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Research Output

Article

Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP

Song, C., Sundqvist, G., Malm, E., de Bruijn, I., Kumar, A., van de Mortel, J., Bulone, V. & Raaijmakers, J., 2015, In : BMC Microbiology. 15, 29.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility

Song, C., Kidarsa, T., van de Mortel, J., Loper, J. E. & Raaijmakers, J. M., 2016, In : Environmental Microbiology. 18, 10, p. 3453-3465

Research output: Contribution to journal/periodicalArticleScientificpeer-review

5 Downloads (Pure)

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity

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, In : New Phytologist. 218, 2, p. 542-553

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Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA

Carrión, V. J., van der Voort, M., Arrebola, E., Gurierrez-Barranquero, J. A., de Vicente, A., Raaijmakers, J. M. & Cazorla, F. M., 2014, In : BMC Microbiology. 14, p. 46

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Massetolide A biosynthesis in Pseudomonas fluorescens

De Bruijn, I., De Kock, M. J. D., De Waard, P., Van Beek, T. A. & Raaijmakers, J. M., 2008, In : Journal of Bacteriology. 190, 8, p. 2777-2789 13 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group

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, In : Biochimica et Biophysica Acta (BBA) - Biomembranes. 1859, 3, p. 331-339 9 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat

Ossowicki, A., Tracanna, V., Petrus, M. L. C., van Wezel, G., Raaijmakers, J. M., Medema, M. H. & Garbeva, P., 2020, In : Proceedings of the Royal Society B-Biological Sciences. 287, 1921, 20192527.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

3 Downloads (Pure)

Microbial extracellular polymeric substances – ecological functions and impact on soil aggregation

Costa, O. Y. A., Raaijmakers, J. M. & Kuramae, E. E., 2018, In : Frontiers in Microbiology. 9, 1636.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Minimum Information about a Biosynthetic Gene cluster: commentary

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., Hadjithomas, M. & 134 others, Haines, A. S., Helfrich, E. J. N., Hillwig, M. L., Ishida, K., Jones, A. C., Jones, C. S., Jungmann, K., Kegler, C., Kim, H. U., Kotter, P., Krug, D., Masschelein, J., Melnik, A. V., Mantovani, S. M., Monroe, E. A., Moore, M., Moss, N., Nutzmann, H-W., Pan, G., Pati, A., Petras, D., Reen, F. J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N. J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A. K., Balibar, C. J., Balskus, E. P., Barona-Gomez, F., Bechthold, A., Bode, H. B., Borriss, R., Brady, S. F., Brakhage, A. A., Caffrey, P., Cheng, Y-Q., Clardy, J., Cox, R. J., De Mot, R., Donadio, S., Donia, M. S., van der Donk, W. A., Dorrestein, P. C., Doyle, S., Driessen, A. J. M., Ehling-Schulz, M., Entian, K-D., Fischbach, M. A., Gerwick, L., Gerwick, W. H., Gross, H., Gust, B., Hertweck, C., Hofte, M., Jensen, S. E., Ju, J., Katz, L., Kaysser, L., Klassen, J. L., Keller, N. P., Kormanec, J., Kuipers, O. P., Kuzuyama, T., Kyrpides, N. C., Kwon, H-J., Lautru, S., Lavigne, R., Lee, C. Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Mendez, C., Metsa-Ketela, M., Micklefield, J., Mitchell, D. A., Moore, B. S., Moreira, L. M., Muller, R., Neilan, B. A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M. S., Ostash, B., Payne, S. M., Pernodet, J-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J. M., Salas, J. A., Schmitt, E. K., Scott, B., Seipke, R. F., Shen, B., Sherman, D. H., Sivonen, K., Smanski, M. J., Sosio, M., Stegmann, E., Sussmuth, R. D., Tahlan, K., Thomas, C. M., Tang, Y., Truman, A. W., Viaud, M., Walton, J. D., Walsh, C. T., Weber, T., van Wezel, G. P., Wilkinson, B., Willey, J. M., Wohlleben, W., Wright, G. D., Ziemert, N., Zhang, C., Zotchev, S. B., Breitling, R., Takano, E. & Glockner, F. O., Sep 2015, In : Nature Chemical Biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Modulation of plant chemistry by beneficial root microbiota

Etalo, D., Jeon, J-S. & Raaijmakers, J. M., 2018, In : Natural Product Reports. 35, 5, p. 398-409

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Molecular and chemical dialogues in bacteria-protozoa interactions

Song, C., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P. C., Watrous, J., van der Voort, M. & Raaijmakers, J., 2015, In : Scientific Reports. 5, 12837.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists

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, In : FEMS Microbiology Ecology. 96, 4, fiaa032.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Natural functions of lipopeptides from Bacillus and Pseudomonas: More than surfactants and antibiotics

Raaijmakers, J. M., de Bruijn, I., Nybroe, O. & Ongena, M., 2010, In : FEMS Microbiology Reviews. 34, 6, p. 1037-1062 26 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

No evidence of modulation of indirect plant resistance of Brassica rapa plants by volatiles from soil-borne fungi

Moisan, K., Lucas-Barbosa, D., Villela, A., Greenberg, L. O., Cordovez, V., Raaijmakers, J. M. & Dicke, M., 2020, In : Ecological Entomology. in press

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

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, In : Science. 366, 6465, p. 606-612

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment

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, In : Plant and Soil. Online

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani

Cordovez, V., Mommer, L., Moisan, K., Lucas-Barbosa, D., Pierik, R., Mumm, R., Carrion, V. J. & Raaijmakers, J. M., 2017, In : Frontiers in Plant Science. 8, 01262.

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Potential for biocontrol of hairy root disease by a Paenibacillus clade

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, In : Frontiers in Microbiology. 8, 447.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Priming of plant growth promotion by volatile compounds of root-associated Microbacterium

Cordovez, V., Schop, S., Hordijk, C. A., Dupré de Boulois, H., Coppens, F., Hanssen, I., Raaijmakers, J. M. & Carrion, V. J., 2018, In : Applied and Environmental Microbiology. 84, 22, e01865-18. .

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces

Avalos, M., Garbeva, P., Raaijmakers, J. M. & van Wezel, G. P., 2020, In : ISME Journal. 14, p. 568-583

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds

Park, Y-S., Dutta, S., Ann, M., Raaijmakers, J. M. & Park, K., 2015, In : Biochemical and Biophysical Research Communications. 461, 2, p. 361-365

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Protozoan-induced regulation of cyclic lipopeptide biosynthesis is an effective predation defense mechanism for Pseudomonas fluorescens

Mazzola, M., De Bruijn, I., Cohen, M. F. & Raaijmakers, J. M., 2009, In : Applied and Environmental Microbiology. 75, 21, p. 6804-6811 8 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Regulation of cyclic lipopeptide biosynthesis in pseudomonas fluorescens by the ClpP Protease

De Bruijn, I. & Raaijmakers, J. M., 2009, In : Journal of Bacteriology. 191, 6, p. 1910-1923 14 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome

Mendes, L. W., Gonçalves De Chaves, M., da Fonseca, M. D. C., Mendes, R., Raaijmakers, J. M. & Tsai, S. M., 2019, In : Frontiers in Microbiology. 10, 2019.02252.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Road MAPs to engineer host microbiomes

Oyserman, B. O., Medema, M. H. & Raaijmakers, J. M., 2018, In : Current Opinion in Microbiology. 43, June , p. 46-54

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25

Cheng, X., Cordovez, V., Etalo, D. W., van der Voort, M. & Raaijmakers, J. M., 18 Nov 2016, In : Frontiers in Plant Science. 7, p. 1706 1 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Saving Seed Microbiomes

Berg, G. & Raaijmakers, J. M., 2018, In : ISME Journal. 12, p. 1167-1170

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Secondary metabolism and interspecific competition affect accumulation of spontaneous mutants in the gacS/gacA regulatory system in Pseudomonas protegens

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, In : mBio. 9, 1, e01845-17.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Soil immune responses

Raaijmakers, J. M. & Mazzola, M., 16 Jun 2016, In : Science. 352, 6292, p. 1392-1393 2 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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10 Downloads (Pure)

The Gac regulon of Pseudomonas fluorescensSBW25

Cheng, X., de Bruijn, I., van der Voort, M., Loper, J. E. & Raaijmakers, J. M., Aug 2013, In : Environmental Microbiology Reports. 5, 4, p. 608-619 12 p.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

The lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms

Bonnichsen, L., Svenningsen, N. B., Rybtke, M., de Bruijn, I., Raaijmakers, J. M., Tolker-Nielsen, T. & Nybroe, O., 2015, In : Microbiology. 161, 12, p. 2289-2297

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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The novel lipopeptide Poaeamide of the endophyte Pseudomonas poae RE*1-1-14 is involved in pathogen suppression and root colonization

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, In : Molecular Plant-Microbe Interactions. 28, 7, p. 800-810

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The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

Mendes, R., Garbeva, P. V. & Raaijmakers, J. M., 2013, In : FEMS Microbiology Reviews. 37, 5, p. 634-663

Research output: Contribution to journal/periodicalArticleScientificpeer-review

8 Downloads (Pure)

The rhizosphere microbiome as an auxiliary breeding component in common bean against Fusarium oxysporum

Mendes, L. W., Raaijmakers, J. M. & Mendes, R., 2018, In : Annual Report of the Bean Improvement Cooperative. LXI, 61, p. 117-118

Research output: Contribution to journal/periodicalArticleScientific

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The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis

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, In : Microbial Biotechnology. 8, 2, p. 296-310

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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The wild side of plant microbiomes

Perez Jaramillo, J. E., Carrion, V. J., De Hollander, M. & Raaijmakers, J. M., 16 Aug 2018, In : Microbiome. 6, 143

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Towards meaningful scales in ecosystem microbiome research

Dini-Andreote, F., Kowalchuk, G. A., Prosser, J. I. & Raaijmakers, J. M., 2020, (Accepted/In press) In : Environmental Microbiology. in press

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors

Garbeva, P. V., Silby, M. W., Raaijmakers, J. M., Levy, S. & De Boer, W., 2011, In : ISME Journal. 5, 6, p. 973-985

Research output: Contribution to journal/periodicalArticleScientificpeer-review

4 Downloads (Pure)

Unravelling the Microbiome of Eggs of the Endangered Sea Turtle Eretmochelys imbricata Identifies Bacteria with Activity against the Emerging Pathogen Fusarium falciforme

Sarmiento-Ramirez, J. M., van der Voort, M., Raaijmakers, J. M. & Dieguez-Uribeondo, J., 2014, In : PLoS One. 9, 4, e95206.

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Volatile affairs in microbial interactions

Schmidt, R., Cordovez, V., De Boer, W., Raaijmakers, J. & Garbeva, P., 2015, In : ISME Journal. 9, p. 2329-2335

Research output: Contribution to journal/periodicalArticleScientificpeer-review

15 Downloads (Pure)

Volatiles from soil-borne fungi affect directional growth of roots

Moisan, K., Raaijmakers, J. M., Dicke, M., Lucas-Barbosa, D. & Cordovez, V., 2020, In : Plant, Cell and Environment. in press

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Open Access

Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores

Moisan, K., Dicke, M., Raaijmakers, J. M., Rachmawati, E. & Cordovez, V., 2020, In : Ecological Entomology. in press

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects

Moisan, K., Cordovez, V., van de Zande, E. M., Raaijmakers, J. M., Dicke, M. & Lucas-Barbosa, D., 15 Jun 2019, In : Oecologia. 190, 3, p. 589-604

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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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

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

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Report

Stille krachten doorgrond: the power of the small: oratie

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

Research output: Book/ReportReportPopularizing

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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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