Biology subjects

Padfield, D.

Publications and source records attributed to Padfield, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Antimicrobial resistance in a warmer world: selection and transfer of kanamycin resistance is temperature dependent in E. coli.

Climate warming consistently correlates with increased antimicrobial resistance (AMR). Understanding the biological mechanisms underpinning this relationship is important for both prediction and mitigation of the future burden of antibiotic resistance in a warmer world, especially given AMR can spread through both selection and horizontal gene transfer. Here, we experimentally measure how temperature alters susceptibility to kanamycin, selection and spread of resistance in Escherichia coli MG1655 carrying the natural plasmids R1 and RP4. We predict that susceptibility should be lowest - and plasmid transfer highest - at maximal growth rate. Thermal performance of bacterial growth peaked at 40{degrees}C and we detected a small plasmid cost - for RP4, but not R1 - in the absence of kanamycin. The thermal performance of plasmid transfer did not mirror that of bacterial growth, instead, R1 transfer peaked at 35{degrees}C with a much narrower thermal tolerance. Susceptibility to kanamycin decreased with increasing growth rate until 31{degrees}C, before increasing again as temperatures approached and exceeded optimal growth temperature. Increasing susceptibility coupled with high growth rates meant that selection was strongest at the highest measured temperature, but the shape of the relationship changed with kanamycin concentration. In mixed populations of resistant and susceptible bacteria, we found that AMR spread most where selection was strongest, irrespective of plasmid transfer. Our findings suggest increased AMR at higher temperatures is predominantly driven by higher growth rates and increased susceptibility, resulting in stronger selection. Our study provides a framework to uncover generalities across antibiotic classes, strains, species, and plasmids, laying the foundation for improved prediction of AMR selection in the environment.

microbiology↗

bioRxiv2025

A Novel Method to Simultaneously Estimate Bacterial Respiration and Growth from Oxygen Dynamics

Bacterial growth and respiration are fundamental metabolic processes that affect how energy is used and impact carbon sequestration at the ecosystem scale. However, these traits are usually quantified independently, growth is quantified with endpoint biomass measurements while respiration is quantified by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration concurrently from a single dissolved oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling the simultaneous inference of both rates in real time. We applied our high throughput method to 15 bacterial strains isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry (R2 > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon-use efficiency increased from cooler temperatures, peaked around the thermal optimum ([~]30-35 {degrees}C), and declined at high temperature. By quantifying respiration and growth simultaneously and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a non-invasive and scalable tool for high throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.

microbiology↗

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

Phage growth rate is significantly affected by host-temperature and phage-temperature interactions

Virus growth depends on host performance in any given environment and has a profound impact spanning fields from climate change to human health. We investigated the intrinsic growth rate of two natural G4-like bacteriophages on four clones of their host (E.coli strain C) that differed in their thermal performance, with significant differences in their maximum growth rate and optimum temperature. The intrinsic population growth rate of the G4-like phage isolates was measured on the four host clones at three temperatures, reflective of a low, optimum and high temperature for one of the phage. The phages intrinsic growth rate was significantly affected by host-temperature and phage-temperature interactions, but not by the interaction between host and phage. Across temperatures, phage growth rate was consistently highest on the host clone with the highest maximum growth rate, but was not, contrary to our expectations, lowest on the host with the lowest growth rate. At any given temperature, phage growth rate followed a directional trend with host growth rate, but this trend was not as apparent when looking between temperatures. Our work demonstrates a significant impact of temperature and the host on phage growth rate, but much work remains to be done to disentangle how variation in host performance impacts virus performance across temperatures.

microbiology↗

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↗

bioRxiv2023

Macroevolutionary dynamics in micro-organisms: generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota.

Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity, but we still know relatively little about how prokaryotes successfully transition and persist across environments, and how this varies between biomes and lineages. Here, we investigate biome transitions and specialisation in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2000 unique Myxococcota lineages, with the majority (77%) being biome specialists and <5% able to live across the salt barrier. Discrete character evolution models revealed that biome specialists very rarely transitioned to specialising in another biome. Instead, generalists mediated transitions between biome specialists. Multistate hidden-state speciation and extinction models found variation in speciation rate across the tree, but this variation was independent of biome association and specialisation. Overall, our results help explain how microbes transition between biomes and are consistent with "the jack-of-all-trades" trade-off, where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists.

microbiology↗

bioRxiv2023

Tradeoffs of increasing temperatures for the spread of antimicrobial resistance in river biofilms

River microbial communities regularly act as the first defense barrier against the spread of antimicrobial resistance genes (ARG) that enter environmental microbiomes through wastewaters. However, how the invasion dynamics of wastewater-born ARGs into river biofilm communities will shift due to increasing average and peak temperatures worldwide through climate change remains unknown. Here we aimed at elucidating the effects of increasing temperatures on both, the natural river biofilm resistome, as well as the river biofilms invadability by foreign, wastewater-born ARGs. To achieve this, natural biofilms were grown in a pristine German river and transferred to artificial laboratory recirculation flume systems at three different temperatures (20{degrees}C, 25{degrees}C, 30{degrees}C). Already after one week of acclimatization to the temperatures, significant increases in the abundance of most naturally occurring ARGs were detected in the biofilms exposed to the highest temperature. Thereafter, biofilms were exposed to a single pulse of wastewater and the invasion dynamics of wastewater-born ARGs were analyzed over a period of two weeks. While initially after one day ARGs were able to invade all biofilms successfully and in equal proportions, the foreign invading ARGs were lost at a far increased rate at 30{degrees}C over time. ARG levels dropped to the initial natural levels at 30{degrees}C after 14 days. Contrary at the lower temperatures ARGs remained far elevated and certain ARGs were able to establish themselves in the biofilms. Overall, we here demonstrate tradeoffs of increasing temperature between increases in naturally occurring and faster loss dynamics of invading ARGs.

microbiology↗

bioRxiv2023

Copper reduces the virulence of bacterial communities at environmentally relevant concentrations

Increasing environmental concentrations of metals as a result of anthropogenic pollution are significantly changing many microbial communities. While there is evidence metal pollution can result in increased antibiotic resistance, the effects of metal pollution on virulence remains largely undetermined. Here, we experimentally test whether metal stress alters the virulence of bacterial communities. We do this by incubating three wastewater influent communities under different environmentally relevant copper concentrations for three days. We then quantify the virulence of the community using the Galleria mellonella infection model, and test if differences are due to changes in the rate of biomass accumulation (productivity), copper resistance, or community composition (quantified using 16S amplicon sequencing). The virulence of the communities was found to be reduced by the highest copper concentration, but not to be affected by the lower concentration. As well as reduced virulence, communities exposed to the highest copper concentration were less diverse and had lower productivity. This work highlights that metal pollution may decrease virulence in bacterial communities, but at a cost to diversity and productivity.

microbiology↗

bioRxiv2021

Bacterial colonisation dynamics of household plastics in a coastal environment

Accumulation of plastics in the marine environment has widespread detrimental consequences for ecosystems and wildlife. Marine plastics are rapidly colonised by a wide diversity of bacteria, including human pathogens, posing potential risks to human health. Here, we investigate the effect of polymer type, residence time and estuarine location on bacterial colonisation of common household plastics, including pathogenic bacteria. To do so, we submerged five main household plastic types: low-density PE (LDPE), high-density PE (HDPE), polypropylene (PP), polyvinyl chloride (PVC) and polyethylene terephthalate (PET) at an estuarine site in Cornwall (U.K.) and tracked bacterial colonisation dynamics. Using both culture-dependent and culture-independent approaches, we found that bacteria rapidly colonised plastics irrespective of polymer type. While biofilm community composition changed with colonisation time, no difference was observed between polymer types. Likewise, the presence of pathogenic bacteria, quantified using the insect model Galleria mellonella, increased over a five-week period, with no consistent differences observed between polymer types. Pathogens isolated from plastic biofilms using Galleria enrichment included Serratia and Enterococcus species and harboured a wide range of antimicrobial resistance genes. Our findings show that plastics in coastal waters are rapidly colonised by a wide diversity of bacteria, including known human pathogens, independent of polymer type.

ecology↗

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↗

bioRxiv2021

The impact of invader number on whole community invasions in biomethane-producing communities

Microbes can invade as whole communities, but the ecology of whole community invasions are poorly understood. Here, we investigate how invader frequency affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of initial invader frequency, which varied between 0.01 and 10%. Invasion resulted in enhanced biogas production (to the level of the pure invading community), but only when invader frequency was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower number of invading taxa (but not individuals) at lower initial invader frequencies, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.

ecology↗

bioRxiv2020

rTPC and nls.multstart: a new pipeline to fit thermal performance curves in R.

O_LIThe quantification of thermal performance curves (TPCs) for biological rates has many applications to problems such as predicting species responses to climate change. There is currently no widely used open-source pipeline to fit mathematical TPC models to data, which limits the transparency and reproducibility of the curve fitting process underlying applications of TPCs. C_LIO_LIWe present a new pipeline in R that currently allows for reproducible fitting of 24 different TPC models using non-linear least squares (NLLS) regression. The pipeline consists of two packages - rTPC and nls. multstart - that allow multiple start values for NLLS fitting and provides helper functions for setting start parameters. This pipeline overcomes previous problems that have made NLLS fitting and estimation of key parameters difficult or unreliable. C_LIO_LIWe demonstrate how rTPC and nls.multstart can be combined with other packages in R to robustly and reproducibly fit multiple models to multiple TPC datasets at once. In addition, we show how model selection or averaging, weighted model fitting, and bootstrapping can easily be implemented within the pipeline. C_LIO_LIThis new pipeline provides a flexible and reproducible approach that makes the challenging task of fitting multiple TPC models to data accessible to a wide range of users. C_LI

ecology↗

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

Spatial heterogeneity of an ecologically relevant environment accelerates diversification and adaptation.

Spatial heterogeneity is a key driver for the evolution of resource specialists and has been shown to both promote and constrain the rate of adaptation. However, direct empirical support for these evolutionary consequences of spatial heterogeneity comes from simplified laboratory environments. Here we address how spatial structure, through its effect on resource heterogeneity, alters diversification and adaptive evolution of the soil bacterium Pseudomonas fluorescens in an ecologically relevant context: soil-based compost. Our data show that environmental heterogeneity can both promote phenotypic diversification and accelerate adaptation. These results suggest that environmental disturbance, which can decrease spatial heterogeneity, may limit diversification and adaptation of microbial populations.

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↗