The Molecular Blueprint for Marine Biomineralization in a Changing Climate

Rapid climate change due to anthropogenic CO2 emissions is having a substantial impact on the marine system. This is particularly true for organisms which calcify, as ocean acidification (OA) progressively challenges their ability to produce their calcium carbonate shells. This biogenic production, surface fluxes to depth, and deep-sea burial of calcium carbonate are all key processes in the global marine carbonate cycle (Carbonate Counter Pump) with a combination of the first two providing an important feedback to atmospheric CO2.

The impact and sensitivity to future climate change (ocean warming, acidification and de-oxygenation) varies between calcifying organisms [1] (foraminifera, coccolithophores and pteropods) due to strong organismal (and hence genetic) control of calcification. This means that we urgently need a better understanding of the genetic response to climate change, and the likely shifts in relative contributions of these marine calcifiers to production, export, and burial, if we are to understand how these different groups will impact on atmospheric CO2 in the future.

This project will focus on a key calcifying taxon, foraminifera. Foraminifera calcify across all marine and coastal habitats, from pole to pole. They buffer ocean carbonate chemistry by shell dissolution in the ocean’s interior and can contribute over 40% [2] of the carbonate buried at the seafloor.

Cellular mechanisms of calcification in foraminifera include seawater vacuolization, transmembrane ion transport, carbon-concentrating mechanisms, and nucleation-promoting organic templates. All are key to understanding foraminiferal calcification, and its evolution and adaptability to a changing climate. One of the few foraminiferal species whose calcification mechanisms have been intensively investigated is the intertidal sediment-inhabiting benthic foraminifer Ammonia sp. T6 [3]. This species is also easily accessible, abundant, and culturable in the lab, making it an ideal model system for the first investigation of the regulation of calcification genes in foraminifera.

The genome and transcriptome of Ammonia sp. T6, is currently being sequenced in the laboratory of Dr Clare Bird, and this PhD project aims to identify key calcification genes and their transcriptional control using molecular tools for DNA and protein analyses. This PhD project will be part of a NERC funded project to investigate biomineralization in both planktonic and benthic foraminifera. As a PhD student on this project, you will become part of a multidisciplinary, international team with considerable experience in foraminifera calcification and ecology, and the mechanisms regulating the ocean’s Carbonate Counter Pump.

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Image Captions

A scanning electron microscope image of the calcium carbonate shell of the benthic foraminifera Ammonia sp. T6


The benthic foraminifera Ammonia sp. T6 can be collected from mudflats on the Forth Estuary, not far from Stirling, and maintained in culture for environmental manipulation experiments at Stirling.

Sequencing, building and analysis of the Ammonia T6 genome is ongoing as part of the wider NERC research project. The sequence information will be interrogated for genes coding for proteins involved in biomineralization such as the ATPase pump, carbonic anhydrase, and bicarbonate pumps, and organic membrane proteins. This will be alongside protein investigations by other members of the team.

You will use molecular biology methods such as PCR, qPCR, RT-qPCR and RNA-seq to amplify genes of interest, analyse gene expression cycles, investigate the transcriptome, and responses to different environmental conditions under experimental laboratory conditions.

Project Timeline

Year 1

This 3.5 year studentship will begin with 6 months for project planning, and literature review, and sourcing bioinformatics training. This will be followed by training in the range of molecular tools to be utilised. Training will also be given in the collection of and picking and processing of live benthic foraminifera. During the first year, genes pertinent to biomineralization will be identified, and initial PCRs tested to develop protocols for investigation of gene expression.

Year 2

Patterns of transcription in organic matrix proteins and other key genes will be explored throughout the life cycle. Manuscript write up and paper submission presenting some key calcification genes and their expression patterns under normal conditions.

Year 3

The project will go on to address changes in gene expression in response to different environmental conditions such as pH shifts and temperature changes. These experiments will be run in the controlled environment facilities in BES and will be followed by manuscript write up and paper submission.

Year 3.5

Final thesis write up and submission.

& Skills

This PhD will principally be held in the vibrant and multidisciplinary research environment at the University of Stirling. The PhD student will be part of the multidisciplinary international research team on the “Blumin” NERC funded project. The PhD student also will become part of the “Environmental Biogeochemisty” research group, made up of various academics and their groups across the department and will be able to attend regular lab group meetings, along with the weekly seminar series giving informal and formal opportunities for research presentation. The student will also participate in the yearly Postgraduate Conference attended by the entire department.
The PhD student will receive training in subject specific and generic skills. Specific skills will include foraminiferal sampling, culture manipulations and microscopy, molecular techniques for DNA, RNA and protein work and bioinformatics. The PhD student will also be encouraged to take on additional bioinformatics training courses as required. More generic skills will include the Stirling R course and IAPETUS2 training available through the IAPETUS2 DTP. The student will also be expected to participate in training opportunities in a range of research and transferable skills offered at Stirling University, for example scientific communication skills (written and verbal) for successful manuscript writing and presentation at conferences.

References & further reading

1Keul et al., 2013. Effect of ocean acidification on the benthic foraminifera Ammonia sp. is caused by a decrease in carbonate ion concentration. Biogeosciences. doi:10.5194/bg-10-6185-2013
2Schiebel (2002) Planktic foraminiferal sedimentation and the marine calcite budget. Global Biogeochemical Cycles, 16, doi: 10.1029/2001GB001459
3Toyofuku et al. 2018. Proton pumping accompanies calcification in foraminifera. Nature Comms. doi: 10.1038/ncomms1414
Ujiié, Y., Ishitani, Y., Nagai, Y., Takaki, Y., Toyofuku, T., and Ishii, S. (2023) Unique evolution of foraminiferal calcification to survive global changes, Sci. Adv., 9, eadd3584, https://doi.org/10.1126/sciadv.add3584.

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