Bacteriophages limit the existence conditions for conjugative plasmids

Bacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome

Valorising nutrient-rich digestate: Dilution, settlement and membrane filtration processing for optimisation as a waste-based media for microalgal cultivation

Digestate produced from the anaerobic digestion of food and farm waste is primarily returned to land as a biofertiliser for crops, with its potential to generate value through alternative processing methods at present under explored. In this work, valorisation of a digestate resulting from the treatment of kitchen and food waste was investigated, using dilution, settlement and membrane processing technology. Processed digestate was subsequently tested as a nutrient source for the cultivation of Chlorella vulgaris, up to pilot-scale (800L). Dilution of digestate down to 2.5% increased settlement rate and induced release of valuable compounds for fertiliser usage such as nitrogen and phosphorus. Settlement, as a partial processing of digestate offered a physical separation of liquid and solid fractions at a low cost. Membrane filtration demonstrated efficient segregation of nutrients, with micro-filtration recovering 92.38% of phosphorus and the combination of micro-filtration, ultra-filtration, and nano-filtration recovering a total of 94.35% of nitrogen from digestate. Nano-filtered and micro-filtered digestates at low concentrations were suitable substrates to support growth of Chlorella vulgaris. At pilot-scale, the microalgae grew successfully for 28 days with a maximum growth rate of 0.62 day−1 and dry weight of 0.86 g⋅L−1. Decline in culture growth beyond 28 days was presumably linked to ammonium and heavy metal accumulation in the cultivation medium. Processed digestate provided a suitable nutrient source for successful microalgal cultivation at pilot-scale, evidencing potential to convert excess nutrients into biomass, generating value from excess digestate and providing additional markets to the anaerobic digestion sector

Landmark Models for Optimizing the Use of Repeated Measurements of Risk Factors in Electronic Health Records to Predict Future Disease Risk.

The benefits of using electronic health records (EHRs) for disease risk screening and personalized health-care decisions are being increasingly recognized. Here we present a computationally feasible statistical approach with which to address the methodological challenges involved in utilizing historical repeat measures of multiple risk factors recorded in EHRs to systematically identify patients at high risk of future disease. The approach is principally based on a 2-stage dynamic landmark model. The first stage estimates current risk factor values from all available historical repeat risk factor measurements via landmark-age-specific multivariate linear mixed-effects models with correlated random intercepts, which account for sporadically recorded repeat measures, unobserved data, and measurement errors. The second stage predicts future disease risk from a sex-stratified Cox proportional hazards model, with estimated current risk factor values from the first stage. We exemplify these methods by developing and validating a dynamic 10-year cardiovascular disease risk prediction model using primary-care EHRs for age, diabetes status, hypertension treatment, smoking status, systolic blood pressure, total cholesterol, and high-density lipoprotein cholesterol in 41,373 persons from 10 primary-care practices in England and Wales contributing to The Health Improvement Network (1997-2016). Using cross-validation, the model was well-calibrated (Brier score = 0.041, 95% confidence interval: 0.039, 0.042) and had good discrimination (C-index = 0.768, 95% confidence interval: 0.759, 0.777)

Using citizen science image analysis to measure seabird phenology

Developing standardized methodology to allow efficient and cost-effective ecological data collection, particularly at scale, is of critical importance for understanding species' declines. Remote camera networks can enable monitoring across large spatiotemporal scales and at relatively low researcher cost, but manually analysing images and extracting biologically meaningful data is time-consuming. Citizen science image analysis could reduce researcher workload and increase output from large datasets, while actively raising awareness of ecological and conservation issues. Nevertheless, testing the validity of citizen science data collection and the retention of volunteers is essential before integrating these approaches into long-term monitoring programmes. In this study, we used data from a Zooniverse citizen science project, Seabird Watch, to investigate changes in breeding timing of a globally declining seabird species, the Black-legged Kittiwake Rissa tridactyla. Time-lapse cameras collected >200 000 images between 2014 and 2023 across 11 locations covering the species' North Atlantic range (51.7°N–78.9°N), with over 35 000 citizen science volunteers ‘tagging’ adult and juvenile Kittiwakes in images. Most volunteers (81%) classified images for only a single day, and each volunteer classified a median of five images, suggesting that high volunteer recruitment rates are important for the project's continued success. We developed a standardized method to extract colony arrival and departure dates from citizen science annotations, which did not significantly differ from manual analysis by a researcher. We found that Kittiwake colony arrival was 2.6 days later and departure was 1.2 days later per 1° increase in latitude, which was consistent with expectations. Year-round monitoring also showed that Kittiwakes visited one of the lowest latitude colonies, Skellig Michael (51.8°N), during winter, whereas birds from a colony at similar latitude, Skomer Island (51.7°N), did not. Our integrated time-lapse camera and citizen science system offers a cost-effective means of measuring changes in colony attendance and subsequent breeding timing in response to environmental change in cliff-nesting seabirds. This study is of wide relevance to a broad range of species that could be monitored using time-lapse photography, increasing the geographical reach and international scope of ecological monitoring against a background of rapidly changing ecosystems and challenging funding landscapes

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

Gene mobility promotes the spread of resistance in bacterial populations

Theory predicts that horizontal gene transfer (HGT) expands the selective conditions under which genes spread in bacterial populations. Whereas vertically inherited genes can only spread by positively selected clonal expansion, mobile genetic elements can drive fixation of genes by infectious HGT. We tested this using populations of Pseudomonas fluorescens and the conjugative mercury resistance (Hg R) plasmid pQBR57. HGT expanded the selective conditions allowing the spread of Hg R: Chromosomal Hg R only increased in frequency under positive selection, whereas plasmid-encoded Hg R reached fixation with or without positive selection. Tracking plasmid dynamics over time revealed that the mode of Hg R inheritance varied across mercury environments. Under mercury selection, the spread of Hg R was driven primarily by clonal expansion while in the absence of mercury Hg R dynamics were dominated by infectious transfer. Thus, HGT is most likely to drive the spread of resistance genes in environments where resistance is useless

Using citizen science image analysis to measure seabird phenology

Developing standardized methodology to allow efficient and cost-effective ecological data collection, particularly at scale, is of critical importance for understanding species' declines. Remote camera networks can enable monitoring across large spatiotemporal scales and at relatively low researcher cost, but manually analysing images and extracting biologically meaningful data is time-consuming. Citizen science image analysis could reduce researcher workload and increase output from large datasets, while actively raising awareness of ecological and conservation issues. Nevertheless, testing the validity of citizen science data collection and the retention of volunteers is essential before integrating these approaches into long-term monitoring programmes. In this study, we used data from a Zooniverse citizen science project, Seabird Watch, to investigate changes in breeding timing of a globally declining seabird species, the Black-legged Kittiwake Rissa tridactyla. Time-lapse cameras collected >200 000 images between 2014 and 2023 across 11 locations covering the species' North Atlantic range (51.7°N–78.9°N), with over 35 000 citizen science volunteers ‘tagging’ adult and juvenile Kittiwakes in images. Most volunteers (81%) classified images for only a single day, and each volunteer classified a median of five images, suggesting that high volunteer recruitment rates are important for the project's continued success. We developed a standardized method to extract colony arrival and departure dates from citizen science annotations, which did not significantly differ from manual analysis by a researcher. We found that Kittiwake colony arrival was 2.6 days later and departure was 1.2 days later per 1° increase in latitude, which was consistent with expectations. Year-round monitoring also showed that Kittiwakes visited one of the lowest latitude colonies, Skellig Michael (51.8°N), during winter, whereas birds from a colony at similar latitude, Skomer Island (51.7°N), did not. Our integrated time-lapse camera and citizen science system offers a cost-effective means of measuring changes in colony attendance and subsequent breeding timing in response to environmental change in cliff-nesting seabirds. This study is of wide relevance to a broad range of species that could be monitored using time-lapse photography, increasing the geographical reach and international scope of ecological monitoring against a background of rapidly changing ecosystems and challenging funding landscapes

Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage 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 gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 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 carriage. 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 up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated 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 (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.</jats:p