Root microbiome

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.

Recent Publications

  • 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
  • Core microbiomes for sustainable agroecosystems (vol 4, pg 247, 2018)
    Toju, H; Peay, KG; Yamamichi, M; Narisawa, K; Hiruma, K; Naito, K; Fukuda, S; Ushio, M; Nakaoka, S; Onoda, Y; Yoshida, K; Schlaeppi, K; Bai, Y; Sugiura, R; Ichihashi, Y; Minamisawa, K; Kiers, ET
    NATURE PLANTS, 4 (9):733-733; 10.1038/s41477-018-0245-3 SEP 2018
  • Keystone taxa as drivers of microbiome structure and functioning
    Banerjee, S; Schlaeppi, K; van der Heijden, MGA
    NATURE REVIEWS MICROBIOLOGY, 16 (9):567-576; 10.1038/s41579-018-0024-1 SEP 2018
  • Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance
    Dennert F; Imperiali N; Staub C; Schneider J; Laessle T; Zhang T; Wittwer R; van der Heijden MG; Smits THM; Schlaeppi K; Keel C; Maurhofer M
    FEMS MICROBIOLOGY ECOLOGY, 94 (8):10.1093/femsec/fiy075 AUG 2018
  • Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
    Lingfei Hu, Christelle AM Robert, Selma Cadot, Xi Zhang, Meng Ye, Beibei Li, Daniele Manzo, Noemie Chervet, Thomas Steinger, Marcel GA van der Heijden, Klaus Schlaeppi & Matthias Erb
    NATURE COMMUNICATIONS 9: 2738 10.1038/s41467-018-05122-7 JUL 16 2018
  • Core microbiomes for sustainable agroecosystems
    Toju H; Peay KG; Yamamichi M; Narisawa K; Hiruma K; Naito K; Fukuda S; Ushio M; Nakaoka S; Onoda Y; Yoshida K; Schlaeppi K; Bai Y; Sugiura R; Ichihashi Y; Minamisawa K; Kiers ET
    NATURE PLANTS, 4 (5):247-257; 10.1038/s41477-018-0139-4 MAY 2018
  • Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (vol 6, 14, 2018)
    Hartman, K; van der Heijden, MGA; Wittwer, RA; Banerjee, S; Walser, JC; Schlaeppi, K
    MICROBIOME, 6 10.1186/s40168-018-0456-x APR 24 2018
  • Detecting macroecological patterns in bacterial communities across independent studies of global soils 
    Ramirez, Kelly S.; Knight, Christopher G.; de Hollander, Mattias; et al. 
    NATURE MICROBIOLOGY, 3 (2): 189-196, 10.1038/s41564-017-0062-x  FEB 2018
  • Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing 
    Walder, Florian; Schlaeppi, Klaus; Wittwer, Raphael; et al. 
  • Continuum of root-fungal symbioses for plant nutrition 
    van der Heijden, Marcel G. A.; Dombrowski, Nina; Schlaeppi, Klaus 
  • Combined Field Inoculations of Pseudomonas Bacteria, Arbuscular Mycorrhizal Fungi, and Entomopathogenic Nematodes and their Effects on Wheat Performance 
    Imperiali, Nicola; Chiriboga, Xavier; Schlaeppi, Klaus; et al. 
Schlaeppi Klaus

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

Tel: +41 61 207 23 10

Research topics

  • 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