Investigating Carbonates in the Field and in the Lab

Why Carbonates?

Our lab, founded in 2008, was initially called the Carbonate Research Group. It was renamed in 2022 to reflect the increased diversity in our research. However, we still very much have a team focusing on carbonate research and it remains a big part of what we do.

Carbonates have a fundamental importance in Earth Sciences: they are chemical sediments that contains rich information about the past conditions of our Earth, and about transformations occuring in the subsurface. Carbonates often form the skeleton of marine organisms, and therefore offer traces of life in the deep-past. Because they require liquid water to precipitate, carbonates are also important to trace the presence of water in our solar system.

Reefs are where the majority of carbonates are being deposited on the seafloor. This example from a dive on the reefs of Bali, Indonesia, illustrates that reefs comprise the remains of living organisms (they are “bioconstructed”), and as such, constitute an archive of past living organisms on Earth.

The range of scientific problems we can address using carbonate minerals range from understanding the evolution of life in the deep past, constrain past climate and sea-level changes, reconstruct diagenetic transformations in the subsurface, understand the thermal history of basins, and determine the 3D spatial geometry and sequence stratigraphy of coral reef deposits.

From the begining, research within the carbonate group has been multi-disciplinary, and has included fieldwork, clumped isotopes analysis, and numerical methods. This multi-prongued approach mixing experimental, field with numerical methods is very powerful, and can be used to solve problems in both the applied and academic fields.

Carbonates in the Field

Stratigraphy is the study of how rocks are organised in space and time. Hence, stratigraphers are interested not just in what the rocks are made of, but also in what processes led to the depositon of the rocks. One of the best way to study the stacking pattern of rocks at the small scale remains to look at outcrops. Therefore, we have studied outcrop and core stratigraphy to reconstruct sea-level changes, past climate change, and the heterogeneities of carbonate rocks at a range of scale

Dolomitized Permian Limestone

This outcrop is hidden in the heart of the Oman moutains. It contains some beautiful examples of the Permian ‘Khuff’ dolomite. It is believed that this dolomitization event occured soon after deposition.

Bivalve Reef, Ras-Al-Khaima

These bivalves lived together and formed a reef in the shallow, tropical sea of the Jurassic in modern-day Ras-Al-Khaima, UAE.

Deserts Deers, Mancos Shale

Male deers are locking horns in front of the Mancos Shale, an Early Cretaceous sedimentary formation from the Interior Seaway, USA.

Hyper-alcaly Tuffa, Colorado

This tuffa deposit was formed recently from the return waters of an unsuccesful oil well.

Paleo-Sabkha Deposits, UK

Sometimes our work takes us undergrounds, in mines. In this instance, we studied the remains of a paleo-sabkha comprising carbonates, evaporites and clastic sediments from the Jurassic Epoch.

Prograding carbonates, morocco

We studied Jurassic carbonates in the High-Atlas of Morocco, and demonstred that a hierarchy of heteorogeneities existed in these carbonates.

Anhydrite deposit, boulby mine, uK

These Permian beds of playa-type anhydrite are located deep under the North Sea, in Boulby Mine, United Kingdom.

Carbonate concretions, uK

Carbonate concretions were formed in the Eocene Barton Clay Formation of South England. These deposits also contain well-preserved aragonitic shells.

Late Hydrothermal Dolomite, Oman

A significant amount of the research we have done in Oman was concerned with understanding late hydrothermal dolomite. This phase can be seen here as brick-red fracture infills on black Neoproterozoic limestones.

Progradding carbonates, USA

The Permian Basin deposits in New Mexico, USA, contain world-class examples of carbonate deposits that progradded from the rim to towards the center of this intra-continental basin.

Sponge Reef, Permian Basin

In the Permian, corals were not the main reef builders. In this example, the reef is mostly composed of sponges and bryozoa.

Marine Hardground, Morocco

During exposure and reflooding of shallow-water Jurassic carbonates in Morocco, the sediments were left for a long-period of time outside of the main area of deposition. This led to the formation of iron-rich hardgrounds.

Hot, Deep diagenesis

In this outcrop of Ras-Al-Khaima (UAE), we observed a spectacular example of dolomite formed during thermo-sulfate reduction processes.

Stratigraphy is the study of how rocks are organised in space and time. Hence, stratigraphers are interested not just in what the rocks are made of, but also in what processes led to the depositon of the rocks. One of the best way to study the stacking pattern of rocks at the small scale remains to look at outcrops. Therefore, we have studied outcrop and core stratigraphy to reconstruct sea-level changes, past climate change, and the heterogeneities of carbonate rocks at a range of scale.

Our outcrop work has taken us all around the world, with a strong focus on the Middle East. For instance, the lab has worked for over 10 years in Oman, using the spectacular outcrops of Oman to advance our understanding of carbonate deposition.

This image from Neoproterozoic limestones in Oman illustrates how fluids emplaced under pressure in the subsurface can fracture limestones, and result in the deposition of a carbonate mineral phase (the white material within the veins and fractures). This is known as hydrofracturing.

For instance, we studied the relationship between fractures, fluids and diagenesis extensively in the salt dome of Jebel Madar in Oman. We also tried to understand how fractures control dolomitization (the transformation from limestone to an Mg Ca carbonate – dolomite) in the Neoproterozoic to Mesozoic carbonate successions of the Central Oman Mountains. For both of these projects, we collected samples and measurements at the outcrop, and combined geochemistry (including clumped isotopes) with petrographe and mineralogy of the samples to understand past fluid flow in the rocks.

Another major topic of outcrop research is stratigraphy. We have worked on some of the best preserved Lower Cretaceous peritidal and lagoonal deposits in the Haushi Huqf High of South Central Oman, and improved the interpretation and correlation of these units to the rest of the Middle East. We also demonstrated the presence of very small scale heterogeneities in Oman, that we interpret as related to storm deposits. We further explored the theme of small-scale heteorogeneities in Jurassic limestones in the Emirat of Ras-Al-Khaima, in the UAE. There, we demonstrated the cyclical nature of the deposits, and how these mimick the much larger-scale Arab Formation cycles.

But fieldwork is not limited to the dry land: we also work on cores recovered from drilling vessel such as the IODP Research Vessels, and we periodically sail as well. The lab has won a very large grant from NERC, and will sail in the Pacific Ocean in 2024: the goal of this seagoing expedition will be to understand the stratigraphy and diagenesis of drowned atolls. This will help us constrain the magnitude of sea-level changes from the Cretaceous to the Eocene, as well as give us an insight on the geometry of atolls through time. We call this project the CARAPACE project.

Forward Stratigraphic Modelling

Sedimentary  processes occur at a range of time and dimensional scales: basin opening and closing are controlled by tectonic, global sea-level changes, sediment supply by rivers  and in-situ production of (carbonate) sediments proceed to fill accomodation space in the basin. The mathematics controlling the shape and distribution of sediment bodies is complex and non-linear, and although the stratigraphic record gives us constraints on the architecture of carbonate sequences, the incomplete nature of this archive impairs quantitative visualization of the geological processes and products.

To overcome this limitation, we combine traditional field methods to gather information on the sediment and stratigraphy of carbonates with a numerical technique called “forward stratigraphic modeling”. The principle is to model forward in time how sediments within a basin are being deposited, eroded and transported, thus allowing to predict the nature of the sediment and the stratigraphic architecture of the rocks. Importantly, uncertainties in the stratigraphic models can be determined by repeating the modeling numerous times, allowing the establishement of uncertainty maps. 

Forward Stratigraphic Modelling of the Lower Cretaceous (Oman). This example shows the use of forward modelling to simulate the deposition of sediments of Cretaceous age in Oman. We can use this numerical laboratory to, for instance, estimate subsidence rates or sediment supply, and use the known stacking pattern of the rock record as our control experiment.

Our workhorse for this type of work is a commercial simulation package called “DionisosFlow” made by Beicip, in France. In DionsisosFlow, we define a region to model (a basin) and a time in the geological past, and from there, we can model forward how sediments are being deposited, eroded and transported in the basin, where the main area of deposition are, what the nature of the sediment deposited is, and the nature of the rocks in the subsurface. Importantly, we can also derive  the uncertainties in our models, e.g. build uncertainty maps. We use diffusion equations to represent sediment flow, an approach that has been shown to work well for sediments modeled over long (>10’000 years) periods.

Examples of problems we solved using this approach include understanding the regional 4D (three dimensional, plus geological time) distribution of carbonate sediments in the Early Cretaceous of Oman, a time periods characterised in the Middle East by the deposition of important hydrocarbon reservoirs. This study is now published in the Journal of Marine and Petroleum Geology (see Al-Salmi et al, 2019), and we demonstrate for instance the need for regional differential tectonic in the Early Cretaceous to explain the stacking patterns of carbonate rocks in this area.

Other examples include understanding the sub-salt of Kazakhstan, where we looked at the Serpukovian Stage of the Karachaganak FIeld. There, we worked on a relatively small (10-20 km) carbonate atoll, and tried to understand the constraints from the data on the geologic models. We demonstrated for instance that the seismic horizon picking needed to be re-evaluated in view of our models, and we also were able to model where and why the most promising reservoir facies would be. And a final example is our work on organic-rich shales of the Najma Formation in the subsurface of Kuwait, where we explore how much oxygen must have existed at the bottom of the shallow sea to account for the amount of organic material preserved in the sediments.

Other numerical approaches

Numerical methods in carbonates are not limited to forward stratigraphic modelling. For instance, we developed pluri-gaussian simulations to model carbonate rocks at a range of scales. This work, writen using the programming language ‘R’, has resulted in a number of publications, for instance Le Blevec et al, 2017. Another example is the work of Peter Fitch who used Eclipse and a experimental design to model the effect of various geologic heterogeneities within a carbonate reservoir on production scenarios (Fitch et al, 2014).

The field of numerical methods is a dynamic and fascinating one, and it benefits from creativity: there are many interesting problems that we can solve using numerical methods combined with domaine-specific expert knowledge.

Clumped Isotopes Lab

For over 15 years, our lab has made its reputation from running a difficult stable isotope method called clumped isotope geochemistry. In short, clumped isotopes consist of measuring isotopologues (i.e. molecules of the same chemical composition, but different isotopic composition) of CO2 either as a gas, or directly from carbonates (in which case the minerals are acidified to release carbone dioxide for analysis). Clumped isotopes are powerful, because they offer a one phase paleo-thermometer. If you want to know more about what clumped isotopes are, and how they are measured, you can read this article on our blog.

What being able to measure clumped isotopes means for research is the ability to read a temperature of formation or of recrystallization of any carbonate (or apatite) phase. Over the past 10 years, this has been a major focus of our research. First, we pioneered a calibration at high-temperature for clumped isotopes, pushing the inital calibration to 250˚C, well beyond the original calibration (70˚C). We also explored potential ‘vital’ effects, i.e. non-temperature related controls on clumped isotopes in groups such as echinoids and in nautiloids. We were the first group to apply clumped isotopes to the mineral magnesite, and to inorganic carbonate-fluoroapatite from the Monterey Formation.

But most of our focus in clumped isotopes has been on understanding carbonate diagenesis. We applied this tool to recrystallized oysters from the Lower Cretaceous of Oman, and demonstrated that these rocks must have been buried deeper than previously expected. We also did some extensive work on early dolomite, and how early dolomite recrystallizes. We showed that fine-grained limestones recrystallize almost at equilibrium with the host rock, giving a good insight on the maximum burial reached by the rocks. We also found evidence that the emplacement of oil inhibits the recrystallization process, and that gas expension in shales could cause transient peak temperatures.

In summary, the clumped isotope paleothermometer offers a window on when and how rocks where formed and recrystallized. This in turn can be used to constrain the processes that impacted subsurface environments in their history.

Historical Analytical Setup

In the current incarnation of our lab, we focus on digital research surrounding clumped isotopes and other isotopic system or geological and environmental problems. But we have a lot of historical experience in running clumped isotopes, and were were the first lab established for clumped isotopes in the UK. For 15 years, we operated a Thermo MAT 253 mass spectrometer attached to an autosampler called “the IBEX”. The IBEX was developed in our lab, and is now a commercially available instrument. Traditionally, the MAT 253 is setup to measure CO2 from acid-dissolution of carbonates: it has three collectors registered for masses 44, 45, and 46. This allows for δ13C and δ18O to be measured. 

The COVID outbreak forced us to shut down our old clumped isotope facilities at Imperial College London in March 2020. However, we were able to reopen it in summer of 2020, thanks to important safety measures put in place at the time. This allowed work to continue for our researchers. The lab stopped operating in early 2024 when we moved our activity to DERI and shifted our focus towards AI and digital solutions for the environment and sustainability.

However, the ‘clumped isotope’ paleothermometers (denoted Δ47) relies on accurately measuring δ47, and therefore the machines at Imperial College have modified collector arrays that allow the simultaneous measurement of masses 44 to 49.

The major issue with measuring δ47 in CO2 is the very low abundance of this mass (in the ppm range), which implies that any contaminents could recombine in the source and produce spurious peaks of mass 47 that would throw the analysis off (see Huntington et al., 2009, for discussion of contamination in clumped isotopes). Therefore, the CO2 gas produced by acid digestion needs to be cleaned prior to analysis. 

The technique we are using on the mass spectrometer to do our measurement is known as ‘dual inlet’. Essentially, we use two reservoir (belows) of gas (a standard and a sample side), and we ensure equal pressure between the two belows by bleeding gas during measurment. This insure greater accuracy of our results.

Initially, we built a series of manual vacuum lines that permit cleaning of the CO2 gas through a poropak column following protocols highlighted in Dennis and Schrag, 2010. The principle of each line is to 1) allow online digestion of carbonates to liberate CO2, 2) trap water in a series of slush traps, and 3) trap any non-water polar contaminants (hydrocarbons, halogenids, etc..). After removal of all contaminants the purified CO2 is analyzed on the MAT 253 mass spectrometer to simultaneously measure Δ47, δ18O and δ13C. A normal measurement cycle is about 1.5 to 2 hours, and each sample is measured at least three times.

The  IBEX: an automated system for clumped isotopes

The clumped isotope paleothermometer is a very powerful method, but it is also very slow: measurements on the mass spetrometer take up to two hours, and the manual line is very work intensive and requires specialized training. This greatly limits the number of samples that can be processed in one day, and also limits accessibility of clumped isotopes to specialized individuals.

An obvious workaround is to develop automated systems for clumped isotopes. Over the last 10 years, we have developed in collaboration with Protium (a company specialized in developing and marketing peripherals for mass spectrometers) an automated device for clumped isotope analysis. We call this automated system the “Imperial Batch EXtraction” system, or IBEX.  The acronym IBEX is also refering to  the Nubian Ibex, a caprinid native to the Arabian peninsula, which highlights the roots of our funding sources for this project.

The Imperial Batch Extraction system (IBEX) is connected to a liquid nigrogen dewar to allow for automatic cooling of the water and CO2 traps, and has a 40 positions autosampler. This allows us to operate the IBEX in an automated manner. This photo was taken in our old lab at Imperial College London.

The IBEX is fully automated, and we have build software to interface with common manufacturers (such as Thermo). The IBEX has a 40 positions autosampler, a common acid bath maintained at a temperature selected by the operator (we operate at 90˚C), two water traps, two CO2 traps, and one hydrocarbon trap. An inlet port allows for the introduction of sample gases, for instance heated gases. The IBEX will also be fitted with an LN2 auto-refill system, meaning that the instrument can run continuously without human intervention for several days. Typically, a full carrousel of samples and standards (about 2 hours per sample) takes 5-6 full days to run. Hence, the IBEX automation offers a real advantage and a much greater throughput.

To be able to keep up with the data coming from the IBEX, we also developed a free software called ‘Easotope’  (see John and Bowen, 2016). Easotope is built as a client-server application in Java, and runs on most standard operating systems that support a Java Virtual Machine (JVM). Easotope is capable of reading the raw format of most mass spectrometer files, saves all data on a server in a central MySQL database, and performs all the necessary corrections based on standards and other parameters. Easotope is a great help for the field of clumped isotope geochemistry, as it makes the management of complex isotope corrections easier and more transparent. This in turn reduces the source of uncertainty in interpreting data.

This top view of the IBEX in our old lab at Imperial College London, showing the system of valves actuated by compressed air, clearly visible from this angle.