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At least 19 recordsLinked to original sources

PubMed1992

Biochemical ecology of deep-sea animals.

Deep-sea ecosystems contain unique endemic species whose distributions show strong vertical patterning in the case of pelagic animals and sharp horizontal patterning in the case of benthic animals living in or near the deep-sea hydothermal vents. This review discusses the biochemical adaptations that enable deep-sea animals to exploit diverse deep-sea habitats and that help establish biogeographic patterning in the deep-sea. The abilities of deep-sea animals to tolerate the pressure and temperature conditions of deep-sea habitats are due to pervasive adaptations at the biochemical level: enzymes exhibit reduced perturbation of function by pressure, membranes have fluidities adapted to deep-sea pressures and temperatures, and proteins show enhanced structural stability relative to homologous proteins from cold-adapted shallow-living species. Animals from the warmest habitable regions of hydrothermal vent ecosystems have enzymes and mitochondria adapted to high pressure and relatively high temperatures. The low metabolic rates of bathypelagic fishes correlate with greatly reduced capacities for ATP turnover in locomotory muscle. Reduced light and food availability in bathypelagic regions select for low rates of energy expenditure in locomotory activity. Deep-sea animals thus reflect the importance of biochemical adaptations in establishing species distribution patterns and appropriate rates of metabolic turnover in different ecosystems.

Adaptation, Physiological↗

PubMed1976

In situ morphologies of deep-sea and sediment bacteria.

Deep-sea and sediment bacteria at the bottom of an approximately 1200-m water column were sampled by means of pressure vessels attached to a remote underwater manipulator. Cells were immediately fixed in situ with glutaraldehyde, and after processing in the laboratory their morphologies were observed with the scanning electron microscope. Most bacteria were coccoid or rod-lide and less than 0.4 mum in diameter or width. Few filamentous bacteria were observed. Bacteria were in aggregates or free-living. It is concluded that morphologies of deep-sea bacteria collected and fixed at the hydrostatic pressure of their environment are, in general, similar to the observed morphologies of deep-sea bacteria determined at 1 atm pressure after collection and decompression during ascent through the water column.

Bacteria↗

PubMed1992

Kynurenine identified as the short-wave absorbing lens pigment in the deep-sea fish Stylephorus chordatus.

A number of deep-sea fish have bright yellow lenses whose coloration is attributable to a variety of largely unidentified short-wave absorbing pigments. Here the pigment of the deep-sea fish Stylephorus chordatus has been isolated and identified by NMR and mass spectroscopy as kynurenine; a pigment also found in the human lens. The degree of this pigmentation is greater in older animals. The fact that the lenses of both a deep-sea fish and man contain the same pigment is of interest, given the vastly different light environments they inhabit.

Animals↗

PubMed2026

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones.

Sea anemones occupy the full depth range of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with publicly available actiniarian data. We find support for a shallow-water origin of Actiniaria through a framework that emphasizes genome-scale changes associated with habitat transitions. Most strikingly, these changes include repeated dismantling of the circadian toolkit across deep-sea lineages. In addition to convergent gene losses in photo- and temperature-regulatory genes, we find that some deep-sea lineages have experienced recurrent loss or pseudogenization of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, and Mlh3), suggesting reduced meiotic capacity in some lineages. Despite this extensive genomic erosion, deep-sea anemones exhibit molecular tuning: specific amino acid substitutions improve enzyme performance under low-temperature conditions relevant to the deep sea, while selective expansions of gene families related to neural excitability, membrane systems, and other functions may help maintain physiological performance in this environment. Functional assays in yeast indicate enhanced performance of the deep-sea variants at 4°C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

Actiniaria↗

PubMed2025

Hologenomic insights into the molecular adaptation of deep-sea coral Bathypathes pseudoalternata.

Deep-sea coral ecosystems support biodiversity and nutrient cycling through interactions with symbionts. However, their molecular mechanisms remain unexplored. Here, hologenomic analyses of Bathypathes pseudoalternata are applied to uncover molecular adaptations underpinning host-symbiont interactions. Genomic evidence reveals that B. pseudoalternata exhibits adaptations in nutrient transport, immune response, and lysosomal digestion, reflecting its genomic adjustments for a stable symbiosis. Candidatus Nitrosopumilus bathypathes (78.43% ± 3.65%) is inferred to oxidize host-derived ammonia to synthesize amino acids and vitamins to provision the host. The presence of CRISPR-Cas and restriction-modification (R-M) systems suggests that Ca. Bathyplasma bathypathes and Ca. Thalassoplasma bathypathes (10.68% ± 2.99%) may protect the host from viral infections. Ca. Bathybacter bathypathes (8.39% ± 1.53%) is hypothesized to synthesize heme, lipoic acid, and glutathione, which serve dual functions as antioxidants and nutrients. These findings collectively provide insights into how the hologenome contributes to the survival of B. pseudoalternata in the extreme environment.

Animals↗

PubMed2025

Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes).

BACKGROUND: The evolutionary relationships within Stomiiformes, a diverse order of deep-sea fishes dominating the mesopelagic and bathypelagic zones, remain contentious due to conflicting morphological and molecular evidence. These fishes, comprising 464 species across four traditionally recognized families (Gonostomatidae, Sternoptychidae, Phosichthyidae, and Stomiidae), exhibit remarkable adaptations such as bioluminescence, ultra-black pigmentation, and extreme jaw morphologies. Their global abundance and ecological significance, including contributions to the biological carbon pump, underscores the need to resolve their phylogeny amid escalating threats from climate change and human activities. RESULTS: We conducted the most comprehensive phylogenomic analysis of Stomiiformes to date, integrating 936 nuclear loci from 60 species and an expanded dataset of 135 species with mitochondrial sequences from publicly available repositories such as the Barcode of Life Data Systems (BOLD) database. We used maximum likelihood and coalescent-based approaches to assess family monophyly and relationships, including extensive quality control to address contamination in public databases. Our analyses reveal unstable tree topologies and complex evolutionary histories that challenge traditional classifications, while our quality control analyses identified 29% of BOLD sequences as misidentified or contaminated, emphasizing rigorous curation for deep-sea taxa. Congruent with a recent taxonomic treatment of Stomiiformes, the families Phosichthyidae and Gonostomatidae exhibit polyphyly and paraphyly, respectively, while subfamilies within Stomiidae are extensively non-monophyletic, leading us to recommend their abandonment. We propose the recognition of eight monophyletic families: Vinciguerriidae, Diplophidae, Gonostomatidae, Yarrellidae, Ichthyococcidae, Phosichthyidae, Sternoptychidae, and Stomiidae, supported by robust molecular and morphological evidence. CONCLUSIONS: This revised classification reflects the morphological and ecological diversity of Stomiiformes, aligning with their evolutionary diversification in the deep sea. Our phylogenomic framework resolves longstanding systematic uncertainties and highlights the power of genome-wide data in tackling taxonomically challenging clades. These findings provide a foundation for understanding deep-sea fish diversification and assessing the potential ecological drivers for their evolutionary diversity.

Animals↗

PubMed2026

Genome mining reveals an architecturally expanded pyoluteorin-associated biosynthetic gene cluster and a divergent flavin-dependent halogenase-like sequence in deep-sea Pseudomonas Aeruginosa from the Gulf of Guinea.

BACKGROUND: Marine deep-sea environments harbour microorganisms with extraordinary biosynthetic potential, yet their secondary metabolite repertoires remain largely uncharacterised. RESULTS: This study reports the isolation, phenotypic characterisation, and whole-genome analysis of Pseudomonas aeruginosa strain E1, recovered from deep Atlantic seawater (Gulf of Guinea, ~2500 m depth), which exhibits antifungal activity against multidrug-resistant Candida parapsilosis. Three presumptive P. aeruginosa isolates (E1, E17, and E44) showed > 99% 16S rRNA gene sequence identity to P. aeruginosa reference sequences, while whole-genome dDDH analysis of strain E1 yielded 95.2% (95% CI: 93.6-96.4%; formula d4) relative to the P. aeruginosa type strain DSM 50071ᵀ (= ATCC 10145ᵀ), supporting its species-level assignment. Antifungal screening and PCR-based detection of flavin-dependent halogenase genes identified strain E1 as the primary candidate for genomic investigation. Illumina whole-genome sequencing produced a 6.33 Mb draft genome assembly (113 contigs, 5862 protein-coding genes, 66.4% GC content). Genome mining with antiSMASH 8.0 identified 27 biosynthetic gene clusters (BGCs) spanning nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), phenazine, terpene, and metallophore pathways. Region 7.1 of strain E1 harbours a predicted 50.8 kb pyoluteorin-associated BGC, comprising 34 genes, substantially larger than its terrestrial counterpart (~ 22 kb, ~ 17 genes), and featuring nine transport genes and three regulatory elements. Phylogenetic analysis resolved three halogenase genes: ctg7_146 showed 98.7% amino acid identity to PltA, and ctg7_149 showed 99.2% amino acid identity to PltM, supporting their annotation as PltA-like and PltM-like components of the predicted pyoluteorin biosynthetic pathway. Among the characterised reference enzymes included in this analysis, ctg7_143 showed the highest amino acid identity to PltM from P. fluorescens Pf-5. However, the identity remained low at approximately 30.4%, supporting its placement as a divergent FDH-like sequence rather than a close PltM orthologue. CONCLUSION: This study provides the first comprehensive genomic characterisation of a pyoluteorin-BGC-harbouring marine P. aeruginosa strain, demonstrating conservation of the core biosynthetic machinery alongside an expanded transport architecture and a divergent FDH-like sequence that may represent a candidate for future biochemical investigation. These findings expand current knowledge of FDH-like sequence diversity in deep-sea bacteria and support further investigation of Gulf of Guinea microorganisms as a potential source of biosynthetic and enzymatic diversity.

Multigene Family↗

PubMed1992

Homeoviscous adaptation under pressure: the pressure dependence of membrane order in brain myelin membranes of deep-sea fish.

Steady-state and time-resolved anistropy of 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence have been used to compare the hydrocarbon order of brain myelin membranes from a shallow water (plaice) and two deep-sea fish species (Coryphenoides rupestris and Coryphenoides armatus). At atmospheric pressure the deep sea fish displayed lower steady-state anisotropies than shallow water species although the pressure dependence of anisotropy was similar in all species. Time-resolved measurements allowed the separate determination of the rate of probe motion from the amplitude of that motion. Anisotropy decays were analysed in terms of two correlation times and a constant (r infinity). The r infinity and mean value of P2 order parameter for all species increased with pressure, the graphs for deep-sea species being translated to higher pressures relative to shallow-water species. The resulting pressure coefficients for C. armatus was distinctly less than for the two shallower species. These time-resolved studies show that the interspecific differences provide for similar order parameters in all three species when corrected to their respective habitat conditions of pressure and temperature. This indicates that myelin order is highly conserved despite the profound ordering effects of high hydrostatic pressure.

Adaptation, Physiological↗

PubMed1976

A comparative study of the pineal complex in the deep-sea fishes Bathylagus Wesethi and Nezumia liolepis.

The pineal complexes of two deep-sea fishes, Bathylagus wesethi (family Bathylagidae) and Nezumia liolepis (family Macrouridae), were studied with both light and electron microscopy. Receptor and supportive cells were identified in the pineals of both species. The presence of receptor cells suggests that the pineals function in photoreception. Ganglion cells could be identified only in B. wesethi. A dorsal sac and a paraphysis were found in B. wesethi; both structures are absent in N. liolepis. Several trends were found when the results of this study were compared with those of a study on the pineal complex of another deep-sea fish, the myctophid Triphoturus mexicanus (McNulty and Nafpaktitis, 1976). Two of these trends, which are correlated with the vertical distributions of the species studied, suggest an increase in the photosensitivity of the pineals. These are: 1) an increase in the average number of outer segment lamellar membranes per receptor cell, and 2) an increase in the ratio of receptor cells to nerve fibers in the pineal stalks. A functional relationship between the dorsal sac, paraphysis, and pineal central lumen was suggested. The relationship may involve secretory activities.

Animals↗

PubMed1975

Survival of human enteric and other sewage microorganisms under simulated deep-sea conditions.

The survival of pure cultures of Escherichia coli, Streptococcus faecalis, Clostridium perfringens, and Vibrio parahaemolyticus under simulated deep-sea conditions of low temperature (4 C), seawater, and hydrostatic pressures ranging from 1 to 1,000 atm was determined over a period exceeding 300 h. The viability of E. coli and total aerobic bacteria in seawater-diluted raw sewage subjected to these deep-sea conditions was also measured. There was a greater survival of both E. coli and S. faecalis at 250 and 500 atm than at 1 atm at 4 C. S. faecalis was quite insensitive to 1,000 atm, whereas with E. coli there was a 10-fold die-off per 50-h exposure to 1,000 atm. In contrast, V. parahaemolyticus and C. perfringens were quite sensitive to pressures exceeding 250 atm, and with both of these species there was a total loss of viability of approximately 10(8) cells per ml within 100 h at 1,000 arm and within 200 h at 500 atm. The viability of the naturally occurring fecal coliforms in sewage exposed to moderate pressures at 4 C was found to be similar to the survival patterns demonstrated with pure cultures of E. coli. The total numbers of aerobic bacteria in these sewage samples, however, stabilized at 500 and 1,000 atm after 100 h, and at 1 and 250 atm there was significant growth of sewage-associated bacteria, which apparently utilized the organic compounds in the seawater-diluted sewage samples. A preliminary classification of some of these bacteria indicated that approximately 90% (160 isolates) of the organisms that survived over a 400-h exposure to 500 and 1,000 atm were Arthrobacter/Corynebacterium species, and the representative organisms capable of growing at 1 and 250 atm in seawater at 4 C were gram-positive cellulose digesters and an unidentified gram-negative coccus. The significance of these results with respect to the contamination of the deep ocean with human pathogens and the possibility of sewage-associated microorganisms growing and competing with indigenous marine microbial flora in situ is discussed.

Arthrobacter↗

PubMed1975

[Para- and tetraplegia caused by decompression accident (deep sea diving). Study of 9 cases with more or less severe sequelae].

The authors report 9 cases of para and tetraplegia due to decompression sickness following deep sea diving. Poor technique was the cause of 8 of these cases, but one remained totally unexplained. The sequelae were serious; 3 dorsal paraplegias, which were functionally complete, 4 incomplete tetraplegias giving rise to permanent disability. In 2 cases there remained some spasticity of the lower limbs, in some cases associated with genito-urinary disorders. The authors review recent physiopathological theories. -- Blood disturbances may be due to the presence of gas bubbles which aggress the organism and give rise to coagulation disorders. -- The formation of the bubbles may be the cause of the spinal lesions, e.g. liberation in situ, gas embolism; the bubbles may form in various parts of the circulation and may cross the pulmonary barrage. Bubbles probably form in the lung itself, in the pulmonary veins and in the aorta, including the spinal capillaries. There is some slowing of the circulation, secondary to increased pressure, and pulmonary stasis may also play a harmful role. Finally, the dorsal spinal segments, which are the most poorly vascularised, are particularly exposed. This corresponds to the clinical findings. As far as treatment is concerned, the authors emphasize that recompression with hyperbaric equipment, should be carried out as an emergency, especially in unconsciuos subjects, together with other appropriate treatment. Such facts are important now that deep sea diving is becoming more and more commonly practised.

Adult↗

PubMedDate not supplied

[Some peculiarities of brain phospholipids in deep sea fishes].

Total phospholipids (PL) as well as the content of various phospholipid classes and their fatty acid composition have been investigated in the brain of mesopelagic and abyssal marine teleosts. These species were compared to shallow water ones. The brain of deep sea fishes was found to be very poor in PL as compared to the brain of mesopelagic ans surface water species. No differences concerning the brain PL content were revealed between the two last mentioned groups. The relative content of separate PL classes was very similar in all the species studied irrespectively of the depth of their habitat. Peculiarities were found in fatty acid composition of individual PL from deep sea species as compared to surface ones. The deeper the habitat, the lower the content of saturated fatty acids, especially of the stearic acid. The lowest content of saturated fatty acids, maximum level of polyenoic fatty acids as well as some peculiarities in the relative content of particular fatty acids were found in the brain of ultraabyssal (6, 000 m) Leucicorus sp.

Adaptation, Physiological↗

PubMed1975

Slow growth rate of a deep-sea clam determined by 228Ra chronology.

The age of a deep-sea clam, Tindaria callistiformis, from 3803 m depth has been determined by 228Ra (6.7 year half-life) chronology of separated size fractions of a captured population. A length of 8.4 mm is attained in about 100 years. Shells of this size fraction show about 100 regularly spaced bands, indicating that the growth feature may be an annual one.

Animals↗

PubMed1977

Degeneria halosauri (Bell 1887) gen. et comb. n. (Digenea: Gorgoderidae) from the deep-sea telost Halosauropsis macrochir.

The earliest reported trematode from a deep-sea fish, Distomum halosauri Bell 1887 collected by the H.M.S. Challenger expedition, is redescribed from fresh material taken from the type host in the northwest Atlantic. The species is assigned to Degeneria gen. et comb. n. Distinguishing characteristics are the combinaion of a pharynx, cirrus pouch with internal seminal vesicle, disposition of the uterus into the forebody, large eggs, and location in the excretory system of the host. The relationship of Degeneria to other gorgoderids is discussed.

Animals↗

PubMed1979

A comparative light and electron microscopic study of the pineal complex in the deep-sea fishes, Cyclothone signata and C. acclinidens.

The pineal complexes of the two closely related deep-sea fished Cyclothone signata and C. acclinidens were compared both qualitatively and quantitatively. Photoreceptor and supportive cells were identified in both species. The deeper-dwelling species, C. acclinidens, had a significantly greater number of photoreceptor-cell outer segment saccules and a higher ratio of receptor cells to nerve fibers in the pineal stalk. It was suggested that these indicate increased photosensitivity of the pineal. Supportive cells were sometimes seen to contain arrays of undulating tubules. The functional significance of these tubules is not understood. A prominent dorsal sac is closely associated with the pineal end-vesicle. Both structures appear to have a common vascular supply suggesting that they are functionally related. Dorsal sac cells contained abundant mitochondria, glycogen, and large filament-like inclusions.

Animals↗

PubMed2026

Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep-Sea Molluscs.

Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon-dated to 1671-1135 years old before present) deep-sea vesicomyid clam shells, including species Archivesica marissinica, A. nanshaensis and A. okutanii, using whole-genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on-target read recovery of UCEs from fresh soft tissue, but < 1% from shell specimens. By contrast, UCE capture in the same specimen increased on-target reads by up to 155-fold, reaching 29.84% in fresh shells and up to 72-fold, reaching 19.89% in ancient shells. Target capture of UCEs recovered 142-1001 loci per sample compared to 0-230 with WGS alone. Ancient shells of A. marissinica and A. okutanii, based on reads mapped with bwa-mem2 and bbmap, exhibited characteristic post-mortem DNA damage signals, with average 5'-end C-to-T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh A. marissinica shells (maximum 1.24%). UCE-based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target-capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells-one of the most abundant invertebrate remains-for evolutionary, biogeographic and conservation studies.

Animals↗

PubMed1977

Influence of hydrostatic pressure on the effects of the heavy metal cations of manganese, copper, cobalt, and nickel on the growth of three deep-sea bacterial isolates.

Increases hydrostatic pressure varied the 72-h growth yield of three bacterial isolates from the deep sea in the presence of heavy metal cations of Mn, Cu, Co, and Ni, depending on the bacterial isolate, the metal cation and its concentration, and the level of hydrostatic pressure. Above atmospheric, hydrostatic pressure was found to have one of the following four effects on the response of culture growth to a heavy metal cation. (i) It could be without effect; (ii) it could enhance inhibition by a metal cation; (iii) it could increase the 72-h growth yield by a metal cation; or (iv) it could protect against a growth inhibitory effect noted at a lower pressure. Possible reasons for these varied responses are discussed.

Bacteria↗

PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333-0.264) and did not reveal population differentiation within our samples (F ST = - 0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗