Biology subjects

Copeland, R.

Publications and source records attributed to Copeland, R..

5 recordsLinked to original sources

bioRxiv2025

Higher levels of antibiotic resistance are less competitive: the hidden ecological cost of no-metabolic cost resistance

Antibiotic resistance is often assumed to be constrained by fitness costs that limit the spread of highly resistant strains. Yet, many resistance mechanisms - including enzymatic antibiotic degradation - can arise with little or no metabolic cost, raising an important question: why is extreme resistance not more widespread? Here, we show that community-level interactions impose a hidden ecological cost on high resistance. By performing experiments with simple communities comprised of antibiotic resistant clinical isolates and an antibiotic susceptible strain, we find that when exposed to betalactam antibiotics, strains with a higher degree of antibiotic resistance can promote the survival of cohabiting susceptible strains. Guided by mean-field modeling, we find that highly resistant bacteria accelerate detoxification of the shared environment, shortening the period during which resistance confers a competitive advantage. Experiments with an engineered strain with tunable resistance level confirm that susceptible cells grow best in the presence of highly resistant strains. Importantly, this effect does not require evolved cooperation or active enzyme secretion; experimental and modeling results show that unavoidable processes, such as cell death or passive leakage, prevent complete privatization of resistance, giving rise to "accidental co-operation". These findings suggest that resistance evolution is not only shaped by intrinsic cellular costs but also by ecological feedback that limits the benefits of incremental increases in resistance. This result may be reflected in the phenotypic responses of the clinical strains tested in this work, which fell into distinct low- and high-resistance classes with no intermediate phenotypes. Thus, this work demonstrates the important role of community dynamics in understanding the evolution of antibiotic resistance and treatment outcomes.

microbiology↗

bioRxiv2025

Cell-substrate friction controls biofilm development

Bacteria often live in biofilms, surface-attached communities that can form on nearly any surface, from coarse sands to smooth glass. It is often hypothesized that cell-substrate friction can impact biofilm growth and development on these disparate surfaces. However, the experimental difficulty in measuring the friction between a biofilm and its surface has limited our understanding of how friction forces impact emergent colony-level behaviors and morphologies. Here, we demonstrate that increasing cell-substrate friction increases the biofilm contact angle, which, in turn, decreases the horizontal biofilm range expansion rate. We first used individual-based simulations to isolate the impact of friction. In this simple model, we found that increasing friction increases biofilm contact angle, and, in turn, that the contact angle emerges from a simple dynamic force balance between cell-substrate friction, cell-cell steric forces, and cell-cell adhesion, reminiscent of Youngs equation for sessile liquid drops. We developed an approach to directly measure the friction between bacterial colonies and agar surfaces, and found that the friction between the substrate and the biofilm is higher on substrates made with higher agar weight percentage. Additionally, we observed that biofilm contact angles increase with friction, following a Young-equation-like balance. Finally, we found that contact angle increases with agar percentage for a wide range of bacteria, suggesting that the biophysical impact of friction may play a role for a wide array of microbes.

biophysics↗

bioRxiv2025

Biofilm Vertical Growth Dynamics Are Captured by An Active Fluid Framework

Bacterial biofilms, surface-attached microbial communities, grow horizontally across surfaces and vertically above them. Although a simple heuristic model for vertical growth was experimentally shown to accurately describe the behavior of diverse microbial species, the biophysical implications and theoretical basis for this empirical model were unclear. Here, we demonstrate that this heuristic model emerges naturally from fundamental principles of active fluid dynamics. By analytically deriving exact solutions for an active fluid model of vertical biofilm growth, we show that the governing equations reduce to the same form as the empirical model in both early- and late-stage growth regimes. Our analysis reveals that cell death and decay rates likely play key roles in determining the characteristic parameters of vertical growth. The active fluid model produces a single, simple equation governing growth at heights above and below the diffusion limit; surprisingly, this "full" expression is simpler than the heuristic. With this theoretical basis, we explain why the vertical growth rate reaches a maximum at a height greater than the previously identified characteristic length scale. These results provide a theoretical foundation for a simple mathematical model of vertical growth, enabling deeper understanding of how biological and biophysical factors interact during biofilm development.

biophysics↗

bioRxiv2024

Evolving a High-Performance Terminal Deoxynucleotidyl Transferase for Enzymatic DNA Synthesis

Enzymatic DNA synthesis, using stepwise nucleotide addition catalyzed by template-independent polymerases, promises higher efficiency, quality, and sustainability than todays industry standard phosphoramidite-based processes. We report on the directed evolution of a terminal deoxynucleotidyl transferase that uses 3-phosphate blocked dNTPs to control the polymerization reaction and demonstrates high activity for these modified substrates and improved template promiscuity and thermostability.

bioengineering↗

bioRxiv2023

Spatial constraints subvert microbial arms race

Biofilms, surface attached communities of microbes, grow in a wide variety of environments. Often, the size of these microbial community is constrained by their physical surroundings. However, little is known about how size constraints of a colony impact the outcome of microbial competitions. Here, we use individual-based models to simulate contact killing between two bacterial strains with different killing rates in a wide range of community sizes. We found that community size has a substantial impact on outcomes; in fact, in some competitions the identity of the most fit strain differs in large and small environments. Specifically, when at a numerical disadvantage, the strain with the slow killing rate is more successful in smaller environments than in large environments. The improved performance in small spaces comes from finite size effects; stochastic fluctuations in the initial relative abundance of each strain in small environments lead to dramatically different outcomes. However, when the slow killing strain has a numerical advantage, it performs better in large spaces than in small spaces, where stochastic fluctuations now aid the fast killing strain in small communities. Finally, we experimentally validate these results by confining contact killing strains of Vibrio cholerae in transmission electron microscopy grids. The outcomes of these experiments are consistent with our simulations. When rare, the slow killing strain does better in small environments; when common, the slow killing strain does better in large environments. Together, this work demonstrates that finite size effects can substantially modify antagonistic competitions, suggesting that colony size may, at least in part, subvert the microbial arms race. Author summaryBiofilms are often crowded with many bacteria in direct contact. As a result, the competition for space and resources often turns deadly. Bacteria have evolved many mechanisms with which to kill each other; this bacterial warfare is often studied in large communities on agar plates or in flow cells [1]. However, in nature these colonies are often smaller, due to spatial constraints or shear forces. It is unclear how bacterial warfare proceeds in small systems. We performed individual based model simulations of bacterial warfare comprising two strains, each capable of killing the other on direct contact. We found that the community size played a substantial role in determining the outcome. When at a numerical disadvantage, the slow killing strain survived at much higher rates in small communities. In fact, there were many conditions in which the slow killing strain survives in small spaces but is completely eliminated in large ones. Conversely, when the slow killing strain is more common, it performs better in large spaces. Together, these observations demonstrate that finite size effects aid the strain that is at a disadvantage, and in some conditions, can even flip which strain increases its abundance. Finally, we experimentally tested the results of these simulations. Two mutual killing strains of V. cholerae were grown unconfined on agar plates (i.e., in large spaces) or confined within square holes with sides 7.5m long (i.e., in small spaces). In these experiments we found that the slow killing strain survived at significantly higher rates in confinement, validating simulation results.

biophysics↗