Taking a deeper look: Quantifying the differences in fish assemblages between shallow and mesophotic temperate rocky reefs

eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental to describe how diverse and distinct the eukaryotic assemblages from the deep layers are compared to shallow ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote deep ocean areas. We analyzed shallow water samples (<30 m) collected via SCUBA diving and adjacent deeper samples (mid-water 30-150 m, deep-water >200 m) obtained with Niskin samplers within 16 locations in a recognized hotspot of marine biodiversity (Gulf of California, Mexico). We sequenced an eDNA metabarcoding library targeting a fragment of the COI gene of eukaryotes. We demonstrated that the diversity of operational taxonomic units (OTUs) did not peak at shallow coastal regions and that the mid-water and deep-water benthic and pelagic samples had similar levels of biodiversity compared to shallow sites, but detected a significant vertical zonation between shallow and deeper habitats. Our results suggest that the deep refugia hypothesis, which posits that deep environments protect biodiversity during environmental changes, enabling species to survive and repopulate shallower regions, is not supported for most taxa and only applies to about a third (34.9%) of the 5,495 OTUs identified that were shared between the shallow and deeper layers. In comparison, the rest of the taxa were exclusive to either shallow (30.8%) or deeper zones (34.28%). The observation that mid-water and deep-water benthic and pelagic communities were as rich but quite distinct as shallow communities supports extending spatial management and conservation tools to deeper habitats to include a significant fraction of unique phylogenetic and functional diversity.

Habitat selection and influence on hunting success in female Australian fur seals

Determining the factors influencing habitat selection and hunting success in top predators is crucial for understanding how these species may respond to environmental changes. For marine top predators, such factors have been documented in pelagic foragers, with habitat use and hunting success being linked to chlorophyll-a concentrations, sea surface temperature and light conditions. In contrast, little is known about the determinants of benthic marine predators. The Australian fur seal (Arctocephalus pusillus doriferus) is a benthic-diving forager that has a breeding and foraging distribution largely restricted to Bass Strait, the shallow (max. depth 80 m) continental shelf region between the Australian mainland and Tasmania. The species forages mostly on benthic prey and represents the greatest resident marine predator biomass in south-eastern Australia. The region is also one of the world's fastest-warming marine areas and oceanographic changes are influencing shifts in prey distribution and abundance. In the present study, GPS-derived locations of benthic dives (n = 288,449) and dive behaviour metrics were used to determine seafloor habitat selection and factors influencing hunting success in 113 lactating adult females from Kanowna Island during the winters of 2006-2021. Individuals non-randomly selected foraging habitats comprised of deeper, steeper sloped, muddy-sandy areas with less gravel and highly disturbed regions (P < 0.01). Hunting success was greatest in shallower rocky reefs (< 30 m) and deep areas (> 40 m) characterised by moderate presence of gravel (25-50%) and substantial rock composition (50-75%) on the seabed. These findings suggest that habitat use and hunting success in adult female Australian fur seals could be impacted by predicted oceanographic changes, such as rising temperature, altered currents and waves which may modify seafloor characteristics and benthic communities.

Vertical structure of reef fish assemblages and light penetration reveal new boundaries of mesophotic ecosystems in the subtropical Southwestern Atlantic

In the Southwest Atlantic, fisheries and in situ observations suggest that mesophotic reefs occur further south than has been reported in the literature, and a description of these subtropical regions is still lacking. We used Baited Remote Underwater stereo-Videos to explore unrevealed patterns in the vertical structure of fish assemblages on subtropical Atlantic reefs, contrasting shallow and mesophotic habitats. Our data on species turnover and light penetration reveal that in the subtropical Atlantic, the boundaries between shallow and mesophotic habitats occur at depths of 18 m, which is shallower than most previous studies have shown. Generalized additive mixed models identified different environmental and management factors as important predictor variables that explain distribution of fish assemblages' attributes. Besides adding new evidence about mesophotic limits, we described variations in the vertical structure of fish assemblages, providing important information for the description and conservation of mesophotic environments in subtropical regions.

Upper mesophotic reef fish assemblages at Bahía de Banderas, Mexico

There is no information on the species associated with the mesophotic reefs of Banderas Bay, located in the central Mexican Pacific. This study analysed the reef fish assemblage from three depths (50, 60 and 70 m) in three sampling sites of the southern submarine canyon of the Bay: Los Arcos, Bajo de Emirio and Majahuitas. Several analyses were performed to test the hypothesis that there are important differences in fish abundance and species composition between sites and depths. Twenty-two species of bony fishes grouped in 14 families were recorded. PERMANOVA results showed that there were no significant differences in fish diversity parameters between sites, indicating a certain uniformity in their distribution. However, nine species were exclusive to one site and depth (five singleton species with only one individual recorded and four unique species recorded only once). On the other hand, there were significant differences between depths, mainly between 50 and 70 m. Diversity decreases with depth and species composition changes. SIMPER, Shade Plot and NMDS analysis show the most representative species at each depth, with at least half of the species (11) recorded only at 50 m and four species at the deeper levels (60 - 70 m). The observed assemblage includes several of the most caught species in the shallow water artisanal fishery, which is the most traditional and common type of fishery in the Bay. In addition, the Pomacanthuszonipectus (Cortés angelfish) is of particular interest, as it has a special protection status in the official Mexican standard (NOM-059-SEMARNAT, 2010) due to its use as an ornamental species in aquaria. We hypothesised that the mesophotic zone may serve as a refuge for these fishes, so we propose that the information obtained is an important basis for new research aimed at the sustainable management of fisheries in the area.

Marine heatwaves in the Great Barrier Reef and Coral Sea: their mechanisms and impacts on shallow and mesophotic coral ecosystems

The Great Barrier Reef (GBR) World Heritage Area and adjacent Coral Sea Marine Park are under serious threat from global climate change. This study used Daily Optimally Interpolated Sea Surface Temperature (DOISST) data to identify major marine heatwaves (MHWs) that have occurred in this region over the last three decades (1992-2022). We then used Himawari-8 (H-8) SST data to map significant MHW events that occurred between 2015 and 2022. We investigated the mechanisms underlying the MHWs, assessed thier impact on shallow and mesophotic coral reef ecosystems and identified potential coral refugia. MHWs in this region have increased in frequency, intensity and spatial extent. El Niño, especially when it is in phase with positive Indian Ocean Dipole, was the key remote driver leading to intense MHWs. However, the more recent strong MHWs (e.g., 2017 and 2022) occurred in the abscence of these climatic events, signifying the impacts of long-term climate change and local drivers. We also found that reduced wind speed and shoaling mixed layer depth, often together with reduced cloudiness, were the main local drivers pre-conditioning these MHWs. Anomalous air-sea heat flux into the ocean, mainly controlled by shortwave solar radiation (cloudiness) and latent heat flux (wind), was the most constant contributor to the 2015-16 and 2019-20 MHW events. However, local oceanographic dynamics, especially horizontal advection and turbulent mixing, played important roles in MHW heat budgets. This study confirmed that shallow-water coral bleaching severity was positively related to the cumulative MHW intensity in the 2015-16 and 2019-20 MHW events. We identified shallow reefs along the path of the North Queensland Current as potential coral refugia from bleaching because of the cooler waters upwelled from the ocean current. We also found that, except during weather events such as tropical cyclones, mesophotic reefs in the Coral Sea Marine Park may be less susceptible to severe bleaching as the MHWs were more confined within the shallow mixed layer.

Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reef

Predatory fishes on coral reefs continue to decline globally despite playing key roles in ecosystem functioning. Remote atolls and platform reefs provide potential refugia for predator populations, but quantitative information on their spatial distribution is required to establish accurate baselines for ongoing monitoring and conservation management. Current knowledge of predatory fish populations has been derived from targeted shallow diver-based surveys (<15 m). However, the spatial distribution and extent of predatory fishes on outer mesophotic shelf environments has remained under described. Middleton Reef is a remote, high-latitude, oceanic platform reef that is located within a no-take area in the Lord Howe Marine Park off eastern Australia. Here we used baited remote underwater stereo video to sample predatory fishes across lagoon and outer shelf habitats from depths 0–100 m, extending knowledge on use of mesophotic depths and habitats. Many predatory fish demonstrated clear depth and habitat associations over this depth range. Carcharhinid sharks and Carangid fishes were the most abundant predators sampled on Middleton Reef, with five predatory fishes accounting for over 90% of the predator fish biomass. Notably, Galapagos shark (Carcharhinus galapagensis) and the protected black rockcod (Epinephelus daemelii) dominated the predator fish assemblage. A higher richness of predator fish species was sampled on reef areas north and south of the lagoon. The more exposed southern aspect of the reef supported a different suite of predator fish across mesophotic habitats relative to the assemblage recorded in the north and lagoonal habitats, a pattern potentially driven by differences in hard coral cover. Biomass of predatory fishes in the more sheltered north habitats was twice that of other areas, predominantly driven by high abundances of Galapagos shark. This work adds to the growing body of literature highlighting the conservation value of isolated oceanic reefs and the need to ensure that lagoon, shallow and mesophotic habitats in these systems are adequately protected, as they support vulnerable ecologically and economically important predator fish assemblages.

ROV assessment of mesophotic fish and associated habitats across the continental shelf of the Amathole region

Understanding how fish associate with habitats across marine landscapes is crucial to developing effective marine spatial planning (MSP) in an expanding and diversifying ocean economy. Globally, anthropogenic pressures impact the barely understood temperate mesophotic ecosystems and South Africa's remote Amathole shelf is no exception. The Kei and East London region encompass three coastal marine protected areas (MPAs), two of which were recently extended to the shelf-edge. The strong Agulhas current (exceeding 3 m/s), which runs along the narrow shelf exacerbates sampling challenges. For the first time, a remotely operated vehicle (ROV) surveyed fish and their associated habitats across the shelf. Results indicated fish assemblages differed between the two principle sampling areas, and across the shelf. The number of distinct fish assemblages was higher inshore and on the shelf-edge, relative to the mid-shelf. However, the mid-shelf had the highest species richness. Unique visuals of rare Rhinobatos ocellatus (Speckled guitarfish) and shoaling Polyprion americanus (wreckfish) were collected. Visual evidence of rhodolith beds, deep-water lace corals and critically endangered endemic seabreams were ecologically important observations. The ROV enabled in situ sampling without damaging sensitive habitats or extracting fish. This study provided information that supported the Amathole MPA expansions, which extended protection from the coast to beyond the shelf-edge and will guide their management. The data gathered provides baseline information for future benthopelagic fish and habitat monitoring in these new MPAs.