The evolutionary ecology of bacteria-phage interactions

Lead Research Organisation: University of Exeter
Department Name: Biosciences

Abstract

Bacteria in the rhizosphere can benefit agriculture by making nutrients available to plants. However, their beneficial effect is thought to be limited by viruses (phage) in soil. CRISPR-Cas adaptive immune systems of bacteria provide phage resistance but it is frequently very difficult to have bacteria evolve this type of phage resistance, and when it evolves, phage can readily escape CRISPR-Cas by point mutation. Recent studies suggest phage resistance may be improved when the adaptive immune system is integrated with an innate immune system, known as restriction-modification (RM). However, synergism between CRISPR and RM has not been clearly demonstrated yet, and because RM systems are highly diverse, it is also unclear whether such synergism would apply to all or only some RM systems. The key aim of this project is therefore to investigate the existence of synergy between different types of RM and CRISPR-Cas, and examine how this synergistic interaction affects bacteria-phage co-evolution. We already have a bacterial host that evolves high levels of CRISPR immunity in response to some, but not all phages. We will use this experimental system to first examine if levels of evolved CRISPR immunity increase when bacteria are equipped with different types of RM systems, to reveal putative synergistic RM-CRISPR interactions. We will then compare the genetic changes that accompany the evolution of CRISPR immunity in the presence and absence of RM, in order to reconstruct the mechanistic basis underlying the synergistic RM-CRISPR interactions. This will be complemented with in vitro biochemical studies that examine how purified RM components digest DNA molecules. Finally, we will investigate how an integrated RM-CRISPR immune response impacts bacteria-phage co-evolution, specifically the ability of phage to overcome immunity, compared to bacteria carrying a single immune mechanism and examine trade-offs associated with encoding multiple immune mechanisms.

The student will receive training in experimental evolution, biochemistry, molecular microbiology and genetics. This interdisciplinary project integrates expertise on CRISPR-Cas (Westra, Exeter), RM (Sczcelkun, Bristol) and bacteria-phage co-evolution (Buckling, Exeter).

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M009122/1 01/10/2015 30/09/2023
1771625 Studentship BB/M009122/1 01/10/2016 30/09/2020 Jack Common
 
Description Featured on the alumni section of the University of Oxford Department of Zoology website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact The Department of Zoology outreach team asked for recently-graduated alumni to answer a few questions about their experience of Biology at Oxford, as well as their current activities. I used this opportunity to share my experience of going to Oxford from a state-school, first-generation background, and the importance of and enthusiasm for my research. This is featured on their website, which is used as part of their outreach to applicants and current undergraduates thinking about their next steps.
Year(s) Of Engagement Activity 2018
URL https://biology.web.ox.ac.uk/people/jack-common
 
Description Speaking to GCSE & 6th form students about higher education and research 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I have given several presentations to GCSE and A-level students from schools in the Falmouth area and Cornwall more generally. I spoke about my career path from state school, through undergraduate study, and onto postgraduate level. I also talk about my research in a way that is accessible to people of this educational level, as well as answering questions and speaking to small groups of students about science, research, and university applications, to name a few.
Year(s) Of Engagement Activity 2017,2018
 
Description Spoke at a "Keg of Knowledge" event at local pub 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Gave a short presentation on my research to members of the public at Beerwolf Books, a pub in Falmouth, followed by questions and informal discussion
Year(s) Of Engagement Activity 2019
URL https://www.facebook.com/events/2503912082971873/
 
Description Spoke to first-year undergraduate students about my research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Delivered a short research seminar about my research, linking it with the course material covered by the 1st year curriculum
Year(s) Of Engagement Activity 2019