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Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species.

Avalos M, Garbeva P, Raaijmakers JM, van Wezel GP.

ISME J. 2019 Nov 7. doi: 10.1038/s41396-019-0537-2. [Epub ahead of print]


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

Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM.

Science. 2019 Nov 1;366(6465):606-612. doi: 10.1126/science.aaw9285.


Harnessing the microbiome to control plant parasitic weeds.

Masteling R, Lombard L, de Boer W, Raaijmakers JM, Dini-Andreote F.

Curr Opin Microbiol. 2019 Jun;49:26-33. doi: 10.1016/j.mib.2019.09.006. Epub 2019 Oct 23. Review.


Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome.

Mendes LW, de Chaves MG, Fonseca MC, Mendes R, Raaijmakers JM, Tsai SM.

Front Microbiol. 2019 Oct 1;10:2252. doi: 10.3389/fmicb.2019.02252. eCollection 2019.


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

Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ.

Microbiome. 2019 Aug 14;7(1):114. doi: 10.1186/s40168-019-0727-1.


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

Moisan K, Cordovez V, van de Zande EM, Raaijmakers JM, Dicke M, Lucas-Barbosa D.

Oecologia. 2019 Jul;190(3):589-604. doi: 10.1007/s00442-019-04433-w. Epub 2019 Jun 15.


Ecology and Evolution of Plant Microbiomes.

Cordovez V, Dini-Andreote F, Carrión VJ, Raaijmakers JM.

Annu Rev Microbiol. 2019 Sep 8;73:69-88. doi: 10.1146/annurev-micro-090817-062524. Epub 2019 May 15.


Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp.

Cordovez V, Schop S, Hordijk K, Dupré de Boulois H, Coppens F, Hanssen I, Raaijmakers JM, Carrión VJ.

Appl Environ Microbiol. 2018 Oct 30;84(22). pii: e01865-18. doi: 10.1128/AEM.01865-18. Print 2018 Nov 15.


The wild side of plant microbiomes.

Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM.

Microbiome. 2018 Aug 16;6(1):143. doi: 10.1186/s40168-018-0519-z. No abstract available.


Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation.

Costa OYA, Raaijmakers JM, Kuramae EE.

Front Microbiol. 2018 Jul 23;9:1636. doi: 10.3389/fmicb.2018.01636. eCollection 2018. Review.


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

Mendes LW, Mendes R, Raaijmakers JM, Tsai SM.

ISME J. 2018 Dec;12(12):3038-3042. doi: 10.1038/s41396-018-0234-6. Epub 2018 Jul 17.


Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.

Carrión VJ, Cordovez V, Tyc O, Etalo DW, de Bruijn I, de Jager VCL, Medema MH, Eberl L, Raaijmakers JM.

ISME J. 2018 Sep;12(9):2307-2321. doi: 10.1038/s41396-018-0186-x. Epub 2018 Jun 13.


Modulation of plant chemistry by beneficial root microbiota.

Etalo DW, Jeon JS, Raaijmakers JM.

Nat Prod Rep. 2018 May 1;35(5):398-409. doi: 10.1039/c7np00057j. Epub 2018 May 3. Review.


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 JM, Steinberg C.

Front Microbiol. 2018 Apr 4;9:568. doi: 10.3389/fmicb.2018.00568. eCollection 2018.


Embracing Community Ecology in Plant Microbiome Research.

Dini-Andreote F, Raaijmakers JM.

Trends Plant Sci. 2018 Jun;23(6):467-469. doi: 10.1016/j.tplants.2018.03.013. Epub 2018 Apr 11. Review.


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

Avalos M, van Wezel GP, Raaijmakers JM, Garbeva P.

Curr Opin Microbiol. 2018 Oct;45:84-91. doi: 10.1016/j.mib.2018.02.011. Epub 2018 Mar 12. Review.


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

Mommer L, Cotton TEA, Raaijmakers JM, Termorshuizen AJ, van Ruijven J, Hendriks M, van Rijssel SQ, van de Mortel JE, van der Paauw JW, Schijlen EGWM, Smit-Tiekstra AE, Berendse F, de Kroon H, Dumbrell AJ.

New Phytol. 2018 Apr;218(2):542-553. doi: 10.1111/nph.15036. Epub 2018 Feb 22.


Secondary Metabolism and Interspecific Competition Affect Accumulation of Spontaneous Mutants in the GacS-GacA Regulatory System in Pseudomonas protegens.

Yan Q, Lopes LD, Shaffer BT, Kidarsa TA, Vining O, Philmus B, Song C, Stockwell VO, Raaijmakers JM, McPhail KL, Andreote FD, Chang JH, Loper JE.

mBio. 2018 Jan 16;9(1). pii: e01845-17. doi: 10.1128/mBio.01845-17.


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 MA, Geurts R, Raaijmakers JM, van Wezel GP.

Antonie Van Leeuwenhoek. 2018 May;111(5):679-690. doi: 10.1007/s10482-018-1014-z. Epub 2018 Jan 15.


Saving seed microbiomes.

Berg G, Raaijmakers JM.

ISME J. 2018 May;12(5):1167-1170. doi: 10.1038/s41396-017-0028-2. Epub 2018 Jan 15. Review.


Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.

Gómez Expósito R, de Bruijn I, Postma J, Raaijmakers JM.

Front Microbiol. 2017 Dec 18;8:2529. doi: 10.3389/fmicb.2017.02529. eCollection 2017. Review.


Road MAPs to engineer host microbiomes.

Oyserman BO, Medema MH, Raaijmakers JM.

Curr Opin Microbiol. 2018 Jun;43:46-54. doi: 10.1016/j.mib.2017.11.023. Epub 2017 Dec 5. Review.


Exploring fish microbial communities to mitigate emerging diseases in aquaculture.

de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM.

FEMS Microbiol Ecol. 2018 Jan 1;94(1). doi: 10.1093/femsec/fix161. Review.


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

Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM.

ISME J. 2018 Jan;12(1):212-224. doi: 10.1038/ismej.2017.158. Epub 2017 Oct 13.


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

Cheng X, Etalo DW, van de Mortel JE, Dekkers E, Nguyen L, Medema MH, Raaijmakers JM.

Environ Microbiol. 2017 Nov;19(11):4638-4656. doi: 10.1111/1462-2920.13927. Epub 2017 Nov 2.


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 VJ, Raaijmakers JM.

Front Plant Sci. 2017 Jul 21;8:1262. doi: 10.3389/fpls.2017.01262. eCollection 2017.


Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits.

Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, de Hollander M, Garcia AAF, Ramírez CA, Mendes R, Raaijmakers JM.

ISME J. 2017 Oct;11(10):2244-2257. doi: 10.1038/ismej.2017.85. Epub 2017 Jun 6.


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, De Mot R, Rozenski J, Rediers H, Raaijmakers JM, Lievens B.

Front Microbiol. 2017 Mar 22;8:447. doi: 10.3389/fmicb.2017.00447. eCollection 2017.


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 JM, Van Loon JJA.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix038.


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

Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC.

Nat Microbiol. 2017 Jan 23;2:17010. doi: 10.1038/nmicrobiol.2017.10. No abstract available.


Editorial: Smelly Fumes: Volatile-Mediated Communication between Bacteria and Other Organisms.

Weisskopf L, Ryu CM, Raaijmakers JM, Garbeva P.

Front Microbiol. 2016 Dec 20;7:2031. doi: 10.3389/fmicb.2016.02031. eCollection 2016. No abstract available.


Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group.

Geudens N, Nasir MN, Crowet JM, Raaijmakers JM, Fehér K, Coenye T, Martins JC, Lins L, Sinnaeve D, Deleu M.

Biochim Biophys Acta Biomembr. 2017 Mar;1859(3):331-339. doi: 10.1016/j.bbamem.2016.12.013. Epub 2016 Dec 20.


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

Cheng X, Cordovez V, Etalo DW, van der Voort M, Raaijmakers JM.

Front Plant Sci. 2016 Nov 18;7:1706. eCollection 2016.


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

Nguyen DD, Melnik AV, Koyama N, Lu X, Schorn M, Fang J, Aguinaldo K, Lincecum TL Jr, Ghequire MG, Carrion VJ, Cheng TL, Duggan BM, Malone JG, Mauchline TH, Sanchez LM, Kilpatrick AM, Raaijmakers JM, De Mot R, Moore BS, Medema MH, Dorrestein PC.

Nat Microbiol. 2016 Oct 31;2:16197. doi: 10.1038/nmicrobiol.2016.197. Erratum in: Nat Microbiol. 2017 Jan 23;2:17010.


ECOLOGY. Soil immune responses.

Raaijmakers JM, Mazzola M.

Science. 2016 Jun 17;352(6292):1392-3. doi: 10.1126/science.aaf3252. No abstract available.


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

Song C, Kidarsa TA, van de Mortel JE, Loper JE, Raaijmakers JM.

Environ Microbiol. 2016 Oct;18(10):3453-3465. doi: 10.1111/1462-2920.13288. Epub 2016 Apr 28.


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

Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits TH, Keel C, Maurhofer M.

ISME J. 2016 Oct;10(10):2527-42. doi: 10.1038/ismej.2016.5. Epub 2016 Feb 19.


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 JM, Mendes R.

Ecol Lett. 2016 Apr;19(4):375-82. doi: 10.1111/ele.12567. Epub 2016 Feb 1.


Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina.

Liu Y, Zachow C, Raaijmakers JM, de Bruijn I.

Int J Mol Sci. 2016 Jan 21;17(1). pii: E140. doi: 10.3390/ijms17010140.


Diversity and Activity of Lysobacter Species from Disease Suppressive Soils.

Gómez Expósito R, Postma J, Raaijmakers JM, De Bruijn I.

Front Microbiol. 2015 Nov 16;6:1243. doi: 10.3389/fmicb.2015.01243. eCollection 2015.


Comparative genomics and metabolic profiling of the genus Lysobacter.

de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J, Patel N, Postma J, Dorrestein PC, Kobayashi D, Raaijmakers JM.

BMC Genomics. 2015 Nov 23;16:991. doi: 10.1186/s12864-015-2191-z.


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

Cordovez V, Carrion VJ, Etalo DW, Mumm R, Zhu H, van Wezel GP, Raaijmakers JM.

Front Microbiol. 2015 Oct 9;6:1081. doi: 10.3389/fmicb.2015.01081. eCollection 2015.


Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms.

Bonnichsen L, Bygvraa Svenningsen N, Rybtke M, de Bruijn I, Raaijmakers JM, Tolker-Nielsen T, Nybroe O.

Microbiology. 2015 Dec;161(12):2289-97. doi: 10.1099/mic.0.000191. Epub 2015 Sep 28.


Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia.

Liu Y, Rzeszutek E, van der Voort M, Wu CH, Thoen E, Skaar I, Bulone V, Dorrestein PC, Raaijmakers JM, de Bruijn I.

PLoS One. 2015 Aug 28;10(8):e0136241. doi: 10.1371/journal.pone.0136241. eCollection 2015.


Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.


Molecular and chemical dialogues in bacteria-protozoa interactions.

Song C, Mazzola M, Cheng X, Oetjen J, Alexandrov T, Dorrestein P, Watrous J, van der Voort M, Raaijmakers JM.

Sci Rep. 2015 Aug 6;5:12837. doi: 10.1038/srep12837.


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

Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM.

Front Microbiol. 2015 Jul 7;6:693. doi: 10.3389/fmicb.2015.00693. eCollection 2015.


Impact of plant domestication on rhizosphere microbiome assembly and functions.

Pérez-Jaramillo JE, Mendes R, Raaijmakers JM.

Plant Mol Biol. 2016 Apr;90(6):635-44. doi: 10.1007/s11103-015-0337-7. Epub 2015 Jun 18. Review.


Investigations into the Biosynthesis, Regulation, and Self-Resistance of Toxoflavin in Pseudomonas protegens Pf-5.

Philmus B, Shaffer BT, Kidarsa TA, Yan Q, Raaijmakers JM, Begley TP, Loper JE.

Chembiochem. 2015 Aug 17;16(12):1782-90. doi: 10.1002/cbic.201500247. Epub 2015 Jul 3.


Fungal invasion of the rhizosphere microbiome.

Chapelle E, Mendes R, Bakker PA, Raaijmakers JM.

ISME J. 2016 Jan;10(1):265-8. doi: 10.1038/ismej.2015.82. Epub 2015 May 29.

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