Plant-Microbe Interactions

Plants accommodate on and inside plant roots a specific and species-rich microbiota. These microbes collectively function as a microbiome and, similar to the microbial communities in human or animal guts, they impact nutrition and health of their host. Individual root microbiota members are known to support plant growth e.g., by improving nutrition acquisition or providing pathogen protection. However, we still have a rudimentary understanding how plants interact with their associated microbial communities.

In our research we focus on the functional contribution of the root microbiota to plant growth and disease protection. A particular interest is how plants communicate with the root microbiota and how they influence their activities. Finally, we asses if we can manipulate the root microbiota for smart and sustainable agriculture.

We mainly investigate plant-microbiome interactions using Arabidopsis thaliana and Zea mays as models. We combine field and lab experiments and make use of methods in microbiomics, molecular biology, microbiology, plant genetics and bioinformatics.

  • Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition (vol 232, pg 1399, 2021)
    Querejeta, Jose Ignacio; Schlaeppi, Klaus; Lopez-Garcia, Alvaro; Ondono, Sara; Prieto, Ivan; et al.
    New Phytologist, 10.1111/nph.17986  MAY 2022
  • Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean
    Liu, Yuanhui; Ma, Bin; Chen, Wenfeng; Schlaeppi, Klaus; Erb, Matthias; et al.
    Frontiers In Microbiology  10.3389/fmicb.2021.709012  DEC 2 2021
  • Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals
    Cadot, Selma; Gfeller, Valentin; Hu, Lingfei; Singh, Nikhil; Sanchez-Vallet, Andrea; Glauser, Gaetan; Croll, Daniel; Erb, Matthias; van der Heijden, Marcel G. A.; Schlaeppi, Klaus
    Plant Cell And Environment  10.1111/pce.14184  DEC 2021
  • Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition
    Ignacio Querejeta, Jose; Schlaeppi, Klaus; Lopez-Garcia, Alvaro; Ondono, Sara; Prieto, Ivan; van Der Heijden, Marcel G. A.; Mar Alguacil, Maria
    New Phytologist 10.1111/nph.17661  NOV 2021
  • Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland
    Alguacil, Maria Del Mar; Schlaeppi, Klaus; Lopez-Garcia, Alvaro; van der Heijden, Marcel G. A.; Querejeta, Jose Ignacio
    Microbial Ecology 10.1007/s00248-021-01886-6  OCT 2021
  • Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field
    Cadot, Selma; Guan, Hang; Bigalke, Moritz; Walser, Jean-Claude; Jander, Georg; Erb, Matthias; van der Heijden, Marcel G. A.; Schlaeppi, Klaus
    Microbiome 10.1186/s40168-021-01049-2  MAY 7 2021
  • Organic and conservation agriculture promote ecosystem multifunctionality
    Wittwer, RA; Bender, SF; Hartman, K; Hydbom, S; Lima, RAA; Loaiza, V; Nemecek, T; Oehl, F; Olsson, PA; Petchey, O; Prechsl, UE; Schlaeppi, K; Scholten, T; Seitz, S; Six, J; van der Heijden, MGA
    Science Advances 10.1126/sciadv.abg6995  AUG 2021
  • Plant chemistry and food web health
    Schlaeppi, Klaus; Gross, Josef J.; Hapfelmeier, Siegfried; Erb, Matthias
    New Phytologist  10.1111/nph.17385  Early Access: MAY 2021
  • Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi
    Bodenhausen, Natacha; Deslandes-Herold, Gabriel; Waelchli, Jan; Held, Alain; van der Heijden, Marcel G. A.; et al.
    Mycorrhiza, 10.1007/s00572-020-01014-1, MAR 2021
  • miCROPe 2019-emerging research priorities towards microbe-assisted crop production
    Hohmann, Pierre; Schlaeppi, Klaus; Sessitsch, Angela
    Fems Microbiology Ecology  DOI: 10.1093/femsec/fiaa177  OCT 2020
  • Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework
    Wasimuddin; Schlaeppi, Klaus; Ronchi, Francesca; Leib, Stephen L.; Erb, Matthias; et al.
    Molecular Ecology Resources  DOI: 10.1111/1755-0998.13215 AUG 2020
  • Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (vol 6, 14, 2018)
    Hartman, Kyle; van der Heijden, Marcel G. A.; Wittwer, Raphael A.; Banerjee, Samiran; Walser, Jean-Claude; et al.
    Microbiome  DOI: 10.1186/s40168-020-00855-4  Published: MAY 17 2020
  • Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation
    Bodenhausen, Natacha; Somerville, Vincent; Desiro, Alessandro; Walser, Jean-Claude; Borghi, Lorenzo; et al.
    Phytobiomes Journal   DOI: 10.1094/PBIOMES-12-18-0057-R  Published: 2019
  • Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
    Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran; Kuramae, Eiko E.; van der Heijden, Marcel G. A.
    Nature Communications,  DOI: 10.1038/s41467-019-12798-y, OCT 24 2019
  • Establishment success and crop growth effects of an arbuscular mycorrhizal fungus inoculated into Swiss corn fields
    Bender, SF; Schlaeppi, K; Held, A; Van der Heijden, MGA
    AGRICULTURE ECOSYSTEMS & ENVIRONMENT, 273 13-24; 10.1016/j.agee.2018.12.003 MAR 1 2019
  • Reply to 'Can we predict microbial keystones?'
    Banerjee, S; Schlaeppi, K; van der Heijden, MGA
    NATURE REVIEWS MICROBIOLOGY, 17 (3):194-194; 10.1038/s41579-018-0133-x MAR 2019
Schlaeppi Klaus

Prof. Dr. Klaus Schläppi
University of Basel
Departement of Environmental Sciences
4056 Basel

Tel: +41 61 207 23 10

  • Structure and function of root microbiomes
  • Microbiota manipulation with synthetic communities in microcosms
  • Communication by root exudates
  • Microbiome diagnostics for improving applications of biologicals
  • Multi-tropic effects of the root microbiome


  • Bioinformatics
  • Microbiology
  • Microbial soil ecology  
  • Sustainable Agriculture