#03 2023

Adding visual pieces to South Africa’s seabed puzzle

By Dr Lara Atkinson, Offshore Marine Scientist, NRF-SAEON Egagasini Node

Like many environmental researchers around the world, the SAEON offshore biodiversity team had not been able to get out into the ocean to conduct biodiversity surveys since the Covid pandemic. Our SkiMonkey towed camera had been sitting securely under its cover for a few years. But all this was about to change. 

We had all the paperwork in place to secure 10 days on the Ellen Khuzwayo research vessel belonging to the Department of Forestry, Fisheries and the Environment (DFFE). The SkiMonkey’s cover had been lifted and all her working parts thoroughly serviced, new sensors installed and she was ready to explore the depths.

It was however with a fair amount of trepidation that all the equipment was loaded onto the vessel – the weather forecast was not looking favourable, with two large frontal systems predicted during the survey. While the Big Wave surfers were waxing their boards and revving their rescue craft engines, we were hoping for less than 2 m swells, less than 10 knot winds and gentle currents! Regardless, we had waited too long for this opportunity and after the calm assurance from the Ellen captain (Captain Raul Mulligan), felt more confident we would find the gaps in the weather to do what we needed to do.

We sailed out of Cape Town on 23 May, one of those perfect calm, clear winter days that Capetonians cherish, yet also call ‘the calm before the storm’. Our first station was strategically placed inside the Robben Island Marine Protected Area (MPA), not too far from Cape Town, for gear trials and a training exercise.

V221 Offshore Biodiversity 2023 Survey scientific team: Front row, from left: Cruise leader Dr Lara Atkinson (SAEON), Kezia Samuels (DFFE), Safiyya Sedick (SAEON) and Zonke Gumede (CapMarine). Back row, from left: Sean Lavis (Sea Technology Services intern), Silke Brandt (UCT PhD student), Grant van der Heever (DFFE Rock Lobster scientist) and JJ Forgus (SAEON).

The real star of the show – SAEON’s towed camera SkiMonkey III.

This survey was the first for SAEON’s newly appointed offshore biodiversity technician, Juan-Jacques (JJ) Forgus, who was going to be learning how to operate the SkiMonkey towed camera. For this in-situ hand-over training, Grant van der Heever (the Egagasini Node’s previous technician) was onboard, joining us for just one day of the cruise (for which we thank his managers at DFFE) to share his knowledge and experience with JJ.

It is always with great excitement and a good dose of anxiety that we all stare at the dark computer screen as the camera descends, watching the depth reading until it is time to turn on the lights at about 10 m from the predicted seabed… we are never sure what we’re going to see – if anything at all! The first deployment at 126 m depth was as exciting as these live-stream visual surveys always are, however, it was not without challenges.

Sean and Grant doing final checks before deployment.

SkiMonkey team pleased with themselves after a successful deployment (Grant, JJ and Sean).

“Movie time” in the ops room – the focus is palpable.

Initially the tow was smooth, and we got some great imagery of mantis shrimp (Pterygosquilla capensis), brittle stars (Ophiomyxa capensis), starfish (Toraster tuberculatus and Anseropoda grandis), sponges, some sea pens, the blush anemone (Bolocera kerguelensis) and darting fish such as dragonettes (Paracallyionomus costatus) and hake (Merluccius spp.). However, towards the end of the transect we kept losing connection with the camera and after four restart attempts, decided it was best to retrieve the system onboard.

Although we are not certain what exactly was causing the camera to disconnect, on retrieval it became evident that the one solid buoy had been crushed by the pressure at 126 m and this may have caused the camera system to become unbalanced and tow strangely. Luckily, we had a spare buoy and with some adjustments we were ready to proceed.

A beautiful blush anemone (Bolocera kerguelensis) on full display inside the Robben Island Marine Protected Area.

Soft coral (Anthomastus giganteus) providing a dreamy refuge for a juvenile jacopever (Helicolenus dactylopterus) and several brittle stars (Ophiura costata costata and Ophiomyxa vivipara capensis).

From left: White anemone (Actinauge granulata), shallow anemone hermit crab (Sympagurus dimorphus), jacopever (Helicolenus dactylopterus) and pancake starfish (Anseropoda grandis).

Master of disguise – angler monkfish (Lophius vomerinus).

South Africa’s most valuable commercially harvested fishery species, hake (Merluccius spp.).

Benguela Muds MPA

After dropping Grant off onshore, we set off overnight aiming to survey the offshore Benguela Muds MPA at first light. Now it was up to JJ Forgus and Sean Lavis (an intern from Sea Technology Services, also gaining his first experience of the SkiMonkey operations) to connect us to the seabed.

The next morning dawned with clear skies, a small swell but a bit of a wind blowing that would build throughout the day. We were all excited to really be out at sea, no land in sight and on the continental shelf edge region.

Just as the sunlight crept onto our faces, the SkiMonkey was plunged into the darkness of 400+ m depths. The 15 minutes it takes for the camera to descend to that depth, through the inky darkness, where we don’t even dare turn on the lights and waste our precious battery power, feels like hours… but according to the carefully recorded data sheets, it really was just 15 minutes before we could see the seabed, 414 m below us.

This level of technology never ceases to amaze me. Who could believe that we can sit warm and dry in the ops room of the ship watching a screen that shows us exactly what is happening at that exact moment on the seabed more than 400 m below us! Exactly this technology, and even more advanced tools operating at extreme depths well over 1000 m, are being deployed every day in some part of the global ocean. For now, it was our turn to absorb the video stream being relayed to us from the seabed of the Benguela Muds MPA.

Some beautiful imagery of brittle stars (Ophiura trimeni) ‘dancing’ on their tippy toes, spiny eels (Notacanthus sexspinis) peeking out from muddy burrows, deep-water anemone hermit crabs (Parapagurus bouvieri) scuttling across the mud and the master of disguise – angler monk fish (Lophius vomerinus) doing its best to remain hidden, flashed across the screen. And then all too soon, the 20-minute transect was completed and JJ called on the radio to our ever-patient bosun, Ronald Nomdoe (the ship winch operator), to bring the camera to the surface.

This 100% successful SkiMonkey deployment and retrieval set the tone for the rest of our survey. We proceeded to collect replicate grab samples for PhD student Silke Brandt’s research and completed another two stations, including a dredge to collect epifauna for processing, before the early winter sunset forced us to end the day’s sampling, but what a successful day it had been.

Orange stripe brittle star (Ophiura trimeni) ‘dancing’ on tippy toes.

Spiny eel (Notacanthus sexspinis) peeking out from a mud borrow, watched by a jacopever (Helicolenus dactylopterus).

Cape Canyon MPA and offshore of St Helena Bay

Steadily, and with continual weather forecast updates from the Captain, we proceeded to tick off our planned station sampling one by one over the next few days, working from the far offshore areas of the Benguela Muds, the mid-shelf area of the Cape Canyon MPA and to the more inshore areas outside St Helena Bay spanning between 414 m and just 64 m depths. Not all stations were easy to sample, and we had some trouble shooting to resolve along the way, but between JJ and Sean, they embraced the learning curve challenges and always had the camera ready for the next deployment.

It was with great excitement and a lot of “fear of missing out” that all seven scientific team members would crowd into the confined ops room to enjoy “movie time”, as the live-stream sessions became known. In areas known to be rocky and not suitable for the towed SkiMonkey camera, we deployed the Drop Camera, which has a similar frame as the SkiMonkey, however has a more rugged and simplified housing that holds a GoPro camera with two lights. The positive of the Drop Camera is that it is rated down to 1750 m depth, however the negative is that there is no live feed so we have to wait until the system is returned to the deck before viewing any imagery.

We also obtained nine grab samples providing seabed sediment for profiling the grain size and the infauna (tiny animals less than 1 mm in size that live within the seabed) and dredge samples of epifauna (larger animals living on the surface of the seabed) from 16 stations. The epifauna were all carefully preserved for barcoding through the SeaMap project of the Foundational Biodiversity Information Programme (FBIP).

SkiMonkey III, with the cone dredge attached, being deployed at first light.

Successful sample from the benthic grab, with Silke Brandt about to collect a sediment sample.

Finding shelter in Hout Bay

Although we had been evading the worst of the frontal systems sweeping across the country, as we proceeded towards our southern stations, the captain cautioned that we needed to seek shelter from a large approaching frontal system that would likely prevent sampling for a few days. After completing two stations on Sunday 28 May, we steamed to the shelter of Hout Bay and set anchor to await the imminent storm.

Although we arrived in Hout Bay to a rather balmy and calm winter’s day, it was just a matter of hours before the wind had increased and churned the ocean into white sheets of spray and began battering the Ellen from all sides. The storm continued through the night and on Monday 29 May the primary focus of the crew was to keep the ship steady on anchor. The top wind speed recorded on the ship anemometer on that Monday was 86 knots (159 km/hour), which is well above the Beaufort Wind Scale category 12 of “Hurricane force” (> 64 knots) and was the highest wind speeds ever experienced by the science team and many of the most experienced ship crew. I now better understand “extreme weather conditions” and the warnings associated therewith.

The arrival of the rain late on Monday, which meant a drop in wind speed, was a welcome relief for all and we could again walk more upright when moving around the ship. We remained on anchor in Hout Bay the whole of Tuesday, waiting for the sea state to calm to within manageable working conditions.

It was again a jubilant atmosphere onboard when we awoke early on Wednesday morning to the sounds of the anchor being hauled, which meant we could exit Hout Bay and attempt to survey and sample our few remaining stations offshore of Cape Point. Although the sea conditions were very challenging at these stations, we persevered and eventually managed to complete the required sampling, including an additional two stations en route back to Cape Town.

True to the wildly diverse moods of the Cape, we sailed into Cape Town harbour in the early evening of another magical, calm winters day which seemed very fitting to welcome us back, full circle, from when we had departed.

Overall, Voyage 221 onboard the R/V Ellen Khuzwayo was a resounding success, with a total of 21 west coast stations visually surveyed in eight different ecosystem types including three marine protected areas, 16 dredge deployments yielding > 300 epifaunal specimens for barcoding, 12 epifaunal specimens and 14 sediment samples collected to target for actinobacteria cultures, nine individual grab samples collected for infaunal community composition and eight sediment samples collected for particle size analysis.

Additionally, we collected some targeted specimens requested for projects being run through Iziko Museum and DFFE Oceans and Coast. All visual imagery and sediment particle size data will contribute towards the forthcoming National Biodiversity Assessment marine ecosystem classification and all specimens collected will contribute towards the barcoding component of the SeaMap project.

This success was only made possible by a large number of people, both behind the scenes on land and every single person onboard the vessel, from the bridge to the deck, the engine room, the galley and the scientists. The professionalism, dedication and flexibility displayed by the captain and crew of the R/V Ellen Khuzwayo was outstanding and much appreciated. The scientific team were equally exceptional and always enthusiastically ready to leap into action and get stuck into the work whenever needed.

After three years of waiting (mostly for the pandemic to end) and planning, I personally feel deeply satisfied with my renewed connection with South Africa’s offshore seabed biodiversity as a result of this research survey. Now for the lengthy data processing and taking the field work to the next level of the value chain.

The R/V Ellen Khuzwayo deck crew and Sean Lavis preparing to deploy the benthic dredge.

A rare moment for the science team to simply appreciate the vast ocean and just being at sea.


With thanks and gratitude to Johan Rademan from DFFE and the Captain and crew of V221 on the R/V Ellen Khuzwayo. SAEON funded the charter of the vessel and SeaMap will fund the DNA and bacteria sample processing.