Biology subjects

Hall, J. P.

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

3 recordsLinked to original sources

bioRxiv2026

Fungicide drives de novo evolution of multidrug resistance in the plant growth promoting rhizobacterium, Pseudomonas fluorescens

Plant growth-promoting rhizobacteria (PGPR) are key members of soil microbial communities, supporting nutrient cycling, plant health, and productivity. In agricultural soils, these beneficial bacteria are often exposed to multiple stressors simultaneously, including fungicides, antibiotics, and rising temperatures. Despite their ecological importance, little is known about how PGPR respond evolutionarily to such combined stressors. Here, we investigated how the model PGPR Pseudomonas fluorescens SBW25 evolves resistance to the fungicide formulation Fubol Gold (metalaxyl-M + mancozeb), under ambient or warming soil conditions. Using a 16-week experimental evolution in soil microcosms with a fully factorial design (fungicide {+/-} warming), we assessed the evolution of fungicide resistance via phenotypic assays and whole-genome sequencing. Fungicide exposure rapidly selected for increased fungicide resistance, detectable as early as week 4, and co-selected for multidrug resistance, likely through mutations in a mexS ortholog that cause efflux pump overexpression. Warming did not alter the evolution of fungicide resistance; however, populations subjected to both fungicide and warming stress went extinct more rapidly, indicating that population evolutionary rescue was less effective under dual stress. Our findings show that fungicides alone can drive multidrug resistance in beneficial soil bacteria, suggesting that strategies to tackle AMR in agriculture should also consider non-antibiotic drivers of resistance.

microbiology↗

bioRxiv2025

Species interactions determine plasmid persistence in a 3-member bacterial community

Microbial communities are shaped by multiple forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community responses to environmental perturbations remains unclear, particularly considering the qualitatively different natures and the complexity of competitive and plasmid transfer interactions. We investigated the role of bacterial and plasmid interaction networks in community responses to single and multiple environmental perturbations, using a model community of three bacteria and two plasmids grown in rich media over five 2-day transfers. Bacterial interactions were the primary driver of community response, to the extent that plasmids were not always retained in the community even when they carried relevant resistance genes. Overall, our results indicate that while bacterial and plasmid interactions both shape community responses to environmental perturbations, bacteria-bacteria interactions may be the primary driver of community dynamics and their response to perturbations.

ecology↗

bioRxiv2018

Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections

AO_SCPLOWBSTRACTC_SCPLOWAntigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of [~]2,000 alleles. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving allelic differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12. The innovative application of ecological diversity analysis to VSG reads enabled characterisation of hierarchical VSG expression in the dataset, and resulted in a novel method for analysing such patterns of variation. Additionally, the long read approach allowed detection of mosaic VSG expression from very few reads - this was observed as early as day 3, the earliest that such events have been detected. Therefore, our results indicate that long read analysis is a reliable tool for resolving diverse allele expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and identifying mosaic gene formation unprecedentedly early during the infection process.

genomics↗