Biology subjects

Hall, J. P. J.

Publications and source records attributed to Hall, J. P. J..

9 recordsLinked to original sources

bioRxiv2026

The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements

Plasmids are extrachromosomal mobile genetic elements that can facilitate rapid bacterial adaptation by transferring genes between individuals. While plasmids are known to exist in diverse habitats and encode a range of traits, most of our knowledge about plasmids comes from clinically-associated antimicrobial resistance (AMR) plasmids that have already been recruited as vectors of drug resistance and have likely been shaped by strong selection for plasmid-encoded resistance. Here, we investigated 26 plasmids from the pQBR collection -- a set of large, co-existing mercury resistance environmental plasmids isolated in Pseudomonas spp. from a field in Oxfordshire in the 1990s -- and explored the ability of pQBR plasmids to mobilise novel chromosomally-encoded traits. New whole genome sequences for 25 plasmids confirmed that these soil-isolated plasmids are generally very large (140-588 kb), constitute at least five distinct genetic groups, and have relatives in various other Pseudomonas species and habitats. Despite significant nucleotide-level divergence, Groups I (pQBR103-like, [~]406 kb) and IV (pQBR57-like, [~]328 kb) showed remarkable ancient similarities in synteny and gene content both with one other, and with the PInc-2 family of plasmids known to mobilise clinically significant drug resistance in Pseudomonas aeruginosa. None of the pQBR plasmids sequenced to date harboured known AMR determinants, but putative phage defence systems and metal resistances were evident. Transposable elements, including the Tn5042 mercury resistance transposon, were responsible for significant structural variation within plasmid groups, consistent with a predominant role of transposons in rapidly remodelling plasmids. To experimentally test the ability of pQBR plasmids to spread new traits, we developed a novel transposon mobilisation assay which showed that certain Group IV pQBR plasmids were especially effective at acquiring the chromosomally-encoded transposon Tn6291, and that this mobilisation was likely due to specific plasmid factors rather than generic conjugation rate. Our work presents a tractable set of sequenced plasmids suitable for exploring the evolution and dynamics of gene acquisition by pre-AMR plasmids, and provides a key case study highlighting the pervasive interplay between plasmids and transposable elements that can drive microbial genome evolution. Repositories: github.com/jpjh/PQBR_PLASMIDS Impact statementPlasmids can drive microbial evolution by acting as vectors for horizontal gene transfer. Because of their central role in disseminating antimicrobial resistance (AMR), plasmids are mainly explored as vehicles for AMR traits, meaning that our knowledge of the diversity and evolutionary dynamics of non-AMR plasmids is more limited. Here, we explore sequences from a set of mercury resistance plasmids isolated in Pseudomonas spp. from pristine agricultural land that lack AMR determinants. By providing new whole genome sequencing analyses we expand the set of sequenced pQBR plasmids to 26, finding globally dispersed relatives from clinical, environmental, and industrial settings, and identifying an ancient plasmid backbone shared amongst divergent modern environmental and clinical AMR plasmids. We experimentally verify the role of pQBR plasmids in readily mobilising chromosomal traits using a novel transposon mobilisation assay, which suggests that specific plasmid-transposon interactions may drive trait spread. Overall, our work expands our understanding of the role of environmental plasmids in mobilising and disseminating adaptive traits.

microbiology↗

bioRxiv2026

Fungicide and warming interact to reduce soil ecosystem functioning

Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bioremediation. However, intensively managed environments such as agricultural soils are increasingly challenged with multiple harsh environmental stressors from the compounding effects of climate change and conventional agricultural practices. Understanding how soil communities will respond to environmental stress along multiple axes is key for predicting how environmental change will impact terrestrial soil ecosystems. We combine experimental evolution with community phenotyping, 16s rRNA metabarcoding, fungicide resistance assays and plant experiments, to show that fungicide and warming temperatures together drive a synergistic reduction in soil community respiration rates, metabolic capacity and plant growth promotion (Hordeum vulgare), which would have been missed by looking at stressor effects independently. Dual stressors caused widespread loss of metabolic activity, particularly for carbohydrates and carboxylic acids, highlighting impairment of community function. Fungicide-evolved soil isolates had a 16-fold increase in fungicide resistance, but only in the absence of warming - suggesting that the dual stressor treatment constrained fungicide adaptation. Together, our findings suggest that the number of stressors (rather than the nuances of individual stressors) may be key for predicting soil microbial community responses to environmental change across multiple axes.

ecology↗

bioRxiv2024

Superiority of chromosomal compared to plasmid-encoded compensatory mutations

Plasmids are important vectors of horizontal gene transfer in microbial communities but can impose a burden on the bacteria that carry them. Such plasmid fitness costs are thought to arise principally from conflicts between chromosomal- and plasmid-encoded molecular machineries, and thus can be ameliorated by compensatory mutations (CMs) that reduce or resolve the underlying causes. CMs can arise on plasmids (i.e. plaCM) or on chromosomes (i.e. chrCM), with contrasting predicted effects upon plasmid success and subsequent gene transfer because plaCM can also reduce fitness costs in plasmid recipients, whereas chrCM can potentially ameliorate multiple distinct plasmids. Here, we develop theory and a novel experimental system to directly compare the ecological effects of plaCM and chrCM that arose during evolution experiments between Pseudomonas fluorescens SBW25 and its sympatric mercury resistance megaplasmid pQBR57. We show that while plaCM was predicted to succeed under a broader range of parameters in mathematical models, experimentally chrCM dominated under all conditions, including those with numerous recipients, due to a more efficacious mechanism of compensation, and advantages arising from transmission of costly plasmids to competitors (plasmid weaponisation). We show analytically the presence of a mixed Rock-Paper-Scissors regime for plaCM, driven by trade-offs with horizontal transmission, that explains the observed failure of plaCM to dominate even in competition against an uncompensated plasmid. Our results reveal broader implications of plasmid-bacterial evolution for plasmid ecology, demonstrating the importance of compensatory mutations for resistance gene spread. One consequence of the superiority of chrCM over plaCM is the likely emergence in microbial communities of compensated bacteria that can act as hubs for plasmid accumulation and dissemination.

microbiology↗

bioRxiv2023

Spatial refuges and nutrient acquisition predict the outcome of evolutionary rescue in evolving microbial populations

Microbial populations are often exposed to environmental stressors that impact their survival and evolution. Eco-evolutionary theory suggests microbial populations may be able to survive a stressor through "spatial refuges" - i.e., areas of low or reduced stress such as within biofilms. However, spatial refuges reduce a populations access to nutrients, so may be detrimental depending on the severity of the stressor they are sheltering from. Using predictions from a general mathematical model, and the experimental evolution of the bacterium Pseudomonas fluorescens SBW25 under salinity stress and varying opportunities to form spatial refuges (i.e., agitated or non-agitated culture conditions), we show that spatial refuges can rescue a population from stressors only when nutrient levels are high. In the surviving high-salinity evolved populations (i.e., non-agitated culture conditions and high-nutrients), clones had an increased salinity resistance, indicating that spatial refuges can facilitate evolutionary rescue. Though whole genome resequencing did not reveal a single specific mutation associated with salt resistance, we found that clones evolved under control conditions (lower salt, high-nutrients, and no agitation) acquired mutations in a putative chemotaxis gene and showed increased motility. This indicates that spatial refuges under high salinity may also constrain adaptations to other environmental factors. Together, our combination of theory, laboratory experiment, and genome re-sequencing demonstrate the value and limits of spatial refuges in alleviating environmental stress within microbial populations.

microbiology↗

bioRxiv2022

Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities

Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their natural environmental niche.

microbiology↗

bioRxiv2022

Horizontal gene transfer increases microbiome stability

Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for mobile resistance genes with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies depending upon the mobility of the resistance gene and the network of ecological interactions within the community. Non-mobile resistance genes can benefit susceptible taxa in cooperative communities, yet damage those in competitive communities. Moreover, whilst the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can, counterintuitively, decrease the stability of the originally resistant donor species. We confirmed these theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together these findings highlight the importance of horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.

evolutionary biology↗

bioRxiv2021

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation, and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation rates for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.

microbiology↗

bioRxiv2021

The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multispecies communities are poorly understood. Here, we show, using experimental multispecies communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the dilution effect; an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from coinfected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid-plasmid interactions reducing the rate of horizontal transmission.

microbiology↗

bioRxiv2021

Plasmid fitness costs are caused by specific genetic conflicts

Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid acquisition are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or expression level. Here we show -- using a combination of experimental evolution, reverse genetics, and transcriptomics -- that fitness costs of two divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid acquisition. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by upregulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained upregulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer due to their propensity for amelioration by single compensatory mutations, explaining why plasmids are so common in bacterial genomes.

microbiology↗