The Dark Side of Coral Reefs

By Manuel Velasco-Lozano, Bárbara Rojas-Montiel and Georgina Ramírez-Ortiz.

Into the mesophotic zone

Imagine yourself nearby a tropical, colorful, and highly diverse coral reef. You only need a diving mask, a snorkel, and a pair of fins to venture into the reef and watch the stunning variety of sea stars, sea urchins, fishes, shrimps, and crabs, among others. The ecosystem where this fauna settles to find shelter, food, and reproduce has been a subject of interest for many researchers over time.

Interestingly, warm-water coral ecosystems are hardly the only reefs inhabiting the ocean; there are also deep cold-water corals, which can settle on the seafloor below 200 m and are only accessible via submersibles. While shallow and deep reefs are isolated ecosystems, a mid-realm lies between the shallow boundary and the deep ocean, ranging from 30 to 150 m: the mesophotic ecosystems.

Mesophotic reef-builders and research techniques

The word mesophotic comes from the Greek terms mesos (middle) and photo (light), hence these ecosystems are characterized by the particular relationship between the intensity of light and their depth range (between 30 m and 150 m). Although the light intensity is reduced at mesophotic depths, light-dependent corals can still be found in clear waters; however, light availability determines differences in benthic composition across the depth gradient, going from a dominance of hard corals at shallow reefs to soft corals at deeper ones. Therefore, since hard reef-building corals are scarce at these depths, mesophotic reef-builders are sea fans, black corals, sponges, algae, and rhodoliths.

Figure 1. Typical distribution of coral morphologies through a depth gradient (0 – 150 m) at a mesophotic coral ecosystem, determined by light intensity (taken from Weiss, 2017).

Thanks to marine expeditions, such as the voyage of HMS Beagle (1826-1843), we have known for centuries now that corals can inhabit surfaces deeper than 30 m. Nevertheless, specimens were collected through trawls or dredges for taxonomic descriptions. Nowadays, the ultimate goal of deep-reef surveys is to understand biological relationships and ecosystem dynamics, which have demanded the use of high-tech to make observations, record videos or photos, collect specimens, and perform environmental characterization (i.e., use of sensors to measure physical and chemical seawater properties). Among the most used methods, technical diving configurations, such as rebreathers (closed-circuit technology that allows the recycling of used oxygen to reach up to 150 m deep) and small remotely operated vehicles (or ROVs), have improved the access to mesophotic ecosystems and, consequently, their exploration and monitoring.

Figure 2. On the left, the set-up of a dome at 89 m using rebreathers (taken from Pyle et al., 2016). On the right, the comparison between a small ROV and two divers (photo taken by Arturo Bocos).

The Deep Reef Refugia Hypothesis

Recent research is trying to determine whether mesophotic ecosystems can act as shelter against natural (e.g., storms, climate change, bleaching events) and anthropogenic or man-made disturbances (e.g., pollution, overfishing) that affect shallow reefs. This assumption, called the Deep Reef Refugia Hypothesis, states that disturbances are dampened in deeper waters and mesophotic reefs because they have more stable environmental conditions that may provide refuge, nourishment, and promote reproduction to several shallow reef species, thus acting as insurance for the persistence of reef ecosystems in the future. In spite of that, the Deep Reef Refugia Hypothesis is yet to proven because there is limited information about the effects of disturbances at mesophotic depths, particularly since, although mesophotic reefs of the Caribbean and Gulf of Mexico have already been described and characterized, many other regions still remain understudied (e.g., Mexican Pacific).

Figure 3. Dense aggregation of Acropora tenella coral species in the Coral Sea that can extend to 110 m (taken from Pinheiro et al., 2019).

Regarding natural disturbances, physical damage to mesophotic coral reefs is mainly caused by debris and coral rubble that buries and eventually kills corals, rather than by the impact of storm-generated waves. In addition, corals have shown to be less resistant to thermal changes at deeper depths and are thus more susceptible to bleaching events than their shallow counterpart. Concerning anthropogenic disturbances, dredging activities and their consequent high sedimentation have a negative effect in the survival rates and abundance of coral species at disturbed sites. Moreover, plastic trash and fishing lines have already reached mesophotic ecosystems, though their effect has not been measured yet.

On the bright side, observations after natural disturbances have shown a boost on the colonization of other invertebrates by providing new habitat and feeding opportunities. Furthermore, there is evidence that deeper coral populations can successfully export larvae to shallow reefs, even though these migrations are driven by oceanographic conditions and the dispersal pattern of each species. On the other hand, research assessing the abundance (total number of individuals of a species) and biomass (weight of living tissue in a given area) of commercially important species at mesophotic reefs has demonstrated they can act as refuges to shallow fish species affected by fisheries. For instance, several species of fishes, lobsters, and shrimps use deep reefs as spawning grounds, but use coastal habitats as nursery grounds, where juveniles are found.


In summary, mesophotic ecosystems are located between 30 m and 150 m and are defined based on the light intensity that reaches these depths. They are mainly composed of soft corals, black corals, sponges, and algae. Mesophotic ecosystems are currently studied using rebreathers and ROVs, but despite the great amount of progress in obtaining and analyzing data to assess and characterize these ecosystems, several regions still lack information to prove the Deep Reef Refugia Hypothesis. According to this assumption, mesophotic ecosystems can safeguard species under natural and human disturbances at shallow reefs, although evidence shows that they are still affected by some of these disturbances. However, research suggests a certain degree of connectivity between shallow reefs and mesophotic ecosystems that could benefit the persistence of reef ecosystems and the use of spawning grounds to some species. Besides, even though natural disturbances negatively affect these ecosystems at first, they may also promote the establishment of other invertebrates.


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Lindfield, S. J., Harvey, E. S., Halford, A. R. & McIlwain J. L. (2016). Mesophotic depths as refuge areas for fishery-targeted species on coral reefs. Coral Reefs, 35, 125–137.

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Smith, T. B., Gyory, J., Brandt, M. E., Miller, W. J., Jossart, J. & Nemeth R. S. (2016). Caribbean mesophotic coral ecosystems are unlikely climate change refugia. Global Change Biology, 22 (8), 2756-2765.

Weiss, K. R. (2017). Into the Twilight Zone. Science, 355 (6328), 900-904.

White, K. N., Ohara, T., Fujii, T., Kawamura, I., Mizuyama M., Montenegro, J., Shikiba, H., Naruse, T., McClelland, T. Y., Denis, V. & Reimer J. D. (2013). Typhoon damage on a shallow mesophotic reef in Okinawa, Japan. PeerJ, 1: e151, 1-12.

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