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Hot, acidified and breathless – biomineralisation of deep sea corals in the oceans of the future

   Ocean and Earth Science

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  Prof Gavin Foster, Prof Sumeet Mahajan, Dr C D’Angelo  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Project Rationale

The skeletons of deep sea stony corals form the foundations for large reefs 100’s to 1000’s of meters below the ocean surface that provide a key habitat for marine life. This deep habitat has insulated them from the threats of anthropogenic climate change to some extent, but the warmth and acidification that is impacting tropical coral reefs is now reaching down into the abyss. Like all stony corals, many reef-forming deep-sea corals make their skeletons from calcium carbonate ultimately derived from seawater. To control and promote calcification, biomineralisation occurs in a micron-sized “privileged space” sandwiched between the animal tissue and existing skeleton (Gilbert et al., 2022). The exact biomineralisation toolkit the coral uses however remains uncertain, with two schools of thought emerging, being either: (i) physiochemically controlled or (ii) biologically induced (Gilbert et al. 2022). The processes that occur in this space are very difficult to observe directly but do leave a mark on the chemical composition of the skeleton that forms (Chalk et al., 2021) and in the proteins expressed by the coral (Drake et al., 2018). In this project we will use a range of techniques from genes to geochemistry to provide a mechanistic understanding of how future ocean warming, ocean acidification and ocean deoxygenation will impact skeletal formation of the keystone deep-sea coral species Lophelia pertusa.  


Lophelia pertusa will be grown at the St. Abbs Marine Station as part of related research (https://marinestation.co.uk/) at various future-relevant temperature, pH and O2 levels. Coral physiological response (e.g. calcification rate) will be examined and the skeletons and tissue sampled for geochemical and genetic analysis as part of this project. This will consist of: (i) differential expression of genes encoding for the proteins involved in calcification (e.g. coral acidic rich proteins; Drake et al., 2018) to explore how the biomineralisation toolkit of L. pertusa is impacted by changing environmental conditions; (ii) the coral skeleton will be scanned using computerised tomography (CT) at the m-VIS X-Ray Imaging Centre at the University of Southampton (www.muvis.org) to examine how the changing environment impacts coral macro- and micro-structure; (iii) the skeleton will be sectioned and subjected to geochemical analysis using boron-based tracers to reconstruct the pH and carbonate system in the privileged calcifying space as a function of seawater pH, temperature and O2 (Chalk et al., 2021; Gilbert et al. 2022). By using the latest laser ablation 2D imaging approaches this geochemistry will be correlated with CT and optical images and the distribution and composition of organic molecules determined using Raman imaging. This will provide a unique mechanistic view of the biomineralisation toolkit and provide valuable information about how future ocean conditions will influence deep-sea coral reefs.


The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at the School of Ocean and Earth Science, National Oceanography Centre Southampton. Specific training will include:

·        RNA extraction, processing and sequencing and the necessary statistical tools required to carry out the analysis of these data.

·        Micro-CT imaging and thin section analysis of coral skeletons.

·        Boron isotopic measurements of coral skeletons by laser ablation multi-collector inductively coupled plasma mass spectrometry

·        Trace element concentration measurements of coral skeletons by laser ablation quadrapole inductively coupled plasma mass spectrometry (ICPMS) and Time of Flight ICPMS

·        Imaging of coral skeletal organics by Coherent anti-Stokes Raman spectroscopy (CARS).

·        Correlative imaging techniques to combine these imaging modalities. 

·        Coral taxonomy and sample preparation techniques.

This mix of cutting edge imaging, genetic and geochemical training will uniquely equip the student to carry out work across a range of areas of environmental science and beyond. Opportunities exist to take part in the coral culturing work that is being done at St. Abbs, go to sea to collect live Lophelia pertusa to put the experimental work in context, and attend international meetings and conferences.  

Funding Notes

Please see https://inspire-dtp.ac.uk/how-apply for details.
To be considered for this project you MUST submit a formal online application form - full details on how to apply can be found here https://inspire-dtp.ac.uk/how-apply


Chalk, T. B., C. D. Standish, C. D’Angelo, K. D. Castillo, J. A. Milton and G. L. Foster (2021). Mapping coral calcification strategies from in situ boron isotope and trace element measurements of the tropical coral Siderastrea siderea. Scientific Reports 11(1): 472.
Drake, J. L., M. F. Schaller, T. Mass, L. Godfrey, A. Fu, R. M. Sherrell, Y. Rosenthal and P. G. Falkowski (2018). Molecular and geochemical perspectives on the influence of CO2 on calcification in coral cell cultures. Limnology and Oceanography 63(1): 107-121.
Gilbert, P., K. D. Bergmann, N. Boekelheide, S. Tambutté, T. Mass, F. Marin, J. F. Adkins, J. Erez, B. Gilbert, V. Knutson, M. Cantine, J. O. Hernández and A. H. Knoll (2022). Biomineralization: Integrating mechanism and evolutionary history. Sci Adv 8(10): eabl9653

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