Dataset and scripts for Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses and enhance maize growth at field scale

Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses and enhance maize growth at field scale by Davide Francioli, Ioannis D. Kampouris, Theresa Kuhl-Nagel, Doreen Babin, Loreen Sommermann, Jan H. Behr, Soumitra Paul Chowdhury, Rita Zrenner, Narges Moradtalab, Michael Schloter, Jörg Geistlinger, Uwe Ludewig, Günter Neumann, Kornelia Smalla, Rita Grosch Abstract Background Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits. Results Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores. Conclusions Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity. Funding This work was supported by the German Federal Ministry of Education and Research (BMBF, Germany) within the framework of the project DiControl (http://dicontrol.igzev.de/de/; grant number 031B0514A- E) as part of the BonaRes funding initiative ‘Soil as a sustainable resource for the bioeconomy’ (https://www.bonares.de).