James P. J. Hall

Thompson CMA, Hall JPJ, Chandra G, Martins C, Saalbach G, Panturat S, Bird SM, Ford S, Little RH, Piazza A, Harrison E, Jackson RW, Brockhurst MA, Malone JG (2023) PLoS Biology 21, e3001988. (doi:10.1371/journal.pbio.3001988)

Plasmids are known to carry important functional genes like those encoding antibiotic resistance enzymes, but plasmids can also be a lot more subtle. Here we explore a family of plasmid translational regulators that mimic members of a highly conserved chromosomally-encoded regulation cascade, and show that, besides providing useful tools, plasmids can manipulate bacterial behaviour and lifestyle in complex ways.

Editors: Hall JPJ, Harrison E, Baltrus D (2022). Philosophical Transactions of the Royal Society B Theme Issue. Volume 377, Issue 1842, 17 January 2022

Mobile genetic elements (MGEs), such as plasmids, transposons, and bacteriophages can have distinct fitness ‘interests’ and evolutionary trajectories as semi-autonomous entities living in symbiosis with microbes. In this theme issue, we take an ‘MGE-eye view’ of microbiology, reflecting the increasing appreciation of the ubiquity, impact, versatility, and diversity of MGEs. Read our introduction to the issue here.

Hall JPJ, Wright RCT, Harrison E., Muddiman K, Wood AJ, Paterson S, & Brockhurst MA (2021). PLoS Biology. doi:10.1371/journal.pbio.3001225

Plasmids impose fitness costs, but what actually causes these costs is obscure. Here, we show that the disruptions caused by acquiring megaplasmids can be resolved by single mutations, indicating that the principal source of plasmid costs is specific gene-gene conflicts, rather than generic properties such as size. Our findings imply that evolution can readily resolve the costs of plasmid carriage, enabling plasmid maintenance in genomes.

Hall JPJ, Harrison E, Pärnänen K, Virta M, Brockhurst MA (2020). Frontiers in Microbiology, 11, 1846. doi: 10.3389/fmicb.2020.01846.

Mobile genetic elements can spread adaptive traits between species. We established species-rich soil microbial communities to understand how selection for mobile genetic elements affects microbial community structure. We show how mercury pollution affects community structure, and, by selecting for acquired mobile genetic elements, enables a focal strain to persist in the face of competitors.

Cazares A, Moore MP, Hall JPJ, Wright LL, Grimes M, Emond-Rhéault J-G, et al. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas (2020). Nat Commun; 11: 1370. doi: 10.1038/s41467-020-15081-7

Drug resistance in Pseudomonas aeruginosa has often been associated with chromosomal determinants. Here we reveal a diverse family of resistance megaplasmids present in 1-2% of Pseudomonas Genbank submissions, and show a high stability of these plasmids with a high rate of conjugation and low fitness costs.

Hall JPJ, Wright RCT, Guymer D, Harrison E, & Brockhurst MA (2019). Microbiology. doi: 10.1099/mic.0.000862.

Plasmids cause fitness costs. These fitness costs can be resolved by compensatory evolution, but it wasn’t clear whether this could occur quickly enough to save plasmids. A fortuitous observation inspired this study, which shows mutations ameliorating a very costly plasmid occurring during the process of colony growth. Compensatory evolution is therefore rapid and potent, and we suggest it may often occur during the process of isolating and selecting individual plasmid-containing clones. Read an interview I did for the ‘Editor’s Choice’ section here.

Hall JPJ, Wood AJ, Harrison E, Brockhurst MA (2016). Proceedings of the National Academy of Sciences, 113(29), 8260–8265, doi:10.1073/pnas.1600974113

Most experimental studies of plasmid dynamics involve single species in broth culture — far cry from the natural environment of most bacteria. Here, we tested how co-culture affected plasmid dynamics in soil microcosms over 450 bacterial generations, and used mathematical models to unpick the findings. We identified a pattern whereby the presence of a plasmid-favourable species maintains community-wide access to plasmids, implying that such plasmid ‘sources’ play a keystone role in facilitating horizontal gene transfer in bacterial communities.