Investigating the nature and implications of archaea-bacteria interactions

OVERVIEW

Due to the relatively recent discovery of the Domain Archaea, they are hugely understudied compared to their bacterial counterparts. Additionally, as microbiome studies have historically focused on the bacterial component, the global importance of bacteria is well-studied and unquestionable, while the role of archaea in many environments remains unclear. 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 importance.

The above studies identified the ability of archaea to directly impact living systems, giving them a new environmental relevance. However, some of our recent work 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 (Megaw et al., 2019), and potential production by archaea of the same signalling molecules that bacteria use to modulate their community behaviour (Megaw and Gilmore, 2017). Other studies have reported failure in isolation of archaea from mixed samples when the bacteria were inhibited. These findings all raise questions about the relationship between archaea and bacteria inhabiting the same environment, concerning the evolution and role of the interactions between these two separate domains of life, and their impact on complex microbial communities.

The overall aim of this project is to characterise some of the positive/negative/neutral interactions that occur between bacteria and archaea inhabiting the same environment, in order to gain a better understanding of the relationship between them. This will involve the use of type strains (and environmental isolates where available). Hypersaline environments (the simplest environment from which to isolate and culture both domains) 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 co-culture 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 and biofilm development, followed by potential identification of active metabolites.

– Transcriptomic analysis to investigate changes in gene expression when key bacterial and archaeal species are grown together vs. separately.

– Screening of archaeal transposon knockouts to identify genes involved in various processes. This will involve molecular biology techniques including PCR and gene sequencing/annotation.

Megaw, J., Kelly, S. A., Thompson, T. P., Skvortsov, T. & Gilmore, B. F. (2019). Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery. FEMS Microbiology Letters https:doi.org/10.1093/femsle/fnz242.

Megaw, J. & Gilmore, B. (2017) Archaeal Persisters: Persister cell formation as a stress response in Haloferax volcanii. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2017.01589.

ENTRANCE REQUIREMENTS

Graduate
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School.

International Students

For information on international qualification equivalents, please check the specific information for your country.

English Language Requirements

Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years).

International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes.

For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs.

If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree.

HOW TO APPLY

Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply.

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