Prof. Dr. Paul Schulze-Lefert

Functional analysis of plant-associated microbial communities using reductionist approaches
Healthy plants in nature are colonized by multi-kingdom microbial communities including bacteria and fungi, termed the plant microbiota, which promote plant growth and health. Our work focuses on the root microbiota and aims at a deeper understanding of the mechanisms underlying the establishment of root-associated microbial communities and their beneficial functions for the host. We have established systematic culture collections of the root microbiota of the crucifer Arabidopsis thaliana, allowing us to culture the majority of bacterial and fungal taxa associated with healthy roots. We then compose defined consortia, called synthetic communities (SynComs), from the isolated root commensals and reconstitute the root microbiota in co-cultivation experiments with germ-free plants to study microbial community functions for the host in laboratory environments. This enabled us to demonstrate that the bacterial root microbiota is crucial for the survival of the host in natural soil by protecting the plant against harmful fungal root endophytes. Our experiments also show that suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial taxa of the plant microbiota. In CEPLAS we investigate the molecular mechanisms underlying a key role of the bacterial root microbiota in iron nutrition of plants in alkaline and acidic soils.

1. Ordon J, Thouin J, Nakano RT, Ma KW, Zhang P, Huettel B, Garrido-Oter R, Schulze-Lefert P (2024) Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota. Nat Microbiol 9(4):1117-1129. doi: 10.1038/s41564-024-01619-8.
2. 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.
3. Ma KW, Niu Y, Jia Y, Ordon J, Copeland C, Emonet A, Geldner N, Guan R, Stolze SC, Nakagami H, Garrido-Oter R, Schulze-Lefert P (2021) Coordination of microbe-host homeostasis by crosstalk with plant innate immunity. Nat Plants. doi: 10.1038/s41477-021-00920-2.
4. Wippel K, Tao K, Niu Y, Zgadzaj R, Kiel N, Guan R, Dahms E, Zhang P, Jensen DB, Logemann E, Radutoiu S, Schulze-Lefert P, Garrido-Oter R (2021) Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nat Microbiol 6(9):1150-1162. doi: 10.1038/s41564-021-00941-9.
5. Harbort CJ, Hashimoto M, Inoue H, Niu Y, Guan R, Rombola AD, Kopriva S, Voges M, Sattely ES, Garrido-Oter R, Schulze-Lefert P (2020) Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. Cell Host Microbe. doi: 10.1016/j.chom.2020.09.006.
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. Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17(3):392-403. doi: 10.1016/j.chom.2015.01.011.
8. Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528(7582):364-369. doi: 10.1038/nature16192.
9. Schlaeppi K, Dombrowski N, Oter RG, Ver Loren van Themaat E, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci U S A 111(2):585-592. doi: 10.1073/pnas.1321597111.
10. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488(7409):91-95. doi: 10.1038/nature11336.