Prof. dr. Jos Raaijmakers

CV
Projecten
Publicaties (highlights)
Peer-reviewed publicaties
Populair-wetenschappelijke publicaties
Links

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

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

Research activities

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)
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
Eline Ampt
Ohana Costa
Kay Moisan
Adam Ossowicki
Anne van der Meij
AnaShein Lee-Diaz
Getahun Mitiku
Sewunet Abera
Stalin Sarango-Flores
Dario Ramirez

Links

Professor Microbial Ecology at IBL, Leiden University

Deciphering the microbiome of fish eggs to mitigate emerging diseases in aquaculture

In aquaculture, diseases caused by the fungal-like oomycete Saprolegnia, but also ectoparasites are causing significant declines in fish and crayfish populations. To date, these diseases are controlled in aquaculture mainly by formalin treatment. However, the use of formalin will be banned in the...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

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

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

Selected Publications

Carrion et al. Medema M, Raaijmakers JM (2019) Pathogen-induced activation of disease-suppressive functions in the endophytic microbiome. Science

Cordovez V, Carrion VJ, Dini-Andreote F, Raaijmakers JM (2019) Ecology and evolution of plant microbiomes. Annual Review Microbiology

Berg G, Raaijmakers JM (2018) Saving Seed Microbiomes. ISME Journal

Oyserman B, Medema M, Raaijmakers JM (2018) Road MAPs to engineer host microbiomes. Current Opinion in Microbiology

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

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

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

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.,... 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
Avalos, M., Garbeva, P., Raaijmakers, J. M., & van Wezel, G. P. (2019). Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces. ISME Journal, Online. https://doi.org/10.1101/450833, https://doi.org/10.1038/s41396-019-0537-2
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.,... 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
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.,... 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.,... 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.,... 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.,... 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.
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
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, 2017(12), 212-224. https://doi.org/10.1038/ismej.2017.158
Perez Jaramillo, 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, 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.,... 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.,... 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.,... 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
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.,... 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.,... 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
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]. https://doi.org/10.3389/fmicb.2016.02031
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.
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]. 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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

International Research Program PROMISE: http://promise.nioo.knaw.nl

NWO-TTW Perspective Program BackToRoots: http://backtoroots.nioo.knaw.nl

International Back2Roots Initiative: http://backrootsproject.wix.com/backroots

Centre for Soil Ecology: http://www.soilecology.eu/

2^nd International Plant Microbiome symposium, Amsterdam 2018

Rhizosphere4 Conference: http://www.rhizo4.org/

Internet search

Prof. dr. Jos Raaijmakers

Head of Department

Microbial Ecology

Research themes
Chemical communication
Disease ecology
Microbiomes

Research expertise
Metagenomics
Microbial Interactions
Molecular microbiology

Links

2019

2018

2017

2016

2015

2014

2013

2011

2010

2009

2008

2007

2006

Contact

Contact Form

Internet search

Prof. dr. Jos Raaijmakers

Head of Department

Microbial Ecology

Research themesChemical communicationDisease ecologyMicrobiomes

Research expertiseMetagenomicsMicrobial InteractionsMolecular microbiology

Links

2019

2018

2017

2016

2015

2014

2013

2011

2010

2009

2008

2007

2006

Contact

Contact Form

Research themes
Chemical communication
Disease ecology
Microbiomes

Research expertise
Metagenomics
Microbial Interactions
Molecular microbiology