Prof. dr. Jos Raaijmakers

Jos Raaijmakers is head of the Microbial Ecology Department at the Netherlands Institute of Ecology (NIOO-KNAW) and Professor at the Institute of Biology at Leiden University. He is board member of the Centre for Soil Ecology and of the PhD graduate School PE&RC. The overall goal of his research program is to unravel the impact of plant domestication on the diversity, dynamics and beneficial functions of microorganisms associated with plants. In this search for 'missing plant microbes', we work together with research institutes and universities in the centres of origin of plant species. The functions of the plant microbes studied in detail are protection of plants against infections caused by fungal pathogens, parasitic weeds and insects. Jos teaches BSc and MSc courses at Leiden University, and organizes (inter)national PhD courses and conferences, including the International Plant Microbiome conference.

CV
NIOO Projects
Peer-reviewed publications
Popular-scientific publications
Ancillary positions

Work experience since graduating

2014 – ... : Head Microbial Ecology Department, NIOO-KNAW

2014 – ... : Professor Microbial Ecology, IBL, Leiden University (https://www.universiteitleiden.nl/en/science/biology/staff)

2014 – 2016 : Honorary Scientist & Advisor, RDA, South Korea

2009 – 2014 : Associate Professor Plant Pathology, Wageningen University

2006 – 2008 : Visiting Professor, University Copenhagen, Denmark

2001 – 2006 : Fellow Royal Dutch Academy of Arts and Sciences (KNAW)

1998 – 2009 : Assistant Professor Plant Pathology, Wageningen University.

1995 – 1998 : Postdoc Soil Microbiology, USDA-ARS, WSU, USA.

1994 – 1995 : Research Associate, Plant Microbiology, Utrecht University

Masters (MSc) / Doctorate (PhD)

Study/University : Biology, Utrecht University, Netherlands (1989)

PhD Topic/University : Rhizosphere microbiology, Utrecht University, Netherlands (1994)

Scientific Publications:

ORCID ID: https://orcid.org/0000-0003-1608-6614

https://publons.com/researcher/2550830/jos-m-raaijmakers/

https://scholar.google.com/citations?hl=nl&user=6-FREKMAAAAJ&view_op=lis...

2018, 2019 - Top 1% most cited - Cross Field category (Clarivate Analytics/Thomson Reuters)

Research activities

2020 - 2030 : Board member and workpackage leader Gravitation program Microp (www.microp.org)

2020 - 2025 : Coordinator NWO Groot project 'Unwiring regulatory networks in the root endosphere'

2019 : Sabbatical Dept. Microbiology, University Malaga, Spain

2016 - 2022 : Coordinator international research program PROMISE (http://promise.nioo.knaw.nl)

2015 - 2021 : Coordinator national STW Perspective Program BACKTOROOTS (http://backtoroots.nioo.knaw.nl)

2013 - present : Coordinator international Back2Roots Initiative (http://backrootsproject.wix.com/backroots)

1997 - present : Supervisor MSc, PhD and postdoc projects

2007 : Sabbatical Oregon State University, USA

2006-2008 : Visiting Professor, Microbiology, University Copenhagen, Denmark

1998 : Sabbatical INRA, Dijon, France

1995 – 1998 : Postdoc USDA-ARS, Washington State University, USA

1985/1986 : MSc-internship at ICARDA, Cairo, Egypt

Other professional activities

Board member Graduate School PE&RC (2020 - present)
Reviewer national and international grant applications
Reviewer for various international scientific journals
Board member of the Dutch Centre for Soil Ecology (2012 - 2020)
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)

Promotor of PhD students

completed: 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 Perez-Jaramillo, Thiago Schlemper, Je-Seung Jeon, Ohana Costa, Anne van der Meij, Du Chao, Kay Moisan
ongoing: Eline Ampt, Kay Moisan, Adam Ossowicki, AnaShein Lee-Diaz, Getahun Mitiku, Sewunet Abera, Stalin Sarango-Flores, Dario Ramirez, Muhammad Rizaludin, Xinya Pan, Linda Gouka

Links

Professor Microbial Ecology at IBL, Leiden University

Harnessing the rhizosphere microbiome to enhance plant productivity

High biomass production of sugarcane needs input of mineral fertilizers in soil. However, since Brazilian sugarcane production technology aims at a sustainable management by recycling straw and vinasse (byproduct of ethanol industry), less mineral fertilizers can be added to soil. In addition,...Read more

Metagenomic mining of the endophytic plant microbiome

The plant microbiome represents an enormous untapped resource for discovering novel microorganisms, traits, genes and bioactive compounds. Endophytic bacteria can promote plant growth, act as biocontrol agents and can be beneficial to their host by producing a range of natural products. Here we...Read more

Meta-omics of disease suppressive soils

Disease suppressive soils (soils in which plant pathogens cause little or no disease due to activities of the resident microbial community) have been described worldwide for many plant species and plant pathogens. For most disease suppressive soils, however, the responsible microbial communities...Read more

Back to the Roots - II

The overall goal of the project is to conduct an in-depth analysis of the biodiversity and functions of microorganisms in the spermosphere and (endo)rhizosphere of ancestors of different crops species grown in their native habitat.Read more

Harnessing the soil microbiome for improved stress tolerance in crop plants

Plants are involved in intimate interactions with microbes during their entire life and these interactions are essential for plant growth and health. Within this project we aim to harness the power of the soil microbiome to protect plants against biotic and abiotic stresses, with main focus on...Read more

2021

Song, C., Jin, K., & Raaijmakers, J. M. (2021). Designing a home for beneficial plant microbiomes. Current Opinion in Plant Biology, 62, [102025]. https://doi.org/10.1016/j.pbi.2021.102025
Kirchner, N., Cano-Prieto, C., Schulz-Finke, A., Gütschow, M., Ortlieb, N., Moschny, J., Niedermeyer, T., Horak, J., Lämmerhofer, M., van der Voort, M., Raaijmakers, J. M., & Gross, H. (2021). Discovery of Thanafactin A, a Linear Proline-containing Octa-Lipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining. Journal of Natural Products, 84(1), 101–109. https://doi.org/10.1021/acs.jnatprod.0c01174
Jeon, J-S., Carreno-Quintero, N., van Eekelen, H. D. L. M., De Vos, R. C. H., Raaijmakers, J. M., & Etalo, D. W. (2021). Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea. Scientific Reports, 11(1), 2781. https://doi.org/10.1038/s41598-021-82238-9
Cordovez, V., Rotoni, C., Dini-Andreote, F., Oyserman, B. O., Carrión, V. J., & Raaijmakers, J. M. (2021). Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome. Science of the Total Environment, 772, [144825]. https://doi.org/10.1016/j.scitotenv.2020.144825
Dini-Andreote, F., Kowalchuk, G. A., Prosser, J. I., & Raaijmakers, J. M. (2021). Towards meaningful scales in ecosystem microbiome research. Environmental Microbiology, 23(1). https://doi.org/10.1111/1462-2920.15276
Moisan, K., Dicke, M., Raaijmakers, J. M., Rachmawati, E., & Cordovez, V. (2021). Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores. Ecological Entomology, 46(2), 240-248. https://doi.org/10.1111/een.12956

2020

Masteling, R., Voorhoeve, L., Ijsselmuiden, J., Dini-Andreote, F., De Boer, W., & Raaijmakers, J. M. (2020). DiSCount: computer vision for automated quantification of Striga seed germination. Plant Methods, 16(60). https://doi.org/10.1186/s13007-020-00602-8
Kirchner, N., Cano-Prieto, C., van der Voort, M., Raaijmakers, J. M., & Gross, H. (2020). Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(21), [00304-20]. https://doi.org/10.1128/MRA.00304-20
Moisan, K., Aragón, M., Gort, G., Dicke, M., Cordovez, V., Raaijmakers, J. M., & Lucas-Barbosa, D. (2020). Fungal volatiles influence plant defence against aboveground and belowground herbivory. Functional Ecology, 34(11), 2259-2269. https://doi.org/10.1111/1365-2435.13633
Ossowicki, A., Tracanna, V., Petrus, M. L. C., van Wezel, G., Raaijmakers, J. M., Medema, M. H., & Garbeva, P. (2020). Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat. Proceedings of the Royal Society B-Biological Sciences, 287(1921), [ 20192527.]. https://doi.org/10.1098/rspb.2019.2527
Rossmann, M., Pérez-Jaramillo, J. E., Kavamura, V. N., Chiaramonte, J. B., Dumack, K., Fiore-Donno, A. M., Mendes, L. W., Ferreira, M. M. C., Bonkowski, M., Raaijmakers, J. M., Mauchline, T. H., & Mendes, R. (2020). Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiology Ecology, 96(4), [fiaa032]. https://doi.org/10.1093/femsec/fiaa032
Moisan, K., Lucas-Barbosa, D., Villela, A., Greenberg, L. O., Cordovez, V., Raaijmakers, J. M., & Dicke, M. (2020). No evidence of modulation of indirect plant resistance of Brassica rapa plants by volatiles from soil-borne fungi. Ecological Entomology, 45(5), 1200-1211. https://doi.org/10.1111/een.12906
Francioli, D., van Rijssel, S. Q., van Ruijven, J., Termorshuizen, A. J., Cotton, T. E. A., Dumbrell, A. J., Raaijmakers, J. M., Weigelt, A., & Mommer, L. (2020). Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant and Soil, Online. https://doi.org/10.1007/s11104-020-04454-y
Avalos, M., Garbeva, P., Raaijmakers, J. M., & van Wezel, G. P. (2020). Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces. ISME Journal, 14, 568-583. https://doi.org/10.1101/450833, https://doi.org/10.1038/s41396-019-0537-2
Gutierrez Landazuri, C. F., Sanabria Gómez, J., Raaijmakers, J. M., & Oyserman, B. O. (2020). Restoring degraded microbiome function with self-assembled communities. FEMS Microbiology Ecology, 96(12), [fiaa225]. https://doi.org/10.1093/femsec/fiaa225
Moisan, K., Raaijmakers, J. M., Dicke, M., Lucas-Barbosa, D., & Cordovez, V. (2020). Volatiles from soil-borne fungi affect directional growth of roots. Plant, Cell and Environment, 44(1), 339–345. https://doi.org/10.1111/pce.13890

2019

Perez Jaramillo, J. E., De Hollander, M., Ramirez, C. A., Mendes, R., Raaijmakers, J. M., & Carrión, V. J. (2019). Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome, 7, [114]. https://doi.org/10.1186/s40168-019-0727-1
Cordovez, V., Dini-Andreote, F., Carrión, V. J., & Raaijmakers, J. M. (2019). Ecology and Evolution of Plant Microbiomes. Annual Review of Microbiology, Online. https://doi.org/10.1146/annurev-micro-090817-062524
Oyserman, B. O., Cordovez, V., Sarango Flores, S. W., Nijveen, H., Medema, M. H., & Raaijmakers, J. M. (2019). Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes. bioRxiv, Preprint. https://doi.org/10.1101/863399
Masteling, R., Lombard, L., De Boer, W., Raaijmakers, J. M., & Dini-Andreote, F. (2019). Harnessing the microbiome to control plant parasitic weeds. Current Opinion in Microbiology, 49(June), 26-33. https://doi.org/10.1016/j.mib.2019.09.006
Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2019). Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness. Soil Biology & Biochemistry, online, 396-406. https://doi.org/10.1016/j.soilbio.2019.05.020
Ampt, E. A., van Ruijven, J., Raaijmakers, J. M., Termorshuizen, A. J., & Mommer, L. (2019). Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands. European Journal of Plant Pathology, 154(1), 141-156. https://doi.org/10.1007/s10658-018-1573-x
Carrión, V. J., Perez Jaramillo, J. E., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz Buck, D., Mendes, L. W., van IJcken, W. F. J., Gómez Expósito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G., Medema, M. H., & Raaijmakers, J. M. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366(6465), 606-612. https://doi.org/10.1126/science.aaw9285
Mendes, L. W., Gonçalves De Chaves, M., da Fonseca, M. D. C., Mendes, R., Raaijmakers, J. M., & Tsai, S. M. (2019). Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome. Frontiers in Microbiology, 10, [2019.02252]. https://doi.org/10.3389/fmicb.2019.02252
Moisan, K., Cordovez, V., van de Zande, E. M., Raaijmakers, J. M., Dicke, M., & Lucas-Barbosa, D. (2019). Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects. Oecologia, 190(3), 589-604. https://doi.org/10.1007/s00442-019-04433-w

2018

Mendes, L. W., Mendes, R., Raaijmakers, J. M., & Tsai, S. M. (2018). Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME Journal, 12, 3038-3042. https://doi.org/10.1038/s41396-018-0234-6
Siegel-Hertz, K., Edel-Hermann, V., Chapelle, E., Terrat, S., Raaijmakers, J. M., & Steinberg, C. (2018). Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Châteaurenard region. Frontiers in Microbiology, 9, 568. https://doi.org/10.3389/FMICB.2018.00568
Dini-Andreote, F., & Raaijmakers, J. M. (2018). Embracing community ecology in plant microbiome research. Trends in Plant Science, 23(6), 467-469. https://doi.org/10.1016/j.tplants.2018.03.013
de Bruijn, I., Liu, Y., Wiegertjes, G. F., & Raaijmakers, J. M. (2018). Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiology Ecology, 94(1), [fix161]. https://doi.org/10.1093/femsec/fix161
Avalos Garcia, M., van Wezel, G. P., Raaijmakers, J. M., & Garbeva, P. V. (2018). Healthy scents: microbial volatiles as new frontier in antibiotic research? Current Opinion in Microbiology, 45(October), 84-91. https://doi.org/10.1016/j.mib.2018.02.011
Al-Jubury, A., lu, C., Walter Kania, P., von Gersdorff Jørgensen, L., Liu, Y., De Bruijn, I., Raaijmakers, J. M., & Buchman, K. (2018). Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis. Journal of Fish Diseases, 41(7), 1147-1152. https://doi.org/10.1111/jfd.12810
Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R., & Tsai, S. M. (2018). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME Journal, 2017(12), 212-224. https://doi.org/10.1038/ismej.2017.158
Van der Meij, A., Willemse, J., Schneijderberg, M. A., Geurts, R., Raaijmakers, J., & van Wezel, G. (2018). Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 111(5), 679-690. https://doi.org/10.1101/222844, https://doi.org/10.1007/s10482-018-1014-z
Carrion, V. J., Cordovez, V., Tyc, O., Etalo, D. W., De Bruijn, I., de Jager, V. C. L., Medema, M. H., Eberl, L., & Raaijmakers, J. M. (2018). Involvement of Burkholderiaceae and sulfurous volatiles in disease suppressive soils. ISME Journal, 12, 2307-2321. https://doi.org/10.1038/s41396-018-0186-x
Le, C. N., Hoang, T. K., Thai, T. H., Tran, T. L., Phan, T. P. N., & Raaijmakers, J. M. (2018). Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam. Biological Control, in press, 256-262. https://doi.org/10.1016/j.biocontrol.2018.03.014
Mommer, L., Cotton, T., Raaijmakers, J. M., Termorshuizen, A. J., van Ruijven, J., Hendriks, M., van Rijssel, S. Q., van de Mortel, J. E., van der Paauw, J. W., Schijlen, E. G. W. M., Smit-Tiekstra, A. E., Berendse, F., de Kroon, H., & Dumbrell, A. J. (2018). Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. New Phytologist, 218(2), 542-553. https://doi.org/10.1111/nph.15036
Costa, O. Y. A., Raaijmakers, J. M., & Kuramae, E. E. (2018). Microbial extracellular polymeric substances – ecological functions and impact on soil aggregation. Frontiers in Microbiology, 9, [1636]. https://doi.org/10.3389/FMICB.2018.01636
Etalo, D., Jeon, J-S., & Raaijmakers, J. M. (2018). Modulation of plant chemistry by beneficial root microbiota. Natural Product Reports, 35(5), 398-409. https://doi.org/10.1039/C7NP00057J
Cordovez, V., Schop, S., Hordijk, C. A., Dupré de Boulois, H., Coppens, F., Hanssen, I., Raaijmakers, J. M., & Carrion, V. J. (2018). Priming of plant growth promotion by volatile compounds of root-associated Microbacterium. Applied and Environmental Microbiology, 84(22), [e01865-18. ]. https://doi.org/10.1128/AEM.01865-18
Oyserman, B. O., Medema, M. H., & Raaijmakers, J. M. (2018). Road MAPs to engineer host microbiomes. Current Opinion in Microbiology, 43(June ), 46-54. https://doi.org/10.1016/j.mib.2017.11.023
Berg, G., & Raaijmakers, J. M. (2018). Saving Seed Microbiomes. ISME Journal, 12, 1167-1170. https://doi.org/10.1038/s41396-017-0028-2
Yan, Q., Lopes, L. D., Schaffer, B. T., Kidarsa, T., Vining, O., Philmus, B., Song, C., Stockwell, V. O., Raaijmakers, J. M., McPhail, K. L., Andreote, F. D., Chang, J. H., & Loper, J. E. (2018). Secondary metabolism and interspecific competition affect accumulation of spontaneous mutants in the gacS/gacA regulatory system in Pseudomonas protegens. mBio, 9(1), [e01845-17]. https://doi.org/10.1128/mBio.01845-17
Mendes, L. W., Raaijmakers, J. M., & Mendes, R. (2018). The rhizosphere microbiome as an auxiliary breeding component in common bean against Fusarium oxysporum. Annual Report of the Bean Improvement Cooperative, LXI(61), 117-118. http://www.bic.uprm.edu/wp-content/uploads/2019/01/BIC-2018-VOL-61-2018.pdf
Perez Jaramillo, J. E., Carrion, V. J., De Hollander, M., & Raaijmakers, J. M. (2018). The wild side of plant microbiomes. Microbiome, 6(143). https://doi.org/10.1186/s40168-018-0519-z

2017

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]. https://doi.org/10.1093/femsec/fix038
Gómez Expósito, R., De Bruijn, I., Postma, J., & Raaijmakers, J. M. (2017). Current insights into the role of rhizosphere bacteria in disease suppressive soils. Frontiers in Microbiology, [2529]. https://doi.org/10.3389/fmicb.2017.02529
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, 19(11), 4638-4656. https://doi.org/10.1111/1462-2920.13927
Perez Jaramillo, J. E., Carrion, V. J., Bosse, M., Ferrão, L. F. V., De Hollander, M., Garcia, A. A. F., Ramirez, C. A., Mendez, R., & Raaijmakers, J. M. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME Journal, 11, 2244-2257. https://doi.org/10.1038/ismej.2017.85
Geudens, N., Nasir, M. N., Crowet, J-M., Raaijmakers, J. M., Fehér, K., Coenye, T., Martins, J. C., Lins, L., Sinnaeve, D., & Deleu, M. (2017). Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1859(3), 331-339. https://doi.org/10.1016/j.bbamem.2016.12.013
Cordovez, V., Mommer, L., Moisan, K., Lucas-Barbosa, D., Pierik, R., Mumm, R., Carrion, V. J., & 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]. https://doi.org/10.3389/fpls.2017.01262
Bosmans, L., de Bruijn, I., Gerards, S., Moerkens, R., Van Looveren, L., Wittemans, L., Van Calenberge, B., Paeleman, A., Van Kerckhove, S., Rozenski, J., de Mot, R., Rediers, H., Raaijmakers, J. M., & Lievens, B. (2017). Potential for biocontrol of hairy root disease by a Paenibacillus clade. Frontiers in Microbiology, 8, [447]. https://doi.org/10.3389/fmicb.2017.00447

2016

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. https://doi.org/10.1016/j.soilbio.2015.12.006
Weisskopf, L., Garbeva, P. V., Ryu, C-M., & Raaijmakers, J. M. (2016). Editorial: Smelly fumes: volatile-mediated communication between bacteria and other organisms. Frontiers in Microbiology, 7, [2031]. https://doi.org/10.3389/fmicb.2016.02031
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. International Journal of Molecular Sciences, 17, [140]. https://doi.org/10.3390/ijms17010140
Chapelle, E., Mendes, R., Bakker, P. A. H. M., & Raaijmakers, J. (2016). Fungal invasion of the rhizosphere microbiome. ISME Journal, 10, 265-268. https://doi.org/10.1038/ismej.2015.82
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. https://doi.org/10.1007/s11103-015-0337-7
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. https://doi.org/10.1111/ele.12567
Nguyen, D., Melnik, A. V., Koyama, N., Lu, X., Schorn, M., Fang, J., Aguinaldo, K., Lincecum Jr., T., Ghequire, M., Carrion, V. J., Cheng, T., Malone, J., Mauchline, T., Sanchez, L., Marm Kilpatrick, A., Raaijmakers, J. M., De Mot, R., Moore, B., Medema, M. H., & Dorrestein, P. C. (2016). Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nature Microbiology, 2, [16197]. https://doi.org/10.1038/nmicrobiol.2016.197
Flury, P., Aellen, N., Ruffner, B., Pechy-Tarr, M., Fataar, S., Metla, Z., Dominguez-Ferreras, A., Bloemberg, G., Frey, J., Goesmann, A., Raaijmakers, J. M., Duffy, B., Hofte, M., Blom, J., Smits, T. H. M., Keel, C., & Maurhofer, M. (2016). Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME Journal, 10, 2527-2542. https://doi.org/10.1038/ismej.2016.5
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. https://doi.org/10.1111/1462-2920.13288
Cheng, X., Cordovez, 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. https://doi.org/10.3389/fpls.2016.01706
Raaijmakers, J. M., & Mazzola, M. (2016). Soil immune responses. Science, 352(6292), 1392-1393. https://doi.org/10.1126/science.aaf3252

2015

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. http://www.nzpps.org/nzpp_abstract.php?paper=681510
De Bruijn, I., Cheng, X., de Jager, V. C. L., Gómez Expósito, R., Watrous, J., Patel, N., Postma, J., Dorrestein, P. C., Kobayashi, D., & Raaijmakers, J. M. (2015). Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics, 16, [991]. https://doi.org/10.1186/s12864-015-2191-z
Mendes, R., & Raaijmakers, J. M. (2015). Cross-kingdom similarities in microbiome functions. ISME Journal, 9, 1905-1907. https://doi.org/10.1038/ismej.2015.7
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]. https://doi.org/10.3389/fmicb.2015.01243
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. https://doi.org/10.3389/fmicb.2015.01081
Liu, Y., Rzeszutek, E., van der Voort, M., Wu, C. H., Thoen, E., Skaar, I., Bulone, V., Dorrestein, P. C., Raaijmakers, J. M., & De Bruijn, I. (2015). Diversity of aquatic Pseudomonas species and their activity against the fish pathogenic oomycete Saprolegnia. PLoS One, 10(8), [e0136241]. https://doi.org/10.1371/journal.pone.0136241
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. https://doi.org/10.1111/1758-2229.12231
van der Voort, M., Meijer, H., Schmidt, Y., Watrous, J., Dekkers, E., Mendes, R., Dorrestein, P. C., Gross, H., & 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]. https://doi.org/10.3389/fmicb.2015.00693
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. https://doi.org/10.1002/cbic.201500247
Song, C., Sundqvist, G., Malm, E., de Bruijn, I., Kumar, A., van de Mortel, J., Bulone, V., & Raaijmakers, J. (2015). Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP. BMC Microbiology, 15, [29]. https://doi.org/10.1186/s12866-015-0367-y
Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., de Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Dusterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A.,... Glockner, F. O. (2015). Minimum Information about a Biosynthetic Gene cluster: commentary. Nature Chemical Biology, 11(9), 625-631. https://doi.org/10.1038/nchembio.1890
Song, C., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P. C., Watrous, J., van der Voort, M., & Raaijmakers, J. (2015). Molecular and chemical dialogues in bacteria-protozoa interactions. Scientific Reports, 5, [12837]. https://doi.org/10.1038/srep12837
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. https://doi.org/10.1016/j.bbrc.2015.04.039
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. https://doi.org/10.1099/mic.0.000191
Raaijmakers, J. (2015). The minimal rhizosphere microbiome. In B. Lugtenberg [Ed.], Principles of Plant-Microbe Interactions (pp. 411-419). (Microbes for sustainable agriculture). Springer. https://doi.org/10.1007/978-3-319-08575-3_43
Zachow, C., Jahanshah, G., de Bruijn, I., Song, C., Ianni, F., Pataj, Z., Gerhardt, H., Pianet, I., Lämmerhofer, M., Berg, G., Gross, H., & 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. https://doi.org/10.1094/MPMI-12-14-0406-R
Song, C., van der Voort, M., van de Mortel, J., Hassan, K., Elbourne, L. D. H., Paulsen, I. T., Loper, J. E., & 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. https://doi.org/10.1111/1751-7915.12190
Schmidt, R., Cordovez, V., De Boer, W., Raaijmakers, J., & Garbeva, P. (2015). Volatile affairs in microbial interactions. ISME Journal, 9, 2329-2335. https://doi.org/10.1038/ismej.2015.42

2014

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. https://doi.org/10.1111/1462-2920.12440
Schmidt, Y., van der Voort, M., Crüsemann, M., Piel, J., Josten, M., Sahl, H-G., Miess, H., Raaijmakers, J. M., & Gross, H. (2014). Biosynthetic Origin of the Antibiotic Cyclocarbamate Brabantamide A (SB-253514) in Plant-Associated Pseudomonas. ChemBioChem, 15(2), 259-266. https://doi.org/10.1002/cbic.201300527
Liu, Y., De Bruijn, I., Jack, A., Drynan, K., van den Berg, A. H., Thoen, E., Sandoval-Sierra, V., Skaar, I., van West, P., Diéguez-Uribeondo, J., van der Voort, M., Mendes, R., Mazzola, M., & Raaijmakers, J. M. (2014). Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. ISME Journal, 8, 2002-2014. https://doi.org/10.1038/ismej.2014.44
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. https://doi.org/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, 5, [567]. https://doi.org/10.3389/fmicb.2014.00567
Carrión, 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. https://doi.org/10.1186/1471-2180-14-46
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]. https://doi.org/10.1371/journal.pone.0095206

2013

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. https://doi.org/10.1038/nrmicro3109
Cheng, X., de Bruijn, I., van der Voort, M., Loper, J. E., & Raaijmakers, J. M. (2013). The Gac regulon of Pseudomonas fluorescensSBW25. Environmental Microbiology Reports, 5(4), 608-619. https://doi.org/10.1111/1758-2229.12061
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. https://doi.org/10.1111/1574-6976.12028

2011

Mendes, R., Kruijt, M., De Bruijn, I., Dekkers, E., Van Der Voort, M., Schneider, J. H. M., Piceno, Y. M., DeSantis, T. Z., Andersen, G. L., Bakker, P. A. H. M., & Raaijmakers, J. M. (2011). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science, 332, 1097-1100. https://doi.org/10.1126/science.1203980
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. https://doi.org/10.1038/ismej.2010.196

2010

Raaijmakers, J. M., de Bruijn, I., Nybroe, O., & Ongena, M. (2010). Natural functions of lipopeptides from Bacillus and Pseudomonas: More than surfactants and antibiotics. FEMS Microbiology Reviews, 34(6), 1037-1062. https://doi.org/10.1111/j.1574-6976.2010.00221.x

2009

De Bruijn, I., & Raaijmakers, J. M. (2009). Diversity and functional analysis of LuxR-type transcriptional regulators of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens. Applied and Environmental Microbiology, 75(14), 4753-4761. https://doi.org/10.1128/AEM.00575-09
Mazzola, M., De Bruijn, I., Cohen, M. F., & Raaijmakers, J. M. (2009). Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens. Applied and Environmental Microbiology, 75(21), 6804-6811. https://doi.org/10.1128/AEM.01272-09
De Bruijn, I., & Raaijmakers, J. M. (2009). Regulation of cyclic lipopeptide biosynthesis in pseudomonas fluorescens by the ClpP Protease. Journal of Bacteriology, 191(6), 1910-1923. https://doi.org/10.1128/JB.01558-08

2008

De Bruijn, I., De Kock, M. J. D., De Waard, P., Van Beek, T. A., & Raaijmakers, J. M. (2008). Massetolide A biosynthesis in Pseudomonas fluorescens. Journal of Bacteriology, 190(8), 2777-2789. https://doi.org/10.1128/JB.01563-07

2007

De Bruijn, I., De Kock, M. J. D., Yang, M., De Waard, P., Van Beek, T. A., & Raaijmakers, J. M. (2007). Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species. Molecular Microbiology, 63(2), 417-428. https://doi.org/10.1111/j.1365-2958.2006.05525.x

2006

Raaijmakers, J. M., De Bruijn, I., & De Kock, M. J. D. (2006). Cyclic lipopeptide production by plant-associated Pseudomonas spp.: Diversity, activity, biosynthesis, and regulation. Molecular Plant-Microbe Interactions, 19(7), 699-710. https://doi.org/10.1094/MPMI-19-0699

2015

Raaijmakers, J. M. (2015). Stille krachten doorgrond: the power of the small: oratie. Universiteit Leiden. http://hdl.handle.net/1887/51605

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Prof. dr. Jos Raaijmakers

Head of Department

Microbial Ecology

Research themes
Chemical ecology
Microbiomes

Research expertise
Metagenomics
Microbial Interactions
Molecular microbiology

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+31 (0)317 473 497

Droevendaalsesteeg 10
6708 PB Wageningen
+31 (0)317 47 34 00

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Internet search

Prof. dr. Jos Raaijmakers

Head of Department

Microbial Ecology

Research themesChemical ecologyMicrobiomes

Research expertiseMetagenomicsMicrobial InteractionsMolecular microbiology

Links

2021

2020

2019

2018

2017

2016

2015

2014

2013

2011

2010

2009

2008

2007

2006

2015

Contact

+31 (0)317 473 497

Droevendaalsesteeg 10 6708 PB Wageningen +31 (0)317 47 34 00

Postbus 50 6700 AB Wageningen

Contact Form

Research themes
Chemical ecology
Microbiomes

Research expertise
Metagenomics
Microbial Interactions
Molecular microbiology

Droevendaalsesteeg 10
6708 PB Wageningen
+31 (0)317 47 34 00

Postbus 50
6700 AB Wageningen