Natural products from marine and terrestrial organisms provide an important resource for medicinal chemistry and drug discovery. Defined as occurring at depths greater than 200 m, most of the ocean, by area and volume, is comprised of deep-sea environments. These contrasting ecosystems exhibit a wide range of temperature, pressure, and environmental chemistry conditions that harbour high phylogenetic diversity. Here we analyse the global distribution of Marine Natural Products (MNPs) from deep-sea organisms, which reveals chronic undersampling of the deep ocean as a reservoir of new and diverse chemical structures and bioactivity. The sources of 2909 compounds and extracts, compiled from published records, show a sampling bias towards benthic and shallower deep-sea habitats, with relatively few from areas beyond national jurisdictions and a concentration of records along geomorphological features that have been the focus of marine scientific interest such as seamounts and hydrothermal vents. The phylogenetic distribution of deep-sea MNPs is dominated by non-metazoan sources (76% of records) and Ascomycota fungi in particular (55%). Polyketides are the most prevalent metabolites in deep-sea MNPs, and cytotoxic and antibacterial properties are the most commonly reported bioactivities. Our analyses highlight a need for systematic sampling and consistent data reporting to explore potential relationships, if any, between, bioactivity, new chemical structures, phylogeny and deep-sea environmental conditions, which could guide targeted biodiscovery in our planet's largest biome and enable better assessment of the benefits of protecting deep-sea biodiversity from human impacts.
For Small Island Developing States, including those in the Caribbean, the deep sea remains a challenging ecosystem to study as it requires expensive technology and specialised expertise. The deep-sea environment of Barbados (200-5,776 m) accounts for 99.8% of its Exclusive Economic Zone (EEZ). Barbados is presently in the initial phases of developing a marine spatial plan for its EEZ. Comprehensive baseline information on the deep-sea ecosystems is crucial for evidence-based decision-making. This research assesses the state of deep-sea biological knowledge in Barbados via a comprehensive review of species records from peer-reviewed and grey literature, as well as museum and biodiversity databases. We found 1,589 biological records constituting 309 families and 624 species and morphospecies for Barbados' deep sea. Strikingly, richness analyses estimate that just 20% of the species and 48% of the families inhabiting Barbados' deep sea have been recorded. We also discuss limitations in existing knowledge, including vast geographic areas and depths still requiring research, as well as the varied methods of deep-sea observation and sampling utilised thus far, and the associated influence on the taxonomic composition of the known deep-sea community. Although limited, this assessment of deep-sea biodiversity information has provided insights to assist with the creation of a road map which decision-makers can utilize to guide future management and research activities.
It is estimated that millions of species exist in the deep-sea environment, such as hydrothermal vents, cold seeps, abyssal plains and seamounts, which have yet to be described. Non-invasive biodiversity assessment methods can be applied using deep-sea environmental DNA (eDNA) metabarcoding, but it can sometimes be limited by the fact that deep-sea taxa are not well represented in curated reference databases. This study proposes a proof-of-concept artificial intelligence (AI)-driven framework for deep-sea eDNA analysis consisting of three different and complementary parts. To learn taxonomically informative sequence representations that cannot be obtained from conventional reference matching, a hybrid CNN Transformer model is presented and trained. The suggested methodology confirmed the practicality of confidence-guided novel taxon discovery with a macro F1 score of 0.847 using simulated data sets drawn from CMLRE expedition metadata. These findings provide the framework for future validation with actual deep-sea sequencing datasets. Second, a module for discovering potential, confidence-based novel taxa has been implemented, which sends low-confidence predictions to an unsupervised workflow that includes UMAP and HDBSCAN. In the simulated evaluation scenario, this module retrieved 91.5% of novel taxa as new taxa, and with 88.2% precision. Third, taxonomic abundance estimations that are suitable for downstream alpha and beta diversity analysis are provided by normalization and ecological profiling modules. The proposed framework consumed one million sequencing reads in 2.1 h across four NVIDIA A100 GPUs, significantly shorter than the processing times used in the different workflows evaluated in this study. Collectively, these findings indicate that deep learning-assisted eDNA analysis could help in biodiversity assessments where there is a lack of extensive reference databases. Due to all quantitative assessments conducted on simulated datasets, the results obtained should be regarded as proof-of-concept results and further testing with real data from deep-sea expeditions needs to be carried out to exercise the operational performance.
Glass sponges constitute an important component of benthic communities, forming structural habitats in the deep-sea. Currently, 146 species of hexactinellids are known to occur in the Atlantic Ocean, with the majority reported at higher latitudes in the North Atlantic. Without a comprehensive understanding of their biodiversity across the entire Atlantic, conservation programs aimed at protecting these important organisms are limited in their effectiveness. To fill-in this knowledge gap, our research focuses on the examination of the glass sponge fauna inhabiting several seamounts (Carter, Gramberg, Knipovich, Vayda) and the Vema fracture zone, all located in Areas Beyond National Jurisdiction across the tropical Atlantic. This study identified 19 glass sponge species from 15 genera and 6 families, using an integrative taxonomic approach. Of these, 13 species are new to science and are herein described and illustrated. Phylogenetic reconstructions of partial mtDNA (COI and 16S rDNA) and nuclear rDNA (28S) markers confirm our taxonomic identifications and support previous studies on the phylogenetic status of these families. In the present work, we increased the number of known species for the Atlantic from 146 to 159. Many of these new species are from rarely studied genera, such as Caulophacella, Tabachnickia, Heterorete, Lonchiphora and Scyphidium. The discovery of such a high number of new species highlights the limited exploration and research in the tropical Atlantic area, where the diversity of deep-sea organisms is yet to be unravelled. This relatively unexplored region contains a substantial diversity of deep-sea life that remains to be fully studied and understood. The discovery of these new species not only enhances our understanding of biodiversity in this region but also provides crucial insights into broad distribution patterns, which is vital for developing new policies to protect these critical habitats.
Deep-sea settings in the Eastern Tropical Pacific remain a poorly understood region with many further species awaiting discovery. Herein, four new species from Costa Rica are described from deep-sea habitats. New occurrences with in situ or living observations are made for eight species. New observations of hippasterine corallivory on deep-sea octocorals are included. A brief summary of Costa Rican species is presented.
In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The 15,923-bp-long sequence displays 98.72% pairwise identity with its closest relative, Mirocaris indica. A significant proportion of the mitochondrial genome (0.63%) corresponds to heteroplasmic sites that were found on 14 of the 37 genes, including cox1, though all such sites induce synonymous mutations. This level of heteroplasmy may serve as the first step for recombination of the mitogenome by paternal leakage and/or a less effective purifying selection in somatic tissues. We also take advantage of the shotgun deep sequencing strategy to assess the metagenomic composition of the sample and are able to detect other deep-sea hydrothermal vent species present at the vent system.
A deep-sea alkaline lipase, MyLip2, fromMoritella yayanosiiwas identified from a metagenomic library of 1,048,576 genes. The wild-type enzyme preferred medium- to long-chain p-nitrophenyl esters, with optimal activity at pH 10.5 and 40 °C, but its specific activity was only 2.93 U/mg toward p-nitrophenyl palmitate. To improve performance, we used a structure- and sequence-guided strategy targeting noncatalytic residues around the catalytic center and lid region. Combinatorial engineering produced triple A271F/V250L/L231P and quadruple A271F/V250L/L231P/T300K (4 M), with comparable specific activities of 743.4 and 745.4 U/mg; 4 M was chosen for its high activity and improved thermal tolerance. This variant showed ∼ 196-fold higher catalytic efficiency (kcat/Km) toward p-nitrophenyl palmitate, with increasedVmax and kcat. Molecular docking, kinetics, and simulations indicated that the substitutions support a more open and catalytically accessible lid conformation, facilitating substrate access and turnover. Comparison with reported lipases indicated that MyLip2 and 4 M combine alkaline preference, medium- to long-chain activity, and improved performance. This work provides a high-performance deep-sea alkaline lipase and suggests that catalytic efficiency can be improved by tuning noncatalytic residues that influence the catalytic-center microenvironment and lid dynamics, without mutating the catalytic triad or redesigning the lid.
A new species of the deep-sea squat lobster genus Munidopsis Whiteaves, 1874, is described from a seamount in the southeastern Arabian Sea, India. Munidopsis hindmahasagaraesp. nov. differs from its close congeners, M. alcocki Ahyong, 2014 and M. treis Ahyong & Poore, 2004 by the presence of a tooth on the distomesial margin of the antennule, a relatively longer distolateral tooth of the second antennal article, and a relatively longer distomesial tooth of the third antennal article. Gonionida comorina (Alcock & Anderson, 1899) is redescribed and illustrated based on fresh material, as well as comparison with photographs and the description of the type specimen. Its re-description enables confirmation of its placement in the genus Gonionida Macpherson & Baba, 2022, owing to a triangular fourth thoracic sternite. Juveniles of Eumunida sp. are compared with congeners from the western Indian Ocean namely, E. funambulus Gordon, 1930, E. similior Baba, 1990, and E. spiridonovi Macpherson, Rodríguez-Flores & Machordom, 2017.
A novel Gram-stain-negative, non-flagellated, non-motile, rod-shaped bacterial strain, designated 502str34T, was isolated from deep-sea sediment. The strain was positive for oxidase, catalase and urease activities. Optimal growth occurred at 28-32 °C, pH 7.0-7.5 and in the presence of 2.0-3.0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 502str34T was most closely related to Pseudooceanicola batsensis HTCC2597ᵀ (97.4%), Pseudooceanicola nitratireducens JLT1210ᵀ (97.3%) and Pseudooceanicola nanhaiensis SS011B1-20ᵀ (97.2%). The genomic G+C content was 67.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain 502str34T and its closest relatives were 20.4-20.9% and 75.5-77.3%, respectively, which are below the accepted thresholds for species delineation. The predominant respiratory quinone was ubiquinone-10. The major cellular fatty acids (>10%) were C16:0, C18:1  ω7c 11-methyl and summed feature 8 (C18:1  ω7c and/or C18:1  ω6c). The polar lipids mainly comprised phosphatidylcholine, phosphatidylglycerol, unidentified aminolipids, unidentified phospholipids, unidentified lipids and an unidentified aminophospholipid. Based on phenotypic, phylogenetic, chemotaxonomic and genomic evidence, strain 502str34T represents a novel species of the genus Pseudooceanicola, for which the name Pseudooceanicola profundus sp. nov. is proposed. The type strain is 502str34T (=KCTC 82133T=JCM 33907T).
Microbially mediated manganese (Mn) oxidation is a key process in the biogeochemical cycling of Mn. While Shewanella is widely recognized for its metal-reducing capabilities, recent studies have shown that certain terrestrial strains can also oxidize Mn2+ during aerobic respiration. Nevertheless, the Mn2+-oxidizing capacity of marine Shewanella strains, which are ubiquitous in oceanic settings, has remained largely unexplored, and the influence of environmental factors on this capacity has not been systematically evaluated. Here, we investigated the ability of the deep-sea bacterium S. piezotolerans WP3 to oxidize Mn2+ under aerobic conditions and examined the effects of temperature (4°C-20°C) and hydrostatic pressure (0.1-20 MPa). We found that S. piezotolerans WP3 efficiently oxidizes Mn2+ to Mn oxides, predominantly forming bixbyite-like minerals and amorphous mixed-valence nanoparticles. This oxidation process was not attributable to a Mn2+-specific enzyme but to bacterially generated reactive oxygen species (ROS), with superoxide (O2 •-) playing the primary role. Both temperature and hydrostatic pressure significantly affected the final extent of Mn2+ oxidation by altering the production of O2 •-. Transcriptomic analysis revealed that exposure to high hydrostatic pressure induced the upregulation of genes involved in antioxidative stress, which likely accounts for the enhanced ROS-mediated Mn2+ oxidation observed in cultures incubated at 20 MPa. Under alternating aerobic and anaerobic conditions, strain WP3 mediated successive Mn oxidation and reduction, ultimately forming rhodochrosite as a secondary mineral. These results suggest that S. piezotolerans WP3 has the potential to mediate Mn redox cycling in marine sediments, coupling ROS-dependent oxidation with anaerobic Mn reduction.
The rare biosphere harbors immense microbial diversity, yet most low-abundance taxa remain uncultured and functionally enigmatic. Here, we isolated strain D14T from deep-sea water, and propose to classify it as a novel species, Metabolovarius oceani sp. nov., within the novel family Metabolovariaceae fam. nov. M. oceani represents the first cultivated member of the candidate family NORP267, a globally distributed but elusive alphaproteobacterial lineage known only from metagenome-assembled genomes. It possesses broad metabolic capabilities, including CO2 fixation, polyhydroxyalkanoate biosynthesis, complete denitrification and thiosulfate oxidation, and is capable of aerobic growth under both heterotrophic and autotrophic conditions and of anaerobic autotrophic denitrification via thiosulfate oxidation. Despite its versatile metabolic repertoire and global distribution, Metabolovariaceae remains consistently low in abundance across diverse habitats. The isolation of M. oceani permits direct experimental insights into the evolutionary adaptations, physiological resilience, and potential ecosystem roles of rare but metabolically versatile microorganisms within the microbial dark matter.
Anaerobic oxidation of methane is a key process reducing methane emissions in oxygen-depleted marine environments such as deep-sea cold seeps. However, the stability and adaptability of microbial interactions driving this process remain poorly understood. Here, we combined stable isotope probing, tracer incubations, and bacterial inhibition experiments to investigate methane-oxidizing communities in sediments from the South China Sea. We found that methane oxidation was sustained by interactions between distinct archaeal and bacterial groups under different electron acceptor conditions. Inhibition experiments revealed tightly coupled microbial partnerships, while community shifts toward alternative metabolic pathways maintained overall methane oxidation rates. These results demonstrate functional redundancy and metabolic flexibility within microbial consortia. Our findings highlighted how dynamic environmental conditions supported multiple overlapping pathways, ensuring stable methane consumption. This work provided insights into the resilience of biogeochemical processes and informs future strategies for methane mitigation.
Aspertetranones are a unique class of marine fungal meroditerpenoids characterized by a highly oxygenated, linear 6/6/6/6 tetracyclic core fused to an α-pyrone scaffold. Although the pathway of aspertetranone biosynthesis in Aspergillus ochraceopetaliformis has been partially elucidated, the full potential of these compounds remains untapped. The structural diversity and enzyme promiscuity of tailoring reactions offer unexplored opportunities for the generation of bioactive derivatives through combinatorial biosynthesis. In this study, we identified the atn biosynthetic gene cluster responsible for aspertetranone production in deep-sea-derived Aspergillus versicolor ADS-F20. Through the systematic heterologous expression of 12 key genes in Aspergillus oryzae, the full pathway reconstitution and targeted biosynthesis of 17 metabolites were achieved, thus expanding the known chemical space of meroterpenoids. Notably, bioactivity screening identified compound 6 as having potent antibacterial and antifungal activities against Vibrio vulnificus ATCC 27562 (MIC = 4.50 μg/mL) and Phytophthora nicotianae (MIC = 9.01 μg/mL). Compound 11 demonstrated broad-spectrum anticancer and cytotoxic effects against the K-562, MCF7, and PATU8988T cell lines. This study underscores the power of pathway reprogramming and catalytic network engineering as versatile strategies for expanding the structural and functional diversity of biosynthetic pathway components.
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Deep sea gastropod fauna in the offshore Colombian Pacific is poorly known. This paper presents results from the first quantitative inventory of gastropods inhabiting soft bottoms in the region, based on samples collected during two scientific expeditions. In 2002, 39 trawl samples were collected at water depths 70-500 m offshore the Colombian Department of Chocó, using the R/V ARC Malpelo. In 2012, 15 trawl samples were collected from 200-1,000 m water depth, with the shrimp boat M/N Perla Verde, offshore of the Department of Nariño. We identified a total of 3,432 mollusks, both live specimens and empty shells. Studied specimens were distributed among four subclasses, eight orders, 36 families, 59 genera, and 85 morphospecies. Information on their abundance, distribution, feeding strategies, and ecology is provided in the present study. The Order Neogastropoda accounted for the greatest number of species (46). Most individuals (95.4%) were collected offshore of Chocó, with the remaining 4.6% from the area offshore of Nariño. The most abundant species in the samples was the scavenger Nassarius miser (Dall, 1908), which comprised 59.2% of the total individuals. The family with the greatest number of species (9) was Pseudomelatomidae. This study identified 39 previously not reported species range extensions in the offshore Colombian Pacific, greatly increasing the known species diversity from the region. We encountered three distinct species assemblages that differed across water depth: i) continental shelf; ii) shelf-slope transition, and iii) upper slope. Water depth was determined to be the primary factor that influenced the distribution of the recorded species, with the greatest species richness observed on the continental shelf. These findings contribute to a broader understanding of the gastropod species that inhabit the Colombian Pacific Ocean, the Panamic Province, and the Tropical Eastern Pacific. Such information is crucial for conservation initiatives in biologically diverse areas offshore of developing countries, particularly in the face of rapid habitat change.
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A new species of tubeworm belonging to the genus Hyalopomatus (Serpulidae) is described from the southern Mexican Pacific. It was found in 2024 attached to a seismograph at nearly 1000 m depth. The new species possesses distinctive features that separate it from the 17 species of this genus currently recognized, including: a white, opaque, smooth tube, with anterior collar-like shallow rings; a tetra-lobed collar; thoracic membranes extending to the second chaetiger; absence of an anterior abdominal achaetous zone; a spherical operculum, with a slightly differentiated distal cap; and a smooth, not annulated, junction between the peduncle and the operculum. Phylogenetic analyses indicate that the new species forms a clade with some other Hyalopomatus species (H. mironovi, H. suelindsayae and H. sp. 1 Jaco Summit) but does not group with an undescribed species from the Gulf of California (H. sp. Guaymas Basin).
Vertically transmitted symbionts experience progressive genome degradation driven by transmission bottlenecks each host generation that reduce genetic diversity and promote fixation of deleterious mutations. Direct estimates remain rare because inference requires scarce parent-offspring samples and sequencing sensitive enough to detect rare variants. Here, we investigate symbiont transmission bottlenecks in a vesicomyid clam by deeply sampling within-host endosymbiont genetic diversity using two ultra-accurate sequencing methods. Demographic modeling revealed an effective bottleneck size of approximately eight symbionts (95% CI: 1-17 genomes) per host generation. This estimate is sharply reduced relative to prior cytological estimates of bottleneck census size, with important implications for understanding the rate and dynamics of endosymbiont genome degradation.
Polyclad flatworms are free-living platyhelminths that inhabit various marine environments; however, their biodiversity in the deep sea remains poorly understood. Herein, we describe a new species of Notocomplana Faubel, 1983, Notocomplana profundasp. nov., based on specimens collected from Bathymodiolus mussel aggregations in a deep-sea hydrocarbon seep off Hatsushima, Japan. This is the first report of a bathyal species of Notocomplana, which is dominated by shallow-water species. The new species is characterized by the absence of tentacles, eyespots, and any color pattern on the dorsal surface of the body and the presence of a seminal vesicle larger than a prostatic vesicle and a long, tubular Lang's vesicle. A molecular phylogenetic analysis based on the partial sequences of two mitochondrial and two nuclear genes suggested that the strategy of N. profundasp. nov. to use mussel aggregations was acquired by its shallow coastal ancestors.
A new species of the genus Stilipes Holmes, 1908, is described and illustrated from a single female specimen collected from the SW Gulf of California, Mexico, in 1500 m depth. Stilipessp. nov. represents the sixth species of this genus worldwide, all documented from 200 to 1060 m depth. Characters that separate the new species from congeners include: head with eyes; first three pereonites subequal in length; presence of a conical subrostral lamina and a vestigial accessory flagellum of antenna 1; 6th coxa forming a very wide, rounded posteroventral lobe; epimeral plate 2 acute, directed posteriorly; epimeral plate 3 rounded; telson length and width subequal. A comparative table of diagnostic characters among species of Stilipes is provided, including the depth range and geographic distribution of each species.