Dr. Stéphane Hacquard

In the Multitrophic Plant-Microbe Interactions group, we aim at understanding the fundamental mechanisms that underlie the structure and the functions of multi-kingdom microbial consortia colonizing plant roots. By combining microbial community profiling data from natural A. thaliana populations, with the use of reference microbial culture collections and gnotobiotic plant systems, we dissect how both host-microbe and microbe-microbe interactions impact microbial community structure and plant health. More recently, we also focused on the fascinating, yet overlooked circuits that connect root microbiota composition belowground with aboveground leaf development. Our projects involve the use of tractable microbial communities, cutting-edge metabolome, microbiome and grafting techniques, as well as genetic engineering methods and advanced gnotobiotic plant growth systems to mechanistically understand and engineer plant microbiota functions.

1. Getzke F, Hassani MA, Crüsemann M, Malisic M, Zhang P, Ishigaki Y, Böhringer N, Jiménez Fernández A, Wang L, Ordon J, Ma KW, Thiergart T, Harbort CJ, Wesseler H, Miyauchi S, Garrido-Oter R, Shirasu K, Schäberle TF, Hacquard S, Schulze-Lefert P (2023) Cofunctioning of bacterial exometabolites drives root microbiota establishment. Proc Natl Acad Sci U S A 120(15):e2221508120. doi: 10.1073/pnas.2221508120.
2. Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Huttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S (2021) Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 12(1):7227. doi: 10.1038/s41467-021-27479-y.
3. Hou SJ, Thiergart T, Vannier N, Mesny F, Ziegler J, Pickel B, Hacquard S (2021) A microbiota-root-shoot circuit favours growth over defence under suboptimal light. Nature Plants 7(8):1078-+. doi: 10.1038/s41477-021-00956-4.
4. Wolinska KW, Vannier N, Thiergart T, Pickel B, Gremmen S, Piasecka A, Pislewska-Bednarek M, Nakano RT, Belkhadir Y, Bednarek P, Hacquard S (2021) Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots. Proc Natl Acad Sci U S A 118(49). doi: 10.1073/pnas.2111521118.
5. Thiergart T, Duran P, Ellis T, Vannier N, Garrido-Oter R, Kemen E, Roux F, Alonso-Blanco C, Agren J, Schulze-Lefert P, Hacquard S (2020) Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nat Ecol Evol 4(1):122-131. doi: 10.1038/s41559-019-1063-3.
6. Duran P, Thiergart T, Garrido-Oter R, Agler M, Kemen E, Schulze-Lefert P, Hacquard S (2018) Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival. Cell 175(4):973-983 e914. doi: 10.1016/j.cell.2018.10.020.
7. Hassani MA, Durán P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6. doi: ARTN 58 doi: 10.1186/s40168-018-0445-0.
8. Hacquard S, Kracher B, Hiruma K, Munch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristan S, Ver Loren van Themaat E, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ (2016) Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat Commun 7:11362. doi: 10.1038/ncomms11362.
9. Hacquard S, Garrido-Oter R, Gonzalez A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley R, Schulze-Lefert P (2015) Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host Microbe 17(5):603-616. doi: 10.1016/j.chom.2015.04.009.
10. Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, van Themaat EVL (2013) Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 110(24):E2219-E2228. doi: 10.1073/pnas.1306807110.