Plant-soil-microbe interactions

The free living and symbiotic microbes that make up these communities  have  profound effects on plant health and productivity, ecosystem processes, and contribute to the regulation of globally-important biogeochemical cycles. In this research theme we use a combination of advanced molecular techniques, high-throughput imaging, state of the art microscopy and biochemical approaches to examine: rhizosphere community ecology, the evolution of symbioses and soil biogeochemistry from a microbe-centric view.

PROJECTS

• MiCrop [Weedon, Kokkoris, Kiers, Stewart, Klein, van Son] We study the evolution of plant-microbiome interactions and identify opportunities for future plant breeding at an unprecedented scale. Our focus is on understanding stress-adaptive microbiomes and their active recruitment by plants across the plant kingdom through a phylogenetic approach. NWO-funded in collaboration with UvA, UU, NIOO-KNAW, WUR.
• Tracking trade across symbiotic networks [Shimizu, Kiers, Oyarte Gálvez, van Son, Bisot, Cargill] In collaboration with AMOLF, we are developing an imaging robot to capture time-lapse imaging of network topologies. We use transformed in-vitro root systems with precisely controlled nutrient landscapes to generate high-resolution datasets for fungal architecture.
• Flows, Structure and Trading in Underground Fungal Networks [Kiers, Oyarte Gálvez, Kokkoris, van Son, Terry, Bisot] The project’s goal is to understand how symbiotic fungi process and share complex information across their bodies to execute trading strategies with their host plants. This includes testing how mycorrhizal networks modulate electrical activity (voltage changes across cell membranes) in response to nutrient stimuli. NWO-funded.
• SPUN [Kiers, Kokkoris, Klein, Stewart, Pringle] In collaboration with researchers, campaigners and local communities, the Society for the Protection of Underground Networks (SPUN) aims to accelerate efforts to protect underground ecosystems largely absent from biodiversity and climate agendas. We are building an open source mapping platform of Earth’s underground fungal biodiversity, developing a methodology for measuring and monitoring network identity and functioning, and translating the science into insights that are accessible to the world. 
• A-LIFE Early Career support program [Kokkoris, Tutucci, van Otterdijk, van Son] This projects lands in the intersection between microbiology, fluorescence microscopy and technology development. Here, via the development of novel imaging and microscopy techniques (DNA/RNA FISH & Immunofluorescence) we examine the mysterious multinucleate biology of the most widespread plant related symbiotic fungi.
• NUCLEAR MIX [Kokkoris, Kiers, van Otterdijk, van Son] By using high resolution molecular techniques, advanced microscopy, image analysis, and DNA/RNA fluorescence in situ hybridization, here, we examine how mycorrhizal fungi connect and exchange nuclei and what is the cost and benefit of these nuclear mixing.