Elucidating spatiotemporal dynamics of soil microbes via belowground microscopy

Soils are the base of our society and our food security, but they are one of the last domains of our modern life to be technologized.

Soil microbes are essential as symbionts, pathogens and drivers of nutrient cycles, but it has been difficult to study them in their natural habitats.

We want to use and develop a novel way to investigate soil microbial communities and species over space and time: With help of microfluidic soil chips and an advanced access system for microscopy we will access natural soil microbial communities to answer questions about their temporal dynamics over weeks and seasons, their interactions such as predator-prey relations and their spatial extent over time.

We will focus on fungal and protist communities in WP1 to understand the connection between their biodiversity and soil ecosystem functions. In WP2 we will focus on chosen fungal pathogen species and their dynamics in agricultural fields.

In WP3 we will develop automated species and community recognition with help of deep-learning algorithms fed with image and metabolic microspectroscopy data, benchmarked against classical DNA profiling.

In parallel, we will engage in soil communication activities with help of an artist and a youtube channel with edu-inspirational videos.

We argue that a strongly improved understanding of soil microbial ecology is crucial for a sustainable agriculture, and a wider education of society on the wonders of soils is important for the conservation of the soils.