Adaptation of bacteriophage to variable environments

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Ayansola, O.T., 2020. Adaptation of bacteriophage to variable environments. PhD, Nottingham Trent University.

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Abstract

Because a virus is an obligate cellular parasite, the host is a key part of its environment. Viruses may expand their ecological niche by switching host. Successful host switching can be influenced by ecological and evolutionary factors, genetic constraints and fitness within new hosts. An outcome of host switching is reduced fitness exhibited by viruses, a phenomenon observed in the evolution of viral disease emergence and resistance. To understand the genetic basis of this cost, investigations are required at the genotypic and phenotypic level.

A host switching paradigm was developed using the model bacteriophage φX174 which was propagated with its laboratory bacterial host Escherichia coli C and with the novel host Salmonella enterica serovar Typhimurium, LT2 strain IJ750 or Escherichia coli K-12 mutant strain JWO196-2 designated as E. coli K-12gmhB-mut. A chemostat was used to achieve steady-state conditions for propagation of φX174 and bacterial cells. Two experiments were performed using this approach. In the first, φX174 was cultured on E. coli K-12gmhB-mut for 3 days (~206 generations). In the second experiment, φX174 was cultured on E. coli C and S. Typhimurium for four consecutive periods of 10 days (~720 generations), alternating between the two hosts.

For the second chemostat experiment, the fitness and attachment rates of each viral population were measured using qPCR in liquid culture in order to identify and characterise fitness costs associated with host-switching. Deep sequencing of chemostat samples was also carried out to identify allelic changes occurring before and after host switches. Viral samples were chosen to capture substitutions associated with each host across the experiment (which might explain observed changes in fitness) and time series were picked to identify the dynamics of adaptation on a new host. Bacterial host strains were not sampled in this study.

The phenotype measures indicated the pleiotropic costs of host switching, that is a reduction in phage fitness was observed when this was tested on the host used prior to switching, and this may be explained by changes in the attachment rate. The genotype data revealed sets of changes that could be identified as signatures of adaptation to each host, although control data indicate that these may arise during DNA preparation, implicating synthesis of replicative form DNA in the host as a source of selective constraint. Some host-specific alleles and some shared alleles were identified and their fitness effects were examined in isolation after reconstruction of these alleles in the ancestor via targeted mutagenesis. The fitness effects observed for reconstructed mutants were in the direction expected although they do not fully account for the observed costs of host switching.

By analysing different phenotypes and genotypes produced during evolution, a detailed view of φX174’s adaptation to different hosts was obtained. The results support the idea that costs associated with pathogen-host adaptation may be host-specific, associated with specific mutations, acquired early and persist. Examining these is relevant for understanding emerging infectious diseases.

Item Type:	Thesis
Creators:	Ayansola, O.T.
Date:	January 2020
Rights:	I hereby declare that the work presented in this thesis is the result of original research carried out by the author, unless otherwise stated. No material contained herein has been submitted for any other degree, or at any other institution. This work is the intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights.
Divisions:	Schools > School of Science and Technology
Record created by:	Linda Sullivan
Date Added:	05 May 2020 14:47
Last Modified:	05 May 2020 14:47
URI:	https://irep.ntu.ac.uk/id/eprint/39790