Mesophotic Reef Ecosystems Research Articles

Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats.

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

Beachrocks of the last low sea level, substrate of the Great Amazon Reef system along the outer Guiana shelf

The Great Amazon Reef System is a living biogenic mesophotic reef ecosystem that has been recently described along the shelf break of Brazil. An oceanographic cruise was carried out in 2019 along the outer edge of the French Guiana Shelf. A side-scan sonar survey was conducted to locate reef outcrops and allowed twelve in situ 80- to 120-m depth dives and sampling of the reef rocks and peripheral sands. The majority of the hard rocks are composed of biological concretions. However, several fragments revealed the inside presence of sandstone clasts. These clasts, more or less enveloped by biogenic coatings, probably represent destroyed clasts of underlying or neighboring beachrock banks. Their dominant cement is micritic (high-magnesian calcite); the intergranular or extragranular porous field was later filled with low-magnesian sparry calcite. The sand or gravel that accumulated near the barrier mainly consists of the blunt debris of coastal fauna and flora associated with different carbonate or ferruginous neoformed ooids. At 104-m depth, ooids extracted from dive 11 samples dated from the start of MIS2 (27,370 cal yr BP) and attest to the presence of a significant coastal accumulation. At this same site, cementing did not take place until about 3500 years later (23,990 cal yr BP). The cement of a nearby beachrock indicates a much more recent age (16,170 cal yr BP). Lastly, the age of 4100 yr BP measured on the barnacles attached to the top of the reef attests to the late Holocene reef's biological activity.

Geomorphological drivers of deeper reef habitats around Seychelles

Mesophotic (30–150 m) and rariphotic (150–300 m) deeper reef habitats are important from an ecological and conservation perspective, yet remain understudied. Key knowledge gaps exist on the environmental patterns and processes that drive and shape their geographical distributions. Understanding these is particularly important for regions as the Western Indian Ocean, where deeper reefs are poorly known but support food security and host economically important species. Spatial predictive models of assemblage occurrences, using terrain variables as predictors, offer a solution to address knowledge gaps around deeper reef distributions. We identified relationships between seafloor geomorphology, quantified at multiple scales, and sessile benthic assemblages in four atoll seascapes in Seychelles using terrain models derived from high-resolution multibeam sonar and underwater video surveys. Using random forests and boosted regression trees, we demonstrated that terrain derivatives extracted over multiple scales perform as reliable predictors of deeper reef assemblages. The most influential environmental predictors were depth, distance to shore, topographic complexity, slope and curvature and substrate characteristics. The relative importance of predictors was explained by assemblage functional characteristics. Assemblage–environment relationships were used to produce probability distribution maps that showed similar distributional patterns for identified assemblages across locations, with high occurrence probabilities linked to complex geomorphological structures. Our results help contribute to a consistent baseline understanding of the relationship between seascape structure and mesophotic reef ecosystems in this area. Complex geomorphological structures, including terraces and paleoshorelines, supported high densities of mesophotic assemblages and could be considered priority habitats for management.

Ecological Links between Pelagic and Mesophotic Reef Fishes in an Oceanic Archipelago of the Equatorial Atlantic Ocean

Geographic isolation, a relatively low species richness and high endemism make oceanic islands excellent natural laboratories for ecological and evolutionary studies. Here we used Baited Remote Underwater stereo-Video systems (stereo-BRUVS) to investigate the taxonomic, trophic and size structures of fish assemblages from pelagic and mesophotic reef ecosystems in the smallest archipelago of the equatorial Atlantic Ocean, the Saint Peter and Saint Paul’s Archipelago (SPSPA). The occurrence of steep reef walls favors studies on the ecological connections between pelagic and reef ecosystems. We performed five pelagic stereo-BRUVS deployments and fourteen benthic stereo-BRUVS deployments, totaling 1440 min of footage. We recorded 14 species from eight families in the pelagic ecosystem, with Carangidae and Balistidae as the most diverse families. The most abundant species were Elagatis bipinnulata (Quoy and Gaimard, 1825), Melichthys niger (Bloch, 1786), and Caranx crysos (Mitchill, 1815), which together accounted for over 75% of the total relative abundance. The carnivores were the most diverse and abundant trophic group. On the mesophotic reefs, 41 taxa were recorded, with carnivores and planktivores being the most diverse, whereas omnivores were the most abundant. Here, the most abundant species were M. niger, Azurina multileneata, Chromis vanbebberae, Seriola rivoliana, Caranx lugubris and Stegastes sanctipauli. Nine species were recorded in both ecosystems, with Melichthys niger, Caranx lugubris and S. rivoliana being the main species linking them (i.e., occurring in both). These species are known to forage in both pelagic and mesophotic reef ecosystems, and thus represent potential ecological links between them. Such links combined with the endangered status of some species, suggest the need for an integrated management strategy in this remote archipelago.

Changes in reef fish assemblages in a cross-shelf euphotic-mesophotic gradient in tropical SW Atlantic

Despite a vast number of studies about shallow reef fish assemblages, and an increasing amount of studies about mesophotic ones, there are very few cross-shelf assessments including both, shallow and mesophotic depths. Herein, we analyze changes in reef fish assemblages in a cross-shelf euphotic-mesophotic (19–72.6 m) gradient in tropical SW Atlantic. Data was obtained using a novel low-cost 360° stationary video system. Sixty-four species from thirty families were identified. Depth, distance offshore and proportion of consolidated substrate were the main predictors of fish assemblages’ structure. Four distinct fish assemblages were identified across the depth gradient (20–30, 30–40, 40–50 and 50–75 m), with marked shifts in composition, abundance, and trophic structure. Abundance of invertebrate feeders and large roving herbivores declined across the shelf and with increasing depth, while abundance of planktivores and piscivores increased, particularly below 50 m. These changes were likely caused by changes in food availability and habitat suitability. Our low-cost video system yielded high-resolution images that enabled us to accurately survey reef fish assemblages, being therefore a useful method for studies focusing on both, euphotic and mesophotic reef ecosystems. Our results contribute to a better understanding of how reef fish assemblages change with increasing depth in SW Atlantic reefs and corroborate the idea that the breakpoint between euphotic and mesophotic fish assemblages is context-dependent rather than previously defined as 30 m depth.

Predicting the distribution of threatened orbicellid corals in shallow and mesophotic reef ecosystems

Orbicellid corals are threatened primary reef-building corals throughout the Caribbean in shallow and mesophotic coral ecosystems (MCEs), yet a poor understanding of where they occur limits population monitoring and management. The goals of this study were to predict suitable habitat for orbicellid coral species and to identify how abiotic environmental factors constrain that habitat on the eastern Puerto Rico Shelf. The probability of occurrence for Orbicella annularis and O. faveolata/O. franksi (combined) from shallow to mesophotic depths on the eastern Puerto Rico Shelf was predicted using maximum entropy models. Contributions of abiotic predictors, including bathymetry, seafloor topography, temperature, wave exposure, and bottom velocity, were assessed. Model performance was assessed using area under the receiver operating characteristic curve, standard error of the replicate model runs, and mean absolute error. Both O. annularis and O. faveolata/O. franksi distributions were best predicted by rugosity, temperature, and wave exposure. O. faveolata/O. franksi occurred at shallow and mesophotic depths, and acted as a proxy for identifying the spatial extent of MCEs, contrary to O. annularis, which was predicted at shallow depths. Results for O. faveolata/O. franksi in mesophotic depths indicated potential for large areas of unexplored and unmonitored MCEs along the southeast shelf of St. Thomas, US Virgin Islands and within the Virgin Passage. These spatial predictions of potential mesophotic reef habitats will provide direction for future MCE exploration efforts.

Insights on the evolution of the living Great Amazon Reef System, equatorial West Atlantic

The Great Amazon Reef (GARS) is an extensive mesophotic reef ecosystem between Brazil and the Caribbean. Despite being considered as one of the most important mesophotic reef ecosystems of the South Atlantic, recent criticism on the existence of a living reef in the Amazon River mouth was raised by some scientists and politicians. The region is coveted for large-scale projects for oil and gas exploration. Here, we add to the increasing knowledge about the GARS by exploring evolutionary aspects of the reef using primary and secondary information on radiocarbon dating from carbonate samples. The results obtained demonstrate that the reef is alive and growing, with living organisms inhabiting the GARS in its totality. Additional studies on net reef growth, habitat diversity, and associated biodiversity are urgently needed to help reconcile economic activities and biodiversity conservation.

Characterizing population structure of coral-associated fauna from mesophotic and shallow habitats in the Caribbean

Symbiotic relationships are a common phenomenon among marine invertebrates, forming both obligatory and facultative dependencies with their host. Here, we investigate and compare the population structure of two crustacean species associated with both shallow and mesophotic ecosystems: an obligate symbiont barnacle (Ceratoconcha domingensis), of the coral Agaricia lamarcki and a meiobenthic, free-living harpacticoid copepod (Laophontella armata). Molecular analyses of the Cytochrome Oxidase Subunit I (COI) gene revealed no population structure between mesophotic and shallow barnacle populations within south-west Puerto Rico (ΦST = 0.0079, P = 0.33). The absence of population structure was expected due to the pelagic naupliar larvae of the barnacles and the connectivity patterns exhibited by the coral itself within the same region. Laophontella armata exhibited significant structure based on the mitochondrial COI gene between the mesophotic reef ecosystem of El Seco, Puerto Rico and mangrove sediments of Curaçao (ΦST = 0.2804, P = 0.0). The El Seco and Curaçao copepods shared three COI haplotypes despite the obligatory benthic development of harpacticoid copepods and the geographic distance between the two locations. Three other COI haplotypes from El Seco exhibited higher than expected (up to 7%) intra-species variability, potentially representing three new cryptic species of harpacticoid copepods or rare, deeply divergent lineages of L. armata. This result is evidence for the urgent need of a deeper investigation into the meiofauna diversity associated with mesophotic coral ecosystems (MCEs), arguably the most diverse metazoan component of MCEs.

Lush underwater forests in mesophotic reefs of the Gulf of Guinea

[Excerpt] The Gulf of Guinea, in West Africa, harbors some of the least known tropical reefs in the world. Shallow reefs in this region are mainly rocky and have limited scleractinian growth (Laborel 1974). Circulation patterns restrict warm waters to the surface layer and cooler waters to below 20–30 m depth (Laborel 1974). Reefs lying below these depths, in cool water, have not yet been described. Here, we report a mesophotic reef ecosystem dominated by black corals between 30 and 50 m depth off Lagoa Azul, northwest Sao Tome Island (0°24′33″N, 6°36′30″E).

Geology and biology of the “Sticky Grounds”, shelf-margin carbonate mounds, and mesophotic ecosystem in the eastern Gulf of Mexico

Shelf-margin carbonate mounds in water depths of 116–135m in the eastern Gulf of Mexico along the central west Florida shelf were investigated using swath bathymetry, side-scan sonar, sub-bottom imaging, rock dredging, and submersible dives. These enigmatic structures, known to fisherman as the “Sticky Grounds”, trend along slope, are 5–15m in relief with base diameters of 5–30m, and suggest widespread potential for mesophotic reef habitat along the west Florida outer continental shelf. Possible origins are sea-level lowstand coral patch reefs, oyster reefs, or perhaps more recent post-lowstand biohermal development. Rock dredging recovered bioeroded carbonate-rock facies comprised of bored and cemented bioclastics. Rock sample components included calcified worm tubes, pelagic sediment, and oysters normally restricted to brackish nearshore areas. Several reef sites were surveyed at the Sticky Grounds during a cruise in August 2010 with the R/V Seward Johnson using the Johnson-Sea-Link II submersible to ground truth the swath-sonar maps and to quantify and characterize the benthic habitats, benthic macrofauna, fish populations, and coral/sponge cover. This study characterizes for the first time this mesophotic reef ecosystem and associated fish populations, and analyzes the interrelationships of the fish assemblages, benthic habitats and invertebrate biota. These highly eroded rock mounds provide extensive hard-bottom habitat for reef invertebrate species as well as essential fish habitat for reef fish and commercially/recreationally important fish species. The extent and significance of associated living resources with these bottom types is particularly important in light of the 2010 Deepwater Horizon oil spill in the northeastern Gulf and the proximity of the Loop Current. Mapping the distribution of these mesophotic-depth ecosystems is important for quantifying essential fish habitat and describing benthic resources. These activities can improve ecosystem management and planning of future oil and gas activities in this outer continental shelf region.

Mesophotic reef fish assemblages of the remote St. Peter and St. Paul’s Archipelago, Mid-Atlantic Ridge, Brazil

Mesophotic reef fish assemblages (30–90 m depth) of the small and remote St. Peter and St. Paul’s Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil, were characterized using remotely operated vehicles. Ordination analyses identified distinct fish assemblages in the upper (30–50 m) and lower (50–90 m) mesophotic zones, the former characterized by high abundances of species that are also abundant at euphotic reefs (Caranx lugubris, Melichthys niger, Stegastes sanctipauli and Chromis multilineata) and the latter dominated by two mesophotic specialists (Prognathodes obliquus and Chromis enchrysura). Planktivores dominated fish assemblages, particularly in the upper mesophotic zone, possibly due to a greater availability of zooplankton coming from the colder Equatorial Undercurrent in mesophotic depths of the SPSPA. Turf algae, fleshy macroalgae and scleractinian corals dominated benthic assemblages between 30 and 40 m depth, while bryozoans, black corals and sponges dominated between 40 and 90 m depth. Canonical correspondence analysis explained 74 % of the relationship between environmental characteristics (depth, benthic cover and complexity) and structure of fish assemblages, with depth as the most important independent variable. Juveniles of Bodianus insularis and adults of P. obliquus and C. enchrysura were clearly associated with branching black corals (Tanacetipathes spp.), suggesting that black corals play key ecological roles in lower mesophotic reefs of the SPSPA. Results from this study add to the global database about mesophotic reef ecosystems (MREs) and provide a baseline for future evaluations of possible anthropogenic and natural disturbances on MREs of the SPSPA.

Reef fish and benthic assemblages of the Trindade and Martin Vaz Island group, southwestern Atlantic

The Trindade and Martin Vaz island group (TMVIG) is located at about 1,120 km off the Brazilian coast. Despite its importance, highlighted by the presence of several endemic fish species, the TMVIG lacks detailed information on the structure of fish and benthic assemblages. Presented here is the first quantitative assessment of reef fish and benthic assemblages of the TMVIG in a depth gradient ranging from 5 to 45 m. Additional qualitative information on reef assemblages between 45 and 100 m was obtained using advanced gas diving techniques (TRIMIX) and a remotely operated vehicle (ROV). Similarly to other Brazilian oceanic islands, the TMVIG possesses depauperated fish and benthic assemblages, possibly due to its isolation and small size in comparison to the mainland. Depth was the most important factor affecting the structure of fish assemblages, with the density of most fish species declining with depth. Deep reefs (> 45 m) were characterized by the presence of extensive rhodolith beds and rocky reefs sparsely covered with crustose coralline algae, black coral (Cirripathes sp.) and a few massive or plate-like reef corals. Part-time or obligatory planktivorous fishes (e.g. Cephalopholis furcifer and Clepticus brasiliensis) also dominated deep reefs. Similar characteristics were recorded in mesophotic reef ecosystems across the Western Atlantic. Evidence of overfishing (obtained here and in other recent studies), the presence of four endemic and restricted range fish species, as well as the increase in number of new (and still undescribed) endemic taxa, indicates that the adoption of precautionary conservation measures are urgently needed in order to maintain the fragile and unique ecosystems of the TMVIG.