Deep-sea Ecosystems Research Articles

First observed dolphin fall in the South China sea: Implications for the biogeography

Cetacean falls provide a large amount of organic matter to the deep ocean, an otherwise oligotrophic environment. These events are now believed to maintain endemic species and offer intermediate habitats for species in other deep-sea ecosystems. Only about 70 modern whale falls have been reported in the world's oceans to date. We discovered the first known dolphin fall in the South China Sea in March 2020, on the middle slope of the Zhongnan seamount. We set up a camera at the site to observe animals visiting the dolphin carcass for 30 consecutive days from March 29 to April 28, 2020 and made four additional HOV dives to the dolphin carcass. In total, we observed 14 visible megafauna species visiting this dolphin fall, including six fish species, five crustacean species, two echinoderm species, and one mollusk species, of which most were scavengers or predators. This was the first record of many of these taxa in the deep South China Sea. Furthermore, two bone-eating worms were found in a piece of the dolphin bone. The worms are identified as new species in the genus Osedax based on DNA analysis. The findings of this work suggest that cetacean falls occur frequently in the South China Sea and help to fill a knowledge gap regarding the biodiversity of cetacean falls in the West Pacific.

Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81.

Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.

Deep-sea impacts of climate interventions

Ocean manipulation to mitigate climate change may harm deep-sea ecosystems.

Bioaccumulation of emerging persistent organic pollutants in the deep-sea cold seep ecosystems: Evidence from chlorinated paraffin.

Persistent organic pollutants (POPs) are highly toxic and can accumulate in marine organisms, causing nonnegligible harm to the global marine ecosystem. The Cold seep is an essential marine ecosystem with the critical ecological function of maintaining the deep-sea carbon cycle and buffering global climate change. However, the environmental impact of emerging POPs in the deep-sea cold seep ecosystem is unknown. Here, we investigated the potential pollution of chlorinated paraffins (CPs) and their bioaccumulation in the cold seep ecosystem. High concentrations of CPs were detected in the cold seep ecosystems, where CPs bioaccumulated by the keystone species of deep-sea mussels can be released into the surface sediment and vertically migrate into the deeper sediment. Furthermore, more toxic CPs were accumulated from transforming other CPs in the cold seep ecosystem. Our study provides the first evidence that high concentrations of POPs are bioaccumulated by deep-sea mussels in the cold seep ecosystem, causing adverse ecological effects. The discovery of CPs bioaccumulation in the deep-sea cold seep ecosystem is a crucial mechanism affecting deep-sea carbon transport and cycling. This study has important guiding significance for revealing the deep-sea carbon cycle process, addressing global climate change, and making deep-sea ecological and environmental protection policies.

Complex sublinear burrows in the deep sea may be constructed by amphipods.

Trails, burrows, and other "life traces" in sediment provide important evidence for understanding ecology-both of the maker and of other users-and behavioral information often lacking in inaccessible ecosystems, such as the deep sea or those that are already extinct. Here, we report novel sublinear rows of openings in the abyssal plains of the North Pacific, and the first plausible hypothesis for a maker of these constructions. Enigmatic serial burrows have now been recorded in the Pacific and Atlantic deep sea. Based on image and specimen evidence, we propose that these Bering Sea excavations represent amphipod burrows, while the maker of the previously known Mid-Atlantic Ridge constructions remains undetermined. We propose that maerid amphipods could create the Pacific burrows by eating-digging horizontally below the surface along a nutrient-rich layer in the sediment, making the serial openings above them as they go, for conveniently removing excavated sediment as the excavation progresses. These striking structures contribute to local biodiversity, and their maker could be considered a deep-sea ecosystem engineer.

Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology.

Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.

Trophic ecology of midwater zooplankton along a productivity gradient in the Southeast Pacific

The environmental regulation of planktonic food web structure is a key determinant for the efficiency of energy transfer through trophic levels, with direct implications for the amount of energy that is available to top-consumers and deep-sea communities. Yet, the complex trophic interplay between the different components of plankton communities under contrasting environmental conditions remains unresolved. Here, we present a comprehensive field study based on compound-specific isotope analysis of amino acids that aims to explore depth-resolved changes in the trophic strategies of various size-classes of mesozooplankton from distinct habitats across the Southeast Pacific. According to the δ15N values of the so-called source amino acids such as phenylalanine, we first identified a clear shift in nitrogen sources for biological production, from nitrate in the productive upwelling waters of the Humboldt Current System to increased inputs of diazotroph-N within the ultra-oligotrophic South Pacific gyre. These shifts in the productivity and in the source of N at the base of the food web were not accompanied by significant changes in the trophic position (TP) of mesozooplankton, which were mainly omnivores (TP = 2.8 ± 0.3, n = 65) in all ecoregions. However, although the planktonic food web length remained relatively unaltered along the productivity gradient, the microbial contribution to mid-trophic level consumers appeared to be more important at relatively high productivities, likely due to more intense remineralization processes in a late successional stage of the upwelling throughout the coastal-transition zone. Altogether, this research work will contribute to a better understanding of the food web functioning in one of the least explored marine regions of the world’s oceans.

Feeding ecology of the pandalid shrimp, Plesionika semilaevis (Spence Bate 1888) in South Eastern Arabian Sea

The feeding ecology of deep-sea crustaceans is crucial in understanding the ecological roles and interactions of deep-sea organisms as they play a critical role in deep-sea food webs as intermediate trophic level organisms. This study provides the first examination of the feeding ecology of deep-sea shrimp Plesionika semilaevis (Spence Bate 1888) and provides new insights into deep-sea community structure. An aggregate number of 2213 individuals (842 males, 1016 berried and 355 non-berried females) were collected from the South Eastern Arabian Sea from 2019 to 2022 and their feeding ecology was studied in relation to the environmental (season) and biological (maturity, sex and size) factors. The index of preponderance values indicates the species has a diversified diet with a wide trophic niche ranging from smaller foraminifera to larger crustaceans and fishes. Frequency of occurrence (FOC) reveals that crustaceans, detritus and foraminifera forms the main prey while fishes, molluscs and sponges form the secondary prey. Berried females had the highest feeding intensity compared to males and non-berried females. Among the studied groups,the percentage of full stomachs was higher during the pre-monsoon period than post-monsoon. Feeding intensity was highest for smaller individuals and decreased gradually with an increase in size. Statistical analyses (ANOVA) also confirmed the significant differences (p<0.05) in the diet composition and feeding intensity of berried and non-berried females, pre-monsoon and post-monsoon samples and, juveniles and adults. The PERMANOVA test showed that there were significant differences in diet in the interaction between sex and size (p=0.003) and between sex and season (p=0.001). The present study also suggests that the seasonal variation in feeding intensity could be attributed to oceanographic phenomena like upwelling prevailing in the South Eastern Arabian Sea.

The lateral transport of zooplankton explains trophic and taxonomic similarities over the zonal gradient of central Chile

The highly productive upwelling zone in the Southeast Pacific provides inputs of C and N to the oceanic deep-water system via lateral transport, although the quality of this organic matter, the organisms being transported, and the controlling mechanisms are unclear. Here, we assessed whether the taxonomic and trophic structure of zooplankton over more oceanic offshore waters differ from that of zooplankton located in the upwelling zone, along with the characterization of the oceanographic processes and variables associated with the lateral transport. For this, epipelagic, mesopelagic, and bathypelagic zooplankton along with oceanographic variables and particulate organic matter (POM) were analyzed at the upwelling zone and adjacent oceanic stations off Central Chile (27–33°S), some of which were located over the Atacama trench, during September 2016. The community structure of size-fractioned zooplankton (<200 μm, 200–500 μm, 500–1000 μm, 1000–2000 μm, and >2000 μm size classes) was assessed by an automated method, along with the analysis of the isotopic niche computed from their δ 15 N and δ 13 C. The isotope signatures of POM indicated that diatoms contributed mostly to production of new organic C, being the main food source for small-sized zooplankton in coastal waters. The zooplankton community structure differed between the upwelling and oceanic areas, but their isotopic signature showed a large overlap (78%). Satellite-derived geostrophic flow and the depth of the mixed layer appeared as the main factors explaining the homogeneity in the isotopic and biogeochemical signatures of zooplankton between the upwelling zone and offshore waters. Cross-shelf advection is thus suggested as a key process promoting zooplankton export to the deep-water ecosystem, including the ultra-deep Atacama Trench. • The organic matter produced in the upwelling zone can be transported over the Atacama trench by strong offshore advection. • Isotopic niches of zooplankton from the Atacama Trench and the upwelling zone exhibit large overlapping (78%). • The upwelling systems acts as a C subsidiary for the offshore deep-sea ecosystem including the Atacama Trench.

Two new deep-water species of squat lobsters (Crustacea: Anomura: Galatheoidea) from the Central and Southwest Indian Ridge

The high diversity and endemism of benthic species on seamounts are extensively documented. Although the number of squat lobster species from seamount habitats has increased, species from the Central Indian Ridge (CIR) and Southwest Indian Ridge (SWIR) systems remain largely unknown. The hydrothermally active Indian Ridge system harbours potential sites for future Seafloor Massive Sulphides (SMS) mining. Since seabed mining may create a long-lasting impact on the deep-sea ecosystems, it could harm the unique deep-sea life associated with mineral deposits. This study identified two undescribed squat lobster specimens: one from the genus Munidopsis Whiteaves, 1874 from the CIR system in water depths ranging from 1981 to 2033 m, and one from the genus Typhlonida Macpherson & Baba in Machordom, Ahyong, Andreakis, Baba, Buckley, Garcia-Jimenez, McCallum, Rodriguez-Flores & Macpherson, 2022 from the SWIR system in depths ranging from 2070 to 2404 m. Both new species may be distinguished morphologically and genetically based on the partial mitochondrial (mtCOI) gene. To generate baseline environmental and biodiversity data, efforts for accurate sampling and correct identification of biological species are required.

Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the northwestern Pacific Ocean

The Thyasiridae is one of the species-richest families in the abyssal and hadal zones of the northwestern Pacific Ocean. Many thyasirid species dominate benthic communities in terms of abundance and play an important role in the functioning of deep-sea ecosystems. Most of the thyasirid species in the region are new to science and have not been described. Based on the material collected from 1954 to 2016 by seven deep-sea expeditions, three new species of Thyasiridae (Parathyasira coani sp. nov., P. pauli sp. nov., and Thyasira kharkovensis sp. nov.) are described from the abyssal and hadal zones (3210–7540 m depth) of the Sea of Okhotsk, the Bering Sea, as well as the Kuril-Kamchatka and Japan trenches. The new species are remarkable among their congeners due to the combination of the following characters: an obliquely-rhomboidal shell with a weak and shallow posterior sulcus and a large prodissoconch with sculpture of lamellated folds. Comparisons with related species are provided.

Macrofauna community of the cold seep area at Site F, South China Sea

A cold seep is one of the typical deep-sea chemical energy ecosystems and a hotspot for studying unique life processes and biogeochemical cycles in the deep sea. Macrofauna, which is one of the most important components of the cold seep ecosystem, has not been thoroughly studied. We examined the macrofauna community at Site F using images collected in 2016 by an imaging and laser profiling system and biological samples collected in 2020 and 2021 by TV grab and a remotely operated vehicle. In total, 41 species were found. The overall number of macrofauna identified at Site F (20,000 m2) reached 252,943 individuals, and the biomass reached 726.15 kg by dry weight. As the dominant species, Gigantidas platifrons and Shinkaia crosnieri reached their highest densities of 629 and 396 individuals/m2, respectively. The comparisons between different stations revealed that the diversity and density, even the biomass of dominant species, were much higher in the south than in the north at Site F in 2020. Correlation analysis showed that methane had a positive effect on macrofauna density. Compared with S. crosnieri, G. platifrons seems to be more adapted to the harsh cold seep environment. Methane consumption rates of the dominant species show that macrofauna are important in influencing seafloor methane fluxes. Our findings provide valuable insights into the ecology, community structure, and biota-environment interaction in the cold seep at Site F.

Optimization of environmental DNA analysis using pumped deep-sea water for the monitoring of fish biodiversity

Deep-sea ecosystems present difficulties in surveying and continuous monitoring of the biodiversity of deep-sea ecosystems because of the logistical constraints, high cost, and limited opportunities for sampling. Environmental DNA (eDNA) metabarcoding analysis provides a useful method for estimating the biodiversity in aquatic ecosystems but has rarely been applied to the study of deep-sea fish communities. In this study, we utilized pumped deep-sea water for the continuous monitoring of deep-sea fish communities by eDNA metabarcoding. In order to develop an optimum method for continuous monitoring of deep-sea fish biodiversity by eDNA metabarcoding, we determined the appropriate amount of pumped deep-sea water to be filtered and the practical number of filtered sample replicates required for biodiversity monitoring of deep-sea fish communities. Pumped deep-sea water samples were filtered in various volumes (5–53 L) at two sites (Akazawa: pumping depth 800 m, and Yaizu: pumping depth 400 m, Shizuoka, Japan) of deep-sea water pumping facilities. Based on the result of evaluations of filtration time, efficiency of PCR amplification, and number of detected fish reads, the filtration of 20 L of pumped deep-sea water from Akazawa and filtration of 10 L from Yaizu were demonstrated to be suitable filtration volumes for the present study. Fish biodiversity obtained by the eDNA metabarcoding analyses showed a clear difference between the Akazawa and Yaizu samples. We also evaluated the effect of the number of filter replicates on the species richness detected by eDNA metabarcoding from the pumped deep-sea water. At both sites, more than 10 sample replicates were required for the detection of commonly occurring fish species. Our optimized method using pumped deep-sea water and eDNA metabarcoding can be applied to eDNA-based continuous biodiversity monitoring of deep-sea fish to better understand the effects of climate change on deep-sea ecosystems.

Insights from the management of offshore energy resources: Toward an ecosystem-services based management approach for deep-ocean industries

The deep ocean comprises complex ecosystems made up of numerous community and habitat types that provide multiple services that benefit humans. As the industrialization of the deep sea proceeds, a standardized and robust set of methods and metrics need to be developed to monitor the baseline conditions and any anthropogenic and climate change-related impacts on biodiversity, ecosystem function, and ecosystem services. Here, we review what we have learned from studies involving offshore-energy industries, including state-of-the-art technologies and strategies for obtaining reliable metrics of deep-sea biodiversity and ecosystem function. An approach that includes the detection and monitoring of ecosystem services, with open access to baseline data from multiple sectors, can help to improve our global capacity for the management of the deep ocean.

Deep-sea biology in undergraduate classrooms: Open access data from remotely operated vehicles provide impactful research experiences

Opportunities for students to conduct research in courses increase feelings of belonging in science, retention in STEM majors, and sense of ownership in a student’s educational experience. However, many research fields are challenging to bring to students: for example, deep-sea biology often requires expensive expeditions, restricting participation and accessibility. Access to deep-sea systems has been expanded by programs such as the National Oceanic and Atmospheric Administration's Ocean Exploration (NOAA Ocean Exploration), which uses telepresence to bring deep-sea exploration to a global audience. Here, we present one example of how remotely operated vehicles can engage students in original research. Students in an undergraduate Marine Biology lab at at the State University of New York at Geneseo investigated the relationship between substrate rugosity and biodiversity of cold-water coral communities and associate fauna. The study site in the Pacific Remote Islands Marine National Monument was explored by NOAA Ocean Exploration using NOAA Ship Okeanos Explorer as part of the 2017 Mountains in the Deep Expedition, EX1705. Organism density was greater at higher rugosity levels, suggesting that complex substrates support higher abundances in deep-sea communities. This research experience enhanced student’s understanding of the scientific process, appreciation for deep-sea communities, and engagement in the course. Open access deep-sea data provide impactful opportunities for students to participate in original research, increasing the accessibility and reach of deep-sea science.

Soft-Bottom Infaunal Macrobenthos of the Avilés Canyon System (Cantabrian Sea)

The Aviles Canyon System (Northern Atlantic coast of Spain) is one of the ten marine regions studied in the Spanish seas by the LIFE+ INDEMARES project, which aims to identify special areas of conservation within the Natura 2000 Network. This study aims to characterize the composition and distribution of the macrobenthic fauna in order to provide baseline data to obtain a basic knowledge of the environment. Three oceanographic surveys were carried out to investigate species and habitats of this deep-sea ecosystem. The stations were sampled using a box corer, in order to evaluate the distribution and biodiversity of the macroinfauna, and to analyse the granulometric composition and the organic matter content. Sediments were mainly sandy in nature, the finest sediments with the highest organic matter content were found in the deepest areas, while coarser sediments were located in shallow stations. Polychaetes were the best represented group in total number of species and individuals, followed by crustaceans and molluscs. Five major macrobenthic assemblages were determined through multivariate analyses. Bathymetry and sedimentary composition were the main factors structuring the benthic community separating shallow and coarser stations from deeper and finer ones.

Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis.

Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.

Deep-Sea Predator-Prey Dynamics Revealed by Biologging and eDNA Analysis

At depths below 200 m, the pelagic deep sea comprises the largest, but least explored, part of the ocean. In this vast environment, animals are hard to find, and interactions among them are even harder to investigate (Robison, 2009). Climate change and industrial exploitation simultaneously impose increasing pressure on deep-sea ecosystems, leading to reduced ecosystem health and services at a global scale. Many of these changes occur outside of the range of human observation and are unrecognized so that effective conservation is limited. Such changes can include interactions between elusive and sometimes giant deep-sea predators such as cetaceans and their prey. The use of on-animal recorders has revealed that multiple species of cetaceans make extensive use of the deep sea, specifically the meso- (200–1,000 m depth) and bathypelagic (1,000–4,000 m depth) zones, to hunt for diverse, often cephalopod-dominated prey populations (Tyack et al., 2006). Because their dives to remote depths are energy consuming, the prey reward needs to be substantial to make the dives profitable. Thus, we expect that deep-diving cetaceans selectively target distinct foraging zones that hold specific prey communities to optimize their foraging performance.

Adapting ecosystem restoration for sustainable development in a changing world

Adapting ecosystem restoration for sustainable development in a changing world

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding.

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.