The Centre for Trace and Experimental Biogeochemistry is a virtual centre located in Stellenbosch and brings in researchers from Stellnbosch University and other local academic institutions together with an aims to gain an improved understanding on biogeochemical cycling of bioactive trace elements in marine environments. The Centre promotes the mandate of international GEOTRACES program and is headed by Prof Roychoudhury from the Department of Earth Sciences at Stellenbosch University.

South Africa had a rich history in the field of chemical oceanography. Over the past 50 years, however, it has declined and only a skeleton remains which is incapable of meeting the requirements of a country surrounded by three oceans. Deteriorating research facilities combined with a lack of impetus in oceanographic research and funding resulted in South Africa experiencing a significant brain drain and subsequent decline in research capacity. South Africa is currently, however, maturing in its democracy and starting to pay more attention to the socio-economic benefits of the natural environment. Change is on the horizon.

Geographically and strategically, the research centre at Stellenbosch is best-placed to study aspects of the Southern Ocean. It is situated at the confluence of three oceans, namely, the Indian, Atlantic and Southern Oceans. Large sectors of these oceans below Africa are understudied and lack scientific data crucial to global climate models or to ascertain variability trends that will help understand linkages between trace metals, primary productivity, biodiversity and long term climate change.

The Center’s research and training activities focus on the Southern Ocean and Southern African coastal waters with a view to understanding long-term impact on the global carbon cycle, ocean acidification and climate change. More specifically, trace nutrients and their impact on productivity in oceans are studied.  The ultimate goal is to become a South African and African Center of Excellence in the highly specialized field of trace metal biogeochemistry . The Center not only helps to develop capacity for the long-term monitoring of the Southern Ocean and contribute to the global dataset for climate monitoring, but it also undertakes cutting edge scientific work thereby raising the quality and quantity of South African and African research output.

Given the specialized nature of the Center’s work, high-level skills sets and specialized land and ship-based laboratories have been developed. We make use of the state of the art ice-breaker ship SA Agulhas II that is fitted with GEOTRACES approved trace CTD rosette with Teflon coated Go-Flo bottles, a towed fish and three container clean labs for trace clean sampling and experiments. On land we boast a temperature controlled Class 10 clean laboratory equipped with Picotrace® laminar flow workstations, Fe-FIA, Sector filed ICP-MS, anaerobic chamber and temperature and light controlled incubators.






RoyRoydchoudhury 003
Prof AN Roychoudhury, Stellenbosch University

My research focus is on biogeochemical dynamics in aquatic environments. In particular I am interested in understanding reaction kinetics and other controls over elemental (carbon, sulfur, nutrients and metals and trace metals) cycling on the global as well as local scales. For more information click here.

Dr S Fietz, Stellenbosch University

My research aims to study modern aquatic systems and sedimentary archives as well as sedimentation processes to help interpretation. This approach provides essential information on past and present environmental conditions for those predicting future local and global changes.

Dr Thato Mtshali, CSIR

My research focusses on the roles of trace metal biogeochemistry, with particular interest of Iron (Fe), and light dynamics in the Southern Ocean primary productivity. This research combines Fe speciation, analytical chemistry, and phytoplankton physiology

Dr Andrea Baker (Postdoc)

My research…

Dr Saumik Samanta (Postdoc)
My research…

Dr Jan-Lukas Menzel (Postdoc)

My research…

Dr Marisa Storm (Postdoc)

My research…




Recently funded projects:

  1. Roychoudhury AN, Mackey B, Vichi M, Findlay, K (2019 – 2023) Humpback whales in changing climate, Donor funding AUD 4,019,503
  2. Roychoudhury AN (2018-2020) Distribution and Speciation of Bioactive Trace Elements in Southern Ocean, NRF SANAP, R 1,820,000
  3. Roychoudhury AN (2017-2019) TraceEx: Establishment of Center of excellence in Trace and experimental Biogeochemistry, Donor funding, R 17 Million
  4. Roychoudhury AN (2017-2019) Nanoparticles at Air-Sea interface. NRF Competitive Rated Researcher Grant, R 1,550,000
  5. Roychoudhury AN (2015) ICP-MS mass spectrometer for ultra-trace metal analysis. National Equipment Program, NRF, R 2,699,000


For details on currently on-going projects click here


Phytoplankton serve as the base of the aquatic food web, sustaining all aquatic life. Through photosynthesis, phytoplankton are responsible for most of the oxygen present in the Earth’s atmosphere. Phytoplankton also consume as much carbon dioxide as forests and other land plants. Worldwide, this “biological carbon pump” transfers approximately 10 gigatonnes of carbon from the atmosphere to ocean each year.

Ocean-atmospheric carbon dioxide exchange in the Southern Ocean in particular plays an important role in global climate change. Recent estimates indicate that approximately 50% of all carbon dioxide emitted by human activity is stored in the Southern Ocean. Despite the importance of the Ocean in improving carbon dioxide  levels  and  reducing  the  impact  of  man-made  climate  change,  its  carbon  cycle  remains  poorly understood.

Even small changes in the production of phytoplankton in the Southern Ocean will influence carbon dioxide uptake and release. This will in turn influence global atmospheric carbon dioxide concentrations, surface temperatures, ocean acidification and climate. In addition, changes in production will also affect the ecological food chain, leading to possible negative impacts on marine ecosystems and biodiversity.

Biologically important trace metals (iron, manganese, cobalt, nickel, copper, zinc and cadmium) are essential for ocean primary productivity – phytoplankton production. Without their presence, production cannot take place. It is therefore important to understand how the bioavailability of these trace elements (the amount available for absorption and utilisation by phytoplankton) increase or limit phytoplankton growth and also how their rate and mode of occurrence influence this growth.

Laboratory Facilities

TracEx laboratories were established/funded purely from research grants to Prof Roychoudhury. The laboratories house equipment totaling over R 30 million and have space to perform wet-chemistry laboratory work including sediment and water sample processing, analytical work as well as conduct experiments on chemical and biological systems. The laboratories are well furnished with equipment that would be of envy to any low-temperature biogeochemistry laboratory in the world.  The equipment are housed in different spaces

  • Metal free Ultra-clean laboratory, a first in Africa, is situated in the back quad of Earth Sciences building and was constructed in collaboration with CSIR as part of the Southern Ocean Observatory node. This is the only metal-free clean laboratory in Africa and is among 40 laboratories in the world validated for measuring trace metals in seawaters. The space is divided into three rooms having clean air quality of Class-10, Class-100 and Class-1000. The space is used for conducting research on bioactive trace metals in the Southern Ocean. The laboratory is equipped with instruments for concentrating and pre-processing of metal and their isotopes in seawater.

Instrumentation in clean lab:

Millipore Ultra-clean water purification system; seaFASTTM-pico SC-4 DX (Elemental Scientific Inc.) for trace metal preconcentration; prepFAST MC (Elemental Scientific Inc.) for metal isotope sample processing; Flow-injection analyzer for Fe measurement; Mini-SIA for Al measurement; Class-10 Pico-trace workbenches; Anaerobic chamber, Incubator; Particle counter, Multi-channel peristaltic pump, Ph Meter; Multiparameter meter; High-volume Aerosol sampler

  • Mobile container clean laboratory located on the university farm was constructed and furnished with donor funds to Prof Roychoudhury. The container has Class-100 clean air environment with wet-chemistry lab facilities for processing samples and is used on ships during cruises to Southern Ocean. The container is equipped with its own trace-clean CTD and custom rosette for collecting seawater samples for trace metals from depths of up to 5000 m.

Instrumentation associated to container lab:

Seabird Scientific CTD; GEOTRACES compliant custom Rosette with Go-Flo bottles; Class-10 Laminar-flow bench; Fume hood; 2 x McLane pumps for in situ high volume seawater filtration; PTFE Diaphragm pump

  • The General geochemistry laboratory is located in Room 1015 and is used for most “dirty” and day to day operational work. The space is divided into three sections
  1. Wet chemistry workbench space – this is the main room where bench space is available for students to work on their samples or set up experiments. The space contains fume-hoods and few equipment used on a daily basis.
  2. Walk-in high-volume cleaning area with acid fume extraction – this area was specially constructed for high volume cleaning of labware, sampling equipment and samplers that are used in trace metal research. Because of large volume of acid stored and used over long periods, the room is restricted for access and a room wide acid fume extraction system is installed.
  3. Sediment digestion HF lab – this section is used for processing sediment samples in a “clean” and closed environment through digestion by Hydrofluoric and other acids. Because of the use of HF, access to the room is strictly restricted.

Instrumentation set-up in General Geochemistry laboratory:

High-precision and general weighing balances; Centrifuge; High-temperature muffle furnace; Organic solvent extractor; Low-temperature Incubator-shaker; Sediment sieve shaker; Desk-top class-100 laminar flow bench; Pico-trace sediment digestion system; Class-100 laminar flow-bench with HF extraction; Auto-Titrator; Fridge and Freezers; Fume-hoods; Large volume peristaltic pump; Sediment core sampler; Water filtration rigs

  • TracEx laboratory located in Room 1029 was constructed and furnished using donor funds to Prof Roychoudhury and is used for developing phytoplankton cultures for experimental purposes. The laboratory is used as a relatively clean working area and has limited work-bench space for processing samples on sensitive analytical equipment, including isotope analyzers, housed in the lab.

Instrumentation in TracEx lab:

2 x Large-volume temperature and light controlled incubators; FTIR; Freeze-drier; UV-Vis Spectrophotometer; Micro-centrifuge; Fluorometer; PICARRO L2130-i δD and δ18O High-Precision Isotopic Water Analyzer; PICARRO G2201-i CRDS Analyzer for Isotopic Carbon in CO2 and CH4; Picarro CRDS analyzer for Isotopic Nitrogen and Oxygen; Air compressor

Details of some of the equipment are below:

Flow-injection Analyzer (Fe)


A highly sensitive flow injection analysis with Chemiluminescence detector (FIA-CL) is installed for determining the concentration of iron in seawater. The equipment is linked to an auto sampler allowing for multiple analyses without the need for constant monitoring. The developed method is an improvement on similar available methods and uses commercially available resin (IDA) as oppose to the one that requires synthesis in the laboratory. Furthermore, the method requires reduced reagent concentrations thereby providing better results in a cost-efficient and easy manner. The improvements resulted in better precision while eliminating the loss of resin through bleeding, a common problem when using 8-HQ resin as per prior methods. The instrument performance is validated using internationally calibrated reference material (SAFe) provided by GEOTRACES and the values obtained are within the error limits of certified range.

seaFASTTM-pico SC-4 DX (Elemental Scientific Inc.)


This is a completely automated sample introduction system for multi-mode determination of ultra-trace metals in undiluted seawater using ICP-MS. The system can be used in direct mode or pre-concentration mode. Our lab uses this system primarily in pre-concentration mode and is routinely used for analyses of: Fe, Mn, Co, Cd, Zn, Cu, Ni, Mo, Pb and REE.

The method for simultaneous measurement of trace metals using seaFAST system in conjunction with ICP-MS (Agilent® triple quad, 8800) has been validated using GEOTRACES SAFe, GSC and GSP standards.

prepFAST MC (Elemental Scientific Inc.)


The prepFAST MC™ is a fully automated, low pressure chromatography system that isolates elements of interest from the sample matrix and collects multiple discrete eluent fractions for precise isotopic analysis. The syringe-driven system allows sample loading, multiple acid washes, column conditioning and elution cycles all at user-defined intervals (time, volume and flow rate).

Currently, the system is being used to prepare samples for the measurement of Pb isotopes in seawater samples. Future plans include sample preparation for Cu and Zn isotopes.

PicoTrace® sediment acid digestion system


For measurement of trace metals in marine particles we have a corrosion protected system to transfer solid samples to solutions using strong acids (HF, HCl, HNO3, and, H2SO4) under elevated temperature and pressures. The digestion vessels are made from ultra clean TFM. Evaporation of the acids takes place under a closed system. Up to 32 samples can be digested at the same time.

PICARRO L2130-i δD and δ18O High-Precision Isotopic Water Analyzer

Picarro isotope analyzer

Picarro’s L2130-i is a cavity ring down spectrometer that provides a platform for advanced research into all aspects of the water cycle: water vapor, liquid water, or water trapped in solids. The instrument is used for measurement of hydrogen and oxygen isotopes of water. This field deployable analyzer has a full suite of accessories for preparation of the different sample forms and can be deployed on the ship for continuous measurement while steaming.

PICARRO G2201-i CRDS Analyzer for Isotopic Carbon in CO2 and CH4


The G2201-i cavity ring down spectrometer is used for analyzing  the isotopic carbon ratio in both CO2 and CH4  at the same time. This instrument combines the capabilities of Picarro’s two carbon isotope instruments for CO2 and CH4 into a single instrument to gather the insights that stable isotope ratios offer. The spectrometer is linked to a combustion module for analyzing isotopic ratios in solid samples. It is small in size and robust, which makes it easy to transport to the field where immediate and continuous results can be obtained.

Other equipment

A number of other equipment are available that include high precision balances, temperature/light controlled incubators, freeze drier, spectrophotometer and FTIR.

The center also has access to other large equipment such as ICP-MS, Atomic Force Microscope, CT-Scanner, SEM, LC-MS, GC-MS, and Flow cytometer through the Central Analytical Facility of Stellenbosch University for imaging and assessing chemical signatures in biogenic and lithogenic systems.

Publications (TracEx project linked)

  1. Tagliabue, Alessandro, Mtshali, T., Aumont, O., Bowie, A. R., Klunder, M. B., Roychoudhury, A. N., and Swart, S (2012) A global compilation of over 13 000 dissolved iron measurements: focus on distributions and processes in the Southern Ocean, Biogeosciences 9, pp. 2333–2349, doi:10.5194/bg-9-2333-2012.
  2. Sebastiaan Swart, Nicolette Chang, Nicolas Fauchereau, Warren Joubert, Mike Lucas, Thato Mtshali, Alakendra Roychoudhury, Alessandro Tagliabue, Sandy Thomalla, Howard Waldron, Pedro M.S. Monteiro(2012) Southern Ocean Seasonal Cycle Experiment – 2012 (SOSCEx2012): Coupling of Climate and Carbon Cycling at the Seasonal Scale, South African Journal of Science.189(3/4), pp 1-3.
  3. Bjorn P. von der Heyden, A.N. Roychoudhury, T.N. Mtshali, T. Tyliszczak and S.C.B. Myneni (2012) Significant Chemical Variations exist in the Fe-rich Nano- and Colloid-sized Particles in the South Atlantic and Southern Oceans. ScienceV338, pp 1199 – 1201.
  4. Treasure, A.M., Moloney, C.L., Bester, M.N., McQuaid, C.D., Findlay, K.P., Best, P.B., Cowan, D.A., de Bruyn, P.J.N., Dorrington, R.A., Fagereng, A., Froneman, P.W., Grantham, G.H., Hunt, B.P.V., Meiklejohn, K.I., Pakhomov, E.A., Roychoudhury, A.N., Ryan, P.G., Smith, V.R., Chown, S.L. and Ansorge, I.J. (2013) South African research in the Southern Ocean: new opportunities but serious challenges. South African Journal of Science. V109, pp 1-4, DOI 10.1590/sajs.2013/a009
  5. Coleen L. Moloney, Sean Fennessy, Mark J. Gibbons, Alakendra Roychoudhury, Frank A. Shillington, Bjorn P. von der Heyden, Kate Watermeyer (2013) What is the evidence for offshore marine ecosystem 1 change in South Africa? African Journal of Marine Science,V 35(3), pp 427-448. DOI:2989/1814232X.2013.836135
  6. Bjorn P. Von der Heyden, Emily J. Hauser, Bhoopesh Mishra, Gustavo A. Martinez, Andrew R. Bowie, Tolek Tyliszczak, Thato N. Mtshali, Alakendra N. Roychoudhury, Satish C.B. Myneni (2014) Ubiquitous presence of Fe(II) in aquatic colloids and its association with organic carbon. Environmental Science & Technology, Letters, 1; pp 387 – 392.
  7. J. Lam, B. S.Twining, C Jendel, A.N. Roychoudhury, J. Resing, W. Geibert, P. Santschi, R. F. Anderson (2015) Methods for analyzing the composition and speciation of marine particles, Progress in Oceanography,V133, pp 32-42
  8. Von der Heyden, B.and Roychoudhury A. N. (2015) A review of colloidal iron partitioning and distribution in the open ocean, Marine Chemistry, V177(1), pp. 9-19, doi:10.1016/j.marchem.2015.05.010
  9. Von der Heyden, B.and Roychoudhury A. N. (2015) Application, Chemical Interaction and Fate of Iron Minerals in Polluted Sediment and Soils. Current Pollution Reports, V 1, pp. 265-279, doi:1007/s40726-015-0020-2
  10. Baker A.R., W.M. Landing, E. Bucciarelli, M. Cheize, S. Fietz, C.T. Hayes, D. Kadko, P.L. Morton, N. Rogan, G. Sarthou, R.U. Shelley, Z. Shi, A. Shiller, M.M.P. van Hulten (2016) Trace Element and Isotope Deposition across the Air – Sea Interface: Progress and Research Needs. Philosophical Transactions of the Royal Society A.374, 20160190, http://rsta.royalsocietypublishing.org/content/374/2081/20160190
  11. von der Heyden, B.; Roychoudhury, A. N.; Tyliszczak. T.; Myneni, S. C. (2017) Investigating nanoscale mineral composition: Iron L3-edge spectroscopic evaluation of iron oxide and oxy-hydroxide coordination. American mineralogist102, pp. 674-685, doi: 10.2138/am-2017-5805
  12. Das, S. Routh, J. Roychoudhury, A.N. Veldhuis, M.J.W. Ismail, H.E. (2017) Connecting pigment composition and dissolved trace elements to phytoplankton population in the southern Benguela Upwelling zone (St. Helena Bay). Journal of Marine Systems176, pp. 13-23.
  13. Von der Heyden, B., Frith, M.G., Bernasek, S., Tylizszak, T., Roychoudhury, A. N., Myneni, S.C.B. (2018) Geochemistry of Al and Fe in freshwater and coastal water colloids from the west coast of Southern Africa. Geochemica et cosmochimica acta, doi: 10.1016/j.gca.2018.08.043
  14. Johannes Viljoen, Raïssa Philibert, Natasha Van Horsten, Thato Mtshali, Alakendra N Roychoudhury, Sandy Thomalla, Susanne Fietz(2018) Phytoplankton response in growth, photophysiology and community structure to iron and light in the Polar Frontal Zone and Antarctic waters. Deep-Sea Research, Part 1, 141, pp. 118 – 129. doi: 10.1016/j.dsr.2018.09.006
  15. Ryan Cloete; Jean C Loock; Thato N Mtshali; Susanne Fietz; Alakendra N Roychoudhury(2018) Winter and summer distributions of Copper, Zinc and Nickel along the International GEOTRACES section GIPY05: Insights into deep winter mixing. Chemical Geology, doi: 10.1016/j.chemgeo.2018.10.023
  16. Mtshali, T.N., van Horsten, N.R., Thomalla, S.J., Ryan-Leogh, T.J., Nicholson, S-A., Roychoudhury, A. N., Bucciarelli, E., Sarthou, G., Tagliabue, A., Monteiro, P.M.S. ( 2019). Seasonal depletion of the dissolved iron reservoirs in the sub-Antarctic zone of the Southern Atlantic Ocean. Geophysical Research Letters, 46, pp. 4386-4395, doi: 10.1029/2018GL081355
  17. Bjorn von der Heyden, Alakendra N Roychoudhury and Satish Myneni (2019) Iron-rich nanoparticles in the natural aquatic environments. Minerals, 9, 287, doi: 10.3390/min9050287
  18. Johan Viljoen, Ian Weir, Susanne Fietz, Ryan Cloete, Jean Loock, Raissa Philibert, Alakendra N. Roychoudhury (2019) Links between phytoplankton community composition, macronutrients and trace metal distribution in the surface waters of the Atlantic Southern Ocean. Frontiers in Marine Sciences: Marine Biogeochemistry doi.org/10.3389/fmars.2019.00295
  19. Menzel Barraqueta, J.L., De Jonhg, T., Samanta, S., Achterberg, E.P., Bowie, A., Croot, P., Cloete, R., Gelado-Caballero, M.D., Klar, J.K.7, Middag, R., Loock, J., Remenyi, T., Wenzel, B., Roychoudhury, A. (2020) A first global oceanic compilation of aluminium observational data and regional statistics. Frontiers in Marine Sciences: Marine Biogeochemistry 7:468, doi: 10.3389/fmars.2020.00468
  20. Bjorn Phillip von der Heyden; Julien Benoit; Vincent Fernandez; Alakendra N Roychoudhury (2020) Synchrotron X-ray radiation and the African earth sciences: a critical review. Journal of African Earth Sciences,172, doi:10.1016/j.jafrearsci.2020.104012.
  21. R. Cloete, J.C. Loock, N.R. van Horsten, S. Fietz, T.N. Mtshali, H. Planquette, A.N. Roychoudhury (2021) Winter biogeochemical cycling of dissolved and particulate cadmium in the Indian sector of the Southern Ocean (GEOTRACES GIpr07 transect). Frontiers in Marine Sciences: Marine Biogeochemistry, 8, doi: 10.3389/fmars.2021.656321
  22. R. Cloete, J.C. Loock, N.R. van Horsten, J-L. Menzel Barraqueta, S. Fietz, T.N. Mtshali, H. Planquette, M. I. Garcia-Ibanez, A.N. Roychoudhury (2021) Winter dissolved and particulate zinc in the Indian sector of the Southern Ocean: Distribution and relation to major nutrients (GEOTRACES GIpr07 transect) Marine Chemistry, V236, doi.org/10.1016/j.marchem.2021.104031
  23. Saumik Samanta, Ryan Cloete, Jean C Loock, Riana Rossouw, Alakendra N Roychoudhury (2021) Determination of trace metal (Mn, Fe, Ni, Cu, Zn, Co, Cd and Pb) concentration in seawater using single quadrupole ICP-MS: A comparison between offline and online preconcentration setups. Minerals, 11(11) doi.org/10.3390/min11111289
  24. Saumik Samanta, Jan Lukas Menzel Barraqueta, Reshmi Das and Alakendra N Roychoudhury (2022) Source apportionment of the atmospheric Pb using a simulation-based inversion model: a case study from India uncovers bituminous road as the prime contributor of petroleum-derived Pb. Applied Geochemistry, V136, doi: 10.1016/j.apgeochem.2021.105164