Publications

2022

Duran, P.*, Flores-Uribe, J.*, Wippel, K., Zhang, P., Guan, R., Garrido-Oter, R. Characterization of the Chlamydomonas reinhardtii phycosphere reveals conserved features of the plant microbiota. Nature Communications (2021).

* co-first authors.

2021

Wippel, K.*, Tao, K.*, Niu, Y., Zgadzaj, R., Guan, R., Dahms, E., Zhang, P., Jensen, D. B., Logemann, E., Radutoiu, S., Schulze-Lefert, P.⁺, Garrido-Oter, R.⁺. Host preference and invasiveness of commensals in the Lotus and Arabidopsis root microbiota. Nature Microbiology (2021).

* co-first authors; + co-corresponding authors.

Zhang,  P., Spaepen, S., Bai, Y., Hacquard,  S., Garrido-Oter, R. Reference-based error correction of amplicon sequencing data from synthetic communities. ISME Communications (2021).

Durán, P., Reinstädler A., Rajakrut A.L., Hashimoto, M., Garrido-Oter, R., Schulze-Lefert, P., Panstruga R. A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota. Environmental Microbiology (2021).

Mahdi, L. K., Miyauchi, S., Uhlmann, C., Garrido-Oter, R., Langen, G., Wawra, S., Niu, Y., Guan, R., Robertson-Albertyn, S., Bulgarelli, D., Parker, J. E., Zuccaro A. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. ISME Journal (2021).

Ma, K.-W.*, Niu, Y.*, Jia, Y.*, Ordon, J., Copeland, C., Emonet, A., Geldner, N., Guan, R., Stolze, S. C., Nakagami, H.,  Garrido-Oter R.⁺, Schulze-Lefert, P.⁺. Coordination of microbe–host homeostasis by crosstalk with plant innate immunity. Nature Plants (2021).

* co-first authors; + co-corresponding authors.

Winkelmüller, T. M.*, Entila, F.*, Anver, S.*, Piasecka, A., Song, B., Dahms, E., Sakakibara, H., Gan, X., Kułak, Sawikowska, A., Krajewski, P., Tsiantis, M., Garrido-Oter, R., Fukushima, K., Schulze-Lefert, P., Laurent, S., Bednarek P., and Tsuda, K.. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. The Plant Cell (2021).

* co-first authors.

Zhang, J., Liu, J.-X., Guo, X., Qin, Y., Garrido-Oter, R.⁺, Schulze-Lefert, P.⁺, Bai, Y.⁺. High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols (2021).

+ co-corresponding authors.

2020

Harbort, C. J.^*, Hashimoto, M.^*, Inoue, H., Niu, Y., Guan, R., Rombolà, A. D., Kopriva, S., Voges, M. J. E. E. E, Sattely, E. S., Garrido-Oter, R.⁺, Schulze-Lefert, P.⁺. Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. Cell Host & Microbe (2020).

* co-first authors; + co-corresponding authors

Thiergart T.*, Durán P.*, Ellis T., Vannier N., Garrido-Oter R., Roux F., Alonso-Blanco C., Ågren J⁺, Schulze-Lefert P.⁺, Hacquard S.+ Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology & Evolution (2020).

2019

Wang, Y., Garrido-Oter, R., Wu, J., Thomas M. Winkelmüller, T. M., Agler, M., Colby, T., Nobori, T., Kemen, T., Tsuda, K. Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis. Nature Communications (2019).

* co-first authors; + co-corresponding authors

Wippel, K., Schulze-Lefert, P.⁺, Garrido-Oter, R.⁺: Rhizobien in der Pflanzenmikrobiota: Evolution der Wurzelknöllchensymbiose und Funktionen der Mikrobiota für den Pflanzenwirt. Biologie in unserer Zeit (2019).

+ co-corresponding authors

Thiergart, T.*, Zgadzaj, R.*, Bozsóki, Z., Garrido-Oter, R., Radutoiu, S.⁺, and Schulze-Lefert, P.⁺ (2019) Lotus japonicus symbiosis genes impact microbial interactions between symbionts and multikingdom commensal communities. mBio (2019).

* co-first authors; + co-corresponding authors

Zhang, J., Liu, Y., Zhang, N., Hu, B., Jin, T., Xu, H., Qin, Y., Yan, P., Zhang, X., Guo, X., Hui, J., Cao, S., Wang, X., Wang, C., Wang, H., Qu, B., Fan, G., Yuan, L, Garrido-Oter, R., Chu C.*, and Bai ,Y. *. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice, Nature Biotechnology (2019).

* co-corresponding authors

Berens, M.L., Wolinska, K.W., Spaepen, S., Ziegler, J., Nobori, T., Nair, A., Krüler, V., Winkelmüller, T.M., Wang, Y., Mine, A., Becker, D., Garrido-Oter, R., Schulze-Lefert, P.*, Tsuda, K.*. Balancing trade-offs between biotic and abiotic stress responses through leaf age-dependent variation in stress hormone crosstalk, PNAS (2019).

* co-corresponding authors

2018

Durán, P.*, Thiergart, T.*, Garrido-Oter, R., Agler, M., Kemen, E., Schulze-Lefert, P.+, Hacquard, S.+. Microbial interkingdom interactions in roots promote Arabidopsis survival. Cell (2018).

* co-first authors; + co-corresponding authors

Garrido-Oter, R.*, Nakano, T. R.*, Dombrowski, N.*, Ma, K., The AgBiome Team, McHardy, A. C. and Schulze-Lefert, P. Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host & Microbe (2018).

* joint first authors.

Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter. R, Fritz, A., Sczyrba, A. and McHardy, A. C. AMBER: Assessment of Metagenome BinnERs. GigaScience (2018).

Robbins, C., Thiergart, T., Hacquard, S., Garrido-Oter, R., Gans, W., Peiter, E., Schulze-Lefert, P.*, Spaepen, S.*: Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels. Phytobiomes (2018).

*co-corresponding authors

2017

Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., et al. Critical Assessment of Metagenome Interpretation – a comprehensive benchmark of computational metagenomics software. Nature Methods (2017).

Hacquard, S., Spaepen, S., Garrido‐ Oter R. and Schulze ‐Lefert, P. Interplay between innate immunity and the plant microbiota. Annu. Rev. Phytopathol. (2017).

Dombrowski, N., Schlaeppi, K., Agler, M., Hacquard, S., Kemen, E., Garrido Oter, R., Wunder, J., Coupland, G. and Schulze-Lefert, P., Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time. ISME Journal (2017).

2016

Hacquard, S., Kracher, B., Hiruma, K, Münch, P. C., Garrido-Oter, R., Thon, M. R., Weimann, A., Damm, U., Dallery, J.-F., Hainaut, M., Henrissat, B., Lespinet, O., Sacristán, S., Ver Loren van Themaat, E., Kemen, E., McHardy, A.C., Schulze-Lefert, P., O’Connell, R. J. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nature Communications (2016).

Zgadzaj, R.*, Garrido-Oter, R.*, Jensen, D.B., Schulze-Lefert P.^# and Radutoiu S.^# Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. PNAS (2016).

* joint first authors, # joint corresponding authors.

2015

Bai, Y.*, Müller, D. B.*, Srinivas, G.*^, Garrido-Oter, R.*, Potthoff, E., Rott, M., Dombrowski, N., Münch, P.C., Spaepen, S., Remus-Emsermann, M., Hüttel, B., McHardy, A., Vorholt, J.A.#, and Schulze-Lefert, P.# Functional overlap of the Arabidopsis leaf and root microbiota. Nature (2015).

* Joint first authors; # joint corresponding authors.

Hacquard, S.*, Garrido-Oter, R.*, González, A.*, Spaepen, S.*, Ackermann, G., Lebeis, S., McHardy, A. C.#, Dangl, J. L.#, Knight, R.#, Ley, R.^#, Schulze-Lefert, P.^# Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host & Microbe (2015).

* Joint first authors; # joint corresponding authors.

2014

Schlaeppi, K., Dombrowski, N., Garrido Oter, R., Ver Loren van Themaat, E., & Schulze-Lefert, P. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. PNAS (2014).