Mesophotic Coral Ecosystems in Indonesia

Mesophotic Coral Ecosystems in Indonesia

Figure 1. Illustration of the vertical transition, from shallow to mesophotic depths.

The Twilight Zone… No, it is neither the name of a fancy new Disneyland attraction, nor the sequel of a famous teenage vampire movie. It is actually the unscientific way of referring to a very peculiar place in our Oceans. It’s a transition area, where the natural sunlight is heavily dimmed as the depth increases. In tropical and sub-tropical environments, this is where we find underwater habitats rarely accessed by scuba divers: the so-scientifically-called Mesophotic Coral Ecosystems (MCEs; Figure 1).

MCEs are composed of a community of light-dependent corals and other associated organisms typically occurring at depths between 30 to 150 metres <2; 3; 5>: sponges, soft corals, fish, invertebrates - you name it (Figure 2). As you go down the reef slope, the pressure increases and you will notice changes in marine communities along this vertical gradient, from shallow to deep. But in actuality, the transition towards mesophotic habitats seems to be more influenced by light rather than depth, as suggested by a recent study by Tamir et al. (2019) <8>. That means that under certain light conditions, MCEs might begin deeper than the 30-40 metres used in the general definition to separate them from shallow coral ecosystems. This currently acknowledged depth-based definition seems to be actually mainly based on SCUBA diving regulations, more than on scientific facts.

Figure 2. Soft coral encountered during our ascent from a deep dive, -66 m.


In any case, these ecosystems are deep. Sometimes very deep. Due to the difficulty of accessing these depths, MCEs are greatly under-studied and, until recently, rarely considered by the scientific community. A 2008 review revealed 87% of all coral reef literature did not report sampling beneath 30 metres. However, it has been suggested that these deeper reefs may play a crucial role in the resilience of coral reefs globally, which is necessary to maintain healthy marine ecosystems <7>. On a case by case basis, MCEs might provide a refuge for some coral and fish species in the face of climate change and increasing anthropogenic pressures in the shallower waters, including fishing, tourism, chemical pollution, habitat destruction, noise pollution from recreational or commercial ships and more (Figure 3) <1; 6>. Interest about MCEs has been publicly confirmed by the recent publication of an exhaustive report from UNEP (“United Nations Environment Programme”), underlining the importance and emergency to study them <1>.

Figure 3. MCEs can also act as nursery grounds. Juvenile three-spot angelfish, Apolemichthys trimaculatus, hiding in a crack on the seafloor, at -60 m.


In spite of Indonesia being located in the heart of the Coral Triangle, a biodiversity hotspot where you can find the highest number of marine species on the Planet, virtually no work has been conducted on MCEs in this country. Surprising, considering many local communities depend directly on coral reefs for their survival.

In recent years, observations have been made year-round on the north-eastern coast of Bali, Indonesia, during technical dives to depths of 60 to 100 metres. Emblematic species of fish like sharks, trevallies, tunas and bump-head sunfish (Mola alexandrini) have been observed regularly. Some of them were displaying a quite interesting behaviour, rarely documented, if ever, at those depths. Indeed, some individuals were engaged in cleaner fish interactions. It means that some specific reef fish were acting as cleaners, removing parasites and dead skin from the surface of bigger fish’s bodies. The sunfish observations are similar to those seen on the shallower reefs in the Nusa Penida Marine Protected Area <4>, a small island in front of Bali, where they are seen by scuba divers during August-October each year <9>. Until now, cleaning events of sunfish on deep reefs in the Bali region have only been reported anecdotally (Figure 4). The bumphead sunfish is the biggest bony fish currently living on the Planet. It is able to reach over three metres in total length, weighing up to two tons, but yet, not much is known about this animal, often confused with its cousin, the ocean sunfish, Mola mola.

Figure 4. Bump-head sunfish, Mola alexandrini, and its cleaner fish, the longfin bannerfish, Heniochus acuminatus, -75 m.


So, to sum up: there is a huge emblematic and mysterious fish displaying undocumented behaviour at those depths in a country considered the epicentre of the Coral Triangle, but where MCEs have virtually never been studied… That is a gold subject for any marine biologist and scientific technical diver! It was quite easy to find motivated and skilled people to help set up a challenging and pioneering pilot project on the matter: Dr. Marianne Nyegaard, world-renown sunfish expert and discoverer of the hoodwinker sunfish, Mola tecta; Marc Crane, CCR instructor who is among the first to have reported those behaviours on deep reefs in Bali, and of course, our Indonesian scientific partner without whom none of this project would have been possible, Dr. I Gede Hendrawan, an experienced oceanographer and conservationist from the Faculty of Marine Sciences and Fisheries of Universitas Udayana in Bali. That was the easy part… Despite the scientific interest of such a project, finding funding is always a challenge and implies a lot of time in front of a computer screen, calculating budget estimates and writing proposals that are sent to various organisations, hoping that at least one of them will accept to help you.

After few months, a great news arrived in the email box: the French Embassy in Indonesia had selected the project and agreed to finance us. This was followed a few months later by another amazing update, the National Geographic Society – the holy grail for most of us scientists – had accepted to support our work as well through an Early Career Grant! From a faraway dream, the project was finally becoming reality. We were lucky to also have trusted technical partners who were involved since the early stages and provided critical tools and equipment necessary for the safety and comfort of the divers and data collection. After all the administrative and legal aspects were taken care of, granting us the right to legally conduct research in Indonesia, it was time to finally jump in the water (Figure 5).

Figure 5. Long hours spent in front of the computer prior to any research activity in Indonesia.


Besides documenting for the first time the general composition of MCEs in the North-East of Bali (Figure 6), one of the main questions we are exploring with this pilot project is if deep “cleaning stations” exist, or if large fish engage in cleaner-fish interactions at random along the reefs? Answering this question could have consequences for future conservation efforts.

Figure 6. Marc Crane filming the life developing inside and around sponges and cnidarians, at -102 m.


Specifically, a better understanding of the use of deep cleaning stations (or areas) by sunfish would help inform policy, as Indonesia has plan to list the bumphead sunfish M. alexandrini as a protected species. With rapidly increasing diver pressure on the shallow reefs of both Bali and the Nusa Penida island group, whereby divers routinely access the top 30 metres and have a presence throughout daylight hours, deeper cleaning stations may provide important backup solutions and more quiet opportunities for sunfish to seek out interactions with cleaner species. Understanding if dedicated cleaning areas or stations are likely to exit at these deeper depths would aid in assessing the need for management of the dive tourism activities in the shallower areas, as well as any need for future protection of deeper areas. Sunfish could then be used as an umbrella species for this latter purpose: protecting them would lead to the protection of entire habitats, where hundreds of other species are thriving. This pilot project also intends to explore the connectivity between MCEs and the Shallow Water Reefs and how the use of technical diving can help bring new light on the function of MCEs. Besides filling a knowledge gap in Indonesia regarding global survey effort, we believe that such insights will seriously help conservation efforts of an often-neglected ecosystem and poorly-known fish species.

Two distinct sites were selected and are investigated at two different seasons, wet and dry. For diving, we use Close Circuit Rebreathers and Hypoxic Trimix mixes to safely access the depth range of -100 metres. During each dive, we follow as closely as possible the same underwater route, to keep the comparability. Any unusual fish behaviour along the way is recorded on video and photo, particularly for species of interest that we know act as cleaners for sunfish: the longfin bannerfish, Heniochus acuminatus (Figure 7), and the emperor angelfish, Pomacanthus imperator (Figure 8).

Figure 7. Longfin bannerfish, Heniochus acuminatus, -56 m.

Figure 8. Emperor angelfish, Pomacanthus imperator, -52 m.


We also deployed a water level logger and some temperature and light loggers that will stay immerged for many months at various depths, in order to precisely evaluate the tidal, temperature and light variations and then compare those physical factors to our naturalist observations (Figure 9).

Figure 9. Configuration of data loggers before underwater deployment.


A bachelor student from Universitas Udayana, Gede Indra Putra Pratama, joined us on the field and when we were underwater, he was deploying a probe from the boat at fixed intervals to measure water parameters such as temperature and salinity (Figure 10).

Figure 10. Deployment of the CTD probe from the boat, on the dive site.


Physical oceanography is an important component of this expedition, as it will allow us to better understand the environmental aspects and variations of the studied area. It can therefore contribute to explain the observations – or lack of observations – made, as habitat composition and fish behaviours are closely linked to physical factors of the surrounding environment. The more data we can collect, the better it is to improve the knowledge of those poorly-studied MCEs. And hopefully, with a better knowledge and understanding comes better preservation, as it can help develop new and more efficient conservation plans.

Colourful life doesn’t stop at the surface of our Oceans (Figure 11). When people are able to see natural wonders, they will be more likely to feel connected to them and protect them. Images are a powerful tool to tell a story and educate. And education is decisive for conservation. That is why the core of this work relies on photos and videos brought back from the depths and used to raise public awareness on the state and fate of our Oceans, to trigger positive emotions and maybe initiate sustainable changes in our daily behaviours. This latter aspect is definitely a priority in the current context of global changes and increasing human pressure on ecosystems and wildlife worldwide.

Figure 11. Colourful assemblage of sponges, crinoids, gorgonians and other soft corals, -98 m.


The first fieldwork took place in February-March 2019, during which we unfortunately didn’t spot any sunfish. Nevertheless, we had many amazing encounters, from small critters to massive tunas roaming the depths. Notably, we ran into the unique redstripe bigeye, Pristigenys meyeri, three times in a row. To our knowledge, it has never been observed in Bali waters and never been photographed in its natural habitats by divers, until now (Figure 12).

Figure 12. Redstripe bigeye, Pristigenys meyeri, -100 m.

Regrettably, we also found plastic waste on the deeper part of the reef, highlighting that no ecosystem is safe and even the deeper ones can be impacted by our careless lifestyle (Figure 14). At those depths, in colder waters and low sunlight, it will take even longer for the plastic to degrade and will remain here impacting wildlife for centuries or even millennia.

A sad reminder that we urgently need to turn off the trash tap by stopping our consumption of single-use products – not only the plastic ones – and reuse and repair as much as possible.

Figure 14. Plastic bottle, -100 m.


The next mission will be held soon, in October 2019, during the famous “mola season”. We hope to have more luck this time regarding sunfish encounters, but nothing is guaranteed! Indeed, the exciting thing to work with Nature is that it is totally unpredictable and you never know what you will find during your dive (Figure 13).

Figure 13. Marc Crane pointing up at a couple of massive tunas suddenly passing just above us, -64 m... Unfortunately too far and too fast to get the shot! But at least this image is showing how big gorgonians can grow in MCEs.

You can follow us on social media @unseenexpeditions for Facebook and Instagram, where we post daily updates, photos and videos about the project. We also have a Youtube channel.

<1> Baker EK, Puglise KA and Harris PT (Eds.) (2016) Mesophotic coral ecosystems – A lifeboat for coral reefs? The United Nations Environment Programme and GRID-Arendal, Nairobi and Arendal, 98 p.

<2> Hinderstein LM, Marr JCA, Martinez FA, Dowgiallo MJ, Puglise KA, Pyle RL, Zawada DG, Appeldoorn R (2010) Theme section on ‘‘Mesophotic coral ecosystems: characterization, ecology, and management’’. Coral Reefs 29:247–251.

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<4> Konow N, Fitzpatrick R, Barnett A (2006) Adult emperor angelfish (Pomacanthus imperator) clean giant sunfishes (Mola mola) at Nusa Lembongan, Indonesia. Coral Reefs, 25:208.

<5> Lesser PM, Slattery M, Leichter JJ (2009) Ecology of mesophotic coral reefs. Journal of Experimental Marine Biology and Ecology, 375:1–8.

<6> Lindfield SJ, Harvey ES, Halford AR, McIlwain JL (2015) Mesophotic depths as refuge areas for fishery-targeted species on coral reefs. Coral Reefs, 35:125.

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<8> Tamir R, Eyal G, Kramer N, Laverick JH, and Loya Y (2019) Light environment drives the shallow-to- mesophotic coral community transition. Ecosphere 10(9):1–18.

<9> Thys T, Ryan JP, Weng KC, Erdmann M, Tresnati J (2016) Tracking a Marine Ecotourism Star: Movements of the Short Ocean Sunfish Mola ramsayi in Nusa Penida, Bali, Indonesia. Journal of Marine Biology, 2016:1–6.


Written by Alexis Chappuis

Alexis Chappuis is a French marine biologist, technical scientific diver and amateur photographer. He has conducted various marine ecological studies worldwide during his young career, logging hours on and under the sea.