Use of TomatO rhizomicrobiome to Predict Yield in Abiotic Stress (UTOPYAS)
Swiss partners
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Université de Fribourg: Laurent Falquet (main applicant)
Partners in the MENA region
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École nationale supérieure agronomique ENSA, Algérie: Bilal Rahmoune (main applicant), Mohamed Tahrine, Meriem Badji
Presentation of the project
There are two main objectives of this project, the first one seeks to determine the shifts in tomato rhizomicrobiome community resulting from various treatments (especially the application of compost), decipher the correlation between cultivation factors, construct computational models for tomato biofertilisation, and ultimately formulate innovative rhizomicrobiome-based fertilizers, using the microbiome engineering methods. The second objective aims to boost research and raise higher education/research capacities in Algeria by providing an extensive training to an Algerian researcher in the field of NGS, bioinformatics and microbiome data analysis tools. In order to accomplish these objectives, a multi-location field trial was conducted using tomato (var fahla) in two regions: Algiers (humid) and Biskra (desert region of Algeria). Following daily monitoring, two samples of rhizosphere soil were carried out, during the full flowering stage and at the full fruits’ maturity stage. Then, microbial DNA were extracted, and the extracts were transferred to the University of Bern's NGS platform for sequencing utilizing PacBio's Full-Length 16S HiFi Sequencing technology. The evaluation of the data revealed that the majority of the sequences obtained have a length between 1400 pb and 1600 pb. Results after bioinformatics and statistics analysis using R dada2, vegan and phyloseq packages showed that cultivation factors (region, development stage and treatment) significantly impact the abundance and structural diversity of tomato rhizomicrobiome. The number of bacterial species observed and the size of the sequences were higher in the ENSA soil than in the Biskra soil. In addition, the enrichment test revealed several distinct groups depending on the factors. When comparing the two locations, the Bacillus, Microvirga and Arthrobacter groups were more abundant in the ENSA, while Lysobacter and Altererythrobacters were predominant in Biskra. Under conditions of salt stress, the Sandaracinaceae group was heavily enriched. Nitrospira andRhodanobacter showed a significant increase in fertilizer treatments, while Flavisolibacter was notable in the control treatments. Furthermore, the results of the training carried out at UniFr between 16/08 and 06/11 enabled the transfer of new knowledge and skills in bioinformatics, R software and the analysis of the metagenomic sequences of the microbiome to the Algerian lead researcher.