SUPER DTP: The impact of environmental change on the ecological and evolutionary dynamics of symbiotic sponge communities - PhD via FindAPhD

Aberdeen University

Aberdeen, UK 🇬🇧

About the Project

Sponges are widespread heterotrophic animals in marine environments, and they perform a critical ecosystem service, i.e. filtration of seawater. Microbial communities are present within these marine animals, and the diversity of the sponge microbiome is related to the sponge species and also 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. The relationship between sponges and their microbial symbiotic communities, including Thaumarchaeota, has been understudied. This has prevented an understanding of the factors controlling the symbiotic specificity and system stability following environmental change. However, this symbiosis is under threat as climate change has important environmental consequences for marine organisms.

Therefore, this project aims to understand the ecological mechanisms controlling for the stability (resilience and resistance) of sponge-microbe symbiosis following environmental perturbations influenced by climate change. Factors such as temperature change, water acidification and increased pollutant amendments are classical threads and several environmental perturbation experiments will be performed to understand the effect of thermal stress, toxicant exposure, substrate fluctuation or alterations of water chemistry on the sponge microbiome, and subsequently on the sponge physiology using a state-of the-art aquarium controlled mesocosm facility. The final choice of the environmental perturbation factor(s) will depend on the student interest and will be based upon literature review. The stability (resistance and resilience) of the system to these different environmental perturbations will help predict the adaptation of this symbiosis to climate change. In addition to time-series microbial community analysis (performed using 16S rRNA amplicon sequencing), metagenomics and metatranscriptomics analyses will be performed to evaluate the role of specific genes implicated in stress response, gene repair and mutation systems on the system stability.

Thaumarchaeota are one of the only archaeal phyla containing both free-living and symbiotic organisms, so this sponge-archaea model will enable analysis of the evolutionary lifestyle transition from free-living to symbiotic state in archaea. 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 sponge sampling in diverse locations (Indonesia, Spain, UK…), this project will focus on symbiotic Thaumarchaeota to reconstruct their potential metabolic capabilities and infer the rates of gene acquisition, gene duplication, gene loss and lateral gene transfer along their evolution. The student will also assess which genomic pathways have the exciting potential to enable Thaumarchaeota to respond to several environmental perturbations linked with climate change.

The student will benefit from an active interdisciplinary collaborative network and 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.

It may be possible to undertake this project part-time, in discussion with the lead supervisor.

Informal enquiries would be welcomed for a discussion. Please contact Dr Cecile Gubry-Rangin ([email protected]) for more information.

Academic Eligibility:

Applicants to the SUPER DTP are expected to have a minimum of a 2:1 UK honours degree (or equivalent). Applicants with a 2:2 at honours level will be considered on the condition they have a distinction at Masters level (or equivalent).

Application Procedure:

  • This studentship is offered to Home/UK candidates only (this includes EU nationals that hold UK settled or pre-settled status).
  • Previous applicants need not apply.
  • Please visit this page for full instructions on how to submit your application
  • Please DO NOT apply through the University application portal

Application enquiries should be made to [email protected] . Please ensure you enter SUPER DTP in the subject box.

Funding Notes

This is a 42 month full time (or 84 months part time), directly funded project as part of the SUPER DTP which provides:
*A Stipend based on RCUK rates
*UK Level Tuition Fees
*Research and Training Costs
*Funding for this project will cover home/UK fees (this includes EU nationals that hold UK settled or pre-settled status).


• Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Thames Consortium, Williams TA, Gubry-Rangin C. (2020) Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Com 11(1):5494.
• Zhao J, Meng Y, Drewer J, Skiba UM, Prosser JI, Gubry-Rangin C. (2020) Differential ecosystem function stability of ammonia oxidising archaea and bacteria upon short-term environmental perturbation. MSystems 5(3):e00309-20.
• Vad J, Lui F, Dunnett, Montagner CC, Roberts JM, Henry TB. 2020. Soaking up the oil: biological impacts of dispersants and crude oil on the sponge Halichondria panicea. Chemosphere 257:127109
• Artal MC, Pereira KD, Luchessi AD, Okura VK, Henry TB, Marques-Souza H, Umbuzeiro GA. 2020. Transcriptome analysis in Parhyale hawaiensis reveal sex-specific responses to AgNP and AgCl exposure. Environmental Pollution 260:113963.
• Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. (2015) Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci USA 112(30):9370-5. (IF: 9.81)
• Gubry-Rangin C, Hai B, Quince C, Engel M, Thompson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW. (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA 108(52):21206-21211.