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Investigating the nature and implications of archaea-bacteria interactions


   School of Biological Sciences

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  Dr Julianne Megaw  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

Studies of the Domain Archaea have historically been considered a small, niche sub-field of microbiology, due to their largely extremophilic nature and consequent restriction to a few key environments. However, recent studies have increasingly shown that archaea are in fact ubiquitous, coexisting and interacting with other microbial species in almost all environments. The precise nature of these interdomain interactions are unclear, and this project aims to gain a better understanding of the nature and implications of such interactions in order to further our understanding of the environmental roles played by this poorly studied domain.

Due to the relatively recent discovery of the Domain Archaea and the extremophilic nature of many of its members, they are hugely understudied compared to their bacterial counterparts. Only within the past few years has it been shown that archaea are present in virtually all environments, and are active participants or major drivers within complex microbial communities in non-extreme terrestrial environments, the ocean, the human body, and in soil, where they carry out vital but poorly understood roles. These findings highlight both the hidden potential of archaea, and the extent of our knowledge gaps regarding their environmental relevance. However, some recent research has shown that archaea may also have an impact in another way: they appear to interact with, and influence the behaviour and function of bacteria. We have shown antibacterial activity of haloarchaea isolated from a local salt mine, and potential production by archaea of the same signalling molecules that bacteria use to modulate their own phenotypes. Other studies have reported failure to isolate archaea from mixed samples when bacteria were inhibited. These findings all raise questions about the relationship between these domains, concerning the evolution and role of their interactions.

The overall aim of this project is to gain a clearer understanding of the relationship between key archaeal and bacterial species by characterising some of the positive/negative/neutral interactions that occur. This will involve the use of type strains (and environmental isolates where available). Hypersaline environments will be used as a model system, but others can also be included. The project will involve the techniques below, in which the student will receive training:

- Development and use of coculture or simulated coculture models to investigate population dynamics of bacterial and archaeal species when grown together short and long-term, and subsequent investigation of the cause of any growth-promoting or -inhibitory activities or other observable changes. This will also involve assessment of the antimicrobial susceptibility of archaea and bacteria, and other standard culturing techniques.

- Investigation of the effects of archaeal metabolic products on bacterial phenotypes (and vice versa), such as growth, survival, and biofilm development, followed by potential identification of active metabolites.

- Various ‘omic analyses to investigate changes in gene/protein expression when key bacterial and archaeal species are grown together vs. separately.

- Screening of archaeal transposon knockouts to identify genes involved key phenotypes. This will involve molecular biology techniques including PCR and gene sequencing/annotation.

Start Date: 1 October 2022

Duration: 3 years

How to apply: All applications must be submitted via: https://dap.qub.ac.uk/portal/user/u_login.php

Skills/experience required: Applications from candidates with prior knowledge or experience of microbial culture techniques, especially of extremophiles, is particularly welcomed.

Note: This project is in competition for DfE funding with a number of other projects. A selection process will determine the strongest candidates across the range of projects, who may then be offered funding for their chosen project.


Funding Notes

Candidates must hold a UK 2.1 Bachelor's degree or qualifications considered to be equivalent by the University.
Candidates must also be normally resident in the UK for the three year period prior to 1 October 2022. For non-EU nationals, the main purpose of residence must not have been to receive full-time education. Non-UK or Irish nationals must also have pre-settled or settled status (EU nationals) or settled status (non-EU nationals).
Full eligibility criteria: https://www.economy-ni.gov.uk/sites/default/files/publications/economy/Postgraduate-studentships-terms-and-conditions.pdf
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