 1224-1234.
• Moodley, L., Middelburg, J.J., Boschker, H.T.S., G.C.A Duineveld, Pel R., Herman, P.M.J., Heip, C.H.R. (2002) Bacteria and Foraminifera: key players in a short-term deep-sea benthic response to phytodetritus. Mar. Ecol. Prog. Ser. 236:23-29
• van Oevelen, D, , Middelburg JJ, Soetaert K, Moodley, LM (2006) The fate of bacterial carbon in an intertidal sediment: Modeling an in situ isotope tracer experiment. Limnol. Oceanogr. 51(3) 1302-1314.
• Woulds, C.  Cowie GL, Levin LA, Andersson H.,  Middelburg J.J., Vandewiele S., Lamont PA, Larkin K, Gooday A, Schumacher S, Whitcraft C., Jeffreys R.,  Schwartz M. (2007) Oxygen as a control on sea floor faunal communities and their roles in sedimentary organic matter cycling. Limnol. Oceanogr. 52: 1698-1709.
• van Nugteren P, Herman PMJ, Moodley  L,Middelburg JJ,  Vos M,  Heip CHR (2009) Spatial distribution of detrital resources determines the outcome of competition between bacteria and a facultative detritivorous worm. Limnol. Ocean 54:1413-1419
• Pace M.L., Carpenter S.R., Cole J.J., Coloso J., Kitchell J.F., Hodgson J.R., Middelburg J.J., Preston N.D., Solomon C. and B. Weidel (2007) Does terrestrial  carbon subsidize plankton in a clear-water lake Limnol. Oceanogr. 52: 2177-2189.
• de Goeij, J.M., van Oevelen, D., Vermeij, M.J.A., Osinga, R., Middelburg, J.J., de Goeij, A.F.P.M. & Admiraal, W. (2013). Surviving in a marine desert: the sponge loop retains resources within coral reefs. Science, 342(6154), 108-110.

5. Studied biogeochemical cycling in coastal ecosystems with an emphasis on tidal estuaries, vegetated ecosystems and the effects of hypoxia and ocean acidification. We found that tidal estuaries are heterotrophic, hot spots of biogeochemistry processing large quantities of carbon and nutrients (Heip et al., 1995; Middelburg and Herman, 2007). We identified the role of vegetated coastal ecosystems in carbon burial (this has led to the concept of blue carbon, Duarte et al., 2005; Bouillon et al., 2008), the role of tidal marshes in silicon cycling (Struyf et al., 2006) and quantified in detail freshwater tidal marsh nitrogen transformations (Gribsholt et al., 2005). More recently, I studied the effect of hypoxia on sediment biogeochemistry and benthic ecology (Middelburg and Levin, 2009) and the effect of ocean acidification on bivalves, coccoliths and marine ecosystems (Gazeau et al., 2007; Soetaert et al., 2007);
• Heip, C.H.R., Goosen N.K., Herman, P.M.J. Kromkamp J., Middelburg, J.J. and Soetaert, K. (1995) Production and consumption of biological particles in temperate tidal estuaries. Oceanogr.Mar. Biol. Ann. Reviews 33, 1-150.
• Middelburg JJ, Herman PMJ (2007) Organic matter processing in tidal estuaries. Mar. Chem. 106: 127-147
• Struyf E, Dausee A, Van Damme S, Bal K, Gribsholt B, Boschker HTS, Middelburg J.J. Meire P (2006). Tidal marshes and biogenic silica recycling at the land-sea interface Limnol. Oceanogr. 51: 838-846.
• Duarte CM, Middelburg JJ and Caraco N (2005) Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences 1: 173-180.
• Bouillon S., Borges, AV, Diele K,  Dittmar T,  Duke N.C., Kristensen, E., Lee S.Y., Marchand C.,  Middelburg J.J., Rivera-Monroy V.H.,  Smith T.J., and Twilley R.R. (2008) Mangrove production and fate: a revision of budget estimates. Glob. Biogeoch. Cycles doi10.1029/2007GB003052
• Gribsholt B, Boschker HTS, Struyf E, Andersson M, Tramper A, De Brabandere L, van Damme S, Brion N,  Meire P, Dehairs F, Middelburg JJ and Heip C (2005) Nitrogen processing in a tidal freshwater marsh: A whole ecosystem 15N labeling study. Limnology & Oceanography 50: 1945-1959.
• Gazeau F., Quiblier, J. Jansen, J.P. Gattuso, J.J. Middelburg and C. Heip (2007) Impact of elevated CO₂ on shellfish calcification Geophysical Research Letters. Doi10.1029/2006GL028554
• Soetaert, K, A. Hoffman, Middelburg, JJ, Meysman FJR, Greenwood J. (2007). The effect of biogeochemical processes on pH. Mar. Chem. 105: 30-51.

6. I have also contributed to larger team efforts that resulted in papers that recognized the role of freshwater systems in the global carbon cycle (Cole et al., 2007; Downing et al., 2006) and elucidated new pathways in the global nitrogen cycling, including the identification of Archaea as ammonia oxidizers in the ocean (Wuchter et al., 2006) and the importance of anthropogenic atmospheric nitrogen for open ocean, pelagic ecosystem functioning (Duce et al., 2008). 
• Cole, J., Prairie, Y., Caraco, N, McDowell, W.,Tranvik, L., Striegl R.,Duarte C.M., Kortelainen P., Downing J., Middelburg, J.J.  and Melack, J.M. (2007)  Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget Ecosystems 10: 171-184.
• J.A. Downing, 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 Limnol. Oceanogr. 51 (5) 2388-2397.
• Wuchter, C, Abbas, B, Coolen M.J.L., Herfort L., Van Bleijswijk J, Timmers P., Strous M., Teira E.,  Herndl G.J., Middelburg, J.J., Schouten, S., Sinninghe Damsté, JS (2006) Archael nitrification in the ocean. Proceeding National Academy Sciences 103: 12317-12322.
• 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.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, L. Zamora (2008) Impacts of Atmospheric Anthropogenic Nitrogen on the Open Ocean. Science 320, 893-897

7. Finally, in the early stages of my career I published geochemical papers on the distribution of oxyanions V, As and Sb in the ocean (Middelburg et al., 1988), mobilization of radiocesium in lake sediments (Comans et al., 1989), weathering of granitic rocks (Middelburg et al., 1988) and on non-steady state diagenesis (sulfidize down and burn-down concepts; Middelburg, 1991; Passier et al., 1996; de Lange et al., 1989) that have had substantial impact.
• Middelburg, J.J., Van der Weijden, C.H. and Woittiez, J.R.W. (1988). Chemical processes affecting the mobility of major, minor and trace elements during weathering of granitic rocks. Chem. Geol., 68,  253-273.
• Middelburg, J.J., Hoede, D., Van der Sloot, H.A., Wijkstra, J. and Van der Weijden, C.H. (1988). Arsenic, antimony and vanadium in the North Atlantic. Geochim. Cosmochim. Acta, 52, 2871-2878.
• De Lange, G.J., Middelburg, J.J. and Pruysers, P.A. (1989). Middle and Late Quaternary depositional sequences and cycles in the eastern Mediterranean. Sedimentol.,  36, 151-158.
• Comans, R.N.J., Middelburg, J.J., Zonderhuis, J., Woittiez, J.R.W., De Lange G.J., Das H.A. and Van der Weijden C.H. (1989). Mobilization of radiocaesium in pore water of lake sediments. Nature, 339, 367-369.
• Middelburg, J.J. (1991) Organic carbon, sulphur and iron in recent semi-euxinic sediments of Kau Bay. Geochim. Cosmochim. Acta, 55, 815-828.
• Passier, H.F., Middelburg, J.J., van Os, B.J.H. and de Lange, G.J. (1996) Diagenetic pyritisation under Eastern Mediterranean sapropels caused by downward sulphide diffusion. Geochimica Cosmochimica Acta 60: 751-763.