2025

  • Barriga-Medina, N., Decker, T. Ramirez-Villacis, D.X., León-Reyes, A.E., Dong, V., Worley, C., Ruales, C., Pieterse, C.M.J. and León-Reyes, A. (2025). Exploring fungal pathogens to control the plant invasive Rubus niveus on Galapagos Island San Cristobal. Scientific Reports 15: 20358. https://doi.org/10.1038/s41598-025-08949-5.
  • Dai, R., Zhang, J., Liu, F., Xu, H., Qian, J.-M., Cheskis, S., Liu, W., Wang, B., Zhu, H., Pronk, L.J.U., Medema, M.H., de Jonge, R., Pieterse, C.M.J., Levy, A., Schlaeppi, K. and Bai, Y. (2025). Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns. Cell 188: 2521-2539. https://doi.org/10.1016/j.cell.2025.02.013.
  • Elhady, A., Alghanmi, L., Sheikh, A.H., Saad, M.M. and Hirt, H. (2025). Coexistence ecology of pathogen-inhibiting microbes in the phytobiome. Trends in Plant Science 30: 1164-1176. https://doi.org/10.1016/j.tplants.2025.05.001.
  • Kuhlmann, A.B., Martin, A. and Sheikh, A.S. (2025). Cross-kingdom insights into the role of m⁶A RNA modifications in immune regulation. Discover Immunity 2: 7. https://doi.org/10.1007/s44368-025-00015-6.
  • Mendel, M., Zuijdgeest, X.C.L., Van den Berg, F., Van der Meer, L., Elberse, J., Skiadas, P., Seidl, M.F., Van den Ackerveken, G. and de Jonge, R. (2025). Exploiting Pseudomonas syringae type 3 secretion to study effector contribution to disease in spinach. Molecular Plant-Microbe Interactions https://doi.org/10.1094/MPMI-04-25-0042-R.
  • Pan, X., Hageman, J.J., Weits, D.A., Caldas, L., Elsayed, S.S., Bayona, L.M., Van Wezel, G.P., Berendsen, R.L., Carrion, V.J. and Raaijmakers, J.M. (2025). Hypoxia induces phenotypic and metabolic shifts in endophytic Flavobacterium sp. 98. ISME Journal 19: wraf269. https://doi.org/10.1093/ismejo/wraf269.
  • Peña-Zuñiga, E., Barriga-Medina, N., Ramirez-Villacis, D., Miranda-Guerrero, M., Pieterse, C.M.J., Raaijmakers, J.M. and Leon-Reyes, A . (2025). First report of Pectobacterium peruviense as the causal pathogen of blackleg and soft rot in Solanum tuberosum cv. Superchola in Canar, Ecuador. Plant Disease 1: 229. https://doi.org/10.1094/PDIS-08-24-1759-PDN.
  • Peña-Zuñiga, E., Barriga-Medina, N., Ramirez-Villacis, D., Llerena-Llerena, S., Pieterse, C.M.J., Raaijmakers, J.M. and León-Reyes, A . (2025). First report of Rhizoctonia solani AG-3 causing Black Scurf on Solanum tuberosum cv. Superchola in Cotopaxi, Ecuador. Plant Disease 1: 1383. https://doi.org/10.1094/PDIS-12-24-2575-PDN.
  • Pieterse, C.M.J. (2025). The extended plant immune system. Molecular Plant-Microbe Interactions 38: 780-795. https://doi.org/10.1094/MPMI-10-25-0144-HH.
  • Ramirez-Villacis, D.X., Leon-Reyes, A., Pieterse, C.M.J. and Raaijmakers, J.M. (2025). Born to rewild: reconnecting beneficial plant-microbiome alliances for resilient future crops. Cell Host & Microbe 33: 1241-1255. https://doi.org/10.1016/j.chom.2025.06.017.
  • Sánchez-Gil,J.J. and de Jonge, R. (2025). ASVNet: Inferring microbes from 16S rRNA amplicon sequencing data. bioRxiv https://doi.org/10.1101/2025.11.21.689717.
  • Secco, N., Sheikh, A.H. and Hirt, H. (2025). Insights into the role of N6-methyladenosine (m6A) in plant-virus interactions. Journal of Virology 99: e01598-24. https://doi.org/10.1128/jvi.01598-24.
  • Selten, G. (2025). Synthetic microbial communities: a systems approach to understanding root microbiome dynamics and functioning. Pp. 1-289, PhD Thesis Utrecht University. PDF of thesis.
  • Selten, G. and De Jonge, R. (2025). Bacillus drives functional states in synthetic plant root bacterial communities. Genome Biology 26: 270. https://doi.org/10.1186/s13059-025-03739-8.  
  • Selten, G., Gómez-Repollés, A., Lamouche, F., Radutoiu, S., and De Jonge, R. (2025). SyFi: Generating and using sequence fingerprints to distinguish SynCom isolates. Microbial Genomics 11: 001461. https://doi.org/10.1099/mgen.0.001461.
  • Shao, Y.D., Gu, S.H., Peng, H.Y., Zhang, L.S., Li, S.D., Berendsen, R.L., Yang, T.J., Dong, C.X., Wei, Z., Xu, Y.C. and Shen, Q.R. (2025). Synergic interactions between Trichoderma and the soil microbiomes improve plant iron availability and growth. NPJ Biofilms and Microbiomes 11: 56. https://doi.org/10.1038/s41522-025-00684-z.
  • Shekhawat, K., Sheikh, A.H., Nawaz, A.F., Alzayed, W., Nagarajan, A.P. and Hirt, H. (2025). m6A methylation attenuates thermotolerance in Arabidopsis. bioRxiv https://doi.org/10.1101/2025.05.22.655480.
  • Singh, K,S, Suarez Duran, H., Del Pup, E., Zafra Delgado, O., Van Wees, S.C.M., Van der Hooft, J.J.J. and Medema, M.H. (2025). MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways. PLoS Biology 23: e3003307. https://doi.org/10.1371/journal.pbio.3003307.
  • Skiadas, P., Mendel, M.N., Elberse, J., Van den Ackerveken, G., de Jonge, R. and Seidl, M.F. (2025). Evolution of resistance breaking in spinach downy mildew revealed through pangenome graph analysis. bioRxiv https://doi.org/10.1101/2025.05.23.655769.
  • Song, Y., Atza, E., Sánchez-Gil, J.J., Akkermans, D., de Jonge, R., De Rooij, P.G.H., Kakembo, D., Bakker, P.A.H.M., Pieterse, C.M.J., Budko, N.V. and Berendsen, R.L. (2025). Seed tuber microbiome can predict growth potential of potato varieties. Nature Microbiology 10: 28-40. https://doi.org/10.1038/s41564-024-01872-x.
  • Song, Y. and Berendsen, R.L. (2025). Potato crop performance is predicted by tuber microbiome. Nature Microbiology 10: 8-9. https://doi.org/10.1038/s41564-024-01893-6.
  • Spooren, J. (2025). Plant-driven assembly of disease-suppressive microbiomes. Pp. 1-229, PhD Thesis Utrecht University. PDF of thesis.
  • Steenbergh, A.K., Arts, G., Bakker, P.A.H.M., De Boer, W., Glandorf, D.C.M., Ter Horst, M.M.S., De Kogel, W.J. and Köhl, J. (2025). Using problem formulation for an efficient, fit-for-purpose risk assessment of microbial plant protection products.  Environmental Sciences Europe 37: 24. https://doi.org/10.1186/s12302-025-01062-4.
  • Uribe Acosta, M. (2025). No boundaries, no benefits: The role of root defense barrieres in microbiome assembly. Pp. 1-223, PhD Thesis Utrecht University. PDF of thesis.
  • Uribe Acosta, M., Pascale, A., Zhou, J., Stringlis, I.A. and Pieterse, C.M.J. (2025). Roots: metabolic architects of beneficial microbiome assembly. Plant Physiology 199: kiaf349. https://doi.org/10.1093/plphys/kiaf349.
  • Van Bentum, S., O'Banion, B., Gates, A., Van Pelt, J.A., Bakker, P.A.H.M., Pieterse, C.M.J., Lebeis, S.L. and Berendsen, R.L. (2025). Microbiome responses to natural Fusarium infection in field-grown soybean plants. Plant and Soil 516: 1347–1363. https://doi.org/10.1007/s11104-025-07798-5.
  • Van Himbeek, R., Geisen, S., Van Schaik, C., Van den Elsen, S., Berendsen, R.L., Betran, A., Schepel, E. and Helder, J. (2025). Patchy distribution of potato cyst nematodes within single arable fields reveals local disease suppressiveness mediated by disparate microbial communities. Environmental Microbiology 27: e70113. https://doi.org/10.1111/1462-2920.70113.
  • Van Nuland, M.E., Averill, C., Stewart, J.D., Prylutskyi, O., Corrales, A., Van Galen, L.G., Manley, B.F., Qin, C., Lauber, T., Mikryukov, V., Dulia, O., Furci, G., Marin, C., Sheldrake, M., Weedon, J.T., Peay, K.B., Cornwallis, C.K., Větrovský, T., Kohout, P., Baldrian, P., Tedersoo, L., West, S.A., Crowther, T.W., Kiers, E.T., SPUN Mapping Consortium and J. Van den Hoogen. Global hotspots of mycorrhizal fungal richness are poorly protected (2025). Nature 645: 414-422. https://doi.org/10.1038/s41586-025-09277-4. [*PMI scientist Dario X. Ramirez-Villacis contributed as part of the SPUN Mapping Consortium].
  • Xu, Y., Wang, Z., Wu, J., Yue, Y., Ren, Y., Pan, Y., Li, J., Liu, C., Borriss, R., Liu, X., Qiao, J., Lee, Y.-W., Wu, H., Dini-Andreote, F., Shen, Q., Xiong, W., Gao, X., Berendsen, R.L. and Gu, Q. (2025). Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH. Cell Host & Microbe 33: 2052-2066. https://doi.org/10.1016/j.chom.2025.10.016.
  • Zdouc, M.M. et al. (2025). MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Research 53: D678-D690. https://doi.org/10.1093/nar/gkae1115. [*contribution by PMI scientist Kumar Saurabh Singh).
  • Zhou, J., Uribe Acosta, M., Stassen, M.J.J., Qi, R., de Jonge, R., White, F., Kramer, G., Dong, L., Pieterse, C.M.J. and Stringlis, I.A. (2025). Arabidiopsis root defense barriers support beneficial interactions with rhizobacterium Pseudomonas simiae WCS417. New Phytologist 248: 2021-2039. https://doi.org/10.1111/nph.70549.