Blueprints of calcification: genome investigation of foraminifera, critical marine calcifiers.

Overview

Contribute to our understanding of the ocean’s feedback mechanisms on atmospheric CO2 through application of molecular tools to investigate the genetic control of calcification in marine organisms.

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 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 organisms1 (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 marine calcifiers to production, export, and burial, if we are to understand how these different groups will feed back 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 at depth 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. T63. This species is also easily accessible, abundant, and cultured in the lab, making it an ideal model system for the first investigation of the 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 will involve analysis of this genetic information and aims to identify key calcification genes and their transcriptional control using molecular tools for DNA and protein analyses.

The direction of this project is flexible, but it is anticipated that the genetic information gained in the benthic species can be applied to investigate calcification in planktonic foraminifera, with the opportunity to gain experience in marine sampling off the coast of Chile, or Oregon, USA.

Methodology

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.

Building and analysis of the Ammonia T6 genome will be undertaken using bioinformatics tools such as wtdbg2 with minimap2 & racon. Genes will be annotated using motifs such as Interpro database and sequence alignments such as UniGene database. The sequence information will be interrogated for the ATPase pump, carbonic anhydrase, bicarbonate pumps etc, and organic membrane proteins.

DNA analysis will be coupled with protein analysis via extraction of the organic matrix proteins and basic peptide sequencing to reference protein and gene sequence to deliver critical improvements in the resolution and expression of the proteins essential for the organic matrix and calcite nucleation.

Molecular biology methods such as QPCR and qRT-PCR will be used for analysis of gene expression cycles and responses to different environmental conditions.

Project Timeline

Year 1

This 3.5 year studentship will begin with 6 months for project planning, literature review, and the training in, and application of, the bioinformatics tools required for genome building and annotation. Genome annotation should be completed in the first year, and a genome announcement manuscript will be submitted.

Year 2

Protein analysis of the shell bound organic matrix will be undertaken during the second year and the protein sequences will enable a clearer identification of the encoding genes. Patterns of transcription in organic matrix 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. During year 2 or 3, there will be opportunity to collect planktonic foraminifera for DNA/RNA extractions and a preliminary investigation as to the applicability of the benthic genome dataset to the planktonic genome.

Year 3

The project will go on to address changes in gene expression in response to different environmental conditions such as pH shifts followed by manuscript write up and paper submission.

Year 3.5

Final thesis write up and submission.

Training
& Skills

This PhD will principally be held in the vibrant and multidisciplinary research environment at the University of Stirling. The PhD student will become part of the “Environmental Biogeochemisty” research group 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

(1) Keul 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
(2) Schiebel (2002) Planktic foraminiferal sedimentation and the marine calcite budget. Global Biogeochemical Cycles, 16, doi: 10.1029/2001GB001459
(3) Toyofuku et al. 2018. Proton pumping accompanies calcification in foraminifera. Nature Comms. doi: 10.1038/ncomms1414

Further Information

Please contact Clare Bird (clare.bird2@stir.ac.uk) to ask questions, gain further information and to make an informal application.

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