Molecular Ecology of the Rhizosphere

research group Prof. Dr. Joost T. van Dongen

Joost van Dongen

Joost T. van Dongen
room 42A216
Tel: 0241-8026632



Dr. Joost van Dongen is professor of molecular ecology at the RWTH Aachen University, Germany and research group leader at the Max-Planck-Institute of Molecular Plant Physiology in Potsdam, Germany. He obtained his PhD-degree in 2001 at Utrecht University, the Netherlands.

His research focusses on the biochemical and molecular responses of plants to low oxygen stress. Among the most prominent findings of this work, there is the description of the bifurcation of the TCA-cycle into an oxidative and reducing branch during low-oxygen stress which is thought to be involved in the regulation of oxygen consumption. Furhtermore, he was involved in the discovery of the sensing mechanism for oxygen in plants.



Hameed MW, Juszczak I, Bock R, van Dongen JT. 2017. Comparison of mitochondrial gene expression and polysome loading in different tobacco tissues. J. Plant Methods. 13:112

Rahmoune B, Morsli A, Khelifi-Slaoui M, Khelifi L, Strueh A, Erban A, Kopka J, Prell J, van Dongen JT. 2017. Isolation and characterization of three new PGPR and their effects on the growth of Arabidopsis and Datura plants. J. Plant Interactions. 12: 1-6.


Schippers JHM, Foyer CH, van Dongen JT. 2016. Redox regulation in shoot growth, SAM maintenance and flowering. Curr. Opin. Plant Biol. 29: 121-128. doi:10.1016/j.pbi.2015.11.009


Antonio C, Päpke C, Rocha M, Diab H, Limami AM, Obata T, Fernie AR, van Dongen JT. 2015. Regulation of primary metabolism in response to low oxygen availability as revealed by carbon and nitrogen isotope redistribution. Plant Physiol. epub. doi:​10.​1104/​pp.​15.​00266

Kosmacz M, Parlanti S, Schwarzländer M, Kragler F, Licausi F, van Dongen JT. 2015. The stability and nuclear localization of the transcription factor RAP2.12 are dynamically regulated by oxygen concentration. Plant Cell Environ. 38:1094-1103. doi: 10.1111/pce.12493.

Zulet A, Gil-Monreal M, Zabalza A, van Dongen JT, Royuela M. 2015. Fermentation and alternative oxidase contribute to the action of amino acid biosynthesis-inhibiting herbicides. J Plant Physiol. 175:102-112. doi: 10.1016/j.jplph.2014.12.004.

Jorge TF, Rodrigues JA, Caldana C, Schmidt R, van Dongen JT, Thomas-Oates J, António C. 2015. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress.. Mass Spectrom Rev DOI: 10.1002/mas.21449.

van Dongen JT, Licausi F.2015. Oxygen sensing and signaling. Annu Rev Plant Biol. 66:345-367. doi: 10.1146/annurev-arplant-043014-114813.


Giuntoli B, Lee SC, Licausi F, Kosmacz M, Oosumi T, van Dongen JT, Bailey-Serres J, Perata P. 2014. A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis. PLoS Biol. 12:e1001950. doi: 10.1371/journal.pbio.1001950.

Weits DA, Giuntoli B, Kosmacz M, Parlanti S, Hubberten HM, Riegler H, Hoefgen R, Perata P, van Dongen JT, Licausi F. 2014. Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat Commun. 5:3425. doi: 10.1038/ncomms4425.


Paparelli E, Parlanti S, Gonzali S, Novi G, Mariotti L, Ceccarelli N, van Dongen JT, Kölling K, Zeeman SC, Perata P. 2013. Nighttime sugar starvation orchestrates gibberellin biosynthesis and plant growth in Arabidopsis. Plant Cell. 25, 3760-3769.

Dolferus R, Powell N, Xuemei JI, Ravash R, Edlington J, Oliver S, van Dongen JT, Shiran B. 2013. The Physiology of Reproductive-Stage Abiotic Stress Tolerance in Cereals. In Molecular Stress Physiology of Plants. pp. 193-216. Springer India.

Pal SK, Liput M, Piques M, Ishihara H, Obata T, Martins MC, Sulpice R, van Dongen JT, Fernie AR, Yadav UP, Lunn JE, Usadel B, Stitt M. 2013. Diurnal changes of polysome loading track sucrose content in the rosette of wildtype Arabidopsis and the starchless pgm mutant. Plant Physiol. 162, 1246-1265. doi:10.1104/pp.112.212258.


Paparelli E, Gonzali S, Parlanti S, Novi G, Giorgi FM, Licausi F, Kosmacz M, Feil R, Lunn JE, Brust H, van Dongen JT, Steup M, Perata P. 2012. Misexpression of a Chloroplast Aspartyl Protease Leads to Severe Growth Defects and Alters Carbohydrate Metabolism in Arabidopsis. Plant Physiol. 160, 1237-1250. doi:10.1104/pp.112.204016.

Schwachtje J, Karojet S, Kunz S, Brouwer S, van Dongen JT. 2012). Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes. Plant Signal. Behav. 7, 623-627. doi:10.4161/psb.20176.

Bailey-Serres J, Fukao T, Gibbs DJ, Holdsworth MJ, Lee SC, Licausi F, Perata P, Voesenek LA, van Dongen JT. 2012. Making sense of low oxygen sensing. Trends in Plant Sci. 17, 129-138. doi:10.1016/j.tplants.2011.12.004.

Siahpoosh MR, Sanchez DH, Schlereth A, Scofield GN, Furbank RT, van Dongen JT, Kopka J. 2012. Modification of OsSUT1 gene expression modulates the salt response of rice Oryza sativa cv. Taipei 309. Plant Science. 182, 101-111. doi:10.1016/j.plantsci.2011.01.001.

Schudoma C, Steinfath M, Sprenger H, van Dongen JT, Hincha DK, Zuther E, Geigenberger P, Kopka J, Koehl K, Walther D. 2012. Conducting molecular biomarker discovery studies in plants. Methods Mol. Biol. 918, 127-150.

Karojet S, Kunz S, van Dongen JT. 2012. Microbacterium yannicii sp. nov., isolated from Arabidopsis thaliana roots. Int. J. Syst. Evol. Microbiol. 62, 822-826. doi:10.1099/ijs.0.026955-0.

Ast C, Schmalzlin E, Lohmannsroben HG, van Dongen JT. 2012. Optical Oxygen Micro and Nanosensors for Plant Applications. Sensors. 12, 7015-7032. doi:10.3390/S120607015.


Schwachtje J, Karojet S, Thormaehlen I, Bernholz C, Kunz S, Brouwer S, Schwochow M, Koehl K, van Dongen JT. 2011. A Naturally Associated Rhizobacterium of Arabidopsis thaliana Induces a Starvation-Like transcriptional Response while Promoting Growth. PLoS One. 6, e29382. doi:10.1371/journal.pone.0029382.

Licausi F, Kosmacz M, Weits DA, Giuntoli B, Giorgi FM, Voesenek LACJ, Perata P, van Dongen JT. 2011. Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature. 479, 419-422. doi:10.1038/nature10536.

Ramirez-Aguilar SJ, Keuthe M, Rocha M, Fedyaev VV, Kramp K, Gupta KJ, Rasmusson AG, Schulze WX, van Dongen JT. 2011. The Composition of Plant Mitochondrial Supercomplexes Changes with Oxygen Availability. J. Biol. Chem. 286, 43045-43053. doi:10.1074/jbc.M111.252544.

Licausi F, Giorgi FM, Schmalzlin E, Usadel B, Perata P, van Dongen JT, Geigenberger P. 2011. HRE-Type Genes Are Regulated by Growth-Related Changes in Internal Oxygen Concentrations During the Normal Development of Potato (Solanum tuberosum) Tubers. Plant Cell Physiol. 52, 1957-1972. doi:10.1093/pcp/pcr128.

Hoehenwarter W, Larhlimi A, Hummel J, Egelhofer V, Selbig J, van Dongen JT, Wienkoop S, Weckwerth W. 2011. MAPA Distinguishes Genotype-Specific Variability of Highly Similar Regulatory Protein Isoforms in Potato Tuber. J. Proteome Res. 10, 2979-2991. doi:10.1021/pr101109a.

Zabalza A, Orcaray L, Igal M, Schauer N, Fernie AR, Geigenberger P, van Dongen JT, Royuela M. 2011. Unraveling the role of fermentation in the mode of action of acetolactate synthase inhibitors by metabolic profiling. J. Plant Physiol. 168, 1568-1575. doi:10.1016/j.jplph.2011.02.015.

Sandmann M, Skłodowski K, Gajdanowicz P, Michard E, Rocha M, Gomez-Porras JL, González W, Correa LGG, Ramirez-Aguilar SJ, Cuin TA, van Dongen JT, Thibaud J-B, Dreyer I. 2011. The K (+) battery-regulating Arabidopsis K(+) channel AKT2 is under the control of multiple post-translational steps. Plant Signal. Behav. 6, 558-562. doi:10.4161/psb.6.4.14908.

van Dongen JT, Nikoloski Z. 2011. Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions. New Phytol. 190, 273-276. doi:10.1111/j.1469-8137.2011.03674.x.

Narsai R, Rocha M, Geigenberger P, Whelan J, van Dongen JT. 2011. Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia. New Phytol. 190, 472-487. doi:10.1111/j.1469-8137.2010.03589.x.

van Dongen JT, Gupta KJ, Ramirez-Aguilar SJ, Araujo WL, Nunes-Nesi A, Fernie AR. 2011. Regulation of respiration in plants: A role for alternative metabolic pathways. J. Plant Physiol. 168, 1434-1443. doi:10.1016/j.jplph.2010.11.004.

Licausi F, Weits DA, Pant BD, Scheible W-R, Geigenberger P, van Dongen JT. 2011. Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability. New Phytol. 190, 442-456. doi:10.1111/j.1469-8137.2010.03451.x.

Gupta KJ, Fernie AR, Kaiser WM, van Dongen JT. 2011. On the origins of nitric oxide. Trends Plant Sci. 16, 160-168. doi:10.1016/j.tplants.2010.11.007.

Gajdanowicz P, Michard E, Sandmann M, Rocha M, Correa LGG, Ramirez-Aguilar SJ, Gomez-Porras JL, Gonzalez W, Thibaud JB, van Dongen JT. Dreyer I. 2011. Potassium (K plus) gradients serve as a mobile energy source in plant vascular tissues. Proc. Natl. Acad. Sci. USA. 108, 864-869. doi:10.1073/pnas.1009777108.


Rocha M, Sodek L, Licausi F, Hameed MW, Dornelas MC, van Dongen JT. 2010. Analysis of alanine aminotransferase in various organs of soybean (Glycine max) and in dependence of different nitrogen fertilisers during hypoxic stress. Amino Acids. 39, 1043-1053. doi:10.1007/s00726-010-0596-1.

Steinfath M, Strehmel N, Peters R, Schauer N, Groth D, Hummel J, Steup M, Selbig J, Kopka J, Geigenberger P, van Dongen JT. 2010. Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach. Plant Biotechnol. J. 8, 900-911. doi:10.1111/j.1467-7652.2010.00516.x.

Licausi F, van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P. 2010. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J. 62, 302-315. doi:10.1111/j.1365-313X.2010.04149.x.

Rocha M, Licausi F, Araujo WL, Nunes-Nesi A, Sodek L, Fernie AR, van Dongen JT. 2010. Glycolysis and the Tricarboxylic Acid Cycle Are Linked by Alanine Aminotransferase during Hypoxia Induced by Waterlogging of Lotus japonicus. Plant Phys. 152, 1501-1513. doi:10.1104/pp.109.150045.

van Dongen JT, Schauer N. 2010). Metabolic marker as selection tool in plant breeding. Information Systems for Biotechnology News Reports, 11, 7-10.

Strehmel N, Praeger U, Koenig C, Fehrle I, Erban A, Geyer M, Kopka J, van Dongen JT. 2010. Time course effects on primary metabolism of potato (Solanum tuberosum) tuber tissue after mechanical impact. Postharvest Biology and Technology. 56, 109-116. doi:10.1016/j.postharvbio.2009.12.008.


Rasmusson AG, Fernie AR, van Dongen JT (2009). Alternative oxidase: a defence against metabolic fluctuations? Physiol. Plant. 137, 371-382. doi:10.1111/j.1399-3054.2009.01252.x.

Gupta KJ, Zabalza A, van Dongen JT. 2009. Regulation of respiration when the oxygen availability changes. Physiol. Plant. 137, 383-391. doi:10.1111/j.1399-3054.2009.01253.x.

Arrivault S, Guenther M, Ivakov A, Feil R, Vosloh D, van Dongen JT, Sulpice R, Stitt M. 2009. Use of reverse-phase liquid chromatography, linked to tandem mass spectrometry, to profile the Calvin cycle and other metabolic intermediates in Arabidopsis rosettes at different carbon dioxide concentrations. Plant J. 59, 824-839. doi:10.1111/j.1365-313X.2009.03902.x.

Zabalza A, van Dongen JT, Froehlich A, Oliver SN, Faix B, Gupta KJ, Schmalzlin E, Igal M, Orcaray L, Royuela M, Geigenberger P. 2009. Regulation of Respiration and Fermentation to Control the Plant Internal Oxygen Concentration. Plant Phys. 149, 1087-1098. doi:10.1104/pp.108.129288.

Vigano I, Holzinger R, Rockmann T, van Dijk A, Keppler F, Greule M, Brand WA, van Weelden H, van Dongen JT. 2009. UV light induces methane emission from plant biomass: Mechanism and isotope studies. Geochimica Et Cosmochimica Acta. 73, A1382-A1382.

van Dongen JT, Frohlich A, Ramirez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P. 2009. Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Ann. Bot. 103, 269-280. doi:10.1093/aob/mcn126.

Maximova E, van Dongen JT, Hartmann J. 2009. Comparative studies on leaf structure and ultrastructure of Peperomia species in vivo and in vitro. In MA Pabst & G Zellnig (Eds.), Proceedings of Microscopy Conference. 75-76.


Hoehenwarter W, van Dongen JT, Wienkoop S, Steinfath M, Hummel J, Erban A, Sulpice R, Regierer B, Kopka J, Geigenberger P, Weckwerth W. 2008. A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics. 8, 4214-4225. doi:10.1002/pmic.200701047.

Oliver SN, Lunn JE, Urbanczyk-Wochniak E, Lytovchenko A, van Dongen JT, Faix B, Schmalzlin E, Fernie AR, Geigenberger P. 2008. Decreased Expression of Cytosolic Pyruvate Kinase in Potato Tubers Leads to a Decline in Pyruvate Resulting in an in Vivo Repression of the Alternative Oxidase. Plant Phys. 148, 1640-1654. doi:10.1104/pp.108.126516.

Rumpler M, Woesz A, Dunlop JWC, van Dongen JT, Fratzl P. 2008. The effect of geometry on three-dimensional tissue growth. J. R. Soc. Interface. 5, 1173-1180. doi:10.1098/rsif.2008.0064.

Rumpler M, Woesz A, Dunlop J, van Dongen JT, Klaushofer K, Fratzl P. 2008. Three-dimensional geometry determines the tissue formation kinetics in vitro. Calcified Tissue International 82, S76-S76.


Schwachtje J, Minchin PE, Jahnke S, van Dongen JT, Schittko U, Baldwin IT. 2006. SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots. Proc. Natl. Acad. Sci. USA. 103, 12935-12940. doi:10.1073/pnas.0602316103.

Kolbe A, Oliver SN, Fernie AR, Stitt M, van Dongen JT, Geigenberger P. 2006. Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Phys. 141, 412-422. doi:10.1104/pp.106.081208.

Udvardi MK, Ott T, Krusell L, Desbrosses G, Voroshilova V, Colebatch G, Wandrey M, Montanari O, Kakar K, Krause K, Guenther C, van Dongen JT, Vigeolas H, Geigenberger P, Kraemer U, Kloska S, Kopka J, Sato S, Nakamura Y, Tabata S, James EK, Kawaguchi M, Miyamoto A, Suganuma N, Sandal N, Stougaard J. 2006. Insights into nodule physiology and metabolism from transcriptomics, metabolomics, bioinformatics, and genetics. In F Sánchez, C Quinto, IM López-Lara, & O Geiger (Eds.), Biology of plant-microbe interactions. 96-102. St. Paul, MN, USA: ISMPMI.


Schmaelzlin E, van Dongen JT, Klimant I, Marmodee B, Steup M, Fisahn J, Geigenberger P, Lohmannsroeben HG. 2005. An optical multifrequency phase-modulation method using microbeads for measuring intracellular oxygen concentrations in plants. Biophys J. 89, 1339-1345. doi:10.1529/biophysj.105.063453.

Geigenberger P, Regierer B, Nunes-Nesi A, Leisse A, Urbanczyk-Wochniak E, Springer F, van Dongen JT, Kossmann J, Fernie AR. 2005. Inhibition of de novo pyrimidine synthesis in growing potato tubers leads to compensatory stimulation of the pyrimidine salvage pathway and a subsequent increase in biosynthetic performance. Plant Cell. 17, 2077-2088. doi:10.1105/tpc.105.033548.

Ott T, van Dongen JT, Gunther C, Krusell L, Desbrosses G, Vigeolas H, Bock V, Czechowski T, Geigenberger P, Udvardi MK. 2005. Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development. Current Biol. 15, 531-535. doi:10.1016/j.cub.2005.01.042.

Oliver SN, van Dongen JT, Alfred SC, Mamun EA, Zhao XC, Saini HS, Fernandes SF, Blanchard CL, Sutton BG, Geigenberger P, Dennis ES, Dolferus R. 2005. Cold-induced repression of the rice anther-specific cell wall invertase gene OSINV4 is correlated with sucrose accumulation and pollen sterility. Plant Cell Env. 28, 1534-1551. doi:10.1111/j.1365-3040.2005.01390.x.

Loehmannsroeben HG, Beck M, Hildebrandt N, Schmaelzlin E, van Dongen JT. 2005. New Challenges in biophotonics: Laser-based fluoroimmuno analysis and in-vivo optical oxygen monitoring. In W Gries & TP. Pearsall (Eds.), Workshop on Laser Applications in Europe. E1570-E1570. doi:10.1117/12.663583.


van Dongen JT, Roeb GW, Dautzenberg M, Froehlich A, Vigeolas H, Minchin PEH, Geigenberger P. 2004. Phloem import and storage metabolism are highly coordinated by the low oxygen concentrations within developing wheat seeds. Plant Phys. 135, 1809-1821. doi:10.1104/pp.104.040980.

van Dongen JT, Borstlap AC. 2004. Aquaporins: Structure, Function and Phylogenetic Analysis. In AR. Hemsley & I. Poole (Eds.), The evolution of Plant Physiology. 109-120. London, UK: Elsevier – Academic Press.


Vigeolas H, van Dongen JT, Waldeck P, Huhn D, Geigenberger P. 2003. Lipid storage metabolism is limited by the prevailing low oxygen concentrations oilseed rape. Plant Phys. 133, 2048-2060. doi:10.1104/pp.103.031963.

van Dongen JT, Schurr U, Pfister M, Geigenberger P. 2003. Phloem metabolism and function have to cope with low internal oxygen. Plant Phys. 131, 1529-1543. doi:10.1104/pp.102.017202.

van Dongen JT, Ammerlaan AMH, Wouterlood M, van Aelst AC, Borstlap AC. 2003. Structure of the developing pea seed coat and the post-phloem transport pathway of nutrients. Ann Bot. 91, 729-737. doi:10.1093/aob/mcg066.

Schuurmans JAMJ, van Dongen JT, Rutjens BPW, Boonman A, Pieterse CMJ, Borstlap AC. 2003. Members of the aquaporin family in the developing pea seed coat include representatives of the PIP, TIP, and NIP subfamilies. Plant Mol. Biol. 53, 655-667. doi:10.1023/B:PLAN.0000019070.60954.77.


van Dongen JT, Laan RGW, Wouterlood M, Borstlap AC. 2001. Electrodiffusional uptake of organic cations by pea seed coats. Further evidence for poorly selective pores in the plasma membrane of seed coat parenchyma cells. Plant Phys. 126, 1688-1697. doi:10.1104/pp.126.4.1688


van Dongen JT, Schuurmans JAMJ, Deen PMT, Borstlap AC. 2000. Analysis of four MIP-like proteins from the developing pea seed coat. In S. Hohmann & S. Nielsen (Eds.) Molecular Biology and Physiology of Water and Solute Transport. 331-338, New York, NY, USA: Kluwer Academic / Springer.