Sex and Death: testing the evolutionary benefit of recombination using a bacterium and bacteriophage model

Lead Research Organisation: University of Exeter
Department Name: Peninsula Medical School

Abstract

General Summary


Background

Although bacteria reproduce through binary fission, they are not purely clonal. On occasion, they are capable of taking up DNA from the environment derived from other bacterial cells and recombine it with their own genetic material. This process is termed transformation. Just as in plant and animal sex, this shuffling of DNA increases the genetic variation in the population. The process of natural selection needs such genetic variation in the population to be able to select the fittest individuals. Populations of organisms that engage in sex (or more generally recombination) could thus be assumed to adapt more quickly to their environment. However, recombination is only favoured when the environment is ever-changing. If not, recombination would eventually disassemble the fittest combinations of DNA it had created. The strongest candidate for both strong and continuously fluctuating selection is that of parasite attack. Parasites and hosts are locked in a continuing arms race: hosts develop resistance against their parasites, and parasites evolve to overcome this resistance and so on and so forth. This scenario is named 'the Red Queen Hypothesis' after Lewis Carroll's book Through the Looking-Glass, where the Red Queen tells Alice: 'It takes all the running you can do, to keep in the same place'.

Aim

The Red Queen Hypothesis is especially likely to be applicable to bacteria for two reasons. First, bacteria are frequently attacked by deadly viruses (bacteriophages), exerting very strong selection for novel resistance. Second, bacterial recombination is 'cheaper' than that of many plants and animals. For instance, bacteria do not rely on sex for reproduction and could resort to it only when needed. Although a lot of theory has been developed, experimental tests of the Red Queen Hypothesis are rare. Here, we propose to experimentally coevolve the aquatic bacterium Aeromonas, known to frequently recombine, with phage. The quality of free DNA available for transformation will be experimentally manipulated. This will allow us to for the first time quantify whether 'bacterial sex' can aid adaptation to parasitic viruses. Transformation results in the reshuffling of all polymorphisms in the population, not only those associated with resistance to phage. We therefore will also include a temperature treatment where high, stressful temperature requires additional adaptation with an expected greater potential benefit of recombination.

Applications and Benefits

Bacteria and phage are an ideal model system to test the Red Queen Hypothesis, but are also of great importance to human health and the economy. Various Aeromonas species are opportunistic pathogens causing a wide range of infections. Aeromonas is a pathogen on the rise and has been found to be the most common cause of soft tissue and skin infections in a study on survivors of the 2004 tsunami in Asia. Bacteriophages are important agents of bacterial mortality. With increasing levels of bacterial resistance to antibiotics, phage therapy has received renewed interest as an alternative strategy to prevent and fight infection by using phages as 'evolving antibiotics'. Importantly, this project will test whether coevolution with phage selects for increased transformation. Phage therapy designed to limit the negative impact of pathogenic bacteria thus could actually result in the increased capability of bacteria to evolve virulence or antibiotic resistance through transformation. Finding any increased benefit of recombination at higher temperature could have important implications for evolutionary change in response to climate change. This will be the first study explicitly linking phage coevolution and transformation, two main evolutionary forces in microbiology, and is bound to yield exciting new insights with special relevance to fighting an opportunistic pathogen.

Planned Impact

Impact Summary

Parasites are ubiquitous in nature and the arms race between hosts and parasites is believed to be a key factor influencing population dynamics, genetic diversity, and the evolution of virulence. Bacteria suffer from infection by parasitic viruses ('phages') and many bacteria are able to take up free DNA from the environment to recombine it into their genome in a process termed transformation. Transformation has the potential to increase genetic variation, facilitating natural selection. This includes adaptation to coevolving phage, but also to the abiotic and human environment.

The results stemming from the proposed project will be of immediate interests to scientists but will also be of great interest to clinicians, the aquaculture sector and policy makers. Our model system Aeromonas is common in aquaculture as a pathogen of fish but it is also an emergent opportunistic pathogen in humans. With increasing levels of bacterial resistance to antibiotics, phage therapy has received renewed interest as an alternative strategy to prevent and fight infection by using phages as 'evolving antibiotics'. Phage therapy designed to limit the negative impact of pathogenic bacteria thus could actually result in the increased capability of bacteria to evolve virulence or antibiotic resistance through this recombination process. This will have great consequences to management practices.

A collection of Aeromonas strains will be screened for their ability to recombine foreign DNA through the process of transformation. By isolating strains from sewage as well as from unpolluted waters, this will allow us to perform a first test of whether human pollution can select for high transformation rate, which is of direct relevance to waste water management and human health. Our experiment will take into account temperature, where high, stressful temperature requires additional adaptation with an expected greater potential benefit of recombination. Finding a increased benefit of recombination at higher temperature could have important implications for evolutionary change in response to climate change and could thus inform environmental policies.

The proposed project will be carried out at the European Centre for Environment and Human Health (ECEHH) which is has a mission to work with businesses to support the development of a knowledge economy in Cornwall. Contact has already been established with Aquatic Water Services (AWS) Ltd. AWS provides consultancy and scientific contracting services to both the Water and Shellfish sectors, important sectors of the Cornish Economy. This contact will be able to open doors to businesses where Aeromonas can be problematic. Planned collaborations with NHS clinical microbiologists at the Royal Cornwall Hospital in Truro allow for the isolation of Aeromonas from human samples to extend our research more directly into the field of human pathology.

Finally, our results can serve to highlight the fundamental process of evolution to the general public due to various outreach activities (see also Pathways to Impact document).
 
Description We investigated the possible benefits of the uptake and recombination of DNA by bacteria from con-specifics, specifically whether resulting increases in genetic variation speed up adaptation to parasites. We find no such effect, but our results point at other benefits associated with transformation. The research has resulted in a manuscript published in Scientific Reports: " No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system." by Amy McLeman, Pawel Sierocinski, Elze Hesse, Angus Buckling, Gabriel Perron, Nils Hülter, Pål Jarle Johnsen and Michiel Vos*. A poster with the same title was presented at SGM in Birmingham 2015.

A second paper on the general topic of bacterial recombination was written in the same period and NERC funding is acknowledged: "A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus" by Sébastien Wielgoss, Xavier Didelot, Roy R. Chaudhuri, Xuan Liu, Gareth D. Weedall, Gregory J. Velicer and Michiel Vos*. In this paper, we report a complete barrier to homologous recombination between two very closely related bacterial genotypes that inhabit the same centimetere-scale patch of soil.
Exploitation Route 1) Change in model system (to Acinetobacter) stimulated further research collaboration and acquiring a 50K NERC pump priming grant.

2) planned BBSRC grant proposal on recombination in this model system. This grant was not funded.

3) The Myxococcus paper has lead to a Leverhulme grant (rejected) and a submitted open round NERC grant

4) This work on recombination indirectly also led to other collaborations on the topic. I published a paper Rates of Lateral Gene Transfer in Prokaryotes: High but Why? with Adam Eyre-Walker and others in Trends in Microbiology (2015). This paper had led to increased discussion with several collaborators with the aim to write new grant proposals.
Sectors Agriculture, Food and Drink,Environment,Healthcare

 
Description The effect of recombination on incipient speciation in bacteria
Amount £50,000 (GBP)
Funding ID NE/L013177/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2014 
End 05/2015
 
Description Acinetobacter transformation 
Organisation University of Tromso
Department Department of Geosciences
Country Norway 
Sector Academic/University 
PI Contribution Pal Jarle Johnsen and Nils Huelter were co-authors on the paper resulting from this grant. I visited with technician and first author Amy Mcleman for a seminar and to discuss this and other projects.
Collaborator Contribution Intellectual input and provision of an engineered strain.
Impact McLeman, Amy, Pawel Sierocinski, Elze Hesse, Angus Buckling, Gabriel Perron, Nils Hülter, Pål Jarle Johnsen, and Michiel Vos. "No effect of natural transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system." Scientific reports 6 (2016): 37144. Although the project is dormant, it could be revived depending on interests of MSc/MbyREs and UGR students in my lab
Start Year 2013
 
Description Invisible You. The Human Microbiome Exposition 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Attending two-day workshop to help develop an educational, interactive project at the Eden Project in Cornwall. A team of (international) scientists, artists and science communicators will develop an exhibit communicating the crucial links between the human body and our microbial inhabitants. (the estimate of people this activity has reached refers to the planned exhibition rather than the attended workshop). Featured in the booklet accompanying the exhibition. In contact with Eden to obtain further Wellcome funding.

Wellcome trust funded (£200.000) project communicating the importance of microbiology in and on our body to our health. I will attend a workshop with other scientists, artists and educators to develop plans and will be involved as a scientific advisor. (I have been involved in discussions on the "Invisible World Eden Project" supported by the University of Exeter to put in a bid to produce a Wellcome Trust Science Learning+ event "The Invisible Biome". Depending on the outcom
Year(s) Of Engagement Activity 2014,2015,2016
URL https://www.edenproject.com/visit/whats-here/invisible-you-the-human-microbiome-exhibition
 
Description coastal pathogens blog 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact my blog coastalpathogens.wordpress.com explains the content of my published papers in an accessible way and features short discussions pertinent to science careers (eg funding)

I get some feedback on the cite, and see that especially topics such as what citation metrics are best continue to get many hits. I have been approached by persons wanting to join the lab based on the blog as well.
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
URL http://coastalpathogens.wordpress.com/
 
Description outreach video 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact video produced by the ECEHH having named postdoc Pawel Sierocinski explaining the project
Year(s) Of Engagement Activity 2013
URL http://www.ecehh.org/research-projects/bacteria-and-viral-resistance/
 
Description student project Camborne Science and International Academy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I supervised a project of five students at the local Camborne Science and International Academy. The students came in the lab 7x two afternoons every fortnight. The project involves the isolation of bacteriophages about which they will make a school presentation (and possibly a presentation for an international science fair).

The Camborne Science and International Academy visit every fortnight with a group of five students (and a teacher); they are supervised to carry out a research project related to the current grant (bacteriophages and transformation). More importantly perh
Year(s) Of Engagement Activity 2014
URL https://coastalpathogens.wordpress.com/2014/07/18/camborne-science-and-international-academy-student...