Work Package 3 – Plant, Soil, and Environment

Plants and their surrounding environments host diverse microbiomes that play crucial roles in supporting agriculture, ecosystem health, and pollution remediation. Plant-associated microbiomes, found on roots and leaves, influence crop productivity, stress tolerance, and disease resistance. Similarly, soil and engineered environmental microbiomes maintain soil health, water quality, and enable remediation of pollution in contaminated sites and wastewater treatment plants. 

While beneficial microbes such as mycorrhizal fungi and nitrogen-fixing rhizobia enhance nutrient uptake and plant growth, harmful bacteria, viruses, and fungi can cause diseases and crop losses. Likewise, soil microbiomes can be disrupted by nutrient overload, organic contaminants, and heavy metals from human activity. Engineered systems like wastewater treatment plants provide controlled environments to study and manipulate microbiomes for targeted pollutant removal and nutrient cycling.

The objectives of WP3 are to:

• Understand the structure, function, and dynamics of plant, soil, and engineered environmental microbiomes through integrative and reverse engineering approaches
• Achieve targeted manipulation of microbiomes by introducing beneficial microbes to enhance plant growth, prevent pathogen invasion, and restore soil health
• Develop microbiome-based strategies for remediation, including complementation of xenobiotic metabolism in soils and targeted nitrogen and phosphorus removal in wastewater treatment granules

WP3 focuses on key model systems including Arabidopsis thaliana and wheat for plant microbiomes, agricultural topsoils, contaminated soils, and wastewater treatment granules as representative environmental microbiomes. The work package aims to identify key microbial players and interactions that underpin plant health and environmental remediation. Predictive models and engineered microbiomes developed through WP3 will support sustainable agriculture, soil restoration, and energy-efficient wastewater treatment, addressing critical challenges of food security, environmental pollution, and climate change.

Work Package Leaders
Prof. Ian Sanders 
University of Lausanne

Prof. Rizlan Bernier-Latmani
EPFL