Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

Chemical Constituents from the deep-sea-derived Fungus Aureobasidium melanogenum LUO5

Three new C10 and C12 aliphatic δ-lactones (1-3), three new fatty acid methyl esters (4-6), and eight known compounds (7-14) were isolated from the marine Aureobasidium sp. LUO5. Their structures were established by detailed analyses of the NMR, HRESIMS, optical rotation, and ECD data. All isolates were tested for their inhibitory effects on nitric oxide production in LPS-induced BV-2 cells. Notably, compound 4 displayed the strongest inhibitory effect with the IC50 value of 120.3 nM.

Benthic foraminifera in Gulf of Mexico show temporal and spatial dynamics of microplastics

Microplastics have accumulated in the environment since plastic production began, with present-day observations that range from marine trenches to mountains. However, research on microplastics has only recently begun so it is unclear how they have changed over time in many oceanic regions. Our study addressed this gap by quantifying the temporal and spatial dynamics of microplastics in two deep-water regions of the Gulf of Mexico (GOM). We isolated agglutinated foraminifera from sediment cores and assessed microplastics that were incorporated into their tests. Our results indicated that microplastics were incorporated by agglutinated foraminifera after plastic production began. Microplastics were higher at deep-water sites and closer to the Mississippi River. This study confirms the presence of microplastic incorporation into agglutinated foraminifera tests and investigates microplastics in deep-water sediments in the GOM. Additional work is needed to fully identify the distribution of microplastics across the GOM and other oceanic basins.

Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes

The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.

Cloning and functional characterization of the oxidative squalene cyclase gene in the deep-sea holothurian Chiridota sp

Saponins derived from holothurians have high potential medicinal value. However, the de novo synthesis of the derivatization of triterpenes is still unclear. Oxidative squalene cyclase (OSC) can catalyze 2,3-Oxidosqualene into diverse products that serve as important precursors for triterpene synthesis. However, the function of theOSCgene in Chiridotasp. hasnot been elucidated. In this study, an OSCgenederived from the deep-sea holothurianChiridota sp. was cloned and characterized functionally in a yeast system. The open reading frame of the OSC gene was 2086 bp, which encoded 695 amino acids. The Chiridota sp. OSC gene has a similarity of 66.89 % to the OSC of other holothurian species and 63.51 % to that of Acanthaster planci. The phylogenetic tree showed that the echinozoan OSCsclustered together, and then they formeda sister group to fungi and plant homologs. Chiridota sp. OSC catalyzed 2,3-Oxidosqualene into parkeol.Under high pressure, the relative enzymatic activity and stability of cyclase inChiridota sp. was higher than that in the shallow-sea holothurianStichopus horrens. The newly cloned OSC of Chiridota sp.provideskey information for the interpretation of the saponin synthesis pathway in deep-sea holothurians.

Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters

Brisingida Fisher 1928 is one of the seven currently recognised starfish orders, and one of the least known taxa as being exclusive deep-sea inhabitants. Modern deep-sea expeditions revealed their common occurrences in various deep-sea settings including seamounts, basins and hydrothermal vent peripheral, underlining the necessity of clarifying their global diversity and phylogeny. In this study, we present a comprehensive molecular phylogeny of Brisingida which encompasses the highest taxonomic diversity to date. DNA sequences (COI, 16S, 12S and 28S) were obtained from 225 specimens collected in the global ocean, identified as 58 species spanning 15 of the 17 extant genera. Phylogenetic relationship was inferred using both maximum likelihood and Bayesian inference methods, revealing polyphyletic families and genera and indicating nonnegligible bias in prior morphology-based systematics. Based on the new phylogeny, a novel classification of the order, consisting of 5 families and 17 genera, is proposed. Families Odinellidae, Brisingasteridae and Novodiniidae (sensu Clark and Mah, 2001) were resurrected to encompass the genera Odinella, Brisingaster and Novodinia. Brisingidae and Freyellidae were revised to include 11 and 3 genera, respectively. A new genus and species, two new subgenera and seven new combinations are described and a key to each genus and family is provided. Transformations of morphological traits were evaluated under the present phylogenetic hypothesis. A series of paedomorphic characters were found in many genera and species, which led to a high degree of homoplasy across phylogenetically distant groups. Our results provide new insights in the phylogeny and ontogeny of the order, and highlight the necessity to evaluate character convergence under sound phylogenetic hypothesis.

Using a food web model to predict the effects of Hazardous and Noxious Substances (HNS) accidental spills on deep-sea hydrothermal vents from the Mid-Atlantic Ridge (MAR) region

Deep-sea hydrothermal vents host unique ecosystems but face risks of incidents with Hazardous and Noxious Substances (HNS) along busy shipping lanes such as the transatlantic route. We developed an Ecopath with Ecosim (EwE) model of the Menez Gwen (MG) vent field (MG-EwE) (Mid-Atlantic Ridge) to simulate ecosystem effects of potential accidental spills of four different HNS, using a semi-Lagrangian Dispersion Model (sLDM) coupled with the Regional Ocean Modelling System (ROMS) calibrated for the study area. Food web modelling revealed a simplified trophic structure with low energy efficiency. The MG ecosystem was vulnerable to disruptions caused by all tested HNS, yet it revealed some long-term resilience. Understanding these impacts is vital for enhancing Spill Prevention, Control, and Countermeasure plans (SPCC) in remote marine areas and developing tools to assess stressors effects on these invaluable habitats.

Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum

The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.

Organic UV absorbents in the deepwater redfish (Sebastes mentella) from the St. Lawrence Estuary and Gulf: Distribution and human health risk assessment

UV absorbents (UVAs), such as organic UV filters (UVFs) and benzotriazole UV stabilizers (BZT-UVs), are used in a wide range of consumer and industrial products and they are contaminants of emerging concern in the environment. However, their occurrence and fate in the deep-sea environments are inadequately understood. This study investigated the occurrence and distribution of five UVFs and ten BZT-UVs in the muscle (n = 127) of 2019-collected deepwater redfish (Sebastes mentella) from the St. Lawrence Estuary and Gulf (SLEG) (Canada) to better understand the accumulation of these contaminants in deep-sea fish. Small redfish (<30 cm) tended to have higher concentrations of UVAs in the muscle than that of larger specimens (>30 cm). The UVF 2-hydroxy-4-methoxybenzophenone (BP3) was the most frequently detected (present in 34 % of all samples) target UVA, with concentrations as high as 413 ng/g (dry weight). According to the δ15N and δ13C data, pelagic-eating redfish, and individuals with lower trophic levels had higher lipid content and accumulated more BP3 in their muscles. Four BZT-UVs were detected in redfish muscle, but the detection frequency was lower than 30 %. The estimated hazard quotient for these contaminants was <2.3 × 10-2 for general Canadian populations, indicating that they are unlikely to pose health risks to humans through redfish consumption. Factors influencing UVAs bioaccumulation in redfish, as well as the effects UVAs may have on deep-sea species, should be researched further.

Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean

Bacillus species have been considered as promising biological control agents due to their excellent antimicrobial ability. Bacillus cereus strain Z4 was isolated from 2000 m deep sea sediments of the Western Pacific Ocean, which possesses significant antifungal activity against Phytophthora nicotianae, the pathogenic fungus of tobacco black shank disease. To reveal the underlying antifungal genetic mechanisms, here, we report the complete genomic sequence of the strain Z4. The genome has one circular chromosome of 5,664,309 bp with a G + C content of 35.31%, 109 tRNAs, and 43 rRNAs. Genomic analysis identified 10 gene clusters related to the biosynthesis of biocontrol active compounds, including bacillibactin, petrobactin, fengycin, and molybdenum cofactor. Meanwhile, 6 gene clusters were responsible for the biosynthesis of metabolites with unknown functions. Strain Z4 also contains a large number of genes encoding carbohydrate-active enzymes and secreted proteins, respectively. The whole genomic analysis of Bacillus cereus Z4 may provide a valuable reference for elucidating its biocontrol mechanism against tobacco black shank.

A review of the genus Muusoctopus (Cephalopoda: Octopoda) from Arctic waters

We report two Arctic species of incirrate octopods new to science. One is formally described here as Muusoctopus aegir Golikov, Gudmundsson & Sabirov sp. nov. while the other, Muusoctopus sp. 1, is not formally described due to a limited number of samples (all are immature individuals). These two species differ from each other, and from other Muusoctopus, especially in: 1) absence of stylets (in M. aegir sp. nov.); 2) proportions of mantle and head; 3) funnel organ morphology (W-shaped with medial and marginal limbs of equal length in M. aegir sp. nov., or medial are slightly longer; V V-shaped with medial limbs slightly longer and broader than marginal in Muusoctopus sp. 1); 4) sucker and gill lamellae counts; 5) relative arm length and sucker diameter; and 6) male reproductive system relative size and morphology. Species of Muusoctopus now comprise four of 12 known Arctic cephalopods. Additionally, this study provides: a) new data on the morphology and reproductive biology of M. johnsonianus and M. sibiricus, and a diagnosis of M. sibiricus; b) the equations to estimate mantle length and body mass from beak measurements of M. aegir sp. nov. and M. johnsonianus; c) a cytochrome c oxidase subunit I gene barcode for M. sibiricus; d) new data on the ecology and distribution of all studied species; and e) a data table for the identification of northern North Atlantic and Arctic species of Muusoctopus.

Spatial distribution and speciation of mercury in a recovering deepwater redfish (Sebastes mentella) population from St. Lawrence Estuary and Gulf, Canada

Mercury (Hg) pollution poses a significant threat to the environment, particularly in the form of methylmercury (MeHg). However, little is known about the distribution and influencing factors of Hg in deep-sea (>200m) fish, which is crucial for assessing potential health risks to fish and humans. In Canada, the deepwater redfish (Sebastes mentella) has been designated as an endangered species. After a 25-year fishing moratorium, the redfish population in the St. Lawrence Estuary and Gulf is recovering, and resuming of commercial fishing and human consumption are expected. This study aimed to investigate the distribution of MeHg and total Hg (THg) in the muscle of redfish, as well as the factors influencing its distribution, and to assess the potential human health risks associated with redfish consumption. The redfish samples (n = 123) were collected by Fisheries and Oceans Canada in 2019. The concentrations of THg and MeHg in redfish muscle were determined to be 93.3 ± 183 ng/g (mean ± SD, wet weight) and 78.2 ± 149 ng/g, respectively. Large redfish (>30 cm) accumulated 20 to 30 times more Hg than small redfish (17-30 cm). Small redfish from the Estuary-Western Gulf had higher levels of MeHg and THg than those from the Laurentian Channel and the Northeast Gulf, but the Hg availability to redfish among the three areas were similar. Significant predictors of MeHg concentrations in redfish muscle were determined to be fish length, muscle moisture, δ15N, and N%. MeHg consumption by the general population with an average fish consumption rate is not anticipated to have adverse effects. This study establishes a baseline for future Hg monitoring in the deep water environments in this region. Further research is required to elucidate the cause-effect relationships between various environmental/biological parameters and Hg accumulation in deep-sea biota.

Persistent Organic Pollutants (POPs) in three bathyal chondrichthyes from the North-Western Mediterranean Sea

The deep-sea can act as a sink for legacy contaminants such as organochlorines (OCs), causing damages in its inhabitants for their persistence and their prolonged effects in the organisms. HCB, DDT and its isomers, and 28 PCBs congeners were detected in muscle and embryonic tissues of three deep-sea chondrichthyes Chimaera monstrosa (n = 16), Dalatias licha (n = 12) and Etmopterus spinax (n = 51) sampled in Ligurian and Tyrrhenian Sea (Mediterranean Sea). Contaminant distribution in E. spinax and C. monstrosa was PCBs > DDTs ≫ HCB while in D. licha was DDTs > PCBs ≫ HCB. Statistically significant differences were highlighted in OC levels among the species, but no such differences were found among sexes. Ratios between DDT isomers highlighted an historical input of the pesticide in the environment. For the first time was also demonstrated maternal transfer in deep water chondrichthyes, specifically in E. spinax where was highlighted that transfer of contaminants increases with increasing compound's Log Kow.

Amphonal, a new polyene aldehyde from a deep-sea-derived Streptomyces amphotericinicus

A new polyene aldehyde, named amphonal (1), and two known (2 and 3) polyketides were isolated from the deep-sea-derived Streptomyces amphotericinicus OUCT16-38 strain. The structure of 1 was determined by extensive MS and NMR spectroscopic analysis. In the cytotoxicity evaluation, compound 2 showed significant growth inhibition against the drug-resistant human lung cancer cell line A549-Taxol with IC50 value of 0.44 μM, which was more potent than the positive control doxorubicin. Meanwhile, 2 showed considerable cytotoxic effect towards H1975, H1299 and HEL cell lines (IC50 = 0.93-4.73 μM) as well.

Non-target analysis of organohalogenated contaminants in deep-sea fishes from the Mediterranean Sea by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry

The enhanced separation power and identification capabilities make comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC - ToF MS) a valuable instrumental alternative for non-target analysis (NTA). In the present study, GC × GC - ToF MS has been used for the NTA of chlorine- and bromine-containing compounds in composite livers of two scarcely investigated Mediterranean deep-sea fish species, hollowsnout grenadier (Coelorinchus caelorhincus) and roughsnout grenadier (Trachyrhinchus trachyrhinchus). Attention focused on the identification of organohalogenated compounds with structural characteristics similar to those of persistent organic pollutants (POPs). In total, 116 Cl-, Br- and mixed Cl/Br-compounds were either positively or tentatively identified in the analyzed liver samples. Up to 88 of these compounds were legacy POPs, being polychlorinated biphenyls (PCBs) and organochlorinated pesticides (OCPs) the most abundant and frequently detected families. The other 28 identified POP-like compounds were analytes not considered by current regulation and environmental monitoring programs, including, among others, degradation products of specific OCPs, naturally produced organohalogen compounds and several perchlorinated diethyldiphenylmethane-derivatives whose presence in the investigated species is reported here for the first time. The presence of other naturally occurring brominated and mixed halogenated compounds in these fish species is also described for the first time. Our results also showed differences in the accumulation profile of the identified compounds in both species. Thereby, anthropogenic POPs showed higher relative abundances in the livers of roughsnout grenadiers than those in hollowsnout grenadiers, while for naturally occurring compounds the opposite trend or similar levels were found in both species.

Hyposterolactone A, a 3α-Hydroxy Steroidal Lactone from the Deep-Sea-Derived Fungus Hypocrea sp. ZEN14

Chemical investigation of the deep-sea-derived fungus Hypocrea sp. ZEN14 afforded a new 3α-hydroxy steroidal lactone, hyposterolactone A (1) and 25 known secondary metabolites (2-26). The structure of the new compound was established by detailed spectroscopic analysis, electronic circular dichroism (ECD) calculation as well as a J-based configuration analysis. Compound 10 showed potent cytotoxicity against Huh7 and Jurkat cells with IC50 values of 1.4 μM and 6.7 μM, respectively.

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.

Antarctic toothfish Dissostichus mawsoni as a bioindicator of trace and rare earth elements in the Southern Ocean

The Antarctic toothfish Dissostichus mawsoni is a Southern Ocean long-lived top predator which is regularly captured on an annual fishery operating in the region. By its biological and ecological characteristics, it is a potential bioindicator for the concentrations of trace and rare earth elements in the Antarctic. As these elements are mainly transferred through the diet and a deficiency or excess of these elements can lead to diverse health problems, it is important to measure their concentrations on the organisms. This study provides, for the first time, the concentration of 27 trace (major essential, minor essential and non-essential) and rare earth elements in the muscle of D. mawsoni captured in three areas of the Amundsen and Dumont D'Urville Seas (Antarctica). Major essential elements had the highest concentrations, with potassium (K) as the most concentrated, and rare earth elements the lowest. Significant differences between areas were found for most of the studied elements. No bioaccumulation nor biomagnification potential was found for the studied elements, with several elements decreasing concentrations towards larger individuals. Decreasing trends are related with the different habitats occupied by D. mawsoni through their life, suggesting that elements' concentrations in the water is determinant for the concentrations in this top predator, and/or there is a dilution effect as the fish grows. Our results also support that Se presents a detoxification potential for Hg in D. mawsoni, but only when Hg concentrations are higher to unhealthy levels. This study supports D. mawsoni as a potential bioindicator for the concentrations of the different trace and rare earth elements in the Southern Ocean, though only when comparing individuals of similar size/age, but also to evaluate annual changes on their concentrations. Furthermore, D. mawsoni can be a good source of major essential elements to humans with concentrations of major essential elements above some of other marine fish worldwide.

Deep-sea in situ determination of sulfide using a sensitized chemiluminescent terbium complex

A new chemiluminescence (CL) method based on the chemiluminescent reaction between sulfide and an acidic permanganate solution was used to quantify sulfide in seawater. A terbium-pipemidic acid complex was used as CL enhancer. The method was used to determine sulfide in the concentration range of 1-30 μmol/L in artificial seawater samples. The limit of detection of the method was 21 nmol/L sulfide. The sensitivity of the CL method was eight times higher than that of the CL method reported previously. Br^- ions, which are conservative ions, interfered with sulfide. We investigated the effects of salinity, water temperature, and interfering chemicals,such asheavy-metal ions and organic matter, on the performance of the CL method. In addition, sulfite-spiked natural seawater samples were analyzed. The results demonstrate that the CL method can be used to develop a deep-sea sulfide analyzer.

Benthic biogeographic patterns on the deep Brazilian margin

The Brazilian continental margin (BCM) extends from the Tropical to the Subtropical Atlantic Ocean, with much of its seafloor within deep waters, supporting rich geomorphological features and under wide productivity gradients. Deep-sea biogeographic boundaries on the BCM have been limited to studies that used water mass and salinity properties of deep-water masses, partly as a result of historical under sampling and a lack of consolidation of available biological and ecological datasets. The aim of this study was to consolidate benthic assemblage datasets and test current oceanographic biogeographical deep-sea boundaries (200-5,000 m) using available faunal distributions. We retrieved over 4,000 benthic data records from open-access databases and used cluster analysis to examine assemblage distributions against the deep-sea biogeographical classification scheme from Watling et al. (2013). Starting from the assumption that vertical and horizontal distribution patterns can vary regionally, we test other schemes incorporating latitudinal and water masses stratification within the Brazilian margin. As expected, the classification scheme based on benthic biodiversity is in overall agreement with the general boundaries proposed by Watling et al. (2013). However, our analysis allowed much refinement in the former boundaries, and here we propose the use of two biogeographic realms, two provinces and seven bathyal ecoregions (200-3,500 m), and three abyssal provinces (>3,500 m) along the BCM. The main driver for these units seems to be latitudinal gradients as well as water mass characteristics such as temperature. Our study provides a significant improvement of benthic biogeographic ranges along the Brazilian continental margin allowing a more detailed recognition of its biodiversity and ecological value, and also supports the needed spatial management for industrial activities occurring in its deep waters.

Six new species of free-living nematodes (Nematoda: Enoplida) from deep-sea cold seeps on Hikurangi Margin, New Zealand

Little is known about the taxonomy of deep-sea nematode species inhabiting cold seep habitats. An opportunity to characterize the nematode species communities of New Zealand cold seeps was provided by a 2019 research voyage to New Zealand's Hikurangi Margin, during which macrofauna cores were obtained at two seeps at approximately 1,250 and 2,000 m water depth. Here, six new species of the orderEnoplida are described. Metacylicolaimus catherinae sp. nov. represents the first record of the genus for the New Zealand Exclusive Economic Zone and for the deep sea globally. Halalaimus talaurinus sp. nov., Thalassoalaimus duoporus sp. nov. and Crenopharynx crassipapilla sp. nov. are only the second species of their respective genera to be described/recorded from New Zealand waters, and Oncholaimus adustus sp. nov. is the eighth species of the genus to be recorded from the region. Rhabdodemania zealandiaensis sp. nov. was among the most abundant and widespread species found at the Hikurangi Margin seep sites. A few specimens had been found in a previous ecological study of meiofaunal nematode communities on Chatham Rise, a submarine ridge south of Hikurangi Margin. It is possible that this species has a preference for seep environments due to elevated food availability, however it does not seem to be exclusively found in seeps. We find no evidence for an affinity between nematode seep communities in New Zealand and elsewhere, which is consistent with the high variability in nematode community observed to date among regions. Ongoing work on the ecology and distribution of nematode communities at the Hikurangi Margin seep sites will help determine spatial patterns in abundance and species distributions in more detail, including the identification of any species/taxa with affinities with seeps.

Mislabeling and nomenclatorial confusion of Typhlotanais sandersi Kudinova-Pasternak, 1985 (Crustacea: Tanaidacea) and establishment of a new genus

Re-examination of historical collections allowed us to resolve the taxonomic status of Typhlotanais sandersi Kudinova-Pasternak, 1985, originally described based on a single specimen from Great-Meteor Seamount. The holotype of this species was considered lost and the species redescribed based on a second specimen from the type locality by Błażewicz-Paszkowycz (2007a), who placed Ty. sandersi on a newly established genus Typhlamia. Thorough morphological analysis of Typhlamia and Typhlotanais species and recently obtained genetic data of typhlotanaids from N Atlantic and NW Pacific waters allow us to conclude that the redescription of Ty. sandersi by Błażewicz-Paszkowycz (2007a) was based on a wrongly labelled specimen that, rather than a type of Ty. sandersi, represents in fact a new species of Typhlamia. The morphological comparison of the type species of Typhlotanais (Ty. aequiremis) with all 'long-bodied' typhlotanaid taxa with rounded pereonites margins (i.e., Typhlamia, Pulcherella, Torquella), and the use of genetic evidence, support the establishment of a new genus to accommodate: Ty. sandersi, Ty. angusticheles Kudinova-Pasternak, 1989, and a third species from N Atlantic waters, that is described here for the first time. Current knowledge on 'long-bodied' typhlotanaids with rounded pereonites is summarised and a taxonomical key for their identification provided.

A large diversity of organohalogen contaminants reach the meso- and bathypelagic organisms in the Bay of Biscay (northeast Atlantic)

Deep-sea ecosystems play a key role in the cycling and vertical transfer of matter and energy in oceans. Although the contamination of deep-sea demersal and benthic organisms by persistent organic pollutants has been proven, deep pelagic species have been far less studied. To fill these gaps, we studied the occurrence of a large variety of hydrophobic organic contaminants including polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), legacy and alternative brominated flame retardants (BFRs) and per- and polyfluoroalkyl substances (PFASs) in crustaceans and fish species collected in the Bay of Biscay, northeast Atlantic. The results highlighted the global predominance of PCBs in fish, followed by OCPs, PFASs and PBDEs, with highly variable concentrations among species. Most of the chlorinated or brominated contaminants showed increasing concentrations with increasing δ¹⁵N values, while most PFASs showed inverse trends. The contaminant profiles and diagnostic ratios revealed species-specific metabolic capacities and peculiar contribution of highly-brominated BFRs.

Complete genome sequence of a multiple-stress-tolerant bacterium Halomonas piezotolerans NBT06E8T isolated from a deep-sea sediment sample of the New Britain Trench

Halomonas piezotolerans NBT06E8T is a Gram-stain-negative, moderately halophilic, piezotolerant, H2O2 and heavy metal-resistant bacterium, isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. Growth of the strain was observed at 4-45 °C (optimum 30 °C), at pH 5-11 (optimum 8-9) and in 0.5-21% (w/v) NaCl (optimum 3-7%). The optimum pressure for growth was 0.1-30 MPa (megapascal) with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerant 15 mM H2O2. Here, we report the complete genome of H. piezotolerans NBT06E8T, which consists of 3,945,801 bp (G + C content of 57.93%) with a single chromosome, 3509 protein-coding genes, 60 tRNAs and 6 rRNA operons. Genomic analysis revealed the capability of utilizing various carbon and nitrogen sources, the presence of multiple toxin-antitoxin systems and strain-specific type VI secretion system benefitting its adaptation to the oligotrophic hadal environments. Multiple respiratory chain components, especially the strain-specific anaerobic enzymes, could allow its survival in both surficial and buried sediments with variable oxygen concentrations. Gene function and metabolic pathway analysis showed that strain NBT06E8T encodes a series of genes related to high hydrostatic pressure tolerance, antioxidative stress and heavy metal resistance, which could also contribute to its deep-sea adaptation strategies. The complete genome sequence of H. piezotolerans NBT06E8T provides further insights into the stress adaptation strategies of deep-sea bacteria and potential biotechnological application of Halomonas species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03283-3.

Brefeldin A from the Deep-Sea-Derived Fungus Fusarium sp. Targets on RIPK3 to Inhibit TNFα-Induced Necroptosis

From the deep-sea-derived Fusarium sp. ZEN-48, four known compounds were obtained. Their structures were established by extensive analyses of the NMR, HRESIMS, and the X-ray crystal-lographic data as brefeldin A (BFA, 1), brevianamide F (2), N-acetyltryptamine (3), and (+)-diaporthin (4). Although BFA was extensively investigated for its potent bioactivities, its role on TNFα-induced necroptosis was incompletely understood. In this study, BFA showed significant inhibition on TNFα-induced necroptosis by disrupting the necrosome formation and suppressing the phosphorylation of RIPK3 and MLKL (IC50 = 0.5 μM). While, it had no effect on TNFα-induced NF-κB/MAPKs activation and apoptosis. The finding raised significant implications of BFA for necroptosis-related inflammatory disease therapy and new drug development from marine fungi.

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R ² = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser ^AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser ^AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.

Bacterial colonisation of plastic in the Rockall Trough, North-East Atlantic: An improved understanding of the deep-sea plastisphere

Plastic pollution has now been found within multiple ecosystems across the globe. Characterisation of microbial assemblages associated with marine plastic, or the so-called 'plastisphere', has focused predominantly on plastic in the epipelagic zone. Whether this community includes taxa that are consistently enriched on plastic compared to surrounding non plastic surfaces is unresolved, as are the ecological implications. The deep sea is likely a final sink for most of the plastic entering the ocean, yet there is limited information on microbial colonisation of plastic at depth. The aim of this study was to investigate deep-sea microbial communities associated with polystyrene (PS) and polyurethane (PU) with Bath stone used as a control. The substrates (n = 15) were deployed in the Rockall Trough (Atlantic), and recovered 420 days later from a depth of 1796 m. To characterise the bacterial communities, 16S rRNA genes were sequenced using the Illumina MiSeq platform. A dominant core microbiome (taxa shared across all substrates) comprised 8% of total ASVs (amplicon sequence variant) and accounted for 92% of the total community reads. This suggests that many commonly reported members of the plastisphere are simply opportunistic which freely colonise any hard surface. Transiently associated species consisted of approximately 7% of the total community. Thirty genera were enriched on plastic (P < 0.05), representing 1% of the total community. The discovery of novel deep-sea enriched taxa included Aurantivirga, Algivirga, IheB3-7, Spirosoma, HTCC5015, Ekhidna and Calorithrix on PS and Candidatus Obscuribacter, Haloferula, Marine Methylotrophic Group 3, Aliivibrio, Tibeticola and Dethiosulfatarculus on PU. This small fraction of the microbiome include taxa with unique metabolic abilities and show how bacterial communities can be shaped by plastic pollution at depth. This study outlines a novel approach in categorising the plastisphere to elucidate the ecological implications of enriched taxa that show an affinity for colonising plastic.

Cladosporioles A and B, Two New Indole Derivatives from the Deep-Sea-Derived Fungus Cladosporium cladosporioides 170056

Two new (cladosporioles A and B, 1 and 2) and fourteen known (3-16) compounds were isolated from the deep-sea-derived fungus Cladosporium cladosporioides 170056. The relative structures of the new compounds were elucidated mainly by detailed analysis of their NMR and HR-ESI-MS spectroscopic data. Their absolute configurations were determined by comparison of the experimental and calculated electronic circular dichroism (ECD) spectra. All isolates were tested for antimicrobial activity against Vibrio parahaemolyticus. Compound 15 exhibited weak effect with the MIC value of 156.25 μg/mL.

Underwater hidden microplastic hotspots: Historical ocean dumping sites

Three ocean dumping sites located in the Yellow Sea (YS) and East Sea (ES) of South Korea have accumulated terrestrial waste from 1988 to 2015. Most of this waste comprised industrial wastewater and sewage sludge, which are sources of microplastics. In this study, we investigated the spatiotemporal distribution and characteristics of microplastics in surface and core sediments of the YS, South Sea (SS) and ES, including at dumping sites (YDP and EDP). The mean abundance of microplastics in surface sediments was ranked in order of EDP (59,457 ± 49,130 particles/kg d.w.), ES (5,047 ± 9,404 particles/kg d.w.), YDP (3,965 ± 3,213 particles/kg d.w.), SS (314 ± 488 particles/kg d.w.) and YS (288 ± 400 particles/kg d.w.). EDP and YDP showed about 14- and 12-fold higher microplastic abundances, and more diverse polymer compositions, than the ES and YS, respectively. The historical trend of microplastic pollution in age-dated core sediments from EDP and YDP aligned well with the amount of historical ocean dumping. As the level of ocean dumping has gradually reduced since 2006, and was finally banned in 2015, the microplastic abundance decreased accordingly. Interestingly, spherical polystyrene (PS) primary microplastic was the dominant type in EDP sediments (78%) and other surface sediments in the ES (52%). More than 60 million tons of sewage and wastewater sludge were dumped at EDP, and extremely high abundances of up to 130,000 particles/kg d.w. were observed in EDP surface sediments. PS primary microplastics were continuously present in the EDP and ES sediment cores in the dumping period and are suspected to have originated from industrial wastewater sludge. The particle transportation model results showed that PS was dispersed throughout the ES during ocean dumping. In addition, deep circulation can contribute to the dispersion of particles after sinking. These results indicate that ocean dumping sites represent an underwater hotspot and source of microplastics in seafloor sediments.

Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment

Background

The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled.

Results

B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size.

Conclusions

Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01302-6.

Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates

Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.

Occurrence and levels of polybrominated diphenyl ethers (PBDEs) in deep-sea sharks from Suruga Bay, Japan

Few studies have investigated the prevalence of polybrominated diphenyl ethers (PBDEs) in deep-sea sharks. In this study, the levels and profiles of PBDEs were determined in liver samples of eight different species of deep-sea sharks collected in Suruga Bay, Japan. Widespread contamination of PBDEs in the deep-sea environment was reconfirmed in this study as these persistent organic pollutants (POPs) were detected in all specimens analyzed. Mean ΣPBDE levels in the deep-sea sharks ranged from 7 to 517 ng/g of lipid weight. The distribution patterns of BDE homologues were similar in all species where tetra-BDEs provided the dominant contribution to total PBDEs (46%). PBDEs levels were similar to, or higher than, those seen in other deep-sea sharks from different regions. The levels of PBDEs were likely to reflect their feeding preferences as higher PBDE levels were seen in species with higher trophic positions.

No recovery of a large-scale anthropogenic sediment disturbance on the Pacific seafloor after 77 years at 6460 m depth

Habitat restoration and recolonisation of benthic communities after physical perturbation in the deep sea has long been thought to be extremely slow. This study reports on a serendipitous opportunity to survey the current state of a large mechanical disturbance of sediments at 6460 m in the Pacific Ocean. The impact was caused 77 years ago by the sinking of the USS Johnston. The surrounding debris field had little impact on the sedimentary habitat, other than in the provision of artificial hard substrates, while the troughs that formed as the ship impacted the seafloor and slid down the slope of the Philippine Trench were still completely void of animal tracks and burrows, or any observable epifauna, and in some areas subsurface stratification was still exposed at the surface. This suggests that mechanical perturbations of sediments in the deep Pacific may remain ecologically significant for, at the very least, 100 years.

The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes

Adaptation to life in the deep-sea can be dramatic, with fish displaying behaviors and appearances unlike those seen in any other aquatic habitat. However, the extent of which adaptations may have developed at a microbial scale is not as clear. Shotgun metagenomic sequencing of the intestinal microbiome of 32 species of deep-sea fish from across the Atlantic Ocean revealed that many of the associated microbes differ extensively from those previously identified in reference databases. 111 individual metagenome-assembled genomes (MAGs) were constructed representing individual microbial species from the microbiomes of these fish, many of which are potentially novel bacterial taxa and provide a window into the microbial diversity in this underexplored environment. These MAGs also demonstrate how these microbes have adapted to deep-sea life by encoding a greater capacity for several cellular processes such as protein folding and DNA replication that can be inhibited by high pressure. Another intriguing feature was the almost complete lack of genes responsible for acquired resistance to known antibiotics in many of the samples. This highlights that deep-sea fish microbiomes may represent one of few animal-associated microbiomes with little influence from human activity. The ability of the microbes in these samples to bioluminesce is lower than expected given predictions that this trait has an important role in their life cycle at these depths. The study highlights the uniqueness, complexity and adaptation of microbial communities living in one of the largest and harshest environments on Earth.

Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environment

Three marine bacterial strains designated YLB-06^T, YLB-08^T and YLB-09 were isolated under high hydrostatic pressure from deep-sea sediment samples collected from the Southwest Indian Ocean. They were Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and motile. In addition, the strains were capable of growing at 0-20 °C (optimum 4-10 °C) and 0.1-40 MPa (optimum 0.1 MPa), were psychrophiles and piezotolerant, and could use trimethylamine N-oxide (TMAO), DMSO, elemental sulfur and insoluble Fe (III) as terminal electron acceptors during anaerobic growth. Strain YLB-06^T could also use nitrate, and strains YLB-08^T and YLB-09 could use nitrite as a terminal electron acceptor. Phylogenetic tree analyses based on 16S rRNA gene sequences and 400 optimized universal marker sequences indicated that the strains belonged to the genus Shewanella. The 16S rRNA gene highest similarity, together with the estimated ANI and DDH values for these strains with their related type strains, were below the respective thresholds for species differentiation. The ANI and DDH values between YLB-08^T and YLB-09 were 99.9% and 91.8%, respectively, implying that they should belong to the same genospecies. The YLB-06^T genome had duplicated genes, and multiple movement modalities, attachment modalities, biofilm synthesis systems, intercellular interactions and a strong antioxidant system, which were all beneficial for survival in an extreme deep-sea environment. The G + C contents of strains YLB-06^T, YLB-08^T and YLB-09 were 45.1, 43.5 and 43.6 mol%, respectively. Based on polyphasic taxonomic properties, two novel psychropiezotolerant species are proposed, Shewanella psychropiezotolerans sp. nov. with YLB-06^T (=MCCC 1A12715^T = KCTC 62907^T) and S. eurypsychrophilus sp. nov with YLB-08^T (=MCCC 1A12718^T = KCTC 62909^T) as type strains.

Embryo and larval biology of the deep-sea octocoral Dentomuricea aff. meteor under different temperature regimes

Deep-sea octocorals are common habitat-formers in deep-sea ecosystems, however, our knowledge on their early life history stages is extremely limited. The present study focuses on the early life history of the species Dentomuricea aff. meteor, a common deep-sea octocoral in the Azores. The objective was to describe the embryo and larval biology of the target species under two temperature regimes, corresponding to the minimum and maximum temperatures in its natural environment during the spawning season. At temperature of 13 ±0.5 °C, embryos of the species reached the planula stage after 96h and displayed a median survival of 11 days. Planulae displayed swimming only after stimulation, swimming speed was 0.24 ±0.16 mm s⁻¹ and increased slightly but significantly with time. Under a higher temperature (15 °C ±0.5 °C) embryos reached the planula stage 24 h earlier (after 72 h), displayed a median survival of 16 days and had significantly higher swimming speed (0.3 ±0.27 mm s⁻¹). Although the differences in survival were not statistically significant, our results highlight how small changes in temperature can affect embryo and larval characteristics with potential cascading effects in larval dispersal and success. In both temperatures, settlement rates were low and metamorphosis occurred even without settlement. Such information is rarely available for deep-sea corals, although essential to achieve a better understanding of dispersal, connectivity and biogeographical patterns of benthic species.

Pseudomonas nanhaiensis sp. nov., a lipase-producing bacterium isolated from deep-sea sediment of the South China Sea

A bacterial lipase producing bacterium, designated SCS 2-3, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA sequence revealed that strain SCS2-3 belonged to the genus Pseudomonas and had 98.56% similarity to P. xinjiangensis NRRL B-51270^T as the closest relative strain. MLSA using four protein-coding genes (dnaK, gyrA, recA, and rpoB) showed strain SCS 2-3 to form a separate branch. ANI and in silico DDH values between strain SCS 2-3 and related type strains of Pseudomonas were less than 81.51% and 23.80%, respectively. Genome comparison showed that strain SCS 2-3 shared 1875 core gene families with other eight closely related type strains in Pseudomonas, and the number of strain-unique genes was 263. Through gene annotations, genes related to lipase were found in the genome. Furthermore, a combination of phenotypic, chemotaxonomic, phylogenetic and genotypic data clearly indicated that strain SCS 2-3 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas nanhaiensis sp. nov. is proposed. The type strain is SCS 2-3^T (= GDMCC 1.2219^T = JCM 34440^T).

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

BACKGROUND

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

METHODS AND RESULTS

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

CONCLUSIONS

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes.

Red and white muscle proportions and enzyme activities in mesopelagic sharks

In the last decade, there has been an increase in the study of the ecology of deep-sea organisms. One way to understand an organism's ecology is the study of its metabolism. According to literature, deep-sea sharks possess a lower anaerobic enzyme activity than their shallow-water counterparts, but no difference has been observed regarding their aerobic enzyme activities. These studies have suggested deep-sea sharks should be slow and listless swimmers. However, other studies based on video observations have revealed differences in cruise swimming speed between different species. The present study examined muscles of squaliform sharks, including both luminous and non-luminous species. We combined measurements of the relative amounts of red and white muscle with assays of enzymes that are used as markers for aerobic (citrate synthase, malate dehydrogenase) and anaerobic (lactate dehydrogenase) metabolism, searching for a relationship with cruising speeds. Non-luminous deep-sea species displayed lower aerobic enzyme activities but similar anaerobic enzyme activities than the benthic shallow-water counterpart (Squalus acanthias). Conversely, luminous Etmopteridae species were found to have similar aerobic enzyme activities to S. acanthias but displayed lower anaerobic enzyme activities. Analyses revealed that red muscle proportion and aerobic enzyme activities were positively related to the cruise swimming speed. In contrast, Dalatias licha, which swims at the slowest cruise swimming speed ever recorded, presented a very low aerobic metabolic phenotype (lower aerobic marker enzymes and less red muscle). Finally, the values obtained for white muscle proportion and anaerobic metabolic phenotype suggested a high burst capacity for D. licha and non-luminous sharks.

Biochemical and metabolic responses of the deep-sea mussel Bathymodiolus platifrons to cadmium and copper exposure

Greater interest in commercial deep-sea mining has been accompanied by mounting environmental concerns, including metal contamination resulting from mining activities. However, little is known about the toxic effects of metal exposure on deep-sea life. Given its ability to accumulate metals from the surrounding environment, its wide distribution at both vents and seeps, and its high abundance, the deep-sea mussel Bathymodiolus platifrons could serve as an ideal model to investigate the toxicological responses of deep-sea organisms to metal exposure. Here, we evaluated metal accumulation, traditional metal-related biomarkers, namely acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase, catalase, reduced glutathione, metallothioneins, and malondialdehyde, as well as metabolic profiles in the gills of B. platifrons after a 7-day exposure to copper (100 μg/L), cadmium (500 μg/L), or copper-plus-cadmium treatments (100 μg/L Cu and 500 μg/L Cd). Metal exposure concentrations selected in this study can be found in deep-sea hydrothermal environments. Metal exposure resulted in significant metal accumulation in the gills of the mussel, indicating that B. platifrons has promise for use as an indicator of deep-sea metal pollution levels. Traditional biomarkers (AKP, ACP, and measured antioxidants) revealed cellular injury and oxidative stress in mussels following metal exposure. Metabolic responses in the three treatment groups indicated that metal exposure perturbed osmoregulation, energy metabolism, and nucleotide metabolism in mussels, in a response marked by differentially altered levels of amino acids, hypotaurine, betaine, succinate, glucose 6-phosphate, fructose 6-phosphate, guanosine, guanosine 5'-monophosphate, and inosine. Nevertheless, several uniquely altered metabolites were found in each treatment exposure group, suggesting dissimilar modes of toxicity between the two metal types. In the Cd-exposed group, the monosaccharide D-allose, which is involved in suppressing mitochondrial ROS production, was downregulated, a response consistent with oxidative stress in Cd-exposed B. platifrons. In the Cu-exposed group, the detected alterations in dopamine, dopamine-related, and serotonin-related metabolites together suggest disturbed neurotransmission in Cu-exposed B. platifrons. In the Cu-plus-Cd group, we detected a decline in fatty acid levels, implying that exposure to both metals jointly exerted a negative influence on the physiological functioning of the mussel. To the best of our knowledge, this is the first study to investigate changes in metabolite profiles in Bathymodiolus mussels exposed to metal. The findings reported here advance our understanding of the adverse impact of metal exposure on deep-sea life and can inform deep-sea mining assessments through the use of multiple biomarkers.

Rare earth and trace elements in deep-sea sponges of the North Atlantic

The available data on trace elements (TE) of deep-sea organisms is scarce and nonexistent for rare earth elements (REE). Hence, this study characterizes REE and TE in five porifera genera (Jaspis, Geodia, Hamacantha, Leiodermatium, Poliopogon) collected in deep-sea areas (between 481 and 2656 m) of the North Atlantic. Aluminium was the most common TE while lead was the less abundant. These sponges showed an increased accumulation of TE compared with other probably influenced by volcanic activity. Poliopogon amadou sampled at the deepest location presented the highest concentration of all REE. All studied species exhibited a Light REE enrichment in comparison to Heavy REE and showed a negative Ce anomaly with a less conspicuous Eu depletion. Besides the establishment of a baseline for future comparisons, this study provides the first record of REE in a sessile deep-sea marine invertebrate group.

Structure and in vitro antiproliferative activity of the acidic capsular polysaccharide from the deep-sea bacterium Psychrobacter submarinus KMM 225T

Psychrobacter submarinus KMM 225^T is a Gram-negative bacterium isolated from a sea-water sample collected at a depth of 300 m in the Northwest Pacific Ocean. Here we report the structure of the capsular polysaccharide from P. submarinus KMM 225^T and its effect on the viability and colony formation of cancer cells. The glycopolymer was purified by ultracentrifugation and chromatography methods, and the structure was elucidated using NMR spectroscopy and composition analyses. The following structure of the acidic capsular polysaccharide, containing 2-acetamido-2,4,6-trideoxy-4-[(S)-3-hydroxybutyramido]-d-glucose [d-QuipNAc4N(S-Hb)] and 4,6-O-[(S)-1-carboxyethylidene]-2-acetamido-2-deoxy-d-glucose [d-GlcpNAc4,6(S-Pyr)] was established: The capsular polysaccharide slightly reduced the viability but effectively suppressed the colony formation of different types of cancer cells, of which the most pronounced inhibition was shown for the human chronic myelogenous leukemia K-562 cells.

Psolidium bathygalego nom. nov. (Echinodermata, Holothuroidea) from bathyal bottoms of Galicia (NW Iberian Peninsula)

It is proposed to name the Atlantic holothuria Psolidium complanatum Cherbonnier, 1969, whose denomination is already occupied by Psolidium complanatum (Semper, 1867) from the Philippines, as Psolidium bathygalego nom. nov. 843 specimens of Psolidium bathygalego nom. nov., collected between 417 and 1191 m deep in the NW and W of Galicia and in the Galicia Bank, were studied. A detailed description of the external and internal anatomy of Psolidium bathygalego nom. nov. is made by studying the ossicles and the skeletal structure by means of scanning electron microscopy (SEM) as well as the introvert, calcareous ring, retractor muscles, water-vascular system, digestive system, respiratory trees, and reproductive system by means of micro-computed tomography (micro-CT). The habitat, feeding system, and geographical distribution of Psolidium bathygalego nom. nov. are also described.

Deep-sea clawed lobster Nephropsis stewarti Wood-Mason, 1872 species complex in the Indo-West Pacific (Crustacea, Decapoda, Nephropidae), with description of a new species

Nephropsisstewarti Wood-Mason, 1872 is the most common species of the deep-sea clawed lobster genus Nephropsis Wood-Mason, 1872 in the Indo-West Pacific. Morphological comparisons and genetic analyses of extensive material referred to this lobster revealed the presence of three species. The three species differ mainly in body size, development of the intermediate carina on the carapace, position of the lateral pair of rostral teeth, whether the pleonal tergum is granulate, and the spination on the large chelipeds. Nephropsisstewarti is restricted to the western central Indian Ocean, and a neotype is selected to fix its identity. The name Nephropsisgrandis Zarenkov, 2006 is revived with neotype selection for the large form found in the West Pacific and northwestern Australia. The smaller form from southern Taiwan and the Philippines is described as Nephropsispygmaeasp. nov.

A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park

Munida diritas sp. nov. is described for the seamounts near Desventuradas Islands, in the intersection of the Salas & Gómez and Nazca Ridges, Chile. Specimens of the new species were collected in the summit (∼200 m depth) of one seamount and observed by ROV at two nearby ones. This species is characterized by the presence of distinct carinae on the thoracic sternites 6 and 7. Furthermore, it is not related with any species from the continental shelf nor the slope of America, while it is closely related to species of Munida from French Polynesia and the West-Pacific Ocean (i.e., M. ommata, M. psylla and M. rufiantennulata). In situ observations indicate that the species lives among the tentacles of ceriantarid anemones and preys on small crustaceans. The discovery of this new species adds to the knowledge of the highly endemic benthic fauna of seamounts of the newly created Nazca-Desventuradas Marine Park, emphasizing the relevance of this area for marine conservation.

Discovery of andrastones from the deep-sea-derived Penicillium allii-sativi MCCC 3A00580 by OSMAC strategy

Andrastones are unusual 6,6,6,5-tetracyclic meroterpenoids that are rarely found in nature. Previously, three andrastones were obtained from the rice static fermentation extract of the deep-sea-derived fungus Penicillium allii-sativi MCCC 3A00580. Inspired by one strain many compounds (OSMAC) approach, the oat static fermentation on P. allii-sativi was conducted. As a result, 14 andrastones were isolated by UV-guided isolation. The chemical structures of the nine new compounds (1-9) was established by comprehensive analysis of the NMR, MS, ECD, and X-ray crystallography and the five known ones (10-14) were assigned by comparing their NMR, MS, and OR data with those reported in literature. Compound 1 bears a novel hemiketal moiety while 2 is the first example to possess a novel tetrahydrofuran moiety via C-7 and C-15. All isolates were tested for anti-allergic bioactivity. Compound 10, 3-deacetylcitreohybridonol, significantly decreased degranulation with the IC₅₀ value of 14.8 μM, compared to that of 92.5 μM for the positive control, loratadine. Mechanism study indicated 10 could decrease the generation of histamine and TNF-α by reducing the accumulation of Ca²⁺ in RBL-2H3 cells. These findings indicate andrastones could be potential to discover new anti-allergic candidate drugs.

PAH and PCB body-burdens in epibenthic deep-sea invertebrates from the northern Gulf of Mexico

There is a paucity of information on the levels of PAHs and PCBs in the deep-sea (≥200 m). In this study, the body-burdens of 16 PAHs and 29 PCBs were measured in: Actinaria (sea anemones), Holothuroidea (sea cucumber), Pennatulacea (sea pens), and Crinoidea (sea lilies) in the deep Gulf of Mexico. All epibenthic species were collected at depths of approximately 2000 m. The PAH and PCB congener profile displayed a similar pattern of bioaccumulation across all four taxa. The high molecular weight PAH, dibenz[a,h]anthracene, was the most abundant PAH in all organisms, ranging from 36 to 53% of sum total PAHs. PCBs 101 and 138 exhibited the highest levels at 20-25% of total congener concentrations in all taxa. The exposure to PAHs and PCBs is likely attributed to contaminated particulate organic matter that is consumed by the deposit and filter feeding epibenthic megafauna sampled in this study.

Measured and predicted acute toxicity of phenanthrene and MC252 crude oil to vertically migrating deep-sea crustaceans

Deep-water column micronekton play a key role in oceanic food webs and represent an important trophic link between deep- and shallow-water ecosystems. Thus, the potential impacts of sub-surface hydrocarbon plumes on these organisms are critical to developing a more complete understanding of ocean-wide effects resulting from deep-sea oil spills. This work was designed to advance the understanding of hydrocarbon toxicity in several ecologically important deep-sea micronekton species using controlled laboratory exposures aimed at determining lethal threshold exposure levels. The current study confirmed the results previously determined for five deep-sea micronekton by measuring lethal threshold levels for phenanthrene between 81.2 and 277.5 μg/L. These results were used to calibrate the target lipid model and to calculate a critical target lipid body burden for each species. In addition, an oil solubility model was used to predict the acute toxicity of MC252 crude oil to vertically migrating crustaceans, Janicella spinacauda and Euphausiidae spp., and to compare the predictions with results of a 48-h constant exposure toxicity test with passive-dosing. Results confirmed that the tested deep-sea micronekton appear more sensitive than many other organisms when exposed to dissolved oil, but baseline stress complicated interpretation of results.

Asperochratides A-J, Ten new polyketides from the deep-sea-derived Aspergillus ochraceus

Ten new C₉ polyketides (asperochratides A-J, 1-10) and 14 known miscellaneous compounds (11-24) were isolated from the deep-sea-derived fungus Aspergillus ochraceus. Structures of the new compounds were elucidated by extensive spectroscopic analyses, modified Mosher's method, Mo₂(OAc)₄ induced circular dichroism (ICD) experiments, and ECD calculations. Structurally, compounds 1-11 and 16-18 share the same polyketide origin of the skeleton and belong to aspyrone co-metabolites. All isolates were tested for cytotoxic, anti-food allergic, anti-H1N1 virus, anti-microbe, and anti-inflammatory activities in vitro. Results showed that compounds 5-8 and 13-17 exerted significant cytotoxic effects on BV-2 cell line, and compound 16 showed the potential of anti-inflammatory activities.