Biology subjects

Castledine, M.

Publications and source records attributed to Castledine, M..

10 recordsLinked to original sources

bioRxiv2025

Community complexity does not weaken pairwise coevolution in a soil bacterial community

Exploitative interactions, such as predator-prey and host-parasite interactions, are ubiquitous in microbial communities. These interactions shape community density and composition, imposing strong selection on members to evolve countermeasures reducing the negative impacts of exploitation. Exploitative coevolution is often studied between species pairs in isolation, which may over-estimate the strength and relevance of pairwise coevolution. Here we studied how community context influences coevolution between Pseudomonas fluorescens (exploited) and Variovorax sp. (exploiter). We evolved these species in pairwise coculture and embedded within a five-species community to investigate evolved changes in pairwise interactions. We found evidence for asymmetrical coevolution: Variovorax evolved more rapidly than Pseudomonas, leading to increased exploitation through time, while Pseudomonas evolved increased tolerance to Variovorax with time lag. The pairwise coevolutionary dynamics were not affected by the presence of other community members. Understanding how coevolutionary patterns change with increasing community complexity can have important implications for community persistence and function.

evolutionary biology↗

bioRxiv2025

Antagonism between bacteriophages and macrophages decreases efficacy of a phage cocktail and increases bacteriophage resistance

Phage therapy, the use of viruses that infect bacteria (bacteriophages), is a promising complement to antibiotics during the antimicrobial resistance crisis, but treatment success is very variable. Evolution of bacterial resistance to bacteriophages and bacteriophage counter-resistance (coevolution) during therapy may explain some of this variation, the dynamics of which may be affected by interactions with the patients immune system. Here, we examine how a pathogenic bacterium, Pseudomonas aeruginosa coevolves with two clinically relevant bacteriophages (14-1 and PNM) when in the presence of macrophages (RAW 264.7 cell line). We show macrophages reduced the rate by which bacteria were killed by bacteriophages, likely by reducing bacteria-bacteriophage contact rates. Over evolutionary time-scales, macrophages increased the proportion of bacteriophage resistant bacteria compared to where macrophages were absent. These differences in resistance rates were likely driven by the early advantage in density offered by macrophages to bacteria, and exclusion of PNM from the bacteriophage cocktail which otherwise increased in frequency in the absence of macrophages. Consequently, macrophages significantly altered the short- and long-term efficacy of a bacteriophage cocktail. In line with a growing body of work, our results suggest that the patients immune system can reduce the efficacy of phage therapy, potentially driving variable outcomes in therapy success in patients. Significance statementPhage therapy, the use of viruses that infect bacteria (bacteriophages), is a promising complement to antibiotics during the antimicrobial resistance crisis. However, treatment success is very variable. One, often overlooked, variable is the immune system and how this influences bacteriophage efficacy, and how bacteria evolve resistance to bacteriophages. We find that macrophages reduce the rate by which bacteria are killed by bacteriophages. Resistance to bacteriophages also increased in the presence of macrophages, showing macrophages affect the short- and long-term efficacy of phage therapy. These results highlight the importance of the immune system in phage therapy, and the need for more research in this area.

evolutionary biology↗

bioRxiv2025

Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study

AimsIn phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study. Methods and ResultsThe patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localised regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites. ConclusionsFor this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection. Impact statementThis work is important for informing whether phage therapy design protocols give accurate insights into clinical outcomes.

pathology↗

bioRxiv2024

Bacteria-phage (co)evolution is constrained in a synthetic community across multiple bacteria-phage pairs

Bacteriophages can be important drivers of bacterial densities, and therefore microbial community composition and function. These ecological interactions are likely to be greatly affected by evolutionary dynamics, because bacteria can rapidly evolve resistance to phage while phage can reciprocally evolve to increase infectivity. Most studies to date have explored eco-evolutionary dynamics using isolated pairs of bacteria-phage but in nature, multiple bacteria and phages coexist and (co)evolve simultaneously. How coevolution plays out in this context is poorly understood. Here, we examine how three coexisting soil bacteria (Ochrobactrum sp., Pseudomonas sp., and Variovorax sp.) interact and evolve with three species-specific bacteriophages over eight weeks of experimental evolution, both as host-parasite pairs in isolation and as a mixed community. Across all species phage resistance evolution was inhibited in polyculture, with the most pronounced effect on Ochrobactrum. Between bacteria-phage pairs there were also substantial differences in the effect of phage on host densities, and evolutionary dynamics including whether pairs coevolved. These contrasts emphasise the difficulty in generalising from monoculture to polyculture, and between bacteria-phage pairs to wider systems. Future studies should consider how multiple bacteria and phage pairs interact simultaneously to better understand how coevolutionary dynamics happen in natural communities. ImportanceThis project is unique in examining evolutionary dynamics among coexisting bacteria and their phages, rather than focus on single focal species - this makes our work more applicable to natural contexts while still working with controlled synthetic communities. While it is commonly assumed that bacteria will evolve phage resistance and coevolve with phage, this may be uncommon in more complex communities due to reduced contact rates and/or reduced mutation rates. Furthermore, the contrast in population dynamics and ability to coevolve between bacteria-phage pairs highlights the need for more pairs to be studied. Over-reliance on model systems that are known to coevolve means we lack an understanding of how wider bacteria-phage pairs interact, and to what extent results can be generalised beyond these pairs.

evolutionary biology↗

bioRxiv2024

Estimates of community stability using the invasion criterion are robust across levels of invader species richness

A key feature of natural communities is that the species within them stably coexist. A common metric used to test community stability is measuring the ability of each species to recover from rare. Here, each species is assumed to have negative frequency dependent fitness and have a greater fitness relative to the other community members. A conceptual issue with measurements of relative invader fitness is that single species are invaded from rare. In natural communities, multiple species would likely decline following perpetuations e.g. antibiotic application, global warming, natural disasters. In our study, we compare previous estimates of community stability in a five species microbial community to experimental results in which multiple species are invaded from rare. Our results showed that single species invasions were broadly predictive of whole community stability when multiple species are invaded simultaneously. Precise values of relative invader fitness were less comparable, however being non-significantly different in most comparisons in 3/5 species. This work provides the first experimental test of the robustness of relative invader fitness metrics under multi-species invasion scenarios.

ecology↗

bioRxiv2024

Bacteriophage resistance increases bacterial productivity by shifting population growth dynamics in the soil bacterium Variovorax sp.

Lytic bacteriophages ( phages) can limit bacterial densities and shape community structure, either directly through lysis or indirectly through costs to resistance. However, phages have also been reported to have no, and in some cases even positive, effects on host densities. Here, we investigate the mechanisms behind an increase in host density in Variovorax sp. populations following a fixation of resistance that was maintained after phage extinction. Our results demonstrate that the density increase was a genetic trait coinciding with resistance emergence. Growth curves showed that phage resistance shifted population growth curves such that density was higher in the death-phase. This density-increasing effect of resistance had important implications for community structure with phage resistant Variovorax decreasing the density of a conspecific. That resistance to lytic phage can increase host densities has implications for wider ecology and phage therapy where lytic phages are presumed to have negative effects on their hosts.

microbiology↗

bioRxiv2021

Parallel evolution of phage resistance - virulence trade - offs during in vitro and nasal Pseudomonas aeruginosa phage treatment

With rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolve to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct "in vitro evolutionary simulations" using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria - evolved in vitro and in vivo - had lower virulence. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro phage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection on de novo mutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolve in vivo, and in vitro experiments may give useful insights for clinical evolutionary outcomes.

evolutionary biology↗

bioRxiv2020

Experimental multi-species microbial (co)evolution results in local maladaptation

Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species populations to (1) the presence of the other four species in general and (2) sympatric vs allopatric communities. We found no evidence for general biotic adaptation: ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates when measured within communities. However, 4/5 species growth rates were significantly lower within the community they evolved in. This "local maladaptation" suggests that species evolved increased competitive interactions to sympatric species populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.

evolutionary biology↗

bioRxiv2020

Short-term relative invader growth rate predicts long-term equilibrium proportion in a stable, coexisting microbial community

Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion from rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time ([~]600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.

ecology↗

bioRxiv2019

Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host.

Thermal performance curves (TPCs) are used to predict changes in species interactions, and hence range shifts, disease dynamics and community composition, under forecasted climate change. Species interactions might in turn affect TPCs. Here, we investigate whether temperature-dependent changes in a microbial host-parasite interaction (the bacterium Pseudomonas fluorescens, and its bacteriophage, SBW[FE]2) changes the host TPC. The bacteriophage had a narrower infectivity range, with their critical thermal maximum [~]6{degrees}C lower than those at which the bacteria still had high growth. Consequently, in the presence of phage, the host TPC had a higher optimum temperature and a lower maximum growth rate. These changes were driven by a temperature-dependent evolution, and cost, of resistance; the largest cost of resistance occurring where bacteria grew best in the absence of phage. Our work highlights how ecological and evolutionary mechanisms can alter the effect of a parasite on host thermal performance, even over very short timescales. Data accessibility statementAll data and R code used in the analysis will be made available on GitHub and archived on Zenodo.

evolutionary biology↗