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Capacity training for SAEON postgraduate student – first-hand experience in Europe

By Athi Mfikili, PhD Candidate, SAEON Elwandle Node and Nelson Mandela University, Port Elizabeth
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I am a PhD student under the Professional Development Programme* of the National Research Foundation based at SAEON’s Elwandle Node and registered at Nelson Mandela University.

I study the sedimentary deposits of low-lying coastal areas, such as estuaries, to investigate the occurrence and recurrence of past extreme marine events along the South African coast with a strong emphasis on tsunamis.

An African proverb that says “the foot has no nose” – known to Xhosa-speaking people as Unyawo alunampumlo (no one knows their destination), defines my journey in the coastal marine sciences. Having enrolled for a BA in Geography and a BA Honours in Environmental Management for my first two degrees, I never planned to have a career in the field of coastal marine science.

Given the novelty of this study in the regional context, I spent the first year of my PhD studying global literature on the subject and its philosophies. For that purpose, I connected with various scientists across the world who gave me significant input into my project. One of the many things I learnt while doing my MSc is that “you don’t have to know someone to work with them”.

One of the people with whom I established contact is Dr Pedro Costa of the University of Lisbon (now at the University of Coimbra in Portugal), who investigated the sedimentological signatures of extreme marine inundation in his PhD. He used a scanning electron microscope (SEM) to analyse grain surface microtextures on quartz, a recent technique in the interpretation of tsunami and storm deposits.

When I told him about my intention to use the SEM technique in my study, he was keen to host me at the University of Lisbon (at zero cost). I also attended a course on Foraminifera, organised by the International School on Foraminifera at the University of Urbino in Italy.

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Athi prepares samples for SEM imaging at the University of Lisbon in Portugal.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

Grain surface microtextural signatures of different samples along the South African coast. Fresh surfaces, V-percussion marks and adhering particles represent imprints generated as a result of particle collision during transport, whereas dissolved mechanical imprints resulted from immobilisation of grain, and bulbous edges represent the typical dune source environment.

My academic journey in the historical city of Lisbon – “the seven hills”

Lisbon, one of the oldest cities in Western Europe, was hit by a tsunami event in 1755. I do not have formal training in geology, but when the possibility of being trained in grain surface microtextures availed itself, I saw it as an opportunity to learn a new technique rather than a challenge.

During my first two days at the University of Lisbon (27 and 28 May 2019), I worked with Pedro to prepare the samples for the SEM imaging before they were sent to the SEM technician, with whom I spent the following morning (29 May) to learn the imaging technique. I spent the afternoons of 29 and 30 May with Pedro, interpreting different grain surface microtextural signatures from my own and his samples.

Although South African students are exposed to a wide variety of state-of-the-art research instruments to conduct our research, such as SEM, interpretation of the results requires significant human skill. I believe the training I received in grain microtextural analyses has provided me with a new skill beneficial to my research project.


Tsunami deposits along the coast of Algarve. A) Athi collects the sediment core using an auger; B) coarse tsunami layer with some evidence of heavy minerals; and C) sediment profile; the yellowish 10 cm thick layer underneath the muddy layer is the tsunami layer.

The visit to Lisbon was not only about the lab work or being behind the laptop to interpret SEM images, but also afforded me an opportunity to visit known tsunami deposits at Martinhal and Boco do Rio along the coast of Algarve. While tsunami sediment differs from place to place, the field trip to the coast of Algarve gave me first-hand experience of paleo-tsunami deposits. A few cores collected on the trip will be analysed for grain surface microtextures and foraminiferal assemblage and compared with the deposits found in the South African coast.

Without a doubt my 13-day visit to Lisbon was a worthwhile experience – I am now independently able to prepare and interpret SEM grain microtextural images.

18-day course on Foraminifera at Urbino

Unlike for modern extreme marine events in which eyewitness accounts and field measurements of both erosional and depositional effects are utilised, foraminifera (calcareous marine species) assemblages, one of the most abundant microfossils in the continental margin, have been utilised to interpret palaeo-marine events.

The 12th course organised by the International School on Foraminifera at the University of Urbino was structured to accommodate beginners and more advanced participants. The 18-day course, which ran from 9 to 28 June, was attended by over 40 participants from more than 20 countries.

The course was presented by 15 experts from over 13 institutes or universities, with specialisation ranging from benthic to planktonic foraminifera. Each component was organised to give insight into theory and practical sessions, with a field excursion on 24 June to the Gubbio area, where we visited two known oceanic anoxic events** and the Cretaceous–Paleogene boundary at Bottacione.

While I am new to the field of Foraminifera sciences, the course has provided me with much needed insight into the taxonomy, ecology, biodiversity and geological history of these species, which I believe will help immensely in my study. During my time in Lisbon, I observed a few foraminifera species during sample preparation for SEM and imaged two Ammonia species. At the time I had no clue what they were, but after attending the course I can happily say that I now know much more about them.

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Athi during the practical session of the foraminifera course at the University of Urbino in Italy.                                                                                                                              

Athi is awarded a certificate at the foraminifera course graduation ceremony. From left: Athi, Dr Marie Rose Petrizzo, Professor Mike Kaminski, Dr Coccioni and Dr Fabrizio Frontalini.

Potential for organisation-wide collaboration

Former president Thabo Mbeki once said in his speech at the African Student Leadership Summit: “As students [our] principal task is to acquire knowledge as well as the capacity to generate new knowledge.” I have no doubt that the skills I gained at the two institutions will not only help me in my PhD project, but will also contribute to the generation of knowledge in our science community.

Although the visit was about acquiring skills to help me successfully complete my PhD study, it also provided me an opportunity to forge relationships with other scientists. Apart from being utilised in paleoclimatic events, foraminifera are also used in biomonitoring studies.

Dr Fabrizio Frontalini, a specialist in benthic foraminifera and one of the organisers of the International School on Foraminifera, has shown interest in visiting our institution should the opportunity arise. As part of my ongoing collaboration with Dr Pedro Costa we plan to publish collaborative papers on grain microtextural signatures.


Athi at Gubbio, one of the most ancient medieval towns of the Umbria region in Italy.

This trip has been a rare opportunity that every postgraduate student dreams about. I would like to express my sincere gratitude to my supervisor, Professor Tommy Bornman, manager of SAEON’s Elwandle Coastal Node, SAEON MD Johan Pauw, SAEON research administrator Beate Hölscher as well as the support staff at the node and the SAEON National Office who have made this trip possible.

* The Professional Development Programme (PDP) of the Department of Science and Innovation and the National Research Foundation aims to accelerate the development of scientists and research professionals in key research areas. 

** Intervals in the Earth's past where portions of oceans became depleted in oxygen at depths over a large geographic area.

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