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

V.J. Carrión; J.E. Perez Jaramillo; V. Cordovez; Vittorio Tracanna; Mattias De Hollander; Daniel Ruiz Buck; Lukas W. Mendes; Wilfried F.J. van IJcken; R. Gómez Expósito; Somayah S. Elsayed; Prarthana Mohanraju; Adini Arifah; John van der Oost; Joseph N.  Paulson; Rodrigo Mendes; Gilles van Wezel; Marnix H Medema; J.M. Raaijmakers

doi:10.1126/science.aaw9285

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

V.J. Carrión (Corresponding author), J.E. Perez Jaramillo, V. Cordovez, Vittorio Tracanna, Mattias De Hollander, Daniel Ruiz Buck, Lukas W. Mendes, Wilfried F.J. van IJcken, R. Gómez Expósito, Somayah S. Elsayed, Prarthana Mohanraju, Adini Arifah, John van der Oost, Joseph N. Paulson, Rodrigo Mendes, Gilles van Wezel, Marnix H Medema, J.M. Raaijmakers

NIOO - Microbial Ecology (ME)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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Abstract

Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.

Original language	English
Pages (from-to)	606-612
Number of pages	7
Journal	Science
Volume	366
Issue number	6465
DOIs	https://doi.org/10.1126/science.aaw9285
Publication status	Published - 2019

Keywords

international

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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

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abstract = "Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.",

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author = "V.J. Carri{\'o}n and {Perez Jaramillo}, J.E. and V. Cordovez and Vittorio Tracanna and {De Hollander}, Mattias and {Ruiz Buck}, Daniel and Mendes, {Lukas W.} and {van IJcken}, {Wilfried F.J.} and {G{\'o}mez Exp{\'o}sito}, R. and Elsayed, {Somayah S.} and Prarthana Mohanraju and Adini Arifah and {van der Oost}, John and Paulson, {Joseph N.} and Rodrigo Mendes and {van Wezel}, Gilles and Medema, {Marnix H} and J.M. Raaijmakers",

note = "6824, ME; Data Archiving: Data archived at Zenodo",

year = "2019",

doi = "10.1126/science.aaw9285",

language = "English",

volume = "366",

pages = "606--612",

journal = "Science",

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Carrión, VJ, Perez Jaramillo, JE, Cordovez, V, Tracanna, V, De Hollander, M, Ruiz Buck, D, Mendes, LW, van IJcken, WFJ, Gómez Expósito, R, Elsayed, SS, Mohanraju, P, Arifah, A, van der Oost, J, Paulson, JN, Mendes, R, van Wezel, G, Medema, MH & Raaijmakers, JM 2019, 'Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome', Science, vol. 366, no. 6465, pp. 606-612. https://doi.org/10.1126/science.aaw9285

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T1 - Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

AU - Carrión, V.J.

AU - Perez Jaramillo, J.E.

AU - Cordovez, V.

AU - Tracanna, Vittorio

AU - De Hollander, Mattias

AU - Ruiz Buck, Daniel

AU - Mendes, Lukas W.

AU - van IJcken, Wilfried F.J.

AU - Gómez Expósito, R.

AU - Elsayed, Somayah S.

AU - Mohanraju, Prarthana

AU - Arifah, Adini

AU - van der Oost, John

AU - Paulson, Joseph N.

AU - Mendes, Rodrigo

AU - van Wezel, Gilles

AU - Medema, Marnix H

AU - Raaijmakers, J.M.

N1 - 6824, ME; Data Archiving: Data archived at Zenodo

PY - 2019

Y1 - 2019

N2 - Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.

AB - Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.

KW - international

UR - http://doi.org/10.5281/zenodo.3405564

U2 - 10.1126/science.aaw9285

DO - 10.1126/science.aaw9285

M3 - Article

SN - 0036-8075

VL - 366

SP - 606

EP - 612

JO - Science

JF - Science

IS - 6465

ER -

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

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