Jos Raaijmakers
Professor Microbial interactions and diversity
- Name
- Prof.dr. J.M. Raaijmakers
- Telephone
- 071 5272727
- j.raaijmakers@nioo.knaw.nl
- ORCID iD
- 0000-0003-1608-6614
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.
More information about Jos Raaijmakers
News
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A computational tool that will transform bacterial genome analysis -
Jos Raaijmakers new member KHMW: ‘Build a bridge between science and society’ -
Two Leiden professors appointed KNAW members -
What Darwin couldn’t see: Expedition to uncover invisible life in Galápagos -
Jos Raaijmakers nominated for Huibregtsenprijs 2022 -
Awaken sleeping antibiotics with ERC Advanced grant -
These eleven Leiden Science researchers are among the most highly cited -
Leiden biologists get awarded 730k NWO grant -
Microbes protect crops from microbes -
IBL coordinates project to search for new medicines in marine biodiversity
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Science Groot funding for Leiden scientists -
Leiden biology appreciated with large NWO grants -
Bacteria inside plant roots battle fungal disease -
Gravitation Grant: more than twenty million for sustainable crops -
Wanted: bacteria that allow plants to flourish -
“Principles of Plant-Microbe Interactions” -
New STW-grant to redirect the plant micro biome: “Back to the Roots”
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
Professor Microbial interactions and diversity
- Science
- Instituut Biologie Leiden
- IBL Microbial Sciences
- Guerrero Egio G., Pintado A., Bretscher K.M., Arias-Giraldo L.M., Paulson J.N., Spaink H.P., Claessen D., Ramos C., Cazorla F.M., Medema M.H., Raaijmakers J.M. & Carrion Bravo V.J. (2024), bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria, Nature Communications 15: 2072.
- Meij A. van der, Elsayed S.S.M.A., Willemse J.J., Du C., Wood T.M., Martin N.I., Raaijmakers J.M. & Wezel G.P. van (2023), The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes, Applied and Environmental Microbiology 89(11): e01239-23.
- Oyserman B.O., Flores S.S., Griffioen T., Pan X., Wijk E. van der, Pronk L., Lokhorst W., Nurfikari A., Paulson J.N., Movassagh M., Stopnisek N., Kupczok A., Cordovez V., Carrión V.J., Ligterink W., Snoek B.L., Medema M.H. & Raaijmakers J.M. (2022), Disentangling the genetic basis of rhizosphere microbiome assembly in tomato, Nature Communications 13: 3228.
- 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): e01116.
- Ossowicki A., Raaijmakers J.M. & Garbeva P. (2021), Disentangling soil microbiome functions by perturbation, Environmental Microbiology Reports 13(5): 582-590.
- 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.
- 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.
- 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.
- 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.
- Masteling Pereira R., Lombard L., Boerr W. de, Raaijmakers J.M. & Dini-Andreote F. (2019), Harnessing the microbiome to control plant parasitic weeds, Current Opinion in Microbiology 49: 26-33.
- 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.
- 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.
- 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.
- 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.
- Raaijmakers J.M. & Mazzola M. (2016), Soil immune responses Soil microbiomes may be harnessed for plant health, Science 352(6292): 1392-1393.
- 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.
- 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.
- 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.
- 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: 1081.
- Hoofd onderzoeksafdeling