Selected work.

Phosphorus stress and spatial confinement lower the quorum-sensing activation threshold for phenazine production in Pseudomonas synxantha

Reinaldo E. Alcalde, Hannah Jeckel, Oumeng Zhang, Rogelio L. Avila, Nathan F. Dalleska, Dmitri V. Mavrodi, Changhuei Yang, Dianne K. Newman

Current Biology · 2026

We wanted to understand how bacteria coordinate chemical production when nutrients are scarce and cells occupy small, confined spaces. We found that phosphorus limitation lowered the signal concentration and cell density needed for Pseudomonas synxantha to activate quorum-sensing-dependent phenazine production, while confinement accelerated activation. The study shows that population density alone cannot explain when bacteria activate these behaviors: nutrient stress changes their responsiveness to signals, and confinement changes how quickly signals accumulate.

Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy

Oumeng Zhang^†, Reinaldo E. Alcalde^†, Haowen Zhou, Siyuan Yin, Dianne K. Newman, Changhuei Yang

Proceedings of the National Academy of Sciences · 2024

† Equal contribution

We wanted to watch microbes around roots and in developing biofilms without losing their three-dimensional context. In collaboration with biophotonics experts, we developed CFAST, which combines quantitative phase imaging over a 100 µm depth with 3D fluorescence imaging over a 20 µm depth, without scanning through successive focal planes. We used it to track microbial growth, competition, and gene expression, including the surface expansion and biofilm thickness shown below. We also observed that phosphorus-sensing and antibiotic-production reporters varied across space and time in surface-attached populations, with patterns distinct from those in free-swimming cultures. CFAST made it possible to connect microbial growth and gene expression with three-dimensional community development in experimental systems relevant to the rhizosphere. These observations motivated our subsequent investigation of how nutrient stress and spatial confinement tune quorum sensing.

The role of chemotaxis and efflux pumps on nitrate reduction in the toxic regions of a ciprofloxacin concentration gradient

Reinaldo E. Alcalde, Christopher M. Dundas, Yiran Dong, Robert A. Sanford, Benjamin Keith Keitz, Bruce W. Fouke, Charles J. Werth

The ISME Journal · 2021

We wanted to understand how antibiotic contamination affects microbial nutrient transformations when antibiotics and nutrients are unevenly distributed. In our earlier ES&T study (2019), we developed microfluidic reactors with controlled chemical gradients and found that swimming Shewanella oneidensis remained active and reduced nitrate in regions containing the bactericidal antibiotic ciprofloxacin at concentrations lethal in well-mixed cultures, without acquiring detectable antibiotic resistance. Nonmotile cells could not sustain the same response.

In this follow-up study, we investigated the mechanisms behind that behavior. Cells unable to navigate chemical gradients showed that chemotaxis toward nitrate was important for sustaining activity in antibiotic-rich regions. Efflux pumps, which export compounds from cells, were important for survival in well-mixed cultures but were not required in the gradients we tested.

The ES&T study established that movement and resource supply can sustain nitrate transformation under antibiotic stress; the ISME study showed that environmental structure can change which cellular mechanisms are required. Together, they demonstrate why uniform-exposure tests alone may not predict microbial activity in contaminated environments.