Deep-sea Ecosystems Research Articles

A new deep-sea species of golden gorgonian (Octocorallia: Scleralcyonacea: Chrysogorgiidae) from Antarctic waters

The Southern Ocean harbours rich deep-sea ecosystems with local hotspots of benthic biodiversity. Still, many species, including deep-water octocorals, remain undescribed despite the fact that the exploration of the deep-sea has improved thanks to recent technological advances. In this context, a new species of golden gorgonian has been collected at 1407–1581 m depth during a recent cruise to Dronning Maud Land in the Eastern Weddell Sea. Currently, after recent changes in Chrysogorgia taxonomy, Chrysogorgia lunae sp. nov. (Octocorallia: Scleralcyonacea) is the only known representative of the genus in Antarctic waters. It corresponds to the "Squamosae typicae" and is characterized by a bushy colony with branching sequence of 2/5L and bell-shaped polyps. A molecular comparison with published sequences of Chrysogorgia species is provided based on a concatenated sequence of two mitochondrial genes, mtMutS and COI, as well as the 28S nuclear ribosomal gene.

A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation.

Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments. Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments. This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.

Discovery of Prevalent Ciliophora, Discoba, and Copepoda Protists in Deep Sea Water by In Situ Nucleotide Extraction

Deep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF), and a multiple in situ nucleic acid collection (MISNAC) method to exhibit differences in the community structures that were collected at ~590–3100 m in the South China Sea (SCS). The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from the V9 variation region revealed higher diversity for MISNAC DNA absorption column samples compared to others. Importantly, the relative abundance of Ciliophora (19.49%), Copepoda (23.31%), and Diplonemea (10.67%) was higher in MISNAC adsorption column samples, while Retaria (48.86%) were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might collect more DNA in situ for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. In conclusion, MISNAC is an effective method for DNA collection of deep-sea eukaryotic microorganisms and provides valuable materials for studying deep-sea microbial ecosystems.

The BBNJ Agreement: Through the Prism of Deep-Sea Vulnerable Marine Ecosystems

On 19 June 2023, member States of the United Nations adopted, by consensus, the Agreement under the United Nations Convention on the Law of the Sea on the Conservation and Sustainable Use of Marine Biological Diversity of Areas Beyond National Jurisdiction (BBNJ Agreement). The BBNJ Agreement seeks to address one of the greatest challenges of the 21st century—managing our deep ocean environment, including its ecosystems and resources, in a way that does not lead to its long-term decline and maintains its potential to meet the needs of present and future generations. This article assesses the BBNJ Agreement through an analysis of its application to deep-sea vulnerable marine ecosystems (VMEs). As VMEs represent a key component of marine biodiversity and are particularly susceptible to anthropogenic disturbance, they provide a useful medium for undertaking a legal analysis of the provisions, rules, and procedures of the recently adopted instrument.

A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems.

The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.

Sea-Pix-GAN: Underwater image enhancement using adversarial neural network

In the last decade, the exploration of deep-sea ecosystems has surged, offering exciting prospects for discovering untapped resources such as medical drugs, food and energy sources, and renewable energy products. Consequently, research in underwater image processing has witnessed substantial growth. However, underwater imaging poses significant challenges, particularly without sophisticated, specialized cameras. Traditional cameras are impacted by absorption and scattering in the aquatic environment, producing hazy images with a blue–green tint. This phenomenon holds implications for marine research and other disciplines that rely on underwater imaging. While hardware advancements have been made over the years, image processing remains a valuable, cost-effective, and practical approach for underwater enhancement. Despite the existence of state-of-the-art techniques for underwater enhancement and restoration, their performance is often inconsistent. While some methods excel in contrast restoration, color restoration remains a pervasive challenge. In this paper, we introduce Sea-Pix-GAN, a Generative Adversarial Network (GAN)-based model that addresses these issues in underwater image enhancement. We redefine the problem as an image-to-image translation task and tailor the objective and loss functions to achieve color, content, and style transfer. The model is trained on a large dataset of underwater scenes, encompassing the diverse color dynamics of underwater subjects. Sea-Pix-GAN demonstrates promising results in restoring color, contrast, texture, and saturation. To validate its effectiveness, we compare the performance of Sea-Pix-GAN quantitatively based on metrics like PSNR, SSIM, and UIQM and qualitatively against several existing techniques.

Xyloplax princealberti (Asteroidea, Echinodermata): A New Species That Is Not Always Associated with Wood Falls

Xyloplax is a genus of three species of sea stars previously found only on sunken wood in the deep ocean. Their circular and petaloid bodies, which lend them their common name “sea daisy”, and their presumed exclusive diet of wood make them an unusual and rare element of deep-sea ecosystems. We describe here the fourth species of Xyloplax from the eastern Pacific Ocean, Xyloplax princealberti n. sp., which ranges from offshore Canada to the Gulf of California (Mexico) and Costa Rica. Though sampled geographically close to another described species of Xyloplax from the northeastern Pacific, X. janetae, this new species is unique morphologically and according to available DNA data. The short abactinal spines are the most obvious feature that distinguishes X. princealberti n. sp. from other Xyloplax. The minimum distance for mitochondrial cytochrome c oxidase subunit I from Xyloplax princealberti n. sp. to the only other available Xyloplax, X. janetae, was 13.5%. We also describe Ridgeia vestimentiferan tubeworm bushes from active hydrothermal vents as a new Xyloplax habitat, the first record of a non-wood substrate, and a new reproductive strategy, simultaneous hermaphroditism, for this genus. We generated the first mitochondrial genome for a member of Xyloplax and analyzed it with other available asteroid data using nucleotide-coding or amino acid (for protein-coding genes) plus nucleotide coding (for rRNA genes). The nucleotide-coding results place Xylopax as part of the clade Velatida, consistent with a previous phylogenomic analysis that included Xyloplax princealberti n. sp. (as Xyloplax sp.), though the placement of Velatida within Asteroidea differed. The amino acid plus nucleotide coding recovered Velatida to be a grade with X. princealberti n. sp. as sister group to all other Asteroidea.

Survival of surface bacteriophages and their hosts in in situ deep-sea environments.

The survival of the sinking prokaryotes and viruses in the deep-sea environment is crucial for deep-sea ecosystems and biogeochemical cycles. Through an in situ deep-sea long-term incubation device, our results showed that viral particles and infectivity had still not decayed completely after in situ incubation for 1 year. This suggests that, via infection and lysis, surface viruses with long-term infectious activity in situ deep-sea environments may influence deep-sea microbial populations in terms of activity, function, diversity, and community structure and ultimately affect deep-sea biogeochemical cycles, highlighting the need for additional research in this area.

Studying the effect of camera tag associated white light on the diving and foraging behavior of Eastern Caribbean sperm whales

Studying the behavior of animals roaming the deep-sea is challenging and is driven by technological developments. The next step to further understand the interactions between predators and prey in the deep sea may be aided by animal-borne camera tags. However, in the darkness of the deep sea, obtaining useful footage requires a light source, which may affect the animal carrying the tag as well as other nearby organisms such as prey. Here we have tested whether the presence of camera associated white light affects the foraging behavior of sperm whales in the Eastern Caribbean Sea. Based on a small dataset of 7 foraging dives with camera lights on, we observed no changes in diving behavior and overall biosonar search behavior. However, we did observed indications of fewer prey capture attempts, which may be due to light induced prey deterrence. For short camera tag deployments this likely does not affect the long term fitness of the whales. However, this effect should be considered and monitored for longer camera tag deployments. Importantly, different deep-sea communities may react differently, we therefore wish to highlight the importance of testing whether research equipment affects the studied animal and its surroundings.

Fine-scale spatial patterns of deep-sea epibenthic fauna in the Laurentian Channel Marine Protected area

Ecological processes at local to global scales impact spatial patterns in abundance and distribution of megafauna. Fine-scale patterns have rarely been investigated through explicitly spatial analytical methods in the deep sea and have been assumed random, uniform, or similar to neighbouring areas. We used spatial statistics (Moran's I, Gi*, and local Moran's I) to identify significant megafaunal patterns (0–100s of meters; 8 focal taxa) in the Laurentian Channel Marine Protected Area, based on imagery from a remotely operated vehicle, using 8 parallel transects at each of 7 stations. Our results included 2 spatial scales, station level (0.256 km2) and paired transect level (0.004 km2). We found local areas with significant aggregations (e.g., Pennatula sp. 2 and Hexacorallia (SC.) spp.) and patches extending for ∼7–27 m, and in one case for ∼155 m. Patchiness also existed between neighbouring images (≤10 m apart). Patterns varied among taxa within stations and for the same taxon among transect pairs. Station-level patterns appear to be related to geological factors, such as BPI (bathymetric position index), benthoscape, pockmarks, and slope. We propose that patterns at the transect level were likely caused by biological factors, possibly related to reproduction due to local currents and retention, or community interactions (e.g., competition). Fine-scale patterns should be considered to ensure effective sampling designs when using fine-scale tools (e.g., imagery), and for establishing accurate community metrics (e.g., abundance and diversity). Our study is relevant to future ecological research, linking patterns to processes, as well as monitoring and conservation in deep-sea ecosystems.

Pollen from New Zealand may be altering remote deep-sea ecosystems

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Biodiversity study of the deep-sea ecosystems in the northwestern part of the Pacific Ocean

The aim of the work was to study some deep-sea bottom communities of the Far Eastern seas of Russia using a remotely operated underwater vehicle.Materials were the data of underwater video and photo profiling, as well as direct sampling, performed in 2011–2013, 2016, 2018, 2020 and 2021.As results, an extensive array of new data on the composition, structure, and patterns of distribution of deep sea biota has been obtained. A primary description of the benthic communities of the Gamovsky Canyon (Sea of Japan), cold seeps of the Deryugin Basin (Sea of Okhotsk), and Piip underwater volcano (Bering Sea) has been prepared. Some features of the composition and structure of communities are revealed, and vertical zonality is described.Practical value: the results can be used in the development of environmental protection measures and measures of rational nature management in the waters of the Far Eastern seas of Russia and in areas of potential development of deep-sea mineral resources in the ocean.

The Nekton Maldives taxonomic workshop: Exploring the biodiversity of shallow, mesophotic and deep-sea communities in Maldives

The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer.

The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents

The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.

Trophodynamics of the Antarctic toothfish (Dissostichus mawsoni) in the Antarctic Peninsula: Ontogenetic changes in diet composition and prey fatty acid profiles.

The Antarctic toothfish (Dissostichus mawsoni) is the largest notothenioid species in the Southern Ocean, playing a keystone role in the trophic web as a food source for marine mammals and a top predator in deep-sea ecosystems. Most ecological knowledge on this species relies on samples from areas where direct fishing is allowed, whereas in areas closed to fishing, such as the Antarctic Peninsula (AP), there are still key ecological gaps to ensure effective conservation, especially regarding our understanding of its trophic relationships within the ecosystem. Here, we present the first comprehensive study of the feeding behavior of Antarctic toothfish caught in the northern tip of the AP, during two consecutive fishing seasons (2019/20 and 2020/21). Stomach content was analyzed according to size-classes, sex and season. Macroscopic morphological analysis was used to identify prey, whereas DNA analysis was used in highly digested prey items. Fatty acid analysis was conducted to determine the prey's nutritional composition. The diet mainly consisted of Macrouridae, Cephalopoda, Anotopteridae, and Channichthyidae. Other prey items found were crustaceans and penguin remains; however, these were rare in terms of their presence in stomach samples. Sex had no effect on diet, whereas size-class and fishing season influenced prey composition. From 27 fatty acid profiles identified, we observed two different prey groups of fishes (integrated by families Anotopteridae, Macrouridae and Channichthyidae) and cephalopods. Our results revealed a narrow range of prey items typical of a generalist predator, which probably consumes the most abundant prey. Understanding the diet and trophic relationships of Antarctic toothfish is critical for a better comprehension of its role in the benthic-demersal ecosystem of the AP, key for ecosystemic fisheries management, and relevant for understanding and predicting the effect of climate change on this species.

Latitudinal gradient and influencing factors of deep-sea particle export along the Kyushu-Palau Ridge in the Philippine Sea

The export of particulate organic matter (POM) to deep-sea is crucial for deep-sea ecosystems. However, in situ measurements of large-scale POM export flux are scarce in the tropical and subtropical western Pacific, leading to reliance on biogeochemical models or sediment trap data from a few stations. To address this gap, the underwater vision profiler was used to measure particulate density and to calculate particulate organic carbon (POC) fluxes along the Kyushu–Palau Ridge (KPR) in the Philippine Sea. The results revealed a significant latitudinal gradient of POC fluxes: 37 % of the POC output from 200 m depth was preserved to 2000 m in the Western Pacific Warm Pool and up to 51 % was preserved in the North Pacific Subtropical Gyre. The near-bottom POC fluxes north of 25°N (1.64 ± 0.80 mg m−2 d−1) were significantly higher than the average near-bottom value of the entire transect (0.60 ± 0.43 mg m−2 d−1). Multiple linear regression analysis showed that the chlorophyll concentration had a significant positive effect on the POC fluxes at all depths, except near the bottom, while local factors such as mesoscale eddies and the interaction effect between the topography and current velocity only had significant effects on the POC fluxes at depths of >2000 m. Particle size spectrum analysis revealed that particles ranging from 64 to 323 μm in size exerted a dominant influence on the increase in the POC fluxes in the near-bottom layers situated north of 25°N. These findings indicated that the spatial heterogeneity of POC fluxes in the western Pacific was governed not only by upper ocean primary productivity but also by mesoscale processes, current velocity, and topography. These results provided crucial fundamental information for cartography of the distribution and simulation of the dynamics of deep-sea organisms along the KPR in the Philippine Sea.

Living in darkness: functional diversity of mesopelagic fishes in the western tropical Atlantic

Mesopelagic zones (200–1,000-m depth) are characterized by relatively low light levels, cold waters, and often limited oxygen, forming a stable yet challenging habitat for their inhabitants. To overcome these constraints, mesopelagic fishes have developed several adaptations that enable them to participate in crucial ecosystem processes such as nutrient cycling, carbon transport, and provisioning of harvestable fish stocks. However, our understanding of the functional diversity of mesopelagic fishes remains limited, while it is of particular importance considering the increase in human threats and possible environmental changes in the deep ecosystems. In this context, functional diversity emerges as a powerful tool and can help assess community assembly rules, including species complementary and redundancy. Here, we take advantage of scientific surveys that collected 200 species taxa identified from over 7,000 specimens to determine the functional diversity of mesopelagic fish assemblages across depths and the day–night period. We created a data set of 17 qualitative functional traits related to feeding, survival, and locomotion functions. Based on this information, functional spaces and diversity indices were calculated, and functional groups were established. Furthermore, the influence on the functional diversity of environmental variables and the day–night period was assessed by generalized additive models (GAMs). The hypothesis of functional complementary was tested. Overall, mesopelagic fishes displayed a high functional diversity and could be grouped into 10 major functional groups. Moreover, 107 species exhibited a unique composition of functional trait values, revealing a vast complementarity of functions within the deep-sea ecosystem. We also showed that functional diversity in mesopelagic ecosystems is neither static nor homogeneous, exhibiting higher values in the deepest layers and varying between day and night. We finally discuss processes that may structure mesopelagic fish assemblages and the implications of our findings for the conservation mesopelagic fishes.

BIODIVERSITY AND BIORESOURCES OF DEEP-SEA ECOSYSTEMS OF THE NORTHWESTERN PACIFIC

Modern problems of the investigation of marine biodiversity and bio-resources and their inventory in the deep-sea of the World Ocean are considered. The discussion of these problems is also based on the data of aseries of deep-water marine expeditions of the National Scientific Center of Marine Biology of the Far Eastern Branch of the Russian Academy of Sciences (NSCMB FEB RAS) in the deepest areas of the Far Eastern Seas and adjacent waters of the North-West Pacific. New results of a series of the deep-sea expeditions within the special RAS Project “Fundamental problems of investigation and conservation of the deep-sea ecosystems in the potentially ore-reach areas in the North-West Pacific” are briefly introduced and discussed (project of RAS № 3.1902.21.0012). Several “unique” deep-sea ecosystems found in the ore bearing sites and the active fishing areas in the North-West Pacific are described. Some safety opportunities for these “unique” ecosystems and possible limitations in the use of dangerous mining and fishing techniques disturbing deep-sea landscapes are considered, including various conservation statuses.

Ocean-based Climate Action and Human Rights Implications under the International Climate Change Regime

Abstract After drawing attention to the crucial role of marine biodiversity, including that of deep-sea ecosystems, in current scientific understanding of the ocean-climate nexus, this article highlights the limited extent to which the international climate change regime has so far addressed the ocean. The focus then shifts to how the international climate change regime could contribute to the protection of marine biodiversity as part of mitigation, adaptation and finance, taking into account human rights impacts and standards, drawing a comparison with REDD+. The article concludes with an original proposal, inspired by the Climate and Clean Air Coalition, to develop urgent, synergistic approaches to ocean- and human rights-based climate action through a multi-actor coalition, including different international treaties and United Nations bodies, to ‘protect and restore the ocean’s contributions to climate regulation, human well-being and planetary health’.

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean.

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.