Current research directions

Microbes and habitats shape each other.

Our work is driven by a fascination with how pore-scale microbial interactions influence larger environmental processes. We study how microbes function and interact in structured environments, including soils and the rhizosphere, connecting microbial physiology, solute transport, and biogeochemistry.

We design experiments around the question at hand, combining molecular biology, microscopy, microfluidics, controlled plant experiments, and chemical analyses. Our research connects three directions: understanding microbial mechanisms in environmental context, investigating microbial approaches to nutrient management, and developing biosensors for soils and water.

Research areas
Environmental microbiology, microbial physiology, solute transport, biogeochemistry, environmental biotechnology, and rhizosphere science.

Mechanisms in context

How do physical, chemical, and biological conditions shape microbial behavior?

Microbes experience environments structured by water, chemical gradients, and neighboring organisms. Well-mixed cultures have enabled fundamental discoveries in microbiology; we build on that foundation by asking how microbial mechanisms operate when we restore environmental context.

We investigate how nutrient availability, hydration, pore structure, and interactions with neighboring microbes and roots influence microbial signaling, metabolism, competition, and cooperation. We are particularly interested in quorum sensing and secondary metabolites: how environmental conditions shape their production, and how these compounds influence microbial interactions and nutrient transformations. We connect cellular regulation with solute transport to understand when and where these processes affect environmental chemistry.

Microfluidic models, physiological and genetic experiments, and rhizosphere imaging allow us to isolate mechanisms while retaining the environmental features that matter. We progressively introduce complexity to test which mechanisms persist, which change, and why.

Fluorescence microscopy image of microorganisms distributed through a porous micromodel — Microbes in a porous micromodel

Syringe pumps connected by tubing to a microfluidic device on the microscope stage — Micromodel imaging with controlled flow

Plant root mounted in a transparent sample holder between microscope objectives for imaging — Root imaging setup

Researchers working at microscopes in a cleanroom during micromodel fabrication — Micromodel fabrication in the cleanroom

Microbial approaches to nutrient management

When can microbial processes support plant growth while reducing fertilizer inputs and nutrient losses?

Microbial communities can mobilize nutrients and influence plant performance, but sustaining these functions around roots requires more than combining organisms with complementary capabilities. We ask how competition, cooperation, and environmental stress shape community function, and how understanding these interactions can inform more reliable approaches to nutrient management.

We use defined microbial communities and controlled plant experiments to investigate nutrient acquisition, transformation, and retention. One focus is mobilizing legacy phosphorus through organic acids, redox-active metabolites, and siderophores. We also investigate how phosphorus mobilization interacts with nitrogen-cycling functions, including nitrogen fixation and nitrate reduction to ammonium, under nutrient and water stress.

We test whether mechanisms identified in controlled microscale systems remain effective in more complex plant and soil settings, including greenhouse studies. Our goal is to support crop growth while reducing dependence on fertilizer inputs and limiting nutrient losses through leaching and runoff. These losses can contaminate groundwater and contribute to eutrophication in downstream waters.

Young plants growing in three transparent experimental chambers — Controlled plant experiment in a culture vessel

Potted plants growing under controlled lighting in a growth chamber — Controlled plant experiment in soil

Seedlings with visible roots growing in a Petri dish — Seedling cultures

Iron oxide suspension swirling in a beaker on a laboratory stir plate — Iron oxide preparation for nutrient studies

Environmental biosensing

How can microbial sensing provide reliable measurements in soils and water?

Microbial responses offer a way to measure the chemical conditions organisms experience in soils and water. We ask how to translate these responses into reliable environmental measurements, accounting for changes in conditions that affect both sensor performance and signal interpretation.

We develop bacterial biosensors that translate cellular responses into measurable signals, with a focus on nutrient availability. We investigate how environmental conditions affect both sensor performance and the meaning of the resulting signals, including the distinction between a chemical’s abundance and its availability to microbes.

A starting point is phosphorus sensing across oxic and anoxic environments. We combine reporter development, optical measurements, and independent chemical analyses to evaluate sensing performance and explore hydrogel-based platforms containing bacterial reporters. These tools support our mechanistic research while advancing our longer-term goal of robust in situ sensing for soil and water quality monitoring. In agricultural settings, such measurements could inform when and where fertilizers are needed, supporting precision nutrient management.

Fluorescent bacterial reporter colonies growing on an agar plate — Fluorescent bacterial reporters

Numbered bacterial selection plate used during mutant strain construction — Mutant selection plate

Gel electrophoresis showing fluorescent DNA bands used in molecular biology experiments — Gel electrophoresis

Hydrogel beads containing bacterial reporters shown beside a ruler for scale — Hydrogel beads containing bacterial reporters