Publicaties
2024
Wetenschappelijke publicaties
Fourie, A., Lopez, J. L., Sánchez-Gil, J. J., Poppeliers, S. W. M., de Jonge, R., & Dutilh, B. E. (2024, May 7). Bacterial family-specific enrichment and functions of secretion systems in the rhizosphere. bioRxiv. https://doi.org/10.1101/2024.05.07.592589
Poppeliers, S. W. M., Sánchez-Gil, J. J., López, J. L., Dutilh, B. E., Pieterse, C. M. J., & de Jonge, R. (2024, Jun 26). High-resolution quantification of the rhizosphere effect along a soil-to-root gradient shows selection-driven convergence of rhizosphere microbiomes. bioRxiv. https://doi.org/10.1101/2024.06.21.600027
Mendel, M., Zuijdgeest, X. C. L., van den Berg, F., van der Meer, L., Elberse, J., Skiadas, P., Seidl, M. F., den Ackerveken, G. V., & de Jonge, R. (2024, Jun 17). Exploiting Pseudomonas syringae Type 3 secretion to study effector contribution to disease in spinach. bioRxiv. https://doi.org/10.1101/2024.06.14.599008
Selten, G., Lamouche, F., Gomez-Repolles, A., Blahovska, Z., Kelly, S., de Jonge, R., & Radutoiu, S. (2024, Aug 22). Functional capacities drive recruitment of bacteria into plant root microbiota. bioRxiv. https://doi.org/10.1101/2024.08.22.609090
Song, Y., Spooren, J., Jongekrijg, C. D., Manders, E. J. H. H., de Jonge, R., Pieterse, C. M. J., Bakker, P. A. H. M., & Berendsen, R. L. (2024). Seed tuber imprinting shapes the next-generation potato microbiome. Environmental Microbiome, 19(1), Article 12. https://doi.org/10.1186/s40793-024-00553-w
https://dspace.library.uu.nl/bitstream/handle/1874/438503/s40793-024-00553-w.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/438503/s40793-024-00553-w.pdf?sequence=1
2023
Wetenschappelijke publicaties
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. Microbiology spectrum, 11(6), Article e0204923. https://doi.org/10.1128/spectrum.02049-23
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. (pp. 1-21). bioRxiv. https://doi.org/10.1101/2023.07.27.549298v1
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. (pp. 1-37). bioRxiv. https://doi.org/10.1101/2023.05.15.539993
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. (2023). Growth rate is a dominant factor predicting the rhizosphere effect. ISME Journal, 17, 1396–1405. 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. Article 102286. https://doi.org/10.1016/j.mib.2023.102286
2022
Wetenschappelijke publicaties
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
Wetenschappelijke publicaties
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. Article 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. Article 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), Article 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
Wetenschappelijke publicaties
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), Article 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. Article 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
Wetenschappelijke publicaties
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
Wetenschappelijke publicaties
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
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
Wetenschappelijke publicaties
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), Article 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
Wetenschappelijke publicaties
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