Prof. dr. Jos Raaijmakers
Head of Department
Microbial Ecology
Other professional activities
- Member VIDI-STW evaluation committee (2014-2015)
- Board member of the Dutch Centre for Soil Ecology (2012 - present)
- Coordinator Research Area I, National NGI-EcoGenomics consortium (2005 – 2011)
- Member International Society for Microbial Ecology (ISME); American Society for Microbiology (ASM); Dutch Society for Microbiology (NVvM); Dutch Phytopathological Society (KNPV)
- Chair KNPV-Phytobacteriology group (2009-2013)
- Member graduate school Experimental Plant Sciences (EPS)
- Coordination of practicals (VWO-Campus) for high school students (2003-2008)
Supervisor/promoter of PhD students
- Jorge T de Souza
- Tran Thi Thu Ha
- Maria Bergsma-Vlami
- Gerbert Hiddink
- Irene de Bruijn
- Le Nhu Cuong
- Song Chunxu
- Xu Cheng
- Yiying Liu
- Viviane Cordovez
- Ruth Gomez Exposito
- Juan Esteban Perez-Jaramillo
- Thiago Schlemper
- Je-Seung Jeon
- Robert Veldman
- Ohana Costa
- Kay Moisan
- Adam Ossowicki
- Anne van der Meij
- Getahun Mitiku
- Sewunet Abera
Summary of ongoing research projects
The overall goal of my current research program is to unravel the diversity, dynamics and functions of microorganisms associated with plants. Several PhD and Postdoc projects aim to elucidate the genomic, genetic and metabolic potential of specific bacterial and fungal species living on or in plant tissues. The functions of the plant microbiome we study in detail are: 1) microbial protection of plants against biotic stress (pests, diseases, parasitic weeds); 2) microbial modulation of root architecture and plant development, and 3) microbial modulation of plant secondary metabolism. The ongoing projects involve model plants species, natural plant species and also crops important for agriculture/horticulture and the bio-based economy. Over the past years, we also initiated new lines of research to investigate microbiomes in aquatic environments. More specifically, we study the diversity of microorganisms associated with fish that suffer from emerging diseases. Understanding the influence of environmental conditions on the dynamics, assembly and activities of microbiomes will help to design strategies to limit the proliferation and spread of these (re-)emerging pathogens in natural and man-made ecosystems. Next to these fundamental scientific aspects, my program also contributes to the discovery of new antimicrobial compounds and the development of new disease control strategies to reduce pesticide use or to control diseases for which no other effective control measures exist.
In my department, several other major themes in the field of microbial ecology are investigated: 1) functional diversity and dynamics of microorganisms involved in biogeochemical cycling (N, P, C) and greenhouse gas emissions (methane, nitrous oxide), 2) bacteria-fungi interactions, 3) chemical microbial ecology with a focus volatiles in microbe-microbe communication, 4) metagenomics and network analyses of soil and plant microbiomes in a changing environment, and 5) evolutionary microbial ecology. For more information, please visit the ME department website at www.nioo.knaw.nl
Scientific Publications:
ORCID ID: orcid.org/0000-0003-1608-6614
Selected Publications
Cheng X, Etalo DW, van de Mortel JE, et al. Raaijmakers JM (2017) Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. Environ Microbiol
Perez, J. E., et al., Raaijmakers, J. M. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME Journal
Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R., & Tsai, S. M. (2017). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME Journal
Cordovez, V., et al, Raaijmakers, J. M. (2017). Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani. Frontiers in Plant Science
Nguyen D., et al. (2016) Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nature Microbiology
Raaijmakers JM & Mazzola M (2016) Soil immune responses. Science
Song C, Kidarsa TA, van de Mortel J, Loper JE, Raaijmakers JM (2016). Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility. Environmental Microbiology
Van der Voort M, Kempenaar M, Van Driel M, Raaijmakers J M, Mendes R (2016) Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecology Letters
M. H. Medema, et al., I. de Bruijn, J. M. Raaijmakers et al., F.O. Glöckner (2015) Minimum Information about a Biosynthetic Gene cluster (MIBiG) specification. Nature Chemical Biology
C Song, M Mazzola, X Cheng, J Oetjen, T Alexandrov, P Dorrestein, J Watrous, M van der Voort, JM Raaijmakers (2015) Molecular and chemical dialogues in bacteria-protozoa interactions. Nature Scientific Reports
Mendes RM and Raaijmakers JM (2015) Cross-kingdom similarities in microbiome functions. The ISME Journal
Liu et al. Raaijmakers JM (2014) Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. The ISME Journal
Philippot L, Raaijmakers JM, Lemanceau P, Van der Putten W (2013) Going back to the roots: ecology of the rhizosphere microbiome. Nature Reviews Microbiology
Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic and human pathogenic microorganisms. FEMS Microbiology Reviews
van de Mortel JE, de Vos R, Dekkers E, Pineda A, Guillod L, Bouwmeester K, Raaijmakers JM (2012) Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101. Plant Physiology
Loper JE, et al. Raaijmakers JM, et al., Paulsen IT (2012) Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLos Genetics
Raaijmakers JM and Mazzola M (2012) Diversity and natural functions of antibiotics produced by beneficial and pathogenic soil bacteria. Annual Review Phytopathology
Watrous J, et al., Raaijmakers JM, Moore BS, Laskin J, Bandeira N and Dorrestein PC (2012) Mass spectral molecular networking of living microbial colonies. Proceedings National Academy of Sciences USA
Mendes R, Kruijt M, et al., Raaijmakers JM (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science
Raaijmakers JM, De Bruijn I, Nybroe O, Ongena M (2010) Natural functions of lipopeptides from Bacillus and Pseudomonas species: more than surfactants and antibiotics. FEMS Microbiology Reviews
- Bosmans, L., De Bruijn, I., Gerards, S., Moerkens, R., Van Looveren, L., Wittemans, L.,... Lievens, B. (2017). Potential for biocontrol of hairy root disease by a Paenibacillus clade. Frontiers in Microbiology, 8, [447]. doi:10.3389/fmicb.2017.00447
- Cheng, X., Etalo, D. W., van de Mortel, J. E., Dekkers, E., Nguyen, L., Medema, M. H., & Raaijmakers, J. M. (2017). Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. Environmental Microbiology, in press, n/a-n/a. doi:10.1111/1462-2920.13927
- Cordovez, V., Mommer, L., Moisan, K., Lucas-Barbosa, D., Pierik, R., Mumm, R.,... Raaijmakers, J. M. (2017). Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani. Frontiers in Plant Science, 8, [01262]. doi:10.3389/fpls.2017.01262
- Geudens, N., Nasir, M. N., Crowet, J-M., Raaijmakers, J. M., Fehér, K., Coenye, T.,... Deleu, M. (2017). Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group. 1859(3), 331-339. doi:10.1016/j.bbamem.2016.12.013
- Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R., & Tsai, S. M. (2017). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME Journal, Online. doi:10.1038/ismej.2017.158
- Pangesti, N., Vandenbrande, S., Pineda, A., Dicke, M., Raaijmakers, J. M., & Van Loon, J. J. A. (2017). Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore. FEMS Microbiology Ecology, 93(4), [fix038]. doi:10.1093/femsec/fix038
- Perez, J. E., Carrion, V. J., Bosse, M., Ferrão, L. F. V., De Hollander, M., Garcia, A. A. F.,... Raaijmakers, J. M. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME Journal, in press. 10.1038/ismej.2017.85
- Chapelle, E., Mendes, R., Bakker, P. A. H. M., & Raaijmakers, J. (2016). Fungal invasion of the rhizosphere microbiome. ISME Journal, 10, 265-268. doi:10.1038/ismej.2015.82
- Cheng, X., Cordovez da Cunha, V., Etalo, D. W., van der Voort, M., & Raaijmakers, J. M. (2016). Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25. Frontiers in Plant Science, 7, 1706. doi:10.3389/fpls.2016.01706
- Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2016). Challenges and opportunities in harnessing soil disease suppressiveness for sustainable pasture production. Soil Biology & Biochemistry, 95(April), 100-111. doi:10.1016/j.soilbio.2015.12.006
- Flury, P., Aellen, N., Ruffner, B., Pechy-Tarr, M., Fataar, S., Metla, Z.,... Maurhofer, M. (2016). Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME Journal, 10, 2527-2542. doi:10.1038/ismej.2016.5
- Liu, Y., Zachow, C., Raaijmakers, J. M., & De Bruijn, I. (2016). Elucidating the diversity of aquatic Microdochium and Trichoderma species and their activity against the fish pathogen Saprolegnia diclina. 17, [140]. doi:10.3390/ijms17010140
- Nguyen, D., Melnik, A. V., Koyama, N., Lu, X., Schorn, M., Fang, J.,... Dorrestein, P. C. (2016). Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. 2, [16197]. doi:10.1038/nmicrobiol.2016.197
- Perez Jaramillo, J. E., Mendes, R., & Raaijmakers, J. (2016). Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology, 90(6), 635-644. doi:10.1007/s11103-015-0337-7
- Raaijmakers, J. M., & Mazzola, M. (2016). Soil immune responses. Science, 352(6292), 1392-1393. doi:10.1126/science.aaf3252
- Song, C., Kidarsa, T., van de Mortel, J., Loper, J. E., & Raaijmakers, J. M. (2016). Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility. Environmental Microbiology, 18(10), 3453-3465. doi:10.1111/1462-2920.13288
- van der Voort, M., Kempenaar, M., van Driel, M., Raaijmakers, J. M., & Mendes, R. (2016). Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecology Letters, 19(4), 375-382. 10.1111/ele.12567
- Weisskopf, L., Garbeva, P. V., Ryu, C-M., & Raaijmakers, J. M. (2016). Smelly fumes: volatile-mediated communication between bacteria and other organisms. Frontiers in Microbiology, 7, [2031]. doi:10.3389/fmicb.2016.02031
- Bonnichsen, L., Svenningsen, N. B., Rybtke, M., de Bruijn, I., Raaijmakers, J. M., Tolker-Nielsen, T., & Nybroe, O. (2015). The lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms. Microbiology, 161(12), 2289-2297. doi:10.1099/mic.0.000191
- Cheng, X., van der Voort, M., & Raaijmakers, J. M. (2015). Gac-mediated changes in pyrroloquinoline quinone biosynthesis enhance the antimicrobial activity of Pseudomonas fluorescens SBW25. Environmental Microbiology Reports, 7(1), 139-147. doi:10.1111/1758-2229.12231
- Cordovez, V., Carrion, V., Etalo, D. W., Mumm, R., Zhu, H., Van Wezel, G. P., & Raaijmakers, J. M. (2015). Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil. Frontiers in Microbiology, 6. doi:10.3389/fmicb.2015.01081
- De Bruijn, I., Cheng, X., de Jager, V. C. L., Gómez Expósito, R., Watrous, J., Patel, N.,... Raaijmakers, J. M. (2015). Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics, 16, [991]. doi:10.1186/s12864-015-2191-z
- Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2015). A bioassay to compare the disease suppressive capacity of pasture soils. New Zealand Plant Protection, 68, 151-159.
- Gómez Expósito, R., Postma, J., Raaijmakers, J. M., & de Bruijn, I. (2015). Diversity and activity of Lysobacter species from disease suppressive soils. Frontiers in Microbiology, 6(1243), [2015.01243]. doi:10.3389/fmicb.2015.01243
- Liu, Y., Rzeszutek, E., van der Voort, M., Wu, C. H., Thoen, E., Skaar, I.,... De Bruijn, I. (2015). Diversity of aquatic Pseudomonas species and their activity against the fish pathogenic oomycete Saprolegnia. PLoS One, 10(8), [e0136241]. doi:10.1371/journal.pone.0136241
- Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K.,... Glockner, F. O. (2015). Minimum Information about a Biosynthetic Gene cluster: commentary. Nature Chemical Biology, 11(9), 625-631. doi:10.1038/nchembio.1890
- Mendes, R., & Raaijmakers, J. M. (2015). Cross-kingdom similarities in microbiome functions. ISME Journal, 9, 1905-1907. doi:10.1038/ismej.2015.7
- Park, Y-S., Dutta, S., Ann, M., Raaijmakers, J. M., & Park, K. (2015). Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds. Biochemical and Biophysical Research Communications, 461(2), 361-365. doi:10.1016/j.bbrc.2015.04.039
- Philmus, B., Shaffer, B., Kidarsa, T., Yan, Q., Raaijmakers, J., Begley, T., & Loper, J. (2015). Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5. ChemBioChem, 16(12), 1782-1790. doi:10.1002/cbic.201500247
- Raaijmakers, J. (2015). The minimal rhizosphere microbiome. In B. Lugtenberg (Ed.), Principles of Plant-Microbe Interactions (pp. 411-419). (Microbes for sustainable agriculture). Springer. doi:10.1007/978-3-319-08575-3_43
- Schmidt, R., Cordovez, V., De Boer, W., Raaijmakers, J., & Garbeva, P. (2015). Volatile affairs in microbial interactions. ISME Journal, 9, 2329-2335. doi:10.1038/ismej.2015.42
- Song, C., van der Voort, M., van de Mortel, J., Hassan, K., Elbourne, L. D. H., Paulsen, I. T.,... Raaijmakers, J. (2015). The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis. Microbial Biotechnology, 8(2), 296-310. doi:10.1111/1751-7915.12190
- Song, C., Sundqvist, G., Malm, E., de Bruijn, I., Kumar, A., van de Mortel, J.,... Raaijmakers, J. (2015). Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP. BMC Microbiology, 15, [29]. doi:10.1186/s12866-015-0367-y
- Song, C., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P. C.,... Raaijmakers, J. (2015). Molecular and chemical dialogues in bacteria-protozoa interactions. Scientific Reports, 5, [12837]. doi:10.1038/srep12837
- van der Voort, M., Meijer, H., Schmidt, Y., Watrous, J., Dekkers, E., Mendes, R.,... Raaijmakers, J. M. (2015). Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Frontiers in Microbiology, 6, [693]. doi:10.3389/fmicb.2015.00693
- Zachow, C., Jahanshah, G., de Bruijn, I., Song, C., Ianni, F., Pataj, Z.,... Raaijmakers, J. M. (2015). The novel lipopeptide Poaeamide of the endophyte Pseudomonas poae RE*1-1-14 is involved in pathogen suppression and root colonization. Molecular Plant-Microbe Interactions, 28(7), 800-810. doi:10.1094/MPMI-12-14-0406-R
- Carrion Bravo, V. J., van der Voort, M., Arrebola, E., Gurierrez-Barranquero, J. A., de Vicente, A., Raaijmakers, J. M., & Cazorla, F. M. (2014). Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA. BMC Microbiology, 14, 46. doi:10.1186/1471-2180-14-46
- Fritsche, K., Van den Berg, M., De Boer, W., Van Beek, T. A., Raaijmakers, J. M., Van Veen, J. A., & Leveau, J. H. J. (2014). Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331. Environmental Microbiology, 16(5), 1334-1345. doi:10.1111/1462-2920.12440
- Liu, Y., De Bruijn, I., Jack, A., Drynan, K., van den Berg, A. H., Thoen, E.,... Raaijmakers, J. M. (2014). Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. ISME Journal, 8, 2002-2014. doi:10.1038/ismej.2014.44
- Sarmiento-Ramirez, J. M., van der Voort, M., Raaijmakers, J. M., & Dieguez-Uribeondo, J. (2014). Unravelling the Microbiome of Eggs of the Endangered Sea Turtle Eretmochelys imbricata Identifies Bacteria with Activity against the Emerging Pathogen Fusarium falciforme. PLoS One, 9(4), [e95206]. doi:10.1371/journal.pone.0095206
- Schmidt, Y., van der Voort, M., Crüsemann, M., Piel, J., Josten, M., Sahl, H-G.,... Gross, H. (2014). Biosynthetic Origin of the Antibiotic Cyclocarbamate Brabantamide A (SB-253514) in Plant-Associated Pseudomonas. ChemBioChem, 15(2), 259-266. doi:10.1002/cbic.201300527
- Song, C., Aundy, K., van de Mortel, J., & Raaijmakers, J. M. (2014). Discovery of new regulatory genes of lipopeptide biosynthesis in Pseudomonas fluorescens. FEMS Microbiology Letters, 356(2), 166-175. doi:10.1111/1574-6968.12404
- Tyc, O., Van den Berg, M., Gerards, S., Van Veen, J. A., Raaijmakers, J., De Boer, W., & Garbeva, P. (2014). Impact of interspecific interactions on antimicrobial activity among soil bacteria. Frontiers in Microbiology: terrestrial microbiology, 5, [567]. doi:10.3389/fmicb.2014.00567
- Mendes, R., Garbeva, P. V., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews, 37(5), 634-663. doi:10.1111/1574-6976.12028
- Philippot, L., Raaijmakers, J. M., Lemanceau, P., & Van der Putten, W. H. (2013). Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11(11), 789-799. doi:10.1038/nrmicro3109
- Garbeva, P. V., Silby, M. W., Raaijmakers, J. M., Levy, S., & De Boer, W. (2011). Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME Journal, 5(6), 973-985. doi:10.1038/ismej.2010.196
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2015
2014
2013
2011
International program PROMISE: http://promise.nioo.knaw.nl
STW Perspective Program BackToRoots: http://backtoroots.nioo.knaw.nl
International Back2Roots Initiative: http://backrootsproject.wix.com/backroots
Centre for Soil Ecology: http://www.soilecology.eu/
Rhizosphere4 Conference: http://www.rhizo4.org/
