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Research Output

Special issue (editorship)

Smelly fumes: volatile-mediated communication between bacteria and other organisms: Research Topic

Weisskopf, L. (Guest ed.), Garbeva, P. V. (Guest ed.), Ryu, C-M. (Guest ed.) & Raaijmakers, J. M., Aug 2017, In : Frontiers in Microbiology.

Research output: Contribution to journal/periodicalSpecial issue (editorship)Scientific

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Report

Stille krachten doorgrond: the power of the small: oratie

Raaijmakers, J. M., 2015, Universiteit Leiden.

Research output: Book/ReportReportPopularizing

Open Access
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8 Downloads (Pure)
Patent

Biocontrol organism

Bosmans, L., Lievens, B., Rediers, H. & Raaijmakers, J. M., 28 Nov 2019, Patent No. US 2019/0357541 A1, 28 Nov 2019

Research output: Patent

Open Access
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5 Downloads (Pure)
Chapter

The minimal rhizosphere microbiome

Raaijmakers, J., 2015, Principles of Plant-Microbe Interactions. Lugtenberg, B. (ed.). Springer, p. 411-419 (Microbes for sustainable agriculture).

Research output: Chapter in book/volumeChapterScientific

Article

A bioassay to compare the disease suppressive capacity of pasture soils

Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A. & Wakelin, S. A., 2015, In : New Zealand Plant Protection. 68, p. 151-159 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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268 Downloads (Pure)

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore

Pangesti, N., Vandenbrande, S., Pineda, A., Dicke, M., Raaijmakers, J. M. & Van Loon, J. J. A., 2017, In : FEMS Microbiology Ecology. 93, 4, fix038.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

1 Downloads (Pure)

Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331

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, In : Environmental Microbiology. 16, 5, p. 1334-1345

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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354 Downloads (Pure)

Biosynthetic Origin of the Antibiotic Cyclocarbamate Brabantamide A (SB-253514) in Plant-Associated Pseudomonas

Schmidt, Y., van der Voort, M., Crüsemann, M., Piel, J., Josten, M., Sahl, H-G., Miess, H., Raaijmakers, J. M. & Gross, H., 2014, In : ChemBioChem. 15, 2, p. 259-266

Research output: Contribution to journal/periodicalArticleScientificpeer-review

1 Downloads (Pure)

Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean

Mendes, L. W., Mendes, R., Raaijmakers, J. M. & Tsai, S. M., 2018, In : ISME Journal. 12, p. 3038-3042

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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188 Downloads (Pure)

Challenges and opportunities in harnessing soil disease suppressiveness for sustainable pasture production

Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A. & Wakelin, S. A., 2016, In : Soil Biology & Biochemistry. 95, April, p. 100-111

Research output: Contribution to journal/periodicalArticleScientificpeer-review

28 Downloads (Pure)

Comparative genomics and metabolic profiling of the genus Lysobacter

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, In : BMC Genomics. 16, 991.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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290 Downloads (Pure)

Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Châteaurenard region

Siegel-Hertz, K., Edel-Hermann, V., Chapelle, E., Terrat, S., Raaijmakers, J. M. & Steinberg, C., 2018, In : Frontiers in Microbiology. 9, p. 568 1 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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118 Downloads (Pure)

Cross-kingdom similarities in microbiome functions

Mendes, R. & Raaijmakers, J. M., 2015, In : ISME Journal. 9, p. 1905-1907

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Current insights into the role of rhizosphere bacteria in disease suppressive soils

Gómez Expósito, R., De Bruijn, I., Postma, J. & Raaijmakers, J. M., 2017, In : Frontiers in Microbiology. 2529.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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224 Downloads (Pure)

Cyclic lipopeptide production by plant-associated Pseudomonas spp.: Diversity, activity, biosynthesis, and regulation

Raaijmakers, J. M., De Bruijn, I. & De Kock, M. J. D., 2006, In : Molecular Plant-Microbe Interactions. 19, 7, p. 699-710 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Deciphering microbial landscapes of fish eggs to mitigate emerging diseases

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, In : ISME Journal. 8, p. 2002-2014

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

Perez Jaramillo, J. E., De Hollander, M., Ramirez, C. A., Mendes, R., Raaijmakers, J. M. & Carrión, V. J., 2019, In : Microbiome. 7, 114.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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116 Downloads (Pure)

Deciphering the rhizosphere microbiome for disease-suppressive bacteria

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, In : Science. 332, p. 1097-1100 4 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

DiSCount: computer vision for automated quantification of Striga seed germination

Masteling, R., Voorhoeve, L., Ijsselmuiden, J., Dini-Andreote, F., De Boer, W. & Raaijmakers, J. M., 01 May 2020, In : Plant Methods. 16, 60

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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36 Downloads (Pure)

Discovery of new regulatory genes of lipopeptide biosynthesis in Pseudomonas fluorescens

Song, C., Aundy, K., van de Mortel, J. & Raaijmakers, J. M., 2014, In : FEMS Microbiology Letters. 356, 2, p. 166-175

Research output: Contribution to journal/periodicalArticleScientificpeer-review

4 Downloads (Pure)

Diversity and activity of Lysobacter species from disease suppressive soils

Gómez Expósito, R., Postma, J., Raaijmakers, J. M. & de Bruijn, I., 2015, In : Frontiers in Microbiology. 6, 1243, 2015.01243.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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260 Downloads (Pure)

Diversity and functional analysis of LuxR-type transcriptional regulators of cyclic lipopeptide biosynthesis in Pseudomonas fluorescens

De Bruijn, I. & Raaijmakers, J. M., 2009, In : Applied and Environmental Microbiology. 75, 14, p. 4753-4761 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil

Cordovez, V., Carrion, V., Etalo, D. W., Mumm, R., Zhu, H., Van Wezel, G. P. & Raaijmakers, J. M., 2015, In : Frontiers in Microbiology. 6

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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520 Downloads (Pure)

Diversity of aquatic Pseudomonas species and their activity against the fish pathogenic oomycete Saprolegnia

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, In : PLoS One. 10, 8, e0136241.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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418 Downloads (Pure)

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

Kirchner, N., Cano-Prieto, C., van der Voort, M., Raaijmakers, J. M. & Gross, H., 2020, In : MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 9

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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53 Downloads (Pure)

Ecology and Evolution of Plant Microbiomes

Cordovez, V., Dini-Andreote, F., Carrión, V. J. & Raaijmakers, J. M., 2019, In : Annual Review of Microbiology. Online

Research output: Contribution to journal/periodicalArticleScientificpeer-review

2 Downloads (Pure)

Editorial: Smelly fumes: volatile-mediated communication between bacteria and other organisms

Weisskopf, L., Garbeva, P. V., Ryu, C-M. & Raaijmakers, J. M., 23 Feb 2016, In : Frontiers in Microbiology. 7, 2031.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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188 Downloads (Pure)

Elucidating the diversity of aquatic Microdochium and Trichoderma species and their activity against the fish pathogen Saprolegnia diclina

Liu, Y., Zachow, C., Raaijmakers, J. M. & De Bruijn, I., 2016, In : International Journal of Molecular Sciences. 17, 140.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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173 Downloads (Pure)

Embracing community ecology in plant microbiome research

Dini-Andreote, F. & Raaijmakers, J. M., 2018, In : Trends in Plant Science. 23, 6, p. 467-469

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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127 Downloads (Pure)

Exploring fish microbial communities to mitigate emerging diseases in aquaculture

de Bruijn, I., Liu, Y., Wiegertjes, G. F. & Raaijmakers, J. M., 2018, In : FEMS Microbiology Ecology. 94, 1, fix161.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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100 Downloads (Pure)

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes

Oyserman, B. O., Cordovez, V., Sarango Flores, S. W., Nijveen, H., Medema, M. H. & Raaijmakers, J. M., 2019, In : bioRxiv. Preprint

Research output: Contribution to journal/periodicalArticleScientific

Open Access
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60 Downloads (Pure)

Fungal invasion of the rhizosphere microbiome

Chapelle, E., Mendes, R., Bakker, P. A. H. M. & Raaijmakers, J., 2016, In : ISME Journal. 10, p. 265-268

Research output: Contribution to journal/periodicalArticleScientificpeer-review

7 Downloads (Pure)

Fungal volatiles influence plant defence against aboveground and belowground herbivory

Moisan, K., Aragón, M., Gort, G., Dicke, M., Cordovez, V., Raaijmakers, J. M. & Lucas-Barbosa, D., 2020, In : Functional Ecology. in press

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Gac-mediated changes in pyrroloquinoline quinone biosynthesis enhance the antimicrobial activity of Pseudomonas fluorescens SBW25

Cheng, X., van der Voort, M. & Raaijmakers, J. M., 2015, In : Environmental Microbiology Reports. 7, 1, p. 139-147

Research output: Contribution to journal/periodicalArticleScientificpeer-review

4 Downloads (Pure)

Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species

De Bruijn, I., De Kock, M. J. D., Yang, M., De Waard, P., Van Beek, T. A. & Raaijmakers, J. M., 2007, In : Molecular Microbiology. 63, 2, p. 417-428 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

van der Voort, M., Meijer, H., Schmidt, Y., Watrous, J., Dekkers, E., Mendes, R., Dorrestein, P. C., Gross, H. & Raaijmakers, J. M., 2015, In : Frontiers in Microbiology. 6, 693.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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235 Downloads (Pure)

Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

Cheng, X., Etalo, D. W., van de Mortel, J. E., Dekkers, E., Nguyen, L., Medema, M. H. & Raaijmakers, J. M., 2017, In : Environmental Microbiology. 19, 11, p. 4638-4656

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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193 Downloads (Pure)

Going back to the roots: the microbial ecology of the rhizosphere

Philippot, L., Raaijmakers, J. M., Lemanceau, P. & Van der Putten, W. H., 2013, In : Nature Reviews Microbiology. 11, 11, p. 789-799

Research output: Contribution to journal/periodicalArticleScientificpeer-review

8 Downloads (Pure)

Harnessing the microbiome to control plant parasitic weeds

Masteling, R., Lombard, L., De Boer, W., Raaijmakers, J. M. & Dini-Andreote, F., 2019, In : Current Opinion in Microbiology. 49, June, p. 26-33

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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96 Downloads (Pure)

Healthy scents: microbial volatiles as new frontier in antibiotic research?

Avalos Garcia, M., van Wezel, G. P., Raaijmakers, J. M. & Garbeva, P. V., 2018, In : Current Opinion in Microbiology. 45, October, p. 84-91

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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167 Downloads (Pure)

Impact of interspecific interactions on antimicrobial activity among soil bacteria

Tyc, O., Van den Berg, M., Gerards, S., Van Veen, J. A., Raaijmakers, J., De Boer, W. & Garbeva, P., 2014, In : Frontiers in Microbiology. 5, 567.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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530 Downloads (Pure)

Impact of plant domestication on rhizosphere microbiome assembly and functions

Perez Jaramillo, J. E., Mendes, R. & Raaijmakers, J., 2016, In : Plant Molecular Biology. 90, 6, p. 635-644

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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301 Downloads (Pure)

Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis

Al-Jubury, A., lu, C., Walter Kania, P., von Gersdorff Jørgensen, L., Liu, Y., De Bruijn, I., Raaijmakers, J. M. & Buchman, K., 2018, In : Journal of Fish Diseases. 41, 7, p. 1147-1152

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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226 Downloads (Pure)

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression

van der Voort, M., Kempenaar, M., van Driel, M., Raaijmakers, J. M. & Mendes, R., 2016, In : Ecology Letters. 19, 4, p. 375-382

Research output: Contribution to journal/periodicalArticleScientificpeer-review

15 Downloads (Pure)

Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness

Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A. & Wakelin, S. A., 2019, In : Soil Biology & Biochemistry. online, p. 396-406

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

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., 31 Oct 2016, In : Nature Microbiology. 2, 16197.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

73 Downloads (Pure)

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R. & Tsai, S. M., 2018, In : ISME Journal. 2017, 12, p. 212-224

Research output: Contribution to journal/periodicalArticleScientificpeer-review

3 Downloads (Pure)

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

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, In : ISME Journal. 10, p. 2527-2542

Research output: Contribution to journal/periodicalArticleScientificpeer-review

16 Downloads (Pure)

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity

Van der Meij, A., Willemse, J., Schneijderberg, M. A., Geurts, R., Raaijmakers, J. & van Wezel, G., 2018, In : Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology. 111, 5, p. 679-690

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access
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147 Downloads (Pure)

Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5.

Philmus, B., Shaffer, B., Kidarsa, T., Yan, Q., Raaijmakers, J., Begley, T. & Loper, J., 2015, In : ChemBioChem. 16, 12, p. 1782-1790

Research output: Contribution to journal/periodicalArticleScientificpeer-review

1 Downloads (Pure)