Biology subjects

Fink, J. W.

Publications and source records attributed to Fink, J. W..

4 recordsLinked to original sources

bioRxiv2026

A theoretical framework for how ecological interactions between microbes affect mutant fitness

The distribution of fitness effects (DFE) for spontaneous mutations characterizes both an organ-isms evolutionary potential as well as its genomic functions. The DFE of a genome depends on the specific environment in which it is measured, and for microbes a major feature of their environment is the presence of interactions with other species, such as competing for or cross-feeding nutrients. Several recent studies have empirically measured how the DFE of one microbial species changes in the presence of interactions with other species. However, the underlying mechanisms by which this happens, and the statistical patterns they are expected to produce, are unknown. Here we classify two types of statistical changes in the DFE: global changes to the DFE, such as to its mean or variance, and idiosyncratic changes in the fitness of individual mutants, summarized by the correlation of mutant fitness between environments. We first show that both types of effects occur in empirically measured DFEs across a wide range of species and interactions; idiosyncratic effects appear to have a maximum limit and constrain the size of global effects. We then show that a minimal model of an ecological interaction (competition for a single resource) is sufficient to generate both types of effects. Finally, we extend this model to arbitrary quantitative traits to reveal two general mechanisms of how interactions alter the DFE: 1) interactions can globally change fitness by altering the community growth rate, and 2) interactions can idiosyncratically change fitness of individual mutants by altering relative selection on different traits affected by those mutations.

evolutionary biology↗

bioRxiv2025

Phage-mediated lysis increases growth rate of surviving bacterial cells

Bacterial phage infection and subsequent lysis are traditionally considered mechanisms of bacterial mortality and viral propagation; additionally, emerging evidence indicates that they may also contribute to nutrient recycling in broader ecological systems. However, it remains unclear how the nutrients released during cell lysis affect the growth dynamics of the remaining bacterial population. Addressing this gap, we built a controlled system consisting of two Escherichia coli lysogenic strains: one carrying a wild-type{lambda} prophage and the other a temperature-inducible variant that can be induced to lyse at 38 {degrees}C. Using this system, we selectively induced phage lysis in a defined fraction of the population and quantified both total biomass and the biomass of surviving, non-lysed cells. We observed that the biomass loss was consistently smaller than expected based on the fraction of lysed cells, supporting the idea that some of the released biomass is rapidly recycled by the non-lysed population. To formalize the observed dynamics and obtain quantitative insight, we developed a mathematical model showing that nutrients released during lysis can transiently enhance the growth rate of the surviving, non-lysed cells. This effect emerges on a short timescale of minutes, consistent with the rapid onset of biomass compensation observed experimentally. The growth rate increase was confirmed in single-cell experiments using microfluidics and time-lapse microscopy, where we cultured wild-type lysogens in lysate-containing culture supernatants. In summary, the results suggest that nutrients released through lysis are rapidly consumed, leading to an acceleration in the growth rate of non-lysed cells. The consequent partial compensation for cell loss can substantially influence the population dynamics, highlighting phage lysis as a direct modulator of bacterial growth. Overall, our findings provide quantitative insights into how phage-mediated lysis affects the physiology of non-lysed bacterial cells, extending beyond its well-established role in biomass recycling.

microbiology↗

bioRxiv2024

Quantifying microbial fitness in high-throughput experiments

Few concepts are as central to evolution as is fitness, and yet the quantification of fitness is often ambiguous. In particular, high-throughput experiments to measure mutant fitness in microbes are increasingly common but vary widely in their definitions of fitness, which makes their results difficult to compare. What are the consequences of these different fitness statistics, and is there a best way to quantify fitness in a given context? Here we systematize the set of possible fitness statistics according to the following three choices: 1) the encoding of relative abundance (e.g., transforming by a log or logit function), 2) the time scale over which to measure the change in relative abundance, and 3) the choice of a reference subpopulation for calculating relative fitness in bulk competition experiments, such as those using DNA-barcoded mutants. We show that these different choices can lead to significantly different interpretations of mutant fitness, affecting the magnitude of fitness effects, the apparent presence of epistasis, and even the fitness ranking across mutants. This can confound predictions for evolutionary dynamics and gene functions. Altogether our results demonstrate the importance of consistent fitness definitions for reproducible results across experiments.

evolutionary biology↗

bioRxiv2022

Microbial population dynamics decouple nutrient affinity from environmental concentration

How the growth rate of a microbial population responds to the environmental availability of chemical nutrients and other resources is a fundamental question in microbiology. Models of this response, such as the widely-used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the environmental concentration of the resource? We survey growth response data across a wide range of organisms and resources. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentration in proportion to the environmental resource concentration, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentration. Our model not only provides testable predictions for laboratory evolution experiments, but it also reveals how an evolved half-saturation concentration may not reflect the organisms environment. In particular, this explains how organisms in resource-rich environments can still evolve fast growth at low resource concentrations. Altogether our results demonstrate the critical role of population dynamics in shaping fundamental ecological traits.

microbiology↗