Diatoms of the Groot River, and other ingredients that made a freshwater ecologist

Mia Otto
20 May 2019

My grandmother must have loved this mountain. As I sit on the back stoep of our little wooden house in Forest Drive looking up at the mountain, in which shadow this little town lies, I try hard to imagine what she must have been thinking when she looked at this green backdrop. She, Chrissie Otto, bought this erf in 1960, together with her brother (Hermanus Lombard) and a family friend (Kok Geel). When they came here for the first time it must have been so wild and densely vegetated, untouched. In many ways, as it still remains today.



The house in Forest Drive which sits at the foot of the mountain that, together with the Tsitsikamma National Park, shelters the town from its surrounding areas.

There are, however, a few things that did not remain the same. When Ted Holmes built our home in the early 1960’s there were no tar roads or electricity in town and this remained, to a large extent, the same till relatively recently. The only telephone could be found at the shop which, in those days, was owned by the Combrincks. This was the time before the Otter Hiking trail and N2 highway. All the traffic heading from Plettenberg Bay to Port Elizabeth had to drive via the Groot River and Bloukrans passes, among others. While many popular things today were not yet developed in that time, the one thing that was and remains so, is the Sout River hiking trail. I remember walking this trail with my grandfather and dad for the first time when I was very young. It is a special place, our own little piece of “The Beach”. A tucked away oasis of calm where river meets sea, and where among the white round stones and tall dark overhanging trees, my love affair with rivers really started.


The Sout River Bay as viewed from the footpath above. The Sout River enters the bay on the right where the lighter brown tannin-loaded waters can be seen.

I spent most of my holidays as a child in Natures Valley. I came here for the very first time when I had just turned 1 year old. Since a very early time in my life the misty mornings filled with the rumbles of high-tide and a Loerie’s call spoke to my soul. I am often asked how I ended up being a freshwater ecologist and I always answer with: “I did not choose it, it chose me”. While there have been many wonderful “coincidences” and opportunities along the way that brought me to writing this article today, it all started, without a doubt, right here in this little town in the forest by the sea. Natures Valley connects all the different aspects of so many ecosystems together in the most beautiful of ways. Marine conservation, for instance, is not independent of inland freshwater conservation. As you all know now, mostly due to recent awareness raising campaigns, plastic is an example of an upstream problem which concentrates on the coast causing catastrophic effects for marine life, coastal ecosystem functioning and human health. With the Groot River estuary, the Groot and Sout Rivers, the mixed fynbos and forest canopy, a rocky shoreline and beautifully conserved sand dune barrier between the houses and the beach, Natures Valley brings together a multitude of ecosystems in one small space on the Garden Route. One easily spends time in more than one of these ecosystems in one day, which is very important when trying to understand our natural ecosystems, how they interact and function and why its important to conserve our natural resources across our own preconceived ideas of ecosystem barriers.


The Groot River opens up into the estuary which in turn, depending on whether the mouth is open or closed, flows into the Indian Ocean.

The preservation of the entire town’s natural assets, to a great extent, have contributed directly to the high level of resilience, ecosystem health and species conservation found here today. It is no wonder then that when my Professor, Jo Van As, asked me where I was planning on sampling diatoms for my PhD, I said: “Anywhere the data is needed and the Groot River at Natures Valley”. He and his wife, Liesl Van As, had never been to Natures Valley and spending time in the town and its surrounding area during my PhD sampling now has an even more special place in my collection of memories, especially since his passing earlier this year.


The Groot River as seen from the bridge looking upstream during January 2015 sampling.

As many people today would realise, water is our most valuable commodity. It is certainly something that made me take an interest in freshwater resource management and conservation as a student, but these days it really has become a responsibility that is shared by each and every person living on this planet. South Africa is a semi-arid country and with expected climate change projections showing that our rainfall will most likely become more infrequent and more intense, ecosystem management towards increased resilience to withstand these events, is of the greatest importance. Natures Valley has been abstracting its water from the Groot River since the very beginning of the town sometime around the 1940’s. Today this river is still considered the lifeline, or main artery, that provides us with the water we require. This places a certain responsibility on the town, its visitors and the surrounding agricultural community to save water, and to not pollute the water. It seems so easy at this small scale, but let’s not forget that the role of the Tsitsikamma National Park cannot be underestimated. The fact that more deforestation and agriculturally intense activities have not developed in the upper catchment is largely due to the terrain and the protected status the ecosystems in town and its surrounding area enjoys by the South African National Parks (SANParks).

NV diat

The town of Natures Valley lies imbedded into the Tsitsikamma National Park’s coastal forest. In the back the Groot River valley can be seen which opens into the Groot River Estuary.

Take for instance the Marine Protected Area (MPA). It spans 80km along the coastline and is one of the oldest and largest MPA’s in the World. It was the first MPA to be declared in Africa back in 1964. It is considered to be our most important marine reserve protecting 11 of our 17 endangered fish species, some more critically endangered than the Rhino. With the ocean stock fish being depleted at incomprehensible rates, areas such as the 5km wide stretch of marine protected ocean running in front of the town are of immeasurable importance for conserving and restocking the ocean. They provide a safe haven for fish to reproduce, feed and grow into strong adults who can migrate into other areas from here. It is therefore very concerning that in November 2015 the Minister of Environmental Affairs announced that the government would allow recreational fishing in what used to be a no-take MPA. On the beach we have seen African Black Oystercatchers re-establish and successfully raise young on a regular basis. This bird is today considered to be near threatened and have found a way to fight back after reckless beach use and driving, coastal developments and habitat loss pushed them to the brink of being declared a species that’s on the way to extinction. The role of national protection either via National Park or MPA cannot be overstated and together with the research and conservation efforts of the Natures Valley Trust (NVT) it gives us hope that these measures and efforts will continue to be successful in future.


The rocky Indian Ocean shoreline that graces Natures Valley. The Tsitsikamma MPA is the oldest one in Africa and one of the largest in the world. It is instrumental in protecting our critically endangered marine species and from a more holistic point of view also the oceans’ biodiversity.

These and many other conservation efforts have to a great extent also enjoyed success due to the role the town and its people have played over the years. The entire town with its green belts running throughout and its overall mindfulness to the other living beings that share the area with us have been instrumental in the conservation efforts. I have no idea why the town has no street lights yet, but I love that it doesn’t, and I hope it stays that way. This may sound like an insignificant decision but to the species dependent on the cover of night for their survival, it is everything. Now while many things have remained the same, some other aspects of the town’s biodiversity have changed over the years. The bush pig for instance did not frequent the backyards of people living in Forest Drive fifty years ago. Also, the baboons were not often found in town. They were most likely too skittish back in those days to come close to humans. However, with increasing human populations and associated suburban developments some species are well documented to have found ways to extort our presence. Rats, hadedas and pigeons are among the species that are well known for this, but the same could be argued for baboons and bush pigs in Natures Valley. While some species suffer tremendously at the hand of human related developments and associated habitat loss, others thrive on the changes we make and the “left-overs” we come with. I personally enjoy having these species in town and stumbling across a bush buck on a morning jog, as long as we remain conscious of the fact that these, and all the other animals in town, are wild animals and should be respected and never be fed. This proved to be a valuable reminder and lesson for many people during the recent baboon incidents.

It was during 2013 that I first discovered South Africa do not use diatoms and other algae as part of their national bio-monitoring program. I was working in South America on a hydroelectrical dam development in the Peruvian Desert when the World Bank, which was funding the development, insisted we sample algae as part of the project. I realized the value of diatoms and decided that I would have to do my PhD on these organisms. At that stage I was working for a consultancy in Cape Town and doing my Masters on riparian vegetation at Stellenbosch University. The leap to diatoms would therefore not be unachievable, but it would put me at a disadvantage compared to international students who had been working on diatoms since their undergraduate years. Still, I knew this was where information was needed and I wanted to make a contribution towards stronger monitoring and management of freshwater resources in South Africa.

I flew up to Bloemfontein and met with Prof Jo and Liesl Van As with whom I had done my undergraduate and hons studies. I asked them if they would be open to the idea of me working on diatoms if I did a PhD at the University of the Free State. I remember being very nervous since not many universities were doing diatom work at that stage, nor were there PhDs readily available on the subject. I was relieved when he said “I don’t care what you want to work on, as long as its aquatic, relevant and good science we will make it work”. He asked me who the top person in this field was in South Africa and I told him that there was only one person, at that stage, that knew the business of diatoms, Jonathan Taylor at the North West University. He gave me a departmental car and instructed me to drive through to Potchefstroom so I could meet with Jonathan and get him onboard. The first good decision I made when I embarked on my PhD was meeting with Prof Jo and Liesl Van As, the second was meeting with Jonathan Taylor and getting him onboard as a co-supervisor. A great team is often the make or break of a project. With supervisors, department and funding sorted, I packed up my life in Cape Town and drove up to Bloemfontein, where I spent the following 18 months playing catch-up on everything related to diatoms. Prof Jo Van As had not worked on diatoms before either, so he had me prepare a 30 min slide show each week on a different aspect of diatoms which he would then have me present to him in his office. Together we explored and discovered the interesting world of diatoms.

Group4On our journey with diatoms there were many opportunities to present the research to a variety of audiences. Pictured here was the final departmental seminar day in 2017 where I received the prize for best PhD research presentation. Left: I am receiving the prize from Prof. Linda Basson and Dr. Charles Haddad. Right: Prof Jo and Liesl Van As with myself at the prize-giving event.

Diatoms are brown algae that keep the river healthy and are at the base of the food web. If the diatoms are not healthy, it is an indication that the water quality is being impacted and that something may be causing the river to become degraded. By looking at different species combinations and numbers in a river you can tell quite easily which aspect of water quality is being impacted. For instance, if the water is suddenly becoming more acidic than usual, some species with a tolerance to more acidic water will be disproportionately abundant compared to others that may be sensitive to this sudden change in pH. Furthermore, by looking at the health of the diatoms (i.e. cell shape/deformations and chloroplast functioning etc.) one can pinpoint the origin or suspected cause of pollution or impact. For instance, pesticides and herbicides associated with agricultural runoff not only impacts the water quality and subsequent diatom community composition, it also causes cellular deformations that provides information on which type of pollutant is leaching into the water. It is because of this reason that diatoms are used world-wide as a diagnostic tool in rivers and other associated freshwater and marine ecosystems. Yes, diatoms are major role players in the ocean as well. In fact, they are so abundant in oceans that they are estimated to remove more carbon from the atmosphere than all the rain forests in the world put together. Diatoms are the proverbial canaries in the cage for freshwater ecosystems. They are an early warning system for changes in freshwater systems, long before other aquatic species start dying or showing the negative side-effects of pollution and degradation.


A makeshift aquatic laboratory is set up in our house in Natures Valley to analyse and photograph live diatom specimens from the Groot River and neighboring catchments. On the right I am back in the Aquatic Laboratory in the Free State where we continued the processing and analysis of samples collected on our fieldtrips.

The aim of this study was to collect diatom information on rivers that had no existing information as far as the National Diatom Collection goes. Some, such as the Great Fish and Sundays Rivers had been sampled before but only back in the 1950’s. No recent up-to-date information was available to support the inclusion of diatoms into biomonitoring programs, and since monitoring is done by means of a reference condition, one had to be established for these rivers. During 2014 and 2015 I travelled across the Eastern Cape and down into the Garden Route to sample diatoms from 26 selected rivers. We did four sampling trips which started in Hogsback and snaked down to the coast via Adelaide, Somerset East, through the Baviaanskloof to Patensie, past the Tsitsikamma River and across many short coastal rivers between Storms River and Wilderness ending the sampling trip at the Kaaimans River between Wilderness and George. Each fieldtrip was unique. The first one served as both a reconnaissance and sampling exercise to see where these rivers were, where their Department of Water Affairs gauging weirs were situated and if it was realistically feasible to sample these sites for another three seasons (if it was dangerous, too far out of the way or if the river was too impacted or degraded to be considered for sampling). My dad accompanied me on two of the four trips, the first one in Oct 2014 and the last one in July 2015. After sampling riparian vegetation with me on rivers in the baking hot Cederberg for my Masters degree, he has become well trained in the role of field assistant over the years. It was during the third trip in autumn that the Profs joined me. We would walk through the streets of Natures Valley in the evenings after dinner and a long day of river sampling, drinking in the quiet and recharging our kindred nature-loving souls. Especially Prof Jo was quite taken with our little town even thinking out loud about perhaps acquiring a property when we were on these walks.


My dad and myself sampling the Groot River during the reconnaissance trip of October 2014. To the right I am at the river about to take water quality measurements with a hand-held water meter

The second trip was in January and I had two Masters students with me. After being pooped on by monkeys during a hail storm in Hogsback, a close encounter with a snake at the Mentz Dam and heat stroke and buffalo fear in the Baviaanskloof we had finally made it out the other side at Patensie. With two shook up students I set out towards the end of the trip to sample the Bloukrans River down at the bridge in the pass. On the way back up we decided to stop for lunch at one of the picnic tables. We had not even set the food down on the cement table when a troop of baboons came down on us from the steep cliffs next to the road. The one female had only one arm and another had half a tail. This was a proper group of bandit baboons and they made it clear they were not going to ask permission to have our food. Chaos erupted as we ran for the car. As soon as I got behind the wheel the one student next to me in the passenger seat started making the strangest wimping sounds like he wanted to yell but was being strangled. All I could see in that moment was an open window (it was so warm that January) and a little hand being placed on the door as she started to climb up towards the student. I tried getting the key into ignition so we could close the window but alas, the next thing I know I see food flying. The student had lost his nerve and there went our lunch flying out the window, buying him time to get away from the little hand that had invoked fear after two weeks of hard fieldwork time. We drove off, watching our apples and sandwiches disappearing behind greedy incisor-lined lips.


We took this picture at the bottom of the Bloukrans Pass in the river after completing our sampling. On the right I am walking towards the picnic table and taking their picture when they suddenly spot baboons descending on us. This picture was taken mere seconds before they started running towards me (and the car).

In total 42 diatom species were identified from the Groot River during this study. As far as we know, no one has ever sampled the Groot River for diatoms before, as was the case for the majority of rivers in this study. The most abundant species throughout all four seasons were; Eunotia incisa, Eunotia minor, Tabellaria flocculosa and Frustulia saxonica. The seasons with the most species diversity was found to be winter and spring. The average pH for the river over the sapling period was 5.16. This is considered to be fairly acidic. However, acidic water is not unexpected for this region as the high level of tannins in the short coastal rivers of the Southern Cape are a natural feature. Tannins are a natural organic material that is a by-product of the break-down of decaying vegetation. Water passes through peaty soil and decaying vegetation and it usually gives the water a yellow-brown or tea-like color. It is completely natural for the Groot River to have high levels of tannins with its characteristic tea colored water and the diatoms confirmed this.

Eunotia minor is known to occur in circumneutral waters, while Eunotia incisa prefers upland streams of an acidic, oligotrophic and electrolyte-poor nature. This makes Eunotia incisa well suited to being a prominent driver of community identity in the Groot River. The river is acidic as discussed above and flows over a short distance to the coast with rapid changes in slope. The Groot River is classified as a mountain stream geomorphological unit type with a slope of 0.256, as per the description by Rowntree et al. (2000) and therefore naturally has lower nutrients available than would be associated with slower flowing lowland rivers. The Groot River is also classified as being part of the Southern Eastern Coastal Belt Ecoregion (Level I).


When diatom samples are chemically cleaned of all organic material, only the glass frustule (diatoms have cellular walls made of silica/glass) remains. Taxonomic identifications are made based on the size, shape and other features (such as striae/lines seen in the pictures) of the frustule. These are pictures of the four most abundant species found in the Groot River during this study.

Tabellaria flocculosa is known to flourish in electrolyte-poor and acidic waters. The cells are linked at the corners forming zigzag colonies. Frustulia saxonica is described as being a cosmopolitan species occurring in dystrophic, acidic, electrolyte-poor waters. It is therefore safe to say that the diatom community showed the water quality to be as expected and that these results showed that the aquatic food web, at its base, can be considered to be in very good health.


These are photographs of live diatoms taken during fieldtrips. Notice how different these organisms can look when alive. On the left: Frustulia saxonica with its very distinct raphe (the line running down the middle of the frustule). On the right: Tabellaria flocculosa (viewed from the side – also known as girdle-view) form zigzag formations by attaching to one another at the corners of their frustules. Notice how different the colony appears when compared to a single cell viewed from the front (valve-view) in the cleaned sample photos above.

It is important to note that four species do not make the river. Another 38 species play an important role in community composition and inter species relationships. They are all part of the ecosystem that provides food to macroinvertebrates, phytoplankton and fish. While these four species were found to be the most abundant during sampling, they are not disproportionately favored due to imbalances in nutrient load or adverse water quality characteristics (i.e. water temperature, dissolved oxygen and conductivity). Over many thousands of years, the diatom community found in this river has become accustomed to the high tannin load and low nutrient availability. The community is therefore well adjusted and suited to the natural water quality characteristics but would because of this very same reason become lopsided if these natural conditions were to suddenly change.

These conclusions on ecosystem health and good water quality were supported by the water quality readings taken at time of sampling. While most of us will know that this result was to be expected, the real value of the data lies in continued monitoring to assess the impact of changing climate patterns and continued developments upstream to diagnose the potential future causes of degradation before it becomes catastrophic. A baseline data set such as this one, which is found to be at near-pristine or natural state of the river, should be used as a reference point for future assessments of water quality and ecosystem sustainability.


In July 2018 I was offered an invitation, and sponsorship, to join the International Diatom Association in Berlin, Germany, to present my research to the international community at their biennial conference. At this conference I presented information on the Groot River, and all the other rivers I had the privilege of sampling during my PhD. I was the only PhD student from Africa at this conference, which is a testimony to the need for more diatomists in Africa, and especially South Africa. Right: The Young Diatomists is a group of early career scientists dedicated to promoting, supporting and connecting young diatomists from around the world. I am happy to be a part of this international community and to have been elected one of their core team members. No matter how late, old or from where you start, nothing is impossible.

Currently the water of the Groot River is sufficient to keep the town going all year round, however, it cannot be overstated how important water-saving is and will continue to become in the future. It is not even too far-fetched to argue that the area might become more fynbos dominated than forest in future. The ability for the ecosystems to continue providing ecosystem services to the species dependent on these resources, including humans, will be directly dependent on human behavior over the next 10 to 30 years. If we all choose to use less single-use plastic, to not waste water, think before we remove plants from our yards, plant indigenous plants when we do landscaping, recycle as much of our trash as we can, not feed the wild animals, use biodegradable soaps, sunscreens and detergents and many more of the ways in which we can each continue to make a contribution, only then will we ensure that our children and grandchildren get to experience and fall in love with the nature in this valley of a town named so appropriately.

For more details on this study feel free to contact me Mia Otto at miaotto2911@gmail.com. Alternatively, the study can be viewed and downloaded here.