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Fixing the fossil record! Experimentally decrypting the altered isotope archive preserved in ancient carbonates

Dr Thomas Mueller (SEE), Dr Tracy Aze (SEE), Dr Sandra Piazolo (SEE)

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This intriguing PhD project will experimentally explore the effects of chemical alteration processes experienced by the fossil and surrounding rock matrix during sedimentation. This geological record provides a direct source of information about the Earth system during greenhouse climates, which can be used to better constrain future predictions of climate change. The student will use a combination of various experimental techniques, state-of-the-art analytical methods and numerical modelling to quantify rates and mechanisms of the chemical alteration processes.

The geological record provides a direct source of information about the Earth system during greenhouse climates, which can be used to better constrain future predictions of climate change. The ratios between different elements and stable isotopes recorded in the shells of planktonic foraminifera have been demonstrated to reflect ambient water chemistry and temperature (Fig. 1). One of the most important tools for generating records of past climate is the oxygen isotope ratio (δ18O) of foraminiferal calcite. The δ18O is primarily controlled by the isotopic ratio of the water in which the calcite is precipitated and the temperature in which precipitation occurs with more negative δ18O values indicating warmer temperatures for calcite growth. Consequently chemical analysis of fossilised foraminifera provides a direct source information about ancient climates as far back as 100 million years ago. However, the robustness and accuracy of these key records can be compromised by alteration of sediments limiting their application to a restricted number of well-preserved samples (Fig. 1).

Similarly, magnesium isotopes in carbonate minerals were proposed as sensitive geochemical tracers for possible sources and sinks in low temperature aqueous systems (Higgins & Schrag 2010) as well as potential tracers for seawater chemistry through the Earth’s history (Eisenhauer et al. 2009). Stable Mg-isotopes may also be a sensitive tracer of the diagenetic history of hydrothermal dolomites that form in the early diagenetic and deep burial environment (Lavoie et al. 2014; Geske et al. 2012). However, due to the effects of dissolution, precipitation, diagenetic resetting and non-equilibrium fractionation processes, hydrothermal dolomites show a wide range of Mg-isotopic values, and there is still a lack of experimental data on Mg-isotope fractionation behaviour under reaction conditions representative of the burial diagenetic environment.

The major problem in using the isotope archive measured in ancient carbonates is that there is currently no quantitative assessment of the mechanisms and rates modifying the geochemical records in carbonates.

The motivation of this project is therefore to experimentally quantify the post-depositional mechanisms and rates of change of the chemical signatures recorded in fossil calcite that are used to generate records of past climates. The results will improve the accuracy of geochemical data interpretation and will provide a framework of predicted isotopic alteration of marine fossils based on depositional environments, burial histories and sediment composition by addressing three main questions:

  1. What are the mechanism and rates of element and isotope exchange of structure forming (Ca-Fe-Mg-Ba-C-O) and trace elements (Fe, Mn, Ba, Sr) in carbonates?

  2. What parameters are controlling element and isotope transport in carbonates under various conditions?

  3. Which are the most suitable elements or isotopes to be used as palaeo-proxies and which are useful to extract kinetic, i.e. time information of geological processes?

Figure 1: Cross plots of multiple-specimen carbon and oxygen stable isotope data from planktonic foraminifera. A) The coloured ovals represent the average carbon and oxygen isotopic signatures of planktonic foraminifera calcite from different tropical ecologies. B) Multiple-specimen carbon and oxygen isotopic values of tropical Eocene planktonic foraminifera. Above the dashed line are data from “glassy” specimens and below the dashed line are data from altered “frosty” specimens. The different symbols represent the same species, from the same time period but with the different preservation histories which show a clear shift in oxygen isotope values between the two data sets. Figure modified from: A)  (Pearson et al. 2007) and B) (Edgar et al. 2015)


In a recent studies of our group, we presented the first results investigating the replacement reaction of single calcite crystals to form Mg-carbonates aiming to simulate dolomitization processes during burial diagenesis (Fig. 2). We have shown that rates of carbonate reactions depend on the effective element flux and control both the phase petrology and the spatial chemical composition of the reaction product. The same experimental approach can now be used to test, whether isotope exchange is coupled to the reaction front or whether isotope exchange is independent of the reaction progress. Detailed knowledge on these parameters allows to predict the element and isotope signatures preserved in natural geological settings and allow thus to reconstruct the temporal evolution more accurately (see review of (Müller et al. 2010) for details). We firmly believe that the next challenge to read the mineral archive preserved in its spatial chemical composition is to quantitatively investigate element and isotope exchange processes.


Figure 2: BSE and schematic model of calcite replacement by layered reaction rims (Jonas et al. 2015). The replacement reaction mechanism is dissolution-precipitation, but the reaction progress is controlled by diffusion of elements in the pore fluid resulting in a compositional zoning of the reaction rim.

The isotope exchange reaction accompanying the recrystallization process will be experimentally simulated by parameter variation to extract quantitative information on the chemistry and microstructural evolution, i.e., transformation from a pristine “glassy” to an altered “frosty” textures and the isotope exchange between foraminifera, carbonate matrix and fluids. The diagenetic recrystallization process is mainly controlled by: 1) temperature, 2) composition of the sediment, 3) composition of the pore fluids, and 4) the rate at which the fluid is flowing through the rock. Therefore, the student will conduct experiments using synthetic rocks composed of selected fossil species with distinct isotope composition being embedded in a calcite ±clay matrix to systematically study the effect and dependence of these four parameters.

In this project, the student will work with experienced scientists at Leeds and their international collaborators to experimentally investigate carbonate reactions under diagenetic conditions.

The successful student will:

  • Carry out experiments to establish quantitative relationships between temperature, salinity, pH and redox conditions describing the kinetically controlled isotope exchange between carbonates (of different type/composition) and surrounding fluid phase in a polyphase setting (foraminifera and carbonate matrix in the presence of fluids).
  • Determine the microscopic processes governing the textural alteration of foraminifer shells.
  • Assess whether the rate of isotope exchange is independent of, or coupled to the textural replacement process.
  • Test whether presence/absence of clay minerals only affects the amount of available pore fluid or whether they enhance or retard the carbonate recrystallization process.

The School of Earth and Environment at Leeds has all the lab facilities needed for this project and the proposed experiments will build on our previous studies on carbonate replacement (Jonas et al. 2015). This setup investigates mineral/rock-water interaction at diagenetic conditions using 1-atm furnaces (with or without controlled fO2) and rapid-quench cold seal apparatus. The setup has been successfully proven to allow for a temporal monitoring of the reaction progress combining analysis of the fluid and solid phases using various state-of-the-science techniques.

Potential for high impact outcome

The project will focus on oxygen and, partly, carbon isotope systems to produce a comprehensive set of quantitative data describing the rate isotope exchange as a function of temperature, fluid composition, the flow rate and matrix composition. The results will provide the framework to extend the study to other commonly used geochemical proxies such as Ca, Mg, Sr, Nd, and B. Recent studies, partly driven by our group (Jonas et al. 2015; Müller et al. 2010; Müller et al. 2012; Mueller et al. 2014), emphasized the role of effective element fluxes on recorded compositional profiles. Likely, this will also affect isotope signatures which are typically used as environmental proxies given that reaction rates of minerals in the crust are, to a specific extent, directly linked to changes in the atmosphere and biosphere. This is in particular true for carbonates as they are a major source and sink of the Earth CO2 budget. A quantitative understanding on the effect of reaction and exchange kinetics on isotope composition of carbonates is crucial to evaluate the robustness of those isotope signatures for its correct interpretation.

The laboratory facilities at Leeds are extremely well equipped to carry out the proposed research, in particular due to the recent add-on of an experimental petrology laboratory. In combination with the superb analytical facilities of the low temperature geochemistry group (Cohen) and the high resolution TIMS and electron optics lab, this infrastructure provided by the School of Earth and Environmental Sciences, makes the University of Leeds one of the unique places at which this project can be successfully achieved. Given the high interest of using stable isotope composition of carbonates as tracer of paleo-conditions, we anticipate the project generating several publications being suitable for submission to a high impact journal with the potential of becoming 4* contributions.

Training & Framework of the project

In this interdisciplinary project the student will work under the supervision of Dr Thomas Müller (IGT), Dr Tracy Aze (ESSI) and Dr Sandra Piazolo (IGT) within the School of Earth and Environment. In addition, depending on the focus of interest of the PhD candidate the project offers and highly encourages the close collaboration with the Cohen research group being part of the ESSI within the School of Earth and Environmental Sciences. This project provides a high level of specialist scientific training in: (i) experimental techniques to study element/isotope transport including experiments with gas-mixing furnaces, cold seal and piston cylinder apparatus and flow-through reactor vessels; (ii) State-of-science analytical methods on the micro to nano-scale (SIMS, TIMS, LA-ICP-MS and RBS); (iii) numerical modelling (finite differences) in multiple programming environments.

The project provides possible interaction with the DFG funded “research priority group” CHARON working on mechanisms, rates and geological implications of carbonate proxies and alteration reactions.

In addition, the successful PhD student will have access to a broad spectrum of training in various analytical and experimental techniques, managing your degree, and preparing for your viva either by the Faculty ( or within collaborations in the UK and/or abroad. Moreover, research results will be presented at national & international meetings to integrate the student in the scientific community working in the field of paleo-proxies, and reactive mass transport.

Student profile

The student should have a minimum of an upper 2:1 degree (or international equivalent) and strong interest in experimental and analytical work, geochemical processes, and ideally paleoclimate research. A strong background in quantitative science (maths, physics and chemistry) and curiosity for interdisciplinary research is desired. Willingness to work within a research team is essential.


Edgar, K.M. et al., 2015. Assessing the impact of diagenesis on δ11B, δ13C, δ18O, Sr/Ca and B/Ca values in fossil planktic foraminiferal calcite. Geochimica Et Cosmochimica Acta, 166, pp.189–209.

Eisenhauer, A., Kisakürek, B. & Böhm, F., 2009. Marine calcification: an alkali earth metal isotope perspective. Elements, 5(6), pp.365–368.

Geske, A. et al., 2012. Impact of diagenesis and low grade metamorphosis on isotope (?? 26Mg, ?? 13C, ?? 18O and 87Sr/ 86Sr) and elemental (Ca, Mg, Mn, Fe and Sr) signatures of Triassic sabkha dolomites. Chemical Geology, 332-333, pp.45–64.

Higgins, J.A. & Schrag, D.P., 2010. Constraining magnesium cycling in marine sediments using magnesium isotopes. Geochimica et Cosmochimica Acta, 74(17), pp.5039–5053.

Jonas, L. et al., 2015. Transport-controlled hydrothermal replacement of calcite by Mg-carbonates. Geology, 43(9), pp.779–783.

Lavoie, D., Jackson, S. & Girard, I., 2014. Magnesium isotopes in high-temperature saddle dolomite cements in the lower Paleozoic of Canada. Sedimentary Geology, 305, pp.58–68.

Mueller, T. et al., 2014. Diffusive fractionation of carbon isotopes in γ-Fe: Experiment, models and implications for early solar system processes. Geochimica et Cosmochimica Acta, 127, pp.57–66.

Müller, T., Cherniak, D. & Bruce Watson, E., 2012. Interdiffusion of divalent cations in carbonates: Experimental measurements and implications for timescales of equilibration and retention of compositional signatures. Geochimica et Cosmochimica Acta, 84, pp.90–103.

Müller, T., Watson, E.B. & Harrison, T.M., 2010. Applications of Diffusion Data to High-Temperature Earth Systems. Reviews in Mineralogy and Geochemistry, 72(1), pp.997–1038.

Pearson, P.N. et al., 2007. Stable warm tropical climate through the Eocene Epoch. Geology, 35(3), pp.211–214.

Related undergraduate subjects:

  • Chemistry
  • Geology