To design effective synthetic microbial communities (SynComs) for plant protection, it is essential to understand how microbiota achieve robustness under natural conditions and which factors shape their composition and stability. The DeCoCt project systematically investigated the abiotic, biotic, and host-related drivers of microbial community dynamics in Arabidopsis thaliana, integrating long-term field studies, computational modeling, and experimental validation.
1) Abiotic factors:
We demonstrated that environmental parameters, especially temperature and precipitation, are key determinants of microbial community stability. Low temperatures, in particular, favor slow-growing, cold-tolerant microbes that persist over winter on Arabidopsis (Almario et al., 2021).
2) Internal and external biotic interactions:
Using machine learning and longitudinal field data, we identified microbial taxa that contribute to disease suppression and community stability (Kemen et al., 2025). SynComs were designed and tested for their ability to protect against Albugo laibachii, revealing that protective function depends on strain identity, community context, and intermicrobial interactions. Specific combinations of Cystofilobasidium and Pseudomonas enhanced robustness, while other microbes introduced instability. Cross-host experiments with Lotus corniculatus confirmed that host-specific communities vary in their ability to persist and function across plant species.
3) Host factors:
By combining microbiome profiles with genomic data from natural Arabidopsis populations over ten years, we quantified the influence of host genotype on community composition. While genetic effects were generally modest, they became more apparent under specific environmental conditions. These findings suggest that host-mediated microbiota recruitment is context-dependent, and that microbial traits such as biofilm formation and iron acquisition often override host effects in shaping communities.
In the final phase of the project, we validated key findings experimentally. SynComs suppressed pathogen infection even in non-sterile environments, showing ecological resilience. We identified traits such as siderophore sharing and antimicrobial peptide production as key mechanisms contributing to this stability (Gómez-Pérez et al., 2023; Höhn et al., 2024). Long-read metagenomics, proteomics, and metabolomics enabled deep functional characterization of SynCom performance.
A major outcome was the release of structured, FAIR-compliant datasets via the NFDI DataPlant infrastructure. The amplicon and genotype data are publicly available under DOI 10.57754/FDAT.61ckt-vm178. The proteomics dataset will be released shortly. These resources are actively disseminated through preprints, peer-reviewed publications, and conference presentations.
The DeCoCt project has achieved its primary goals. It has demonstrated that predictive and stable SynCom design is feasible and has uncovered the complexity and context dependence of microbiome function. These insights provide a foundation for microbiota-based strategies in sustainable agriculture.
