Forest Microbiome & Ecosystem Ecology
Soils are alive. Incredibly diverse forest microbial communities have profound impacts on our world that we are just beginning to grasp. My team studies the forest microbiome. How does incredible microbial diversity affect which trees are in a forest, forest carbon sequestration and climate change forecasts? We focus on the ecology of mycorrhizal fungi - fungi that form a symbiosis with the roots of most plants on Earth – however we are broadly interested in links between microbes and ecosystems.
We use a diversity of approaches to link microbiome composition to emergent ecosystem function. Work spans manipulative microbiology, field experiments, big data analysis and simulation modeling. We see this combination of approaches as critical to scaling how molecular scale interactions within microbial communities ripple through ecosystems to affect the patterning and function of global forests.
I am always interested in recruiting motivated PhD students and postdocs looking to work together or lead their own project. If you are interested please consider the PhD fellowship and postdoc fellowship opportunities at ETH Zürich and then send me an email. Our group is nested within the Crowther Lab at ETH Zürich, an incredibly collaborative environment broadly interested in all aspects of global ecology.
Big Data
Ecologists have access to larger data sets than ever before. We use big data approaches to understand the biogeography of forests, fungi and bacteria, and link this biogeography to forest carbon sequestration. We make heavy use of large-scale microbial sequence data, forest inventory data sets, and soil carbon data sets. We embrace frequentist, Bayesian, and machine learning frameworks to achieve this, depending on which approach best fits the question at hand.
Theory and Models
Mathematical models underpin ecological theory, as well as how theory is applied to represent ecology within ecosystem and Earth-system models. We build first-principles mathematical models to demonstrate how explicit representation of microbial ecology can change both ecological theory and carbon cycle predictions under global change.
Restoring the Forest Microbiome
There is surging interest in large-scale tree-planting as climate mitigation and biodiversity conservation strategies. However, when we plant trees, we rarely “plant” the soil microbiome. Our group is performing randomized controlled reforestation trials to test the impact of soil microbiome inoculation on reforestation success and carbon sequestration rates. We currently run a 9-hectare field experiment in Wales, U.K. in collaboration with The Carbon Community, and a 12-hectare field experiment on the Yucatan Peninsula in Mexico in collaboration with Plant for the Planet.
Model Ecosystems
Model systems and reductionist approaches have enabled breakthroughs across biology, yet are rarely used to study ecosystem ecology. We have a developed a reduced “model mycorrhizal ecosystem” to study interactions between plants, ectomycorrhizal fungi, free-living soil microbes and soil carbon dynamics. We grow Pinus taeda in symbiosis with the ectomycorrhizal fungus Suillus cothurnatus. By growing these systems in the lab we can choose whether or not Suillus is present within model ecosystems, and then use stable isotopes to trace the impact of this fungus on soil carbon processes without disrupting the plant-mycorrhizal-soil interface. Genome sequencing, transcriptomics, and gene editing allow us to understand the causal molecular links between fungal ecology and the carbon cycle. This work is supported by The U.S. Department of Energy (DOE) Joint Genome Institute, the DOE Environmental and Molecular Science Laboratory, and the DOE Terrestrial Ecosystem Science program.
Soils are alive. Incredibly diverse forest microbial communities have profound impacts on our world that we are just beginning to grasp. My team studies the forest microbiome. How does incredible microbial diversity affect which trees are in a forest, forest carbon sequestration and climate change forecasts? We focus on the ecology of mycorrhizal fungi - fungi that form a symbiosis with the roots of most plants on Earth – however we are broadly interested in links between microbes and ecosystems.
We use a diversity of approaches to link microbiome composition to emergent ecosystem function. Work spans manipulative microbiology, field experiments, big data analysis and simulation modeling. We see this combination of approaches as critical to scaling how molecular scale interactions within microbial communities ripple through ecosystems to affect the patterning and function of global forests.
I am always interested in recruiting motivated PhD students and postdocs looking to work together or lead their own project. If you are interested please consider the PhD fellowship and postdoc fellowship opportunities at ETH Zürich and then send me an email. Our group is nested within the Crowther Lab at ETH Zürich, an incredibly collaborative environment broadly interested in all aspects of global ecology.
Big Data
Ecologists have access to larger data sets than ever before. We use big data approaches to understand the biogeography of forests, fungi and bacteria, and link this biogeography to forest carbon sequestration. We make heavy use of large-scale microbial sequence data, forest inventory data sets, and soil carbon data sets. We embrace frequentist, Bayesian, and machine learning frameworks to achieve this, depending on which approach best fits the question at hand.
Theory and Models
Mathematical models underpin ecological theory, as well as how theory is applied to represent ecology within ecosystem and Earth-system models. We build first-principles mathematical models to demonstrate how explicit representation of microbial ecology can change both ecological theory and carbon cycle predictions under global change.
Restoring the Forest Microbiome
There is surging interest in large-scale tree-planting as climate mitigation and biodiversity conservation strategies. However, when we plant trees, we rarely “plant” the soil microbiome. Our group is performing randomized controlled reforestation trials to test the impact of soil microbiome inoculation on reforestation success and carbon sequestration rates. We currently run a 9-hectare field experiment in Wales, U.K. in collaboration with The Carbon Community, and a 12-hectare field experiment on the Yucatan Peninsula in Mexico in collaboration with Plant for the Planet.
Model Ecosystems
Model systems and reductionist approaches have enabled breakthroughs across biology, yet are rarely used to study ecosystem ecology. We have a developed a reduced “model mycorrhizal ecosystem” to study interactions between plants, ectomycorrhizal fungi, free-living soil microbes and soil carbon dynamics. We grow Pinus taeda in symbiosis with the ectomycorrhizal fungus Suillus cothurnatus. By growing these systems in the lab we can choose whether or not Suillus is present within model ecosystems, and then use stable isotopes to trace the impact of this fungus on soil carbon processes without disrupting the plant-mycorrhizal-soil interface. Genome sequencing, transcriptomics, and gene editing allow us to understand the causal molecular links between fungal ecology and the carbon cycle. This work is supported by The U.S. Department of Energy (DOE) Joint Genome Institute, the DOE Environmental and Molecular Science Laboratory, and the DOE Terrestrial Ecosystem Science program.
