Professor of Microbial interactions and diversity
Jos Raaijmakers is Head of Department of the Microbial Ecology Department at NIOO KNAW and collaborates on various projects with the Institute of Biology Leiden.
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
- Tracanna V., Ossowicki A., Petrus M.L.C., Overduin S., Terlouw B.R., Lund G., Robinson S.L., Warris S., Schijlen E.G.W.M., Wezel G.P. van, Raaijmakers J.M., Garbeva P. & Medema M.H. (2021), Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics, mSystems 6(3).
- Ossowicki A., Raaijmakers J.M. & Garbeva P. (2021), Disentangling soil microbiome functions by perturbation, Environmental Microbiology Reports 13(5): 582-590.
- Masteling Pereira R., Voorhoeve L., IJsselmuiden J., Dini-Andreote F., Boer W. de & Raaijmakers J.M. (2020), DiSCount: computer vision for automated quantification of Striga seed germination, Plant Methods 16(1): 60.
- Avalos M., Garbeva P., Raaijmakers J.M. & Wezel G.P. van (2020), Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species, The ISME journal 14(2): 569-583.
- Carrión V.J., Perez-Jaramillo J., Cordovez V., Tracanna V., Hollander M. de, Ruiz-Buck D., Mendes L.W., Ijcken W.F.J. van, Gomez-Exposito R., Elsayed S.S., Mohanraju P., Arifah A., Oost J. van der, Paulson J.N., Mendes R., Wezel G.P. van, Medema M.H. & Raaijmakers J.M. (2019), Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Science 366(6465): 606-612.
- Avalos Garcia M., Wezel G.P. van, Raaijmakers J.M. & Garbeva P. (2018), Healthy scents: microbial volatiles as new frontier in antibiotic research?, Current Opinion in Microbiology 45: 84-91.
- Meij A. van der, Willemse J.J., Schneijderberg M.A., Geurts R., Raaijmakers J.M. & Wezel G.P. van (2018), Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity, Antonie van Leeuwenhoek 111(5): 679-690.
- Ma H., Pineda A., Wurff A.W.G. van der, Raaijmakers J.M. & Bezemer T.M. (2017), Plant-soil feedback effects on growth, defense and susceptibility to a soil-borne disease in a cut flower crop: species and functional group effects, Frontiers in Plant Science 8: 2127.
- Weisskopf L., Ryu C.M., Raaijmakers J.M. & Garbeva P. (2016), Smelly Fumes: Volatile-Mediated Communication between Bacteria and Other Organisms, FRONTIERS IN MICROBIOLOGY 7: 2031.
- Cheng X., Cordovez V., Etalo D.W., Voort M. van der & 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.
- Song C., Kidarsa T.A., Mortel J.E. van de, 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.
- Raaijmakers J.M. & Mazzola M. (2016), Soil immune responses Soil microbiomes may be harnessed for plant health, Science 352(6292): 1392-1393.
- Perez-Jaramillo J.E., Mendes R. & Raaijmakers J.M. (2016), Impact of plant domestication on rhizosphere microbiome assembly and functions, PLANT MOLECULAR BIOLOGY 90(6): 635-644.
- Voort M. van der, Kempenaar M., Driel M. van, 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.
- Liu Y., Zachow C., Raaijmakers J.M. & Bruijn I. de (2016), Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 17(1): 140.
- Raaijmakers J.M. (13 November 2015), Stille krachten doorgrond: the power of the small (Inaugural address, Science, Leiden). Leiden: Universiteit Leiden.
- Cordovez V., Carrion V.J.J., Etalo D.W., Mumm R., Zhu H., Wezel G.P. van & Raaijmakers J.M. (2015), Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil, Frontiers in Microbiology 6.
No relevant ancillary activities