Research

 
 

microbial evolution

Microbes are ubiquitous, diverse, versatile, and can evolve quickly in response to changes in their environments. For many challenges we face — from antimicrobial resistance, to plant health and productivity, to greenhouse gas emissions — microbes are both part of the problem and part of the solution. My group researches how and why microbes evolve. We are particularly interested in a remarkable and powerful mode of microbial evolution: horizontal gene transfer. 

 
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Horizontal gene transfer

Horizontal gene transfer is when individuals acquire genes from sources other than their parents, such as from neighbours or the local environment. Many of the bacterial traits we are interested in (for medical, industrial, environmental reasons and more) are spread between different species and strains of bacteria thanks to horizontal gene transfer. 

 
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ecology & evolution of Mobile genetic elements

In most cases, horizontal gene transfer is enabled by mobile genetic elements — entities which are adapted to moving DNA between cells. Amongst these, conjugative plasmids are thought to be particularly important vehicles of gene exchange. But plasmids are also entities evolving in their own right, and they don't always get along with the bacteria that carry them, resulting in conflicts. Our aims to understand these interactions and their consequences, using experimental evolution, molecular biology, and genomics. 

 

Science communication

I like talking about science. I've produced several science comics. Once I made a giant trypanosome for a Mardi Gras parade. 

The science comic I’m most proud of is Luna & Simon: Bizarre Bacteria and Peculiar Plasmids. Read it here!

Click here to see a full list of my science comics.

African trypanosome antigenic variation

African trypanosomes undergo rapid within-host evolution of their surface coat to escape their hosts' adaptive immune systems. This amazing survival strategy was the subject of my PhD at the University of Glasgow, and I have a long-standing interest in how trypanosomes deploy a diversity phenotype to such great effect.

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Microbial diversity

Microbiology is fascinating because it brings mystery to the mundane. That handful of soil contains a complex ecosystem with a biological richness we are only just beginning to understand. That muddy puddle is full of predators, prey, symbioses, and competition. The microscope revealed that life on earth goes so much deeper than our eyes can see, and now the genomics revolution is revealing how dynamic, resilient, and creative the microscopic world can be.

Anybody can start to explore the microbial world! It doesn’t have to be expensive or complicated. Some ideas:

Papers

My most up-to-date list of papers can be found here, or on my Google Scholar profile. My work is open access, but depending on the journal, this can sometimes be difficult to navigate. Please get in touch if you cannot access any of my papers you would like to read.

Here are some highlights:

Papers Highlights
Plasmids manipulate bacterial behaviour through translational regulatory crosstalk
Plasmids manipulate bacterial behaviour through translational regulatory crosstalk

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.

The Secret Lives of Microbial Mobile Genetic Elements
The Secret Lives of Microbial Mobile Genetic Elements

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.

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

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.

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer
The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer

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.

A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas
A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas

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.

Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways
Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways

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.

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

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.