Deep-sea Samples Research Articles

Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress.

Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.

A pressure-triggered isobaric sequential liquid sampling system for full-ocean-depth: Design and field deployment

Collecting pressure-retaining deep-sea liquid samples is important for the research on in-situ environment and life. A pressure-triggered isobaric sequential liquid sampling system (PTISLSS) was developed for the collection of seawater at target depths. The sampling system comprises six independent seawater collection modules, each containing a titanium sample container and a pre-charged accumulator. A motor-driven sampling mechanism was designed to open and close the fluid channels at depth. Theoretical studies have indicated that the mechanism can generate a contact pressures of up to 160 MPa to ensure the sealing of the samples. The relationship between the pressure of pre-charged gas and the volume of fluid sample has been derived considering the effects of seal friction. The sampling system was built for full-ocean-depth sampling operation and the reliability of the system was tested at a pressure of 120 MPa. The field test was conducted in the West Philippine Basin on a recent scientific research cruise. Pressurized seawater from depths of 2000 to 4500 meters was recovered, and the pressure-retaining rate exceeded 93.5%. The developed sampling system presents satisfactory performance and high operational efficiency, and it will have a wide range of applications in the field of large-scale deep-sea sampling.

Element recognition of laser-induced breakdown spectroscopy by comparing vectors of peak quantities

Element recognition of laser-induced breakdown spectroscopy (LIBS) can be achieved by analyzing the corresponding peaks of plasma emissions. However, it is still challenging to make quick judgments due to database disagreements, such as wavelength or line-ratio. This study presents a simple method to conduct element recognition based on comparing vectors established by the quantities of spectral peaks, which allows an accurate recognition of the principle elements regardless of wavelength shifts. By examining deep-sea samples, this method demonstrates the recognition effectiveness for rare earth elements (REEs) with an accuracy over 80%. The developed method proves to be practical in LIBS qualitative analysis, and it can serve as an effective complement to existing approaches for element identification.

Experimental study of self-locking seal structure based on full ocean depth sediment pressure retaining sampler

The full ocean depth environment is characterized by high pressure, low temperature, and high corrosiveness, making it difficult for the current deep-sea sampling equipment to obtain pressure-retaining sediment samples from the seafloor. A new self-locking seal structure is designed with an automatic centering plus floating valve core structure to ensure that the long needle valve core only carries the axial load and autonomously fits the sealing cone of the pressure retaining device. The novel self-locking seal design makes the sampler seal more reliable under high pressure. We conducted a series of experiments to verify the sealing performance of the self-locking seal structure, and the test results show that the self-locking seal structure has better sealing performance when the pressure difference between the inside and outside is larger. This new self-locking seal structure has been used for the full ocean depth sediment sampler during the TS-21 cruise in 2021 and was tested in situ at a depth of 7700 m in the West Philippine Basin, retrieving pressure-retaining sediment samples with 94 % pressure retention.

Deep-sea freezer

Recovery of samples from the deep ocean in pristine condition is difficult due to large environmental differences between the deep and surface waters through which the samples necessarily must be transported. Here, we propose a concept for deep-sea sample recovery: a deep-sea freezer using thermoelectric cooling capable of generating ice in the deep and recover them frozen on-board ships. As a proof of concept, we present the DSF-α, a prototype Deep-Sea Freezer based on Peltier device rated at 2000 m. In situ assessments of the DSF-α on remotely operated vehicles showed its capacity to reach freezing (-13.0°C) temperatures in the deep, as well as recovering seawater frozen on deck. Although the DSF-α is limited in that achieving sufficient freezing for useful sample recovery is time consuming, the deep-sea freezer opens a whole frontier of new possibilities for preserving various types of deep-sea samples and has the potential to be adapted according to various needs of the deep-sea research community. With the first literal ‘marine snow’ in the deep, we offer a glimpse to a future where the recovery of reliable bathyal samples is no longer laborious.

Actinobacteria from Arctic and Atlantic deep-sea sediments-Biodiversity and bioactive potential.

The deep-sea covers over 70% of the Earth's surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.

Means and methods for testing bottom soils

One of the main methods of engineering-geological studies of bottom soils is the selection of soil samples using marine samplers for their subsequent analysis in a ship laboratory.Marine samplers are devices that allow obtaining a surface sample of bottom sediments (grabs, dredges) or a soil sample (core) from a depth of up to 5...10 meters from the seabed surface (ground tubes, box-shaped samplers). The analysis of selected soil samples and the measurement of their strength properties are carried out by laboratory methods in on-board or coastal conditions. Sampling is the simplest and cheapest means of studying deep-sea soils and has been used only by oceanologists for a long time. Later, it began to be used in offshore exploration work on the shelf and in marine engineering and geological studies. The possibility of using sampling from non-specialized ships, the efficiency and relatively low cost of work have led to the widespread use of sampling in marine engineering practice. The disadvantages of sampling include the low accuracy of determining the physical and mechanical properties of bottom soils due to violations of the structure of samples during sampling (porosity, density, cohesion), as well as when they rise to the day surface due to changes in the envi15. ronment (pressure, temperature, etc.). etc.). Deep-sea sampling also allows you to analyze soils for particle size distribution, identify the main types, types and varieties of soils. The following samplers are used: types: soil tubes, clamshell, box-shaped, cassette, autonomous self-floating. Testing from underwater platforms and dredging are also used.

A new ROV storage device for deep-sea sampling.

Sampling deep-sea biota is a significant challenge because of the logistics required, in terms of vessels and equipment, to obtain minimally preserved specimens. Traditional methods (trawls, nets, and dredges) cause physical damage, stress, and even contamination during the process of removal from the seabed and their displacement through the water column to the surface. Preserving conditions similar to those found in situ is particularly important when the sampling strives to maintain living organisms and for analyses where contamination or degradation by stress or damage may interfere with the results. Therefore, for the sampling and storage of this biota with less interference, a polypropylene box was designed based on the model of Kellogg et al. (2009) incorporating adaptations to be used by a Remotely Operated Vehicle (ROV). This new device has been successfully used in eight oceanographic campaigns, adequately performing for sediment and biota sampling, including coral reef forming or framework species (Scleractinia), octocorals, associated fauna, and rhodoliths, at depths between 50 and 900 m.

Confocal Raman microscopy for assessing effects of preservation methods on symbiotic deep-sea mussel gills

Confocal Raman microscopy (CRM) is a powerful tool for biological research, which can provide information regarding the composition and distribution of biomolecules in an in situ, label-free, non-destructive manner and with high spatial resolution. Sample preservation is often an unavoidable step, especially for symbiotic deep-sea samples. Moreover, protocols for the preservation of samples for CRM have not been established and specific effects of different preservation methods on biomolecules have not been studied for relevant samples. In this study, we used deep-sea mussel Gigantidas platifrons, an ideal model in the study of deep-sea symbiosis and investigated the effect of four common preservation methods on the results of CRM imaging and signals. The methods included snap-freeze (SF), SF followed by rapid fixation in methanol (SF-MeOH), 2.5% glutaraldehyde and 2% paraformaldehyde fixation (SF-GP), and 4% paraformaldehyde and alcohol fixation (PS-PA). The results of this study indicate that SF was the most effective method for the comprehensive analysis of the biomolecular composition although the sectioning success rate was relatively low. Moreover, SF-MeOH was found to be effective when SF is not sufficient in obtaining good morphology in sections, or when the effect of chemical bonding on the composition of biomolecules upon SF-MeOH can be neglected. Finally, SF-GP and PS-PA were found to be the most effective methods considering the overall morphological observation. However, they were less suitable for metabolic studies. We believe our results can provide guidance for further studies of Raman on symbiotic deep-sea biological samples. It is of great importance for the wide application of Raman technique.

A Review of Diterpenes from Marine-Derived Fungi: 2009–2021

Marine-derived fungi are important sources of novel compounds and pharmacologically active metabolites. As an important class of natural products, diterpenes show various biological activities, such as antiviral, antibacterial, anti-inflammatory, antimalarial, and cytotoxic activities. Developments of equipment for the deep-sea sample collection allow discoveries of more marine-derived fungi with increasing diversity, and much progress has been made in the identification of diterpenes with novel structures and bioactivities from marine fungi in the past decade. The present review article summarized the chemical structures, producing organisms and biological activities of 237 diterpenes which were isolated from various marine-derived fungi over the period from 2009 to 2021. This review is beneficial for the exploration of marine-derived fungi as promising sources of bioactive diterpenes.

Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean.

The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.

High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea

Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.

Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences

SummaryPrecise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.

Active temperature-preserving deep-sea water sampler configured with a pressure-adaptive thermoelectric cooler module

Warming poses a significant threat to the utility of deep-sea samples. This study developed an active temperature-preserving deep-sea water sampler to use at full ocean depths. The most important component of the sampler is the pressure-adaptive thermoelectric cooler module; laboratory experiments validated its high-pressure resistance and waterproof capability under 110 MPa water conditions. The overall structure of the sampler was then designed, and computational fluid dynamics modeled the samples’ temperature distribution. The simulation results were consistent with experimental data. Finally, a sampler prototype was constructed and then tested in the Mariana Trench zone at a large depth of up to 6000 m. Preliminary results indicated that it functioned well during sea trials. The developed sampler should help preserve the in situ temperature of deep-sea samples throughout the recovery process and thus improve the sample quality.

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential.

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.

A Treasure of Bioactive Compounds from the Deep Sea.

The deep-sea environment is a unique, challenging extreme habitat where species have had to adapt to the absence of light, low levels of oxygen, high pressure and little food. In order to survive such harsh conditions, these organisms have evolved different biochemical and physiological features that often have no other equivalent in terrestrial habitats. Recent analyses have highlighted how the deep sea is one of the most diverse and species-rich habitats on the planet but less explored compared to more accessible sites. Because of their adaptation to this extreme environment, deep-sea species have the potential to produce novel secondary metabolites with potent biological activities. Recent advances in sampling and novel techniques in microorganism culturing and chemical isolation have promoted the discovery of bioactive agents from deep-sea organisms. However, reports of natural products derived from deep-sea species are still scarce, probably because of the difficulty in accessing deep-sea samples, sampling costs and the difficulty in culturing deep-sea organisms. In this review, we give an overview of the potential treasure represented by metabolites produced by deep marine species and their bioactivities for the treatment and prevention of various human pathologies.

Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions

Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culturing, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.

Horizontal Distribution of Deep Sea Microplankton: A New Point of View for Marine Biogeography

An investigation on microplankton composition and spatial distribution has been carried out around Italian seas. The analysis of 53 samples, collected in 2017 at two depths in 27 different stations, has led to a scenario of horizontal distribution of microplankton. Dinophyta and Ciliophora were chosen as representatives of the whole microplankton community. A total of 60 genera were identified. Cluster analysis of data regarding taxa presence and abundance led us to recognize that similarities between surface stations were more evident than those between deep ones. Furthermore, we conducted an inter-annual comparison with available data from the South Adriatic Sea (2013, 2015). The higher dissimilarity between deep sea samples was also confirmed in a relatively smaller geographic area. The dissimilarity of deep-sea samples does not correspond to a higher habitat diversification, in terms of abiotic parameters. It has been suggested that the negligible biological connectivity in the deep, for those micro-organisms not able to perform wide spatial migrations, could produce such a biological diversification.

Deep-sea Ophiuroidea (Echinodermata) from the Danish Galathea II Expedition, 1950-52, with taxonomic revisions.

The brittle star samples collected by the Danish cruise 'Galathea II' (1950-52) had not been studied completely. We examined the remaining deep-sea samples (400 m) and present the species inventory, discussing taxonomic issues in relation to recent phylogenetic data. About 235 samples were examined, over 9,300 individuals, from 67 species and 74 sampling localities, at depths of 425-5340 m. The species complex Amphiophiura bullata (Thomson, 1877) is morphologically not well separated, but molecular data suggest at least two clades. We propose to apply A. bullata for Atlantic and Australian populations and A. convexa (Lyman, 1878) for the North Pacific clade. We consider A. bullata pacifica Litvinova, 1971 conspecific with A. convexa. Ophiuroglypha irrorata (Lyman, 1878) and its subspecies are a polyphyletic group with unclear morphological boundaries. We propose to transfer Ophiura ossiculata (Koehler, 1908), Ophiura plana (Lütken Mortensen, 1899) and Ophiura scomba Paterson, 1985 to Ophiuroglypha. Silax Fell, 1962, until now synonymised with Amphioplus Verrill, 1899, is proposed as a valid genus with the species S. verrilli (Lyman, 1879), S. consors (Koehler, 1908), S. daleus (Lyman, 1879), S. patulus (Lyman, 1879) and S. magnificus (Koehler, 1907). Triplodia Turner Hallen, 2011 (a replacement name for Triodia A. M. Clark, 1970, due to homonymy) is synonymised with Silax, and possible specimens of its type species Triodia abdita A. M. Clark, 1970 are analysed. The species limits of Ophiacantha cosmica Lyman, 1879 and Ophiacantha pacifica Lütken Mortensen, 1899 could not be confirmed morphologically, but published molecular data suggest two clades. We propose to apply O. pacifica to the Northern/Central Pacific population and O. cosmica to the Southern Pacific/Antarctic population.

Some Deep-Sea Cephalopods from the Northeastern Mediterranean Sea (Mersin Bay, Turkey)

Deep-sea sampling was conducted by a commercial trawl in the International Waters of Mersin Bay between 14 and 17 May 2018. The sampling depth ranged between 274 and 641 meters. A total of 13 trawling operations were performed, and each trawling operation lasted approximately 4 hours. During the sampling, six of the deep-sea cephalopods species were caught. All specimens were preserved in ethyl alcohol and were deposited in the Museum of the Systematic, Faculty of Fisheries, Mersin University (Catalog no: MEUCC-18-11-2- MEUCC-18-11-7). A total of two cuttlefish species belonging to the families of Sepiidae were identified. The others were represented by the families of Sepiolidae, Octopodidae, Bathypolypodidae, and Ommastrephidae.