Research Topics

Multi-stability and Temporal Dynamics of Microbial Communities

Across biological scales—from cellular processes to populations and ecosystems—life is shaped by the interplay of deterministic and stochastic processes. By constructing frameworks that integrate these components, we aim to uncover principles common to developmental biology, ecology, and beyond.

Historically, studies of intracellular processes and studies of organismal or ecological dynamics have progressed as distinct fields. However, with genomic and transcriptomic tools now widely available, it is becoming possible to trace unifying principles that operate across biological hierarchies.

Our lab quantifies natural and experimental biological diversity using molecular techniques and microscopy, while also developing computational platforms grounded in mathematical biology, nonlinear dynamics, statistical physics, and network science.

Species Interactions and Ecosystems

Climate change and conflicts over food, water, and energy increasingly threaten global health, security, and the economy. Organisms move quantities of greenhouse gases between the atmosphere and soil that far exceed anthropogenic emissions. Thus, enhancing soil carbon sequestration offers tremendous potential for mitigating climate change.

In soils, fungi absorb water and nutrients and deliver them to plants. Harnessing these underground networks may improve reforestation efficiency and promote sustainable agricultural systems.

Our group aims to develop new environmental science frameworks by elucidating the belowground ecosystems long considered “black boxes.” Through large-scale genomic analyses and cutting-edge computational theory, we seek to provide fundamental yet applicable insights into belowground biological networks and their ecological potential.

We study all organisms that inhabit the belowground ecosystem, developing methods to understand whole ecosystems rather than isolated taxa. This requires integrating traditionally separate disciplines, including ecology, plant physiology, mycology, evolutionary biology, molecular biology, and phylogenetics.

Diversity of Mycorrhizal Symbioses

Early plant fossils dating back ~450 million years already show evidence of mycorrhizal partnerships. These symbioses, which shaped terrestrial ecosystems, include arbuscular, ectomycorrhizal, ericoid, and many other types. Recently, numerous plant–fungus symbioses that do not fit traditional definitions have been uncovered.

Through field surveys in forests, grasslands, and agricultural lands, as well as controlled experiments that create “miniature forest ecosystems,” we aim to map the full diversity of these hidden belowground networks.

Hidden Interactions Among Organisms

Ecosystems contain countless organisms engaged in interactions that are largely invisible to humans. Our understanding of natural processes remains extremely limited.

How can we uncover what a 3-mm spider eats as it roams the forest floor at night? When do insects perched on vegetation become infected by entomopathogenic fungi? By developing new analytical methods, we aim to answer such fundamental questions.