Dr. R. (Ronnie) de Jonge

Hugo R. Kruytgebouw
Padualaan 8
Kamer N205
3584 CH Utrecht

Dr. R. (Ronnie) de Jonge

Assistant Professor
Plant-Microbe Interactions
+31 30 253 6860
r.dejonge@uu.nl

Publications

2023

Scholarly publications

Vacheron, J., Heiman, C. M., Garneau, J. R., Kupferschmied, P., de Jonge, R., Garrido-Sanz, D., & Keel, C. (2023). Molecular and evolutionary basis of O-antigenic polysaccharide driven phage sensitivity in environmental pseudomonads. bioRxiv. https://doi.org/10.1101/2023.05.15.539993
Song, Y., Spooren, J., Jongekrijg, C. D., Manders, E. HH., de Jonge, R., Pieterse, C. MJ., Bakker, P. AHM., & Berendsen, R. L. (2023). Seed tuber imprinting shapes the next-generation potato microbiome. bioRxiv.
Verbon, E. H., Liberman, L. M., Zhou, J., Yin, J., Pieterse, C. M. J., Benfey, P. N., Stringlis, I. A., & de Jonge, R. (2023). Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions. Molecular Plant, 16(7), 1160-1177. https://doi.org/10.1016/j.molp.2023.06.001
López, J. L., Fourie, A., Poppeliers, S. W. M., Pappas, N., Sánchez-Gil, J. J., de Jonge, R., & Dutilh, B. E. (Accepted/In press). Growth rate is a dominant factor predicting the rhizosphere effect. ISME Journal. https://doi.org/10.1038/s41396-023-01453-6
Sánchez-Gil, J. J., Poppeliers, S. W. M., Vacheron, J., Zhang, H., Odijk, B., Keel, C., & de Jonge, R. (2023). The conserved iol gene cluster in Pseudomonas is involved in rhizosphere competence. Current Biology, 33(15), 3097-3110.e6. https://doi.org/10.1016/j.cub.2023.05.057
Poppeliers, S. WM., Sánchez-Gil, J. J., & Jonge, R. D. (2023). Microbes to support plant health: understanding bioinoculant success in complex conditions. Current Opinion in Microbiology, 73, 1-10. [102286]. https://doi.org/10.1016/j.mib.2023.102286

2022

Scholarly publications

López, J. L., Pappas, N., Poppeliers, S. WM., Sanchez-Gil, J. J., Fourie-Fouche, A., Jonge, R. D., & Dutilh, B. E. (2022). Copiotrophs dominate rhizosphere microbiomes and growth rate potential is a major factor explaining the rhizosphere effect. (pp. 1-23). bioRxiv. https://doi.org/10.1101/2022.11.24.517860
Spanner, R., Neubauer, J., Heick, T. M., Grusak, M. A., Hamilton, O., Rivera-Varas, V., de Jonge, R., Pethybridge, S., Webb, K. M., Leubner-Metzger, G., Secor, G. A., & Bolton, M. D. (2022). Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet (Beta vulgaris) Fruit Tissue. Phytopathology, 112(5), 1016-1028. https://doi.org/10.1094/PHYTO-03-21-0113-R
Verbon, E. H., Liberman, L. M., Zhou, J., Yin, J., Pieterse, C. MJ., Benfey, P. N., Stringlis, I. A., & Jonge, R. D. (2022). Cell-type specific transcriptomics reveals roles for root hairs and endodermal barriers in interaction with beneficial rhizobacterium. bioRxiv. https://doi.org/10.1101/2022.05.09.491085
Skiadas, P., Klein, J., Quiroz Monnens, T., Elberse, J., de Jonge, R., Van den Ackerveken, G., & Seidl, M. F. (2022). Sexual reproduction contributes to the evolution of resistance breaking isolates of the spinach pathogen Peronospora effusa. Environmental Microbiology, 24(3), 1622-1637. https://doi.org/10.1111/1462-2920.15944

2021

Scholarly publications

Harting, R., Starke, J., Kusch, H., Pöggeler, S., Maurus, I., Schlüter, R., Landesfeind, M., Bulla, I., Nowrousian, M., de Jonge, R., Stahlhut, G., Hoff, K. J., Aßhauer, K. P., Thürmer, A., Stanke, M., Daniel, R., Morgenstern, B., Thomma, B. P. H. J., Kronstad, J. W., ... Braus, G. H. (2021). A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. Molecular Plant Pathology, 22(8), 939-953. https://doi.org/10.1111/mpp.13071
Bernal, P., Eberl, L., de Jonge, R., Lepek, V. C., & Malone, J. G. (2021). Understanding plant-microorganism interactions to envision a future of sustainable agriculture. Environmental Microbiology, 23(4), 1809-1811. https://doi.org/10.1111/1462-2920.15479
Rangel, L. I., Hamilton, O., de Jonge, R., & Bolton, M. D. (2021). Fungal social influencers: secondary metabolites as a platform for shaping the plant-associated community. Plant Journal, 108(3), 632-645. https://doi.org/10.1111/tpj.15490
Ebert, M. K., Rangel, L. I., Spanner, R. E., Taliadoros, D., Wang, X., Friesen, T. L., de Jonge, R., Neubauer, J. D., Secor, G. A., Thomma, B. P. H. J., Stukenbrock, E. H., & Bolton, M. D. (2021). Identification and characterization of Cercospora beticola necrosis-inducing effector CbNip1. Molecular Plant Pathology, 22(3), 301-316. https://doi.org/10.1111/mpp.13026
Li, E., Zhang, H., Jiang, H., Pieterse, C. M. J., Jousset, A., Bakker, P. A. H. M., & de Jonge, R. (2021). Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens. mBio, 12(3), 1-21. [e0092721]. https://doi.org/10.1128/mBio.00927-21
Li, E., de Jonge, R., Liu, C., Jiang, H., Friman, V-P., Pieterse, C. M. J., Bakker, P. A. H. M., & Jousset, A. (2021). Rapid evolution of bacterial mutualism in the plant rhizosphere. Nature Communications, 12(1), 1-13. [3829]. https://doi.org/10.1038/s41467-021-24005-y
Yu, K., Stringlis, I. A., van Bentum, S., de Jonge, R., Snoek, B. L., Pieterse, C. M. J., Bakker, P. A. H. M., & Berendsen, R. L. (2021). Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication. Microorganisms, 9(3), [575]. https://doi.org/10.3390/microorganisms9030575
Pieterse, C. M. J., Berendsen, R. L., de Jonge, R., Stringlis, I. A., Van Dijken, A. J. H., Van Pelt, J. A., Van Wees, S. C. M., Yu, K., Zamioudis, C., & Bakker, P. A. H. M. (2021). Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium. Plant and Soil, 461(1-2), 245-263. https://doi.org/10.1007/s11104-020-04786-9

2020

Scholarly publications

Sánchez-Vallet, A., Tian, H., Rodriguez-Moreno, L., Valkenburg, D. J., Saleem-Batcha, R., Wawra, S., Kombrink, A., Verhage, L., de Jonge, R., van Esse, H. P., Zuccaro, A., Croll, D., Mesters, J. R., & Thomma, B. P. H. J. (2020). A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization. PLoS Pathogens, 16(6), [e1008652]. https://doi.org/10.1371/journal.ppat.1008652
Rangel, L. I., Spanner, R. E., Ebert, M. K., Pethybridge, S. J., Stukenbrock, E. H., de Jonge, R., Secor, G. A., & Bolton, M. D. (2020). Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. Molecular Plant Pathology, 21(8), 1020-1041. https://doi.org/10.1111/mpp.12962
Fourie, A., de Jonge, R., van der Nest, M. A., Duong, T. A., Wingfield, M. J., Wingfield, B. D., & Barnes, I. (2020). Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families. Fungal Genetics and Biology, 143, 1-16. [103433]. https://doi.org/10.1016/j.fgb.2020.103433
Bakker, P. A. H. M., Berendsen, R. L., Van Pelt, J. A., Vismans, G., Yu, K., Li, E., Van Bentum, S., Poppeliers, S. W. M., Sanchez Gil, J. J., Zhang, H., Goossens, P., Stringlis, I. A., Song, Y., de Jonge, R., & Pieterse, C. M. J. (2020). The soil-borne identity and microbiome-assisted agriculture: Looking back to the future. Molecular Plant, 13(10), 1394-1401. https://doi.org/10.1016/j.molp.2020.09.017

2019

Scholarly publications

Webb, K. M., Shrestha, S., Trippe III, R., Rivera‐Varas, V., Covey, P. A., Freeman, C., de Jonge, R., Secor, G. A., & Bolton, M. D. (2019). Phylogenetic relationships and virulence assays of Fusarium secorum from sugar beet suggest a new look at species designations. Plant Pathology, 68(9), 1654-1662. https://doi.org/10.1111/ppa.13082
Fernández, I., Cosme, M., Stringlis, I., Yu, K., de Jonge, R., van Wees, S. C. M., Pozo, M. J., Pieterse, C. M. J., & van der Heijden, M. G. A. (2019). Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism. New Phytologist, 223(2), 867-881. https://doi.org/10.1111/nph.15798
Stringlis, I., De Jonge, R., & Pieterse, C. M. J. (2019). The Age of Coumarins in Plant-Microbe Interactions. Plant and Cell Physiology, 60(7), 1405-1419. https://doi.org/10.1093/pcp/pcz076
Ebert, M. K., Spanner, R. E., de Jonge, R., Smith, D. J., Holthusen, J., Secor, G. A., Thomma, B. P. H. J., & Bolton, M. D. (2019). Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi. Environmental Microbiology, 21(3), 913-927. https://doi.org/10.1111/1462-2920.14475

2018

Scholarly publications

Stringlis, I., Yu, K., Feussner, K., de Jonge, R., Van Bentum, S., van Verk, M. C., Berendsen, R. L., Bakker, P. A. H. M., Feussner, I., & Pieterse, C. M. J. (2018). MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proceedings of the National Academy of Sciences of the United States of America, 115(22), 5213-5222. https://doi.org/10.1073/pnas.1722335115
Stringlis, I., Zhang, H., Pieterse, C. M. J., Bolton, M. D., & de Jonge, R. (2018). Microbial small molecules – weapons of plant subversion. Natural Product Reports, 35(5), 410-433. https://doi.org/10.1039/C7NP00062F
de Jonge, R., Ebert, M. K., Huitt-Roehl, C. R., Pal, P., Suttle, J. C., Spanner, R. E., Neubauer, J. D., Jurick, W. M., Stott, K. A., Secor, G. A., Thomma, B. P. H. J., Van de Peer, Y., Townsend, C. A., & Bolton, M. D. (2018). Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum. PNAS, 115(24), E5459–E5466. https://doi.org/10.1073/pnas.1712798115
https://dspace.library.uu.nl/bitstream/handle/1874/364942/deJonge_etal_2018_PNAS.pdf?sequence=1
Berendsen, R. L., Vismans, G., Yu, K., Song, Y., de Jonge, R., Burgman, W. P., Burmølle, M., Herschend, J., Bakker, P. A. H. M., & Pieterse, C. M. J. (2018). Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME Journal, 12, 1496–1507. https://doi.org/10.1038/s41396-018-0093-1
Bakker, P. A. H. M., Pieterse, C. M. J., de Jonge, R., & Berendsen, R. L. (2018). The Soil-Borne Legacy. Cell, 172(6), 1178-1180. https://doi.org/10.1016/j.cell.2018.02.024

2017

Scholarly publications

de Jonge, R., Ebert, M. K., Huitt-Roehl, C. R., Pal, P., Suttle, J. C., Spanner, R. E., Neubauer, J. D., Jurick, W. M., Stott, K. A., Secor, G. A., Thomma, B. PHJ., Van de Peer, Y., Townsend, C. A., & Bolton, M. D. (2017). Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum. bioRxiv. https://doi.org/10.1101/100545
Hammoudi, V., Vlachakis, G., de Jonge, R., Breit, T. M., & van den Burg, H. A. (2017). Genetic characterization of T-DNA insertions in the genome of the Arabidopsis thaliana sumo1/2 knock-down line. Plant Signaling and Behavior, 12(3), [e1293216]. https://doi.org/10.1080/15592324.2017.1293216
Kombrink, A., Rovenich, H., Shi-Kunne, X., Rojas-Padilla, E., van den Berg, G. C. M., Domazakis, E., de Jonge, R., Valkenburg, D-J., Sanchez-Vallet, A., Seidl, M. F., & Thomma, B. P. H. J. (2017). Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts. Molecular Plant Pathology, 18(4), 596-608. https://doi.org/10.1111/mpp.12520

2016

Scholarly publications

Pieterse, C. M. J., de Jonge, R., & Berendsen, R. L. (2016). The soil-borne supremacy. Trends in Plant Science, 21, 171-172. https://doi.org/10.1016/j.tplants.2016.01.018