Disentangling the Genotype Palaeoproxy Challenge in the Humboldt Current System and Beyond


During this PhD you will collect and work with marine planktonic foraminifera from the Humboldt Current System (HCS) off Chile. You will acquire skills in molecular biology (genotyping and metabarcoding), geochemistry (laser ablation) and electron microscopy to develop understanding of the HCS through time. This work will contribute to the development of tools for the reconstruction of past climates; a requirement for ground-truthing climate models.

The Humboldt Current System (HCS) of the southeast Pacific Ocean is one of the most complex and productive upwelling systems in the world, which supports large fisheries on which the people of the region depend. It is heavily influenced by the cycles of El Niño–Southern Oscillation (ENSO) and recent evidence shows that the coastal upwelling dynamics are changing, potentially forced by global warming. This has cascading impacts on the coastal ecosystems, threatening the world’s largest fishery, and negatively affecting oceanic and terrestrial biodiversity and the food security and livelihoods of resident populations. Predicting how ENSO patterns will alter the HCS as climate changes, is one of the biggest challenges in climate science today.

To model future climate scenarios, it is important to understand how the regional climate has changed in the past in response to previous global warming. To do so, we use the assemblage and chemical composition of shells of microscopic marine planktonic organisms called foraminifera (forams) as “proxies” for past conditions. Because these shells accumulate in the seafloor sediments over hundreds of thousands of years, we can use them to reconstruct oceanic and climatic conditions in the past. In this way the foram fossil record represents the foundation stone of palaeoceanography, providing an unparalleled long-term dataset with which to test and improve models for climate change projections.

The use of forams as a palaeoceanographic tool, however, needs to be filtered through a lens of biological understanding. The differing biology of foram species influences shell composition, leading to the routine use of species-specific proxies by palaeoceanographers. However, more recent research has shown that many species have evolved into genetically distinct groups called genotypes, driven by exploitable diverse niches in the water column. We now know that genotypes may look alike and contribute to the same fossil record. Yet, they occupy different niches, interact with different organism and/or are separated seasonally, all of which influence shell composition and lead to a requirement for genotype-specific proxies. Grouped as a single species in the fossil record, these genotypes supply an average temperature for the region, which is useful for understanding past climate over long time scales. However, analysing each genotype independently, or indeed analysing single specimens to understand changes in seasonal patterns through time allows for a much more refined understanding of changing oceanographic and climate patterns. This of course requires knowledge of the genotypes present and their biological preferences, both of which are currently unknown in the HCS, as it is the last remaining globally important oceanographic region to be genetically assessed.

The overarching aim of this project is to establish the foraminiferal species and genotypes present in the upwelling and OMZ waters of the HCS. We will then use our developed molecular approach to link these genotypes to their unique biology. We will combine this molecular data with eSEM imaging of genotyped individuals and genotype-specific measurements of shell composition to develop genotype-specific proxies. These methods will be directly applicable for research in other ocean regions and will provide palaeoceanographers with the most accurate tools to reconstruct past oceanic conditions, and climate modellers with finely tuned seasonal datasets for ground truthing of climate models.

This PhD will be part of a wider NERC funded project “Disentangling the Genotype Palaeoproxy Challenge in the Humboldt Current System and Beyond.” It would be advantageous for the successful candidate to have some experience in at least one of the following: molecular biology; shell geochemical analysis; eSEM; foraminiferal geology. However, training will be provided throughout the PhD in each of these areas. In addition, the PhD student will gain experience in participating in short cruises in the southeast Pacific and will receive training in catching live foraminifera using plankton nets.


To date, planktonic foraminifera genotyping projects have targeted the major oceanic ecosystems where most palaeoenvironmental effort has been focused. Yet despite its critical importance in the Earth System the distinctive planktonic biomes of the HCS remain neglected. We will target the regional biomes of upwelling, deeper thermocline, and oxygen minimum zones off northern and central Chile, to screen for regionally specific genotypes and identify their microbiomes. Sampling infrastructure is already in place, led by our Chilean project partners.

The focus of this PhD project will be on 16S/18S metabarcoding of single specimens to document their genotype, their trophic and microbial interactions, along with documentation of metadata to identify their preferred environmental/physico-chemical conditions. There is also some methodological development associated with the project, for e.g., DNA extraction buffer testing for its influence on shell geochemistry. Importantly, to test potential morphological and geochemical links to genotype and the fossil record, the shells of genotyped individuals will be imaged using environmental scanning electron microscopy (eSEM) and analysed geochemically

Project Timeline

Year 1

This 3.5-year studentship will begin with two tasks. Firstly, a literature review will be necessary for the candidate to get a broad understanding of the topic. Secondly, the candidate will be involved in the planning and preparation for the field work and will take part in the field work off the coast of Chile during January 2023. The second six months will be used to train the candidate in the methods required (genotyping, metabarcoding, eSEM) and to begin processing the samples collected off Chile. Relevant training in QIIME and/or R will be accessed during the first year.

Year 2

Metabarcoding and data analyses should be completed during year 2, including analysis of both water and foraminiferal samples. The student will also carry out the testing of DNA extraction buffers and perform DNA extractions while retaining shells from genotyped specimens for geochemical analysis and eSEM. This data will be used to link genotype to the corresponding shell geochemistry and morphology.

Year 3

Shell processing will continue, progressing to eSEM imaging and morphometrics. The student will then visit our collaborator at the University of Western Australia where they will train in the geochemical analysis of the shells of single specimens, using laser ablation of genotyped and imaged specimens to measure elemental ratios in the shell.

Year 3.5

Final thesis write up and submission.

& Skills

This PhD will 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 group meetings, along with the weekly seminar series giving informal and formal opportunities for research presentations. The student is also expected to participate in the yearly Postgraduate Conference attended by the entire department. Strong links will be maintained with project partners at Heriot Watt University which has an energetic geochemistry based foraminiferal research group led by co-supervisor Dr Babette Hoogakker, and collaborators at the University of Concepcion in Chile. There will be opportunity to take part in public outreach will Chilean partners in the production of a bilingual short film.
The PhD student will receive training in subject specific and generic skills. Specific skills will include foraminiferal sampling and shipboard work (including sea survival training), molecular techniques and bioinformatics. The PhD student will also be encouraged to take on additional bioinformatics training courses if 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

Sadekov, A. Y. et al. Palaeoclimate reconstructions reveal a strong link between El Niño-Southern Oscillation and Tropical Pacific mean state. Nat Commun 4, 2692 (2013).

Ford, H. L., Ravelo, A. C. & Polissar, P. J. Reduced El Niño–Southern Oscillation during the Last Glacial Maximum. Science 347, 255–258 (2015).

Bird, C. et al. 16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktic foraminifer). PLOS ONE 13, e0191653 (2018).

Further Information

Please contact Clare Bird (clare.bird2@stir.ac.uk) for informal enquires.

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