Trace element and isotope partitioning in carbonates in simulated biological environments
Lead Research Organisation:
University of St Andrews
Department Name: Earth and Environmental Sciences
Abstract
Many marine organisms produce calcium carbonate structures e.g. corals produce skeletons, bivalves produce shells and foraminifera (single-celled organisms) produce tests. These mineral structures provide organisms with tissue support and/or protection from predators and the physical environment. The chemistry of calcium carbonate is affected by environment. In particular seawater temperatures affect how trace elements substitute in place of calcium and the ratio of oxygen isotopes (forms of oxygen with different masses) in the mineral structure. Thus the geochemistry of the calcium carbonate structures provides information on the temperature and chemistry of seawater at the time the organism lived and grew. The mineral structures are preserved after the death of the organism e.g. as coral reefs, and the analysis of fossil specimens offers an excellent route to reconstruct records of past environmental conditions. Such records help us to understand past changes and interactions in global climate and to predict 21st century climate change. Understanding how other factors affect the chemistry of the shells and reefs is key to accurate interpretation of the climate information recorded in fossil specimens.
Coral skeletons and foraminifera tests form at specialist calcification sites, either in or adjacent to the organism. The calcification sites contain both soluble and insoluble organic biomolecules (e.g. proteins, lipids), which control and guide the precipitation and growth of the mineral. These biomolecules also affect the chemistry of the mineral. In this research we will analyse modern and fossil corals and foraminifera to determine how the concentrations and compositions of organic biomolecules at the calcification site have varied throughout time. We will then precipitate CaCO3 minerals in vitro under conditions replicating those of past and present calcification sites to determine how variations in biomolecules affect mineral chemistry. In particular we will explore how biomolecules interact with other ions at the calcification site over a range of temperature to control mineral chemistry. We will calculate how relationships between coral skeleton and foraminifera test chemistry and seawater temperature have varied throughout time. By applying these calculations to fossils, we will optimise the accuracy of past seawater temperature estimates. We will also use advanced microscopy techniques to visualise the structure of the mineral precipitated under different conditions and to watch the formation of minerals in real time. These observations will help us to understand how variations in the calcification environment affect the incorporation of trace elements and isotopes in calcium carbonate.
Coral skeletons and foraminifera tests form at specialist calcification sites, either in or adjacent to the organism. The calcification sites contain both soluble and insoluble organic biomolecules (e.g. proteins, lipids), which control and guide the precipitation and growth of the mineral. These biomolecules also affect the chemistry of the mineral. In this research we will analyse modern and fossil corals and foraminifera to determine how the concentrations and compositions of organic biomolecules at the calcification site have varied throughout time. We will then precipitate CaCO3 minerals in vitro under conditions replicating those of past and present calcification sites to determine how variations in biomolecules affect mineral chemistry. In particular we will explore how biomolecules interact with other ions at the calcification site over a range of temperature to control mineral chemistry. We will calculate how relationships between coral skeleton and foraminifera test chemistry and seawater temperature have varied throughout time. By applying these calculations to fossils, we will optimise the accuracy of past seawater temperature estimates. We will also use advanced microscopy techniques to visualise the structure of the mineral precipitated under different conditions and to watch the formation of minerals in real time. These observations will help us to understand how variations in the calcification environment affect the incorporation of trace elements and isotopes in calcium carbonate.
Planned Impact
Our improved palaeoproxy calibrations will increase the accuracy of past seawater temperature for surface and deep ocean waters and ice volume estimates. These data will facilitate understanding of past climate by improving models which explore how interactions in the ocean and atmosphere drive climate change. Such models underpin our current predictions of the magnitude and geography of future climate change. Increasing the accuracy of these models enables us to plan for future climate change more efficiently.
Researchers studying biomineralisation and the impact of future changes in seawater temperature and pCO2 (ocean acidification) will benefit from our research which will demonstrate how biomolecules can facilitate or suppress calcium carbonate precipitation over different temperatures and pH. Understanding this aspect of biomineralisation is crucial to estimating the future behaviours of calcareous organisms which are of key economic importance e.g. shallow and deep water corals provide important habitat space for fisheries while bivalves are a food source. Approximately 1 in 6 people on the planet rely on coral reefs for their livelihoods and understanding the coral biomineralisation processes is fundamental for predicting their futures.
The UK government is committed to reducing UK greenhouse gas emissions by investing in low-carbon energy sources, improving fuel standards in cars and increasing energy efficiency wherever possible. Encouraging the general public to reduce their carbon footprint will be key to successfully implementing these greenhouse gas reductions. Raising awareness of the negative impacts of CO2 emissions at a local and global scale is an important component of this. Our research, exploring the relationships between temperature, pH and biocarbonate production, provides an excellent route to highlight the negative effects of increasing atmospheric CO2 (and ocean acidification) and to demonstrate their wider impacts e.g. reduction in coral reef production and associated loss of tourism income, coastal protection and fisheries, impacts on UK bivalve aquaculture etc. We will communicate our research to school children (through the University of St. Andrews Geobus) and to the general public through exhibits at Dundee Science Centre (Sensations) and the University of St. Andrews Science open day.
Researchers studying biomineralisation and the impact of future changes in seawater temperature and pCO2 (ocean acidification) will benefit from our research which will demonstrate how biomolecules can facilitate or suppress calcium carbonate precipitation over different temperatures and pH. Understanding this aspect of biomineralisation is crucial to estimating the future behaviours of calcareous organisms which are of key economic importance e.g. shallow and deep water corals provide important habitat space for fisheries while bivalves are a food source. Approximately 1 in 6 people on the planet rely on coral reefs for their livelihoods and understanding the coral biomineralisation processes is fundamental for predicting their futures.
The UK government is committed to reducing UK greenhouse gas emissions by investing in low-carbon energy sources, improving fuel standards in cars and increasing energy efficiency wherever possible. Encouraging the general public to reduce their carbon footprint will be key to successfully implementing these greenhouse gas reductions. Raising awareness of the negative impacts of CO2 emissions at a local and global scale is an important component of this. Our research, exploring the relationships between temperature, pH and biocarbonate production, provides an excellent route to highlight the negative effects of increasing atmospheric CO2 (and ocean acidification) and to demonstrate their wider impacts e.g. reduction in coral reef production and associated loss of tourism income, coastal protection and fisheries, impacts on UK bivalve aquaculture etc. We will communicate our research to school children (through the University of St. Andrews Geobus) and to the general public through exhibits at Dundee Science Centre (Sensations) and the University of St. Andrews Science open day.
Publications
Castillo Alvarez C
(2024)
Insights into the response of coral biomineralisation to environmental change from aragonite precipitations in vitro
in Geochimica et Cosmochimica Acta
Kellock C
(2022)
Optimising a method for aragonite precipitation in simulated biogenic calcification media.
in PloS one
Penkman K
(2020)
Through the Looking-Glass, and What Amino Acids Found There
Description | Coral skeletons and foraminifera tests form at specialist calcification sites, either in or adjacent to the organism. The calcification sites contain both soluble and insoluble organic biomolecules (e.g. proteins, lipids), which control and guide the precipitation and growth of the mineral. Our study has shown that the biomolecules which occur in coral skeletons can both accelerate and inhibit the precipitation of aragonite (the calcium carbonate mineral in the skeleton). These biomolecules also alter the morphology of the mineral crystals and may affect trace element content. Under ocean acidification conditions, the organic content of coral skeletons is increased but the concentration of biomolecules at the coral calcification site is unknown so it is unclear if this increases serves to promote or inhibit formation of the coral skeleton. |
Exploitation Route | The skeletal chemistry of marine organisms may record information on the local environmental conditions prevailing at the time of their deposition and the analysis of fossil specimens can be used to estimate past climate. Understanding how biomolecules influence the trace element and isotope chemistry of biominerals will enhance the accuracy of these estimates of past climate. |
Sectors | Environment |
Description | A deep-sea perspective on coral resilience in a changing world |
Amount | £641,689 (GBP) |
Funding ID | NE/X00127X/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 01/2023 |
End | 01/2026 |
Description | Emerging from lockdown grant: Do organic contaminants influence the formation of calcium carbonate structures in simulated biological environments |
Amount | £1,500 (GBP) |
Organisation | Marine Alliance for Science and Technology for Scotland |
Sector | Academic/University |
Country | United Kingdom |
Start | 05/2021 |
End | 11/2021 |
Description | Groundtruthing the d11B pH proxy in coral aragonite |
Amount | £36,000 (GBP) |
Funding ID | IMF689/0519 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 12/2020 |
End | 12/2021 |
Description | Hawaiian Drowned Reefs: Climate variability and coral reef response to environmental change in the sub-tropical Pacific over the last 500 ky |
Amount | £31,242 (GBP) |
Funding ID | NE/Y005503/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 07/2023 |
End | 08/2025 |
Description | NERC Discipline Hopping for Discovery Science Fund: How do biomolecules alter the material properties of biominerals? |
Amount | £21,131 (GBP) |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 01/2023 |
End | 03/2023 |
Description | St Leonards Global leading PhD scholarship |
Amount | £100,000 (GBP) |
Organisation | University of St Andrews |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2022 |
End | 03/2026 |
Description | St Leonards World leading PhD scholarship, The role of lipids in coral biomineralisation |
Amount | £100,000 (GBP) |
Organisation | University of St Andrews |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2020 |
End | 03/2024 |
Title | B/Ca of synthetic aragonites |
Description | Supplementary data in support of 'B(OH)4-and CO32- do not compete for incorporation into aragonite under typical coral calcification media conditions', Castillo Alvarez et al., submitted to Geochimica et Cosmochimica Acta July 23 |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | This data supports a publication |
URL | https://data.mendeley.com/datasets/cvd66cs5y2/1 |
Title | Insights into the response of coral biomineralisation to environmental change from aragonite precipitations in vitro |
Description | This dataset includes the data in Insights into the response of coral biomineralisation to environmental change from aragonite precipitations in vitro , submitted to Geochimica et Cosmochimica Acta. The dataset includes Fig. S1 (showing different conditions tested for Raman spectroscopy) and tables of the seawater conditions and aragonite precipitation rates observed in experiments conducted with variable pHNBS and O with no biomolecule (Table S1) and with 2 mM of aspartic acid (Table S3), glutamic acid (Table S4) and glycine (Table S5), with variable [amino acid] (Table S2) and at different temperatures with and without aspartic acid (Table S6). |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | This data supports a publication |
URL | https://data.mendeley.com/datasets/b5bpfw97cg/1 |
Description | Expedition member IODP 389: Hawaiian Drowned Reefs |
Organisation | International Ocean Discovery Programme (IODP) |
Country | United States |
Sector | Charity/Non Profit |
PI Contribution | I am an expedition member for IODP 389: Hawaiian Drowned Reefs. I participated in the onshore science party in February 2024. As part of the team I will work to reconstruct past climate in the Central Pacific and to determine the reef response to this change. |
Collaborator Contribution | The IODP team is 31 scientists from a range of countries who will work together to reconstruct climate and reef history in Hawaii. |
Impact | This is a multi-disciplinary partnership. |
Start Year | 2023 |
Description | Article on chiral amino acid analysis for Chemistry World, Mar 2020 |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Article on chiral amino acid analysis and its importance for understanding the past; Chemistry World, Mar 2020 |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.chemistryworld.com/news/unlocking-geological-time-capsules-with-analytical-chemistry/401... |
Description | Contributer to 'Dive In- Protecting our Oceans' exhibition at the Wardlaw Museum, St. Andrews |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | This exhibition ran for 4 months and highlighted stressors in the marine environment and how these could be reduced by individuals decision making. |
Year(s) Of Engagement Activity | 2021,2022 |
URL | https://divein.wp.st-andrews.ac.uk/?msclkid=11c6e22da5d811eca909bfdeea0451f7 |
Description | Departmental seminar - Aberystwyth University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Departmental seminar at Aberystwyth University |
Year(s) Of Engagement Activity | 2020 |
Description | Departmental seminar - University of Oxford |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Departmental seminar at the University of Oxford |
Year(s) Of Engagement Activity | 2021 |
Description | Dundee Science Festival 2020 |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | An online video demonstration of how corals build skeletons and how this is affected by ocean acidification |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.dundeesciencefestival.org/corals-and-ocean-acidification.html |
Description | Mapping Ocean Change workshop |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Guided walk for 25 people collecting intertidal organisms and follow up microscope session discussing impacts of seawater temperature rise and ocean acidification on marine organisms. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.mappingoceanchange.org/events/mapping-ocean-change-workshop-scottish-oceans-institute |
Description | Meet the 2020 Blavatnik Award UK Chemistry Honorees youtube video |
Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | A youtube video about the winners of the 2020 Blavatnik chemistry honorees. The video feactures a section on Kirsty Penkman's research. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.youtube.com/watch?v=_iX_AqNxMNU |
Description | Outreach event at York Festival of Ideas |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Outreach activity; audience of all ages. |
Year(s) Of Engagement Activity | 2022 |
URL | https://yorkfestivalofideas.com/2022/be-part/ |
Description | Poster at INQUA conference, Dublin, July 2019 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Poster Presentation at the 2019 INQUA (International Quaternary) congress, Dublin. Details: Kirsty Penkman, Beatrice Demarchi, Molly Crisp, Peter Tomiak, Marc Dickinson, Lucy Wheeler, Martina Conti & Sheila Taylor, 2019. Through the Looking-Glass, and What Amino Acids Found There. INQUA 2019 Congress, Dublin, Ireland. |
Year(s) Of Engagement Activity | 2019 |
URL | http://www.inqua2019.org/ |
Description | Prepared and contributed specimens to Chaos Terrain sculpture by Ilana Halperin |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | I prepared and contributed pieces of coral to a sculpture by Ilana Halperin which is now displayed in the Bute Building at the University of St. Andrews. The sculpture was unveiled during an event for ~ 30 people and is now on permanent display. |
Year(s) Of Engagement Activity | 2022 |
URL | https://museumblog.wp.st-andrews.ac.uk/2022/11/09/marble-preservation-society/ |
Description | School visit (Madras High school, St. Andrews) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | We held workships on climate change and ocean acidifcation for S1 pupils (ages 12-13) at the local high school. Pupils discussed the causes and consequences of climate change and reported that they felt better informed after the workshops. |
Year(s) Of Engagement Activity | 2020 |
Description | Talk at QRA conference, Leeds, 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote presentation at the QRA Annual Discussion Meeting, Leeds, 2020. Details: Kirsty Penkman, 2020. Through the Looking-Glass, and What Amino Acids Found There. QRA Annual Discussion Meeting, Leeds, 2020 |
Year(s) Of Engagement Activity | 2020 |
URL | https://qraleeds2020.com/ |
Description | Talk at University Open Day, Sep 2019 |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Research talk at University of York Open Day, showcasing inter-disciplinary science. |
Year(s) Of Engagement Activity | 2019 |
Description | Talk for Manchester Literary & Philosophical Society |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | Talk given to a scientific society; sparked questions & discussions afterwards. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.manlitphil.ac.uk/resources/summer-2022-programme |