The big societal challenge is to secure food production for the growing human population and at the same time reducing the environmental impacts of agrochemicals. For this we need to find alternative solutions to mineral fertilizers. Plant microbiomes comprise beneficial microbes such as arbuscular mycorrhizal fungi (AMF) that can enhance plant productivity. AMF promote soil fertility and contribute to plant nutrition by providing phosphorus (up to 90% of plant P can originate from AMF). Field inoculations with AMF can enhance crop yield, however, inoculation success is highly variable between field sites. Here, we investigated whether soil microbiome diagnostics can be used to specifically predict the conditions for successful AMF field inoculation. Conceptually similar to ‘personalized medicine’, we pre-diagnose the soil (chemical measurements and microbiome profiling) to match AMF inoculant and given soil conditions. We performed a large campaign inoculating maize in diverse field soils using Rhizoglomus irregulare SAF22 (our reference AMF) and we find it functioned in of fields with yield increases between 12% and up to 40% per field. The key achievement of this project is that we have demonstrated at very large field scale that field inoculations with AMF present a true option for real-life agriculture. In addition to yield, we collected measures of soil chemistry and soil microbiomes and we are now working on a model to predict yield increase from this soil data. Our final goal is to develop an algorithm that could be used to predict AMF inoculation success for a given field. Our vision is that soil microbiome diagnostics becomes a tool for ‘smart farming’ through which the targeted application of microbials becomes a reliable and sustainable agronomic alternative to mineral fertilizers.

In this project, we develop soil microbiome diagnostics so that beneficial AMF can be inoculated to field soils in a targeted manner. Goals are to improve the reliability of AMF applications and to predict under which conditions AMF inoculations will be successful.
Our approach is conceptually similar to ‘personalized medicine’, we pre-diagnose the soil (chemical measurements and microbiome profiling) and then we choose the AMF inoculant that best fits the local soil conditions. Our vision is that soil microbiome diagnostics becomes a tool for ‘smart farming’ through which the targeted application of microbials becomes a reliable and sustainable agronomic alternative to the usage of mineral fertilizers.

This project has started in early 2018 and includes large-scale field experiments over three field seasons. In 2018, we have inoculated 22 field sites with AMF, in 2019 additional 25 fields and in 2020 further 12 fields to test their potential to enhance maize yield. We find a significant positive effect of AMF inoculation on maize yield in about of the fields with yield increases of 12 up to 40%. As expected, we find not all fields and soil conditions responding positively to AMF inoculation – this is the problem that we what want to explain and solve in the framework of this project. We are continuing to developed the algorithm that predicts AMF inoculation success from soil chemical and/or biological soil data. The overall idea is that the developed algorithms will targeted the inoculations of the AMF based on precedent soil microbiome diagnostics.

Natacha Bodenhausen, Julia Hess, Alain Valzano, Gabriel Deslandes-Hérold, Jan Waelchli, Reinhard Furrer, Marcel G. A. van der Heijden, Klaus Schlaeppi, Predicting soil fungal communities from chemical and physical properties, Journal of Sustainable Agriculture and Environment, 12.6.2023.
Bodenhausen N, Somerville V, Desirò A, Walser J-C, Borghi L, van der Heijden MGA, Schlaeppi K. 2019. Petunia- and Arabidopsis-Specific Root Microbiota Responses to Phosphate Supplementation. Phytobiomes Journal 3: 112–124.
Hohmann P, Schlaeppi K, Sessitsch A. 2020. miCROPe 2019 - emerging research priorities towards microbe-assisted crop production. FEMS microbiology ecology.
Bodenhausen N, Deslandes-Hérold G, Waelchli J, Held A, van der Heijden MGA, Schlaeppi K. 2021. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. Mycorrhiza.
Frick C, Hohmann P, van der Heijden M. 2020. Mehr als ein Nährstofflieferant. Zeitschrift Bioaktuell: Band 9: Seiten 12-13.

Bodenfruchtbarkeit verbessern: Bauern gesucht, Schweizer Bauer, 8.3.2019