Biology subjects

Svenningsen, S. L.

Publications and source records attributed to Svenningsen, S. L..

6 recordsLinked to original sources

bioRxiv2026

Pushing for survival: Spatial intermixing and indirect resistance enable collective growth

The survival of bacterial communities depends on complex dynamics at molecular, cellular, and ecosystem levels. Understanding antibiotic resistance requires a broader community context, as emergent dynamics can lead to unexpected outcomes, such as the persistence of susceptible populations or community collapse. We capture these behaviors by integration of microscopy and mathematical modeling to understand how bacterial interactions and spatial organization shape bacteriostatic antibiotic resistance in a two-strain community. We show that local chloramphenicol detoxification and mechanical pushing shape bacterial coexistence and spatial organization, promoting the survival and growth of otherwise susceptible bacteria. Additionally, the timing of antibiotic administration critically determines the growth dynamics, co-existence, local diversity of susceptible and resistant bacteria, and overall community resistance. Together, these insights highlight how community-level interactions fundamentally reshape antibiotic responses and open new avenues to understand and control bacterial resilience. SIGNIFICANCE STATEMENTAntibiotic resistance is usually treated as a property of individual bacterial strains, yet bacteria typically grow in dense, spatially structured communities where physical interactions matter. We find that under bacteriostatic (growth pausing) antibiotic stress, resistant bacteria can create highly localized protective environments that allow sensitive cells to survive and proliferate. This protection arises not only from antibiotic detoxification, but also from growth-driven mechanical pushing that maintains close cell-cell proximity. As a result, antibiotic tolerance emerges as a collective, spatially dependent property rather than an intrinsic trait of single cells. These findings show that spatial organization, physical forces, and treatment timing can strongly reshape therapy outcomes, with implications for how resistance is understood and managed in microbial communities.

biophysics↗

bioRxiv2024

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarum

Exposure of bacterial populations to phage infection pressure is a significant driver of phage-host co-evolution and diversification. However, the impact of the spatial organization of bacterial population co-existence and co-evolution dynamics remains poorly understood. Here, we investigated how the spatial structure of the host population affects phage-host interactions by co-cultivating a Vibrio anguillarum strain with the lytic T4-like vibriophage KVP40 under conditions that resulted in either a homogenous, well-mixed population or a heterogeneous population with bacterial aggregates. We observed markedly different temporal dynamics associated with the two population structures over a 30-day adaptive laboratory evolution experiment. Phage and host dynamics suggested that phage-sensitive subpopulations retained in the aggregates substantially prolonged the coexistence of phages and bacteria, relative to the homogenous environment. However, the limited phage propagation on the sensitive subpopulations was insufficient for host range expansion to occur. In contrast, daily supplementation of sensitive host bacteria in parallel experiments readily led to the emergence of phage mutants with enhanced infective capability and an expanded host range. These results underscore the importance of bacterial spatial organization in determining the outcome of phage attacks and highlight the complex interplay between genomic processes and ecological conditions in driving evolutionary innovations.

microbiology↗

bioRxiv2023

The dynamics of phage predation on a microcolony

Phage predation is an important factor for controlling the bacterial biomass. At face value, dense microbial habitats are expected to be vulnerable to phage epidemics due to the abundance of fresh hosts immediately next to any infected bacteria. Despite this, the bacterial microcolony is a common habitat for bacteria in nature. Here we experimentally quantify the fate of microcolonies of Escherichia coli exposed to virulent phage T4. It has been proposed that the outer bacterial layers of the colony will shield the inner layers from the phage invasion and thereby constrain the phage to the colonys surface. We develop a dynamical model that incorporates this shielding mechanism and fits the results with experimental measurements to extract important phage-bacteria interaction parameters. The analysis suggests that, while the shielding mechanism delays phage attack,T4 phage are able to diffuse so deep into the dense bacterial environment that colony level survival of the bacterial community is challenged. SignificanceThe shielding mechanism of bacterial microcolonies against phage invasion has been experimentally quantified, and the result was analyzed by using a mathematical model. The analysis suggests that while forming a dense colony delays phage attack by limiting the infection closer to the colony surface,T4 phage can diffuse so deep into the dense bacterial environment that colony-level survival of the bacterial community is challenged. This finding highlights the importance of the interplay between the phage infection dynamics and the physical structure of bacterial colonies in controlling the microbial population.

microbiology↗

bioRxiv2020

Screening for highly transduced genes in Staphylococcus aureus reveals both lateral and specialized transduction

Bacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer in the human pathogen, Staphylococcus aureus. Transduction involves packaging of bacterial DNA by viruses and enables transmission of virulence and resistance genes between cells. To learn more about transduction in S. aureus, we searched a transposon mutant library for genes and mutations that enhanced transfer mediated by the temperate phage, {varphi}11. Using a novel screening strategy, we performed multiple rounds of transduction of transposon mutant pools selecting for an antibiotic resistance marker within the transposon element. When determining the locations of transferred mutations, we found that, within each pool of 96 mutants the screen had selected for just 1 or 2 transposon mutant(s). Subsequent analysis showed that the position of the transposon, rather than inactivation of bacterial genes, was responsible for the phenotype. Interestingly, from multiple rounds we identified a pattern of transduction that encompassed mobile genetic elements, as well as chromosomal regions both upstream and downstream of the phage integration site. The latter was confirmed by DNA sequencing of purified phage lysates. Importantly, transduction frequencies were lower for phage lysates obtained by phage infection rather than induction. Our results confirm previous reports of lateral transduction of bacterial DNA downstream of the integrated phage, but also indicate specialized transduction of DNA upstream of the phage, likely involving imprecise excision of the phage from the bacterial genome. These findings illustrate the complexity of transduction processes and increase our understanding of the mechanisms by which phages transfer bacterial DNA. ImportanceHorizontal transfer of DNA between bacterial cells contributes to the spread of virulence and antibiotic resistance genes in human pathogens. For Staphylococcus aureus, bacterial viruses are particularly important. These viruses, termed bacteriophages, can transfer bacterial DNA between cells by a process known as transduction, which despite of its importance is only poorly characterized. Here, we employed a transposon mutant library to investigate transduction in S. aureus. We show that the location of bacterial DNA in relation to bacteriophages integrated in the bacterial genome is a key decider of how frequently that DNA is transduced. Based on serial transduction of transposon mutant pools and direct sequencing of bacterial DNA in bacteriophage particles, we demonstrate both lateral and specialized transduction. The use of mutant libraries to investigate the patterns of bacterial DNA transfer between cells could help understand how bacteria evolve virulence and resistance and may ultimately lead to new intervention strategies.

microbiology↗

bioRxiv2020

Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse

The vast majority of a bacterial population is quickly killed when treated with a lethal concentration of antibiotics. The time scale of this killing is often comparable with the bacterial generation time before addition of antibiotics. Yet, a small subpopulation typically survives for an extended period. However, the long-term killing dynamics of bacterial cells has not been fully quantified even in well-controlled laboratory conditions. We constructed a week-long killing assay and followed the survival fraction of Escherichia coli K12 exposed to a high concentration of ciprofloxacin. We found that long-term survivors were formed during exponential growth, with some cells surviving at least 7 days. The long-term dynamics contained at least three timescales, which greatly enhances predictions of the population survival time compared to the biphasic extrapolation from the short term behavior. Furthermore, we observed a surprisingly long memory effect of a brief carbon starvation pulse, which was dependent on the (p)ppGpp synthase relA. Specifically, one hour of carbon starvation prior to antibiotics exposure increased the surviving fraction by nearly 100-fold even after 4 days of ciprofloxacin treatment.

microbiology↗

bioRxiv2020

Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate

Stationary phase is the general term for the state a bacterial culture reaches when no further increase in cell number occurs due to the exhaustion of nutrients in the growth medium. Depending on the type of nutrient that is first depleted, the metabolic state of the stationary phase cells may vary greatly, and the subsistence strategies that best support cell survival may differ. As ribosomes play a central role in bacterial growth and energy expenditure, ribosome preservation is a key element of such strategies. To investigate the degree of ribosome preservation during long-term starvation, we compared the dynamics of ribosomal RNA (rRNA) levels of carbon-starved and phosphorus-starved Escherichia coli cultures for up to 28 days. The starved cultures contents of full-length 16S and 23S rRNA decreased exponentially and phosphorus starvation resulted in much more rapid rRNA degradation than carbon starvation. Bacterial survival kinetics were also quantified over the starvation period. Upon replenishment of the nutrient in question, carbon-starved cells resumed growth faster than cells starved for phosphate for the equivalent amount of time, and for both conditions, the lag time increased with the starvation time. While these results are in accordance with the hypothesis that cells with a larger ribosome pool recover more readily upon replenishment of nutrients, we also observed that the lag time kept increasing with increasing starvation time, also when the amount of rRNA per viable cell remained constant. ImportanceBacteria grow exponentially consuming nutrients, and then starve until the next nutrient is added. To elucidate the survival kinetics of the cells under starvation, we performed month-long, carbon and phosphorus starvation experiments of Escherichia coli monitoring ribosomal RNA levels and survival of the cells. The starved cultures concentration of ribosomal RNA dropped exponentially with time, and the speed of degradation was much quicker under the phosphorus starvation than the carbon starvation. We have also quantified the lag time, i.e., the time needed to resume growth when the starved cells are transferred into fresh media. The observation revealed that the lag time increases with starvation time and the phosphorus starvation has a greater impact on the increase of the lag time.

microbiology↗