EXPLORING
The Shallow and Mesophotic Reefs of Comoros
Deep Reefs in Comoros May Provide Refuge for Large Fish and Corals
Mesophotic coral reef ecosystems—reefs that extend below conventional shallow-water diving depths—remain among the least studied parts of coral reef ecosystems, particularly in the Western Indian Ocean. Yet these deeper reefs can support distinct biodiversity and may provide refuge for species affected by climate change and fishing on shallower reefs.
In our latest study, led by Rhodes University’s Anthony Bernard and co-authored by CORDIO Director Melita Samoilys and other experts, we investigated how reef fish communities and their habitats change from shallow to mesophotic depths in the Comoros Archipelago.
Published in Diversity, the research surveyed reefs from approximately 10 to 100 m depth across three islands of Comoros. It found distinct shallow, upper-mesophotic and lower-mesophotic fish communities, while also revealing that light-dependent coral reefs extend unusually deep in Comoros. The presence of large fishery species on deeper reefs further suggests that mesophotic habitats may provide an important refuge from fishing pressure.
The findings highlight the importance of considering the full depth range of coral reef ecosystems in fisheries management, marine spatial planning and conservation in Comoros and across the Western Indian Ocean.
Overview
Most coral reef monitoring in the Western Indian Ocean has historically focused on shallow reefs accessible to divers. Much less is known about mesophotic coral ecosystems, despite their potential importance for biodiversity and resilience.
Mesophotic reefs can support both depth-specialist species, which occupy relatively narrow depth ranges, and depth-generalist species, which occur across shallow and deeper habitats. The latter may be particularly important because deeper habitats can potentially provide refuge from disturbances affecting shallow reefs, including fishing and thermal stress.
The study set out to understand how fish communities change across the shallow-to-mesophotic depth gradient in Comoros and how these changes relate to environmental conditions, including light, temperature and reef habitat. It also examined whether deeper reefs could potentially provide refuge for fishery species affected by fishing on shallow reefs.
Study Area and Methodology
The research was conducted around Ngazidja (Grand Comore), Mwali (Moheli) and Ndzuani (Anjouan), spanning reefs from approximately 10 to 100 m depth.
Researchers used stereo-Baited Remote Underwater Video Systems (BRUVS) to survey fish communities and reef habitats. In total, 85 BRUVS samples were collected from seven sites across the three islands, covering depths from 10 to 98 m.
The cameras recorded fish species and abundance as well as characteristics of the seafloor and benthic communities. Researchers also measured environmental conditions, particularly temperature and photosynthetically active radiation (PAR)—the light available for photosynthesis—to examine how changing environmental conditions corresponded with changes in reef communities.
Read or download the full paper, top.
Findings
Three distinct reef fish depth zones
The surveys recorded 334 fish species and revealed clear changes in fish communities with habitat and depth.
On higher-relief reefs, fish communities separated into three main zones:
- Shallow photic reef: 12–45 m
- Upper-mesophotic reef: approximately 45–62 m
- Lower-mesophotic reef: 63–98 m
Reef substrate and structural relief were particularly important in determining fish community composition. More diverse fish communities occurred on higher-relief reefs, while sand and low-relief sand/reef habitats supported less diverse assemblages.
Importantly, deeper communities were not simply smaller subsets of shallow reef communities. Differences among depth zones were driven predominantly by species replacement, demonstrating that the mesophotic reefs support distinct fish communities in their own right.
Comoros’ shallow coral reefs extend unusually deep
The boundary between the shallow photic reef and the upper-mesophotic reef occurred at around 45 m, deeper than the approximately 30–40 m transition commonly reported for coral reefs elsewhere.
Shallow reefs were characterised by reef-building stony corals. At greater depths, these transitioned towards communities dominated by non-light-dependent soft corals, sea fans, sea whips and black corals.
Some reef-building corals were nevertheless recorded down to approximately 60 m. The study suggests that the unusually deep extent of these corals could potentially increase their resilience by allowing some species to persist in deeper, cooler habitats, although further research is required to establish the extent of this potential refuge.
Light helps explain the transition between fish communities
The study also found a close relationship between changing light conditions and fish-community depth zones.
The transition between the upper- and lower-mesophotic fish communities occurred at approximately 62–63 m, close to the depth at which available light reached about 1% of surface levels—the theoretical lower boundary of the euphotic zone.
This provides further evidence that depth itself is not the only factor structuring mesophotic communities. Light, habitat complexity and other environmental conditions interact to determine which species can occupy different parts of the reef.
Deeper reefs may provide refuge for fishery species
One of the study’s most significant findings was the presence of large-bodied fishery species on deeper reefs.
Depth-generalist groupers, trevallies and snappers were prominent in the lower-mesophotic zone. Two large groupers, Epinephelus tukula and E. malabaricus, were recorded only at depths greater than 50 m, despite being capable of living on shallow reefs.
Previous shallow-water surveys in Comoros have found these species absent or extremely rare. Together with evidence of fishing pressure on shallow reefs, their occurrence at depth suggests that deeper habitats may allow some fishery species to persist where access by small-scale fishers is more difficult.
The researchers caution that further work—including measurements of fish biomass, size and fishing pressure—is needed to test the strength of this refuge effect. Nevertheless, the finding could have important implications for both fisheries management and food security.
Significance and Recommendations
The study provides an important new baseline for understanding mesophotic reefs in Comoros and demonstrates why coral reef ecosystems should not be viewed or managed only through their shallow-water components.
The findings suggest that deeper reefs may contribute to ecosystem resilience in two important ways: by providing habitat for some reef-building corals at greater depths, and by supporting large fishery species that have become scarce on shallow reefs. At the same time, the lower-mesophotic zone contains its own distinctive community of depth-specialist fishes and is therefore important for biodiversity in its own right.
Priorities for Coral Reef Management:
-
Include mesophotic reefs in marine spatial planning and conservation, including considering the extension of marine protected areas into deeper waters.
-
Incorporate deeper reefs into fisheries assessments and management, particularly for large-bodied target species that may use these habitats as refuges.
-
Expand coral monitoring across the full depth range of the photic reef to determine whether deeper coral populations provide meaningful refuge from thermal stress.
-
Improve understanding of connectivity between islands and depths, including whether protected or deeper populations can contribute recruits to neighbouring reefs and fisheries.
-
• Continue monitoring environmental conditions and fishing pressure to establish how persistent these apparent refuge effects are over time.
CORDIO will continue to undertake research demonstrating the importance of incorporating deeper reef habitats into fisheries management and conservation.
About this Publication
Paper: Depth Zonation and Environmental Characteristics of Shallow and Mesophotic Coral Reef Fish Assemblages in Comoros
Authors: Anthony T. F. Bernard, Melita Samoilys, Roxanne Juby, Peter Musembi, Youssouf E. Abdou, Paris Stefanoudis, Ibrahim Mohamed-Toihir, Lucy Woodall and Jean Harris
Published in: Diversity (2026), 18, 532
DOI: 10.3390/d18090532
Study area: Comoros Archipelago, Western Indian Ocean