Current Research
RAM Physiology
Colorful, redox active metabolites (RAMs) are made by many different microbes. Their redox activity makes them fun to work with because they change color depending on their oxidation state. Historically overlooked as "secondary" metabolites, we have shown that phenazine RAMs play critical roles in helping Pseudomonas aeruginosa survive under stressful conditions at low power outputs, including in the cores of biofilms. Using a variety of approaches, including genetics and high-throughput electrochemistry, we continue to deepen our understanding of RAM-based maintenance metabolism; this work has direct relevance for controlling bacterial populations and communities in diverse contexts.
Related Recent Publications:
Shan, Xiaoyu; Trindade, Ines B. et al. (2026) Discovery of a phenazine-thiol conjugase from sparse data using genome-informed machine learning, PNAS, 123:e2607571123.
Thalhammer, Korbinian O.; Scurria, Matthew et al. (2026) Redox-dependent lipophilicity of phenazine metabolites is modulated by intramolecular hydrogen bonds and controls their biological distribution, ACS Chemical Biology 21:2253-62.
Ciemniecki, John A.; Glasser, Nathaniel R. et al. (2026) Facilitated fermentation--an underappreciated mode of energy conservation, mBio 17:e02494-25
Horak, Richard D.; Ciemniecki, John A. et al. (2024) Bioenergetic suppression by redox-active metabolites promotes antibiotic tolerance in Pseudomonas aeruginosa, PNAS 121(46):e2406555121
Ciemniecik, John A.; Ho Chia-Lun; et al. (2024) Mechanistic study of a low-power maintenance state using high-throughput electrochemistry, Cell 187:6882-95.e8. See commentary here
Chronic Infections
Chronic human infections cause major harm, including destroying the lungs of individuals living with cystic fibrosis and resulting in limb amputations due to wound healing failure in diabetics. The opportunistic pathogens causing these infections are found in biofilms--multicellular populations or communities, encased within self-produced polymeric materials--that are physiologically tolerant to conventional antibiotics. We iterate between developing means to characterize the microenvironments in which these pathogens thrive in situ, and using reductionist approaches to understand how they do so (see section on RAM Physiology); insights from this iterative approach are helping reveal novel therapeutic targets for biofilm control.
Related Recent Publications:
Li, Jinyang; Squyres, Georgia R. et al. (2026) Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness, PNAS, 123:e2528666123.
Squyres, Georgia R. and Newman, Dianne K. (2025) Single-cell lysis patterns morphogenesis of eDNA in the matrix of Pseudomonas aeruginosa biofilms, PNAS, 122(41): e2514210122. See commentary here
Wang, Renee Z.; Lonergan, Zachery R. et al. (2024) Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N2O under anoxia, PNAS, 121 (25): e2319960121.
Dar, Daniel; Dar, Nina et al. (2021) Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution, Science; 373(6556): eabi4882. See commentary here
Rhizosphere Studies
In 1962, Rachel Carson wrote in Silent Spring: "There are few studies more fascinating, and at the same time more neglected, than those of the teeming populations that exist in the dark realms of the soil. We know too little of the threads that bind the soil microorganisms to each other and to their world, and to the world above." These words are more resonant today than ever, especially in the context of climate change and the critical role soil plays in carbon cycling and food security. Accordingly, we have begun to study phenazine-based microbial community interactions in diverse rhizospheres, testing the hypothesis that phenazines are "keystone metabolites".
Related Recent Publications:
Kwiecinksi, Jarek V., Squyres, Georgia R. et al. (2026) Dynamic and distinct physiological responses by a soil bacterium promote survival along a dessication continuum, mBio, e01903-26.
Alcalde, Reinaldo. E., Jeckel Hannah et al. (2026) Phosphorus stress and spatial confinement lower the quorum-sensing threshhold for phenazine production in Pseudomonas synxantha, Current Biology, 36:3233-44.e8. See commentary here
Shan, Xiaoyu; Cao, Karen et al. (2026) Drought drives elevated antibiotic resistance across soils, Nature Microbiol. 11: 867–876. See commentary here and here and here and here and here.
McRose, Darcy L. & Newman, Dianne K. (2021) Redox-active antibiotics enhance phosphorous bioavailability, Science; 371:1033-1037. See commentary here