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  Ecological and evolutionary dynamics of sponge-associated microbial communities


   School of Biological Sciences

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  Prof Cecile Gubry-Rangin, Dr Ted Henry  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Microbial communities are present within many hosts, including sponges, which perform a critical ecosystem service, i.e. filtration of seawater. The diversity of the sponge microbiome is related to the sponge species and to the environment in which the sponges live. One of the key waste products of seawater filtration is ammonia and removal of ammonia is facilitated by microbial ammonia oxidisers such as Thaumarchaeota, as they use ammonia as a substrate for their energy generation.

This project aims to understand the ecological and evolutionary mechanisms controlling for the host and niche specialisation and stability (resilience and resistance) of sponge-associated microbes following environmental perturbations influenced by climate change.

  • As many organisms are under climate thread, the first aim of this PhD will be to perform a comparative analysis of microbial communities under diverse environmental pressures for determining the effect of climate change on sponge-associated microbes. In addition to general microbial diversity, a particular focus will be on Thaumarchaeota (Gubry-Rangin et al., 2011 and 2015), which are potentially important symbionts.
  • Thaumarchaeota contain both free-living and sponge-associated organisms. A second aim of this PhD will be to cultivate sponge-associated Thaumarchaeota, to physiologically characterise these isolates and to compare their genomic content, metabolism and physiology to the collection of free-living Thaumarchaeota available in our laboratory (Lehtovirta-Morley et al., 2016).
  • Finally, a diverse set of free-living representative genomes has been recently assembled and used to infer ancestral evolutionary history of this lineage using metagenomic assemblies, phylogenomic reconstruction and associated bioinformatic evolutionary approaches (Sheridan et al., 2020). Following available (and potential additional) sponge sampling in diverse locations (Indonesia, Spain, UK…), the third aim of this PhD will be to analyse the evolutionary lifestyle transition from free-living to symbiotic state in Thaumarchaeota. The student will then assess which genomic pathways have the exciting potential to enable these microbes to respond to several environmental perturbations linked with climate change.
  • Based on their interest, there will also be some scope for the student to develop their own line of research.

The student will join an active research group focused on microbial ecology and evolution and more information about the group can be found on our website (https://www.gubry-rangin.com/). The student will also benefit from an interdisciplinary network of collaborators with strong expertise in sponges. Such collaboration will offer some great sampling opportunities and fantastic access to collection databases. Among the diverse approaches applicable to answer these key questions of eco-evo dynamics of symbiotic microbial communities, a combination of novel DNA sequencing and metagenome reconstruction and microbial cultivation would be included. The student will be trained in a series of cutting-edge lab- and computer-based approaches to provide exciting novel discoveries that will contribute to understanding the mechanisms underlying microbial ecology and evolution in natural environments.

Our laboratory is located in the North-East of Scotland, close to the sea and the mountains, with numerous opportunities for outdoor activities and wildlife spotting.

Candidate Background:

Candidates should hold, or expect to achieve a minimum of a 2.1 UK Honours degree (or international equivalent) in a biological based subject. Experience in bioinformatics, molecular biology or microbiology is recommended.

Candidates with a 2:2 at undergraduate level may be considered if they hold a Commendation or Distinction at masters level or have significant commensurate experience.

We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

Informal enquiries are encouraged, please contact Cecile Gubry-Rangin ([Email Address Removed]) for further information.

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APPLICATION PROCEDURE:

  • Formal applications can be completed online: https://www.abdn.ac.uk/pgap/login.php
  • You should apply for Biological Sciences (PhD) to ensure your application is passed to the correct team for processing.
  • Please clearly note the project title and lead supervisor in the respective fields on the application form
  • Your application must include: A personal statement, an up-to-date copy of your academic CV, and clear copies of your educational certificates and transcripts.
  • Please provide 2 Academic References
  • Please note: you DO NOT need to provide a research proposal with this application
  • If you require any additional assistance in submitting your application or have any queries about the application process, please don't hesitate to contact us at [[Email Address Removed]]
Biological Sciences (4)

Funding Notes

Funding will cover tuition fees and stipend (currently £18,622 per annum for 2023/2024). Eligibility is not constrained by nationality.

Funding for international students does not cover visa costs (either for yourself or for accompanying family members), immigration health surcharge or any other additional costs associated with relocation to the UK.


References


1. Gubry-Rangin, C., Hai, B., Quince, C., Engel, M., Thomson, B.C., James, P., Schloter, M., Griffiths, R.I., Prosser, J.I., Nicol, G.W., 2011. Niche specialization of terrestrial archaeal ammonia oxidizers. Proceedings of the National Academy of Sciences 108, 21206–21211. doi:10.1073/pnas.1109000108
2. Gubry-Rangin, C., Kratsch, C., Williams, T.A., McHardy, A.C., Embley, T.M., Prosser, J.I., Macqueen, D.J., 2015. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proceedings of the National Academy of Sciences 112, 9370–9375. doi:10.1073/pnas.1419329112
3. Lehtovirta-Morley, L.E., Ross, J., Hink, L., Weber, E.B., Gubry-Rangin, C., Thion, C., Prosser, J.I., Nicol, G.W., 2016. Isolation of “Candidatus Nitrosocosmicus franklandus”, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology 92, fiw057. doi:10.1093/femsec/fiw057
4. Sheridan, P.O., Raguideau, S., Quince, C., Holden, J., Zhang, L., Thames Consortium, Williams, T.A., Gubry-Rangin, C., 2020. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nature Communications 11, 5494. doi:10.1038/s41467-020-19132-x

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