Deep Bottom Research Articles

Stable microbial community diversity across large-scale Antarctic water masses

The distinctive environmental attributes of the Southern Ocean underscore the indispensability of microorganisms in this region. We analyzed 208 samples obtained from four separate layers (Surface, Deep Chlorophyll Maximum, Middle, and Bottom) in the neighboring seas of the Antarctic Peninsula and the Cosmonaut Sea to explore variations in microbial composition, interactions and community assembly processes. The results demonstrated noteworthy distinctions in alpha and beta diversity across diverse communities, with the increase in water depth, a gradual rise in community diversity was observed. In particular, the co-occurrence network analysis exposed pronounced microbial interactions within the same water mass, which are notably stronger than those observed between different water masses. Co-occurrence network complexity was higher in the surface water mass than in the bottom water mass. Yet, the surface water mass exhibited greater network stability. Moreover, in the phylogenetic-based β-nearest taxon distance analyses, deterministic processes were identified as the primary factors influencing community assembly in Antarctic microorganisms. This study contributes to exploring diversity and assembly processes under the complex hydrological conditions of Antarctica.

Healthy assemblages of Isidella elongata unintentionally protected from trawling offshore of Asinara Island (northwestern Sardinia, NW Mediterranean Sea)

Deep-sea coral assemblages are marine biodiversity hot spots. Because of their life history traits, deep-sea corals are highly vulnerable to the impacts of human activities such as fishing. The critically endangered “bamboo coral” Isidella elongata is a key structuring species of deep muddy bottoms that is susceptible to habitat destruction, particularly from trawling. A shallow population of this species was recently discovered by a multibeam and ROV survey offshore of the Asinara Island marine protected area (MPA) (northwestern Sardinia, NW Mediterranean Sea). This vulnerable marine assemblage has been found under healthy conditions at depths ranging from 110 to 298 m. Isidella elongata occurs on a muddy seafloor locally characterised by boulders associated with black coral species (Parantipathes larix and Antipathes dichotoma). The lush colonies of I. elongata seem to be related to natural protection from bottom trawling activity; nevertheless, the presence of lost fishing artisanal nets has been observed in the study area. These structuring species are indicators of vulnerable marine ecosystems, and their conservation is essential for preserving marine biodiversity. Therefore, enlarging the perimeter of the Asinara Island MPA into its deeper western waters is suggested to ensure the protection of these valuable and vulnerable marine ecosystems.

Reduced Deep Convection and Bottom Water Formation Due To Antarctic Meltwater in a Multi‐Model Ensemble

AbstractThe additional water from the Antarctic ice sheet and ice shelves due to climate‐induced melt can impact ocean circulation and global climate. However, the major processes driving melt are not adequately represented in Coupled Model Intercomparison Project phase 6 (CMIP6) models. Here, we analyze a novel multi‐model ensemble of CMIP6 models with consistent meltwater addition to examine the robustness of the modeled response to meltwater, which has not been possible in previous single‐model studies. Antarctic meltwater addition induces a substantial weakening of open‐ocean deep convection. Additionally, Antarctic Bottom Water warms, its volume contracts, and the sea surface cools. However, the magnitude of the reduction varies greatly across models, with differing anomalies correlated with their respective mean‐state climatology, indicating the state‐dependency of the climate response to meltwater. A better representation of the Southern Ocean mean state is necessary for narrowing the inter‐model spread of response to Antarctic meltwater.

Structural Basis for Substrate Binding and Catalytic Mechanism of the Key Enzyme VioD in the Violacein Synthesis Pathway.

Violacein is a pigment synthesized by gram-negative bacteria with various biological activities such as antimicrobial, antiviral, and anticancer activities. VioD is a key oxygenase converting protodeoxyviolaceinic acid (PDVA) to protoviolaceinic acid in violacein biosynthesis. To elucidate the catalytic mechanism of VioD, here, we resolved two crystal structures of VioD, a binary complex structure containing VioD and a FAD and a ternary complex structure composed of VioD, a FAD and a 2-ethyl-1-hexanol (EHN). Structural analysis revealed a deep funnel like binding pocket with wide entrance, this pocket is positively charged. The EHN is located at the deep bottom of the binding pocket near isoalloxazine ring. Further docking simulation help us to propose the mechanism of the hydroxylation of the substrate catalyzed by VioD. Bioinformatic analysis suggested and emphasized the importance of the conserved residues involved in substrate binding. Our results provide a structural basis for the catalytic mechanism of VioD. This article is protected by copyright. All rights reserved.

Ancient Deep Sea Bottom in Modern Mountains: New Aspects of Geoheritage from Guzeripl in Southwestern Russia

Geoheritage studies have different perspectives, among which treatment of geological features in relation to particular areas and settlements seems to be promising for better local planning and tourism organization. The small town of Guzeripl in the Western Caucasus (southwestern Russia) experiences tourism-triggered development. Five localities, which are parts of two earlier established geosites, are found directly in this settlement and in its vicinity. They show representative siliciclastic deposits dominated by shales, which accumulated on the deep bottom of the Caucasian Sea in the Early Middle Jurassic. New field investigations allowed for the collection of information regarding the improvement of the geological knowledge of this study area and the reconsideration of its geoheritage in relation to the settlement’s needs. Particularly, the tentative approach for the functional assessment of the localities was proposed and applied. It is established that the localities represent not only deep-marine siliciclastic deposits, trace fossils, and specific palaeoenvironment, but also the structural elements (anticline, syncline, and fault) of the complex deformed domain. They differ by functional value, with two of the most valuable localities directly in Guzeripl, and all of them can be employed for the settlements’ needs. Geoscientists, guided student groups, and geotourists can choose Guzeripl to collect new data, train, and for new impressions. Importantly, geotourism based on the considered localities can diversify the experience of visitors, and it can be combined with and facilitated by ecotourist activities already offered by the Caucasus State Nature Biosphere Reserve, which is famous for its natural heritage. The study area focuses on the spatial distribution of geoheritage relatively to the touristic patterns.

A Nonlinear Schrеdinger Equation for Gravity-Capillary Waves on Deep Water with Constant Vorticit

The surface gravity-capillary waves on deep water with constant vorticity in the regionbounded by the free surface and the infinitely deep plane bottom are considered. A nonlinear Schrödinger equation is derived from a system of exact nonlinear integro-differential equations in conformal variables written in the implicit form taking into account surface tension. In deriving the nonlinear Schrödinger equation, the role of the mean flow is taken into account. The nonlinear Schrödinger equation is investigated for modulation instability. A soliton solution of the nonlinear Schrödinger equation that represents a soliton of the “ninth wave” type is obtained. bounded by the free surface and the infinitely deep plane bottom are considered. A nonlinear Schrödinger equation is derived from a system of exact nonlinear integro-differential equations in conformalvariables written in the implicit form taking into account surface tension. In deriving the nonlinear Schrödinger equation, the role of the mean flow is taken into account. The nonlinear Schrödinger equation is investigated for modulation instability. A soliton solution of the nonlinear Schrödinger equation that represents a soliton of the “ninth wave” type is obtained.

Unconventional Surface Charging Within Deep Cavities on Airless Planetary Bodies: Particle‐In‐Cell Plasma Simulations

AbstractSurface charging properties of a nonconducting surface that has a deep cavity and is in contact with the solar wind plasma are investigated by means of the particle‐in‐cell plasma simulations. The modeled topography is an abstract representation of deep depressions found on the irregular surfaces of solid planetary bodies. The simulations have revealed unconventional charging features in that the cavity bottom is charged up to positive values even without any electron emission processes such as photoemission, provided that the surface location is accessible to a portion of incoming solar wind ions. The major driver of the positive charging is identified as drifting ions of the solar wind plasma, and an uncommon current ordering where ion currents exceed electron currents is established at the innermost part of the deep cavity. This also implies that the deep cavity bottom may have a positive potential of several hundred volts, which is similar in magnitude to the kinetic energy of an ion drift motion. The present study also clarifies the role of photoelectrons in developing the distinctive charging environment inside the cavity. The photoemitted electrons can no longer trigger positive charging at the cavity bottom, but rather exhibit the effect of relaxing positive potentials caused by the solar wind ions. The identified charging process, which is primarily due to the solar wind ions, is localized at the depths of the cavity and may be one possible scenario for generating intense electric fields inside the cavity.

High polychaete diversity in the Gulf of Guinea (West African continental margin): The influence of local and intermediate scale ecological factors on a background of regional patterns

The Tropical East Atlantic is one of the least studied areas in the world's oceans, and thus a blank spot on the map of marine studies. Shaped by dynamic currents and shifting water masses, it is a key region in discussions about marine ecology, biodiversity, and zoogeography, while facing numerous, poorly understood, and unmonitored threats associated with climate change, acidification, and pollution. Polychaete diversity was assessed along four transects along the Ghana coast, from shallow to deep bottoms and distributed along the whole upwelling marine ecoregion. Despite high sampling effort, steep species accumulation curves demonstrated the necessity of further sampling in the region. We observed zonation of fauna by depth, and a decrease in species richness from 25 m to 1000 m depth. Polychaete communities were influenced by sediment type, presence of oxygen minimum zones, and local disturbances caused by elevated barium concentrations. Similar evenness along the depth gradient reflected the importance of rare species in the community structure. Differences in phylogenetic diversity, as reflected by taxonomic distinctness, were small, which suggested high ecosystem stability. The highly variable species richness at small scale (meters) showed the importance of ecological factors giving rise to microhabitat diversity, although we also noticed intermediate scale (50–300 km) differences affecting community structure. About 44 % of the species were rare (i.e. recorded only in three or fewer samples), highlighting the level of patchiness, while one fifth was distributed on all transects, therefore along the whole upwelling ecoregion, demonstrating the influence of the regional species pool on local communities at particular stations. Our study yielded 253 species, increasing the number of polychaetes known from this region by at least 50 %. This casts doubt on previous findings regarding Atlantic bioregionalization, biodiversity estimates and endemism, which appear to have been more pronouncedly affected by sampling bias than previously thought.

Terrigenous leaf-utilizing life of the tube-bearing annelid Anchinothria cirrobranchiata (Annelida: Onuphidae) in the deep sea

AbstractDeep-sea ecosystems are generally oligotrophic because they lack photosynthesizing producers. On deep-sea slopes near land, however, various terrestrial plant remains flow to and are deposited on near-shore deep bottoms. From a depth of 300 m off the Pacific coast of Owase, central Japan, we collected an onuphid polychaete, Anchinothria cirrobranchiata (Annelida: Onuphidae), which lives in a dorsoventrally flattened portable tube. The polychaete tubes were made of sand, as well as leaves and twigs of terrestrial evergreen trees. The leaves glued on the portable tubes were chartaceous, blackish and tough; they belonged mainly to two genera of Fagaceae, Castanopsis and Quercus, which are dominant components of coastal evergreen oak forests. In aquaria, the polychaetes fed on the leaves on their tubes, as well as autochthonous sedimented leaves, suggesting utilization of terrigenous plant litter as food. As to the evolution of Anchinothria, a molecular phylogenetic analysis suggests that Anchinothria is monophyletic with other Hyalinoeciinae (Nothria, Leptoecia, Hyalinoecia).

Additional records of bathyal ascidians (Tunicata) from the New Caledonia region

Two expeditions EXBODI (2011) and SPANBIOS (2021) sampled the invertebrate fauna of deep bottoms on each side of New Caledonia. Many ascidians were collected and the most part are already known species. Among the 13 species described and figured, two are new to science. All have typical characters of a deep habitat. Variability of the internal anatomy is described for abundant specimens of the same species from the same location. There is no concordance with the littoral ascidian fauna.

Coastal cliff erosion as a source of toxic, essential and nonessential metals in the marine environment

Due to the rising environmental awareness, emissions and releases of pollutants, including metals, have been considerably reduced in the last decades. Therefore, the remobilization of natural and anthropogenic contaminants is gaining importance in their biogeochemical cycle. In the marine coastal zone, this process occurs during the erosion of a shore, especially the most vulnerable cliffs. The research was conducted in the Gulf of Gdańsk (southern Baltic Sea) from 2016 to 2017. The sediment cores were collected from four cliffs; additionally, marine surface sediments were also taken. The concentrations of essential (Cr, Mn, Fr, Cu, Zn) and nonessential (Rb, Sr, Y, Zr, Ba) metals were analyzed using the XRF technique. The levels of the analyzed metals were relatively low, typical of nonpolluted areas. However, considering the mass of eroded sediments, the annual load of metals introduced into the sea in this way is significant. In the case of Cu, Zn, and Y the load can amount to a few kilograms, for Cr and Rb – over ten kilograms, for Mn, Sr, and Zr – several tens of kilograms, for toxic Ba – over 100 kg, and in the case of Fe – 4.8 tonnes. During strong winds and storms, when the upper part of a cliff is eroded, especially the load of Zn and Cr entering the sea may increase. The content of Cr, Zr, and Ba in the cliffs was higher compared to marine sediments from the deep accumulation bottom, which indicates that coastal erosion may be an important source of these metals.

Numerical and Experimental Investigations on Hydrodynamic Performance of a Newly Designed Deep Bottom Trawl

In this paper, a new type of bottom trawl was designed for target fishing vessels to use in deep-water fishing grounds. The trawl’s hydrodynamic performance was investigated using numerical simulation and physical modeling methods, and a numerical model based on the finite element method was proposed for estimating hydrodynamic forces and predicting performances. A series of physical model tests based on Tauti’s law were carried out in a towing tank to explore the hydrodynamic performance of the trawl and to assess the applicability of the numerical simulation method. The results showed that the working towing speed of the trawl was 3.5 kn. The drag force and the height of net opening were 50 kN and 5.62 m, respectively, and the swept area was 128 m2 at that speed. The simulated result was close to the experimental result, with a maximum relative error less than 20%, and an average relative error of 10%. The net shape and tension distribution of the trawl were analyzed using the numerical simulation method, and the hanging ratio in T-direction of the mesh of the codend was 0.25 at the working towing speed. The newly designed deep bottom trawl had a superior hydrodynamic performance for high catch efficiency and selectivity and may be applied to commercial fishing operations.

Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome

BackgroundHadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench.ResultsThe results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria.ConclusionsThis study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.

Deep Learning-Based High Accuracy Bottom Tracking on 1-D Side-Scan Sonar Data

The bottom tracking is to confirm the first bottom return signal in each ping to divide the data into the seabed area and the water column area, which is an essential part of side-scan sonar (SSS) data processing. More than that, SSS is usually affected by water flow or suspended solids, resulting in serious noises, which make the bottom tracking more difficult and complex. Some existing methods follow ideas such as abnormal point detection or filtering, resulting in unsatisfactory bottom tracking effects. Inspired by the semantic segmentation mission in deep learning, we innovatively transform the bottom tracking into a binary-class semantic segmentation mission on 1-D SSS data. Following this idea, we propose a semantic segmentation-based bottom tracking method and modify two image semantic segmentation models, SegNet and U-Net, so that they can achieve bottom tracking on 1-D SSS data. Benefiting from the large receptive field brought by convolution and down-sampling, our method has made significant progress in accuracy and antinoise performance compared with the existing method. According to the experimental result, our method has obvious improvement compared with the existing method on the testing set; not only that, our method also performs better on the unused data.

Physical-Chemical Characteristic and Trophic Status of Some Small Lakes in Ciliwung Watershed, West Java Indonesia

Small lakes are important freshwater resources to support the quality of human life. However, small lakes in the watershed are becoming threatened ecosystems because of increasing land-use changes and anthropogenic activity. The study aimed to determine characteristic physical-chemical parameters and trophic status some small lake in Ciliwung Watershed to support the sustainable management of small lakes in the Ciliwung watershed in preventing eutrophication effects. The data was collected in April and June 2021. Measurement and analysis of water quality parameters were conducted by insitu and Laboratory. Some parameters were not in accordance with the Government Regulation number 22/2021 for class II water quality criteria (WQC), including TSS (>50 mg.L-1)., TP (>0.03 mg.L-1), COD (>25 mg.L-1) and DO (<3 mg.L-1), especially for Lake Sunter and Lake Cincin.There are two groups of lakes based on water quality and trophic status. Lake Telaga Warna Lake Cikaret, and Lake Cilodong were classified as eutrophic while lake Sunter and Lake Cincin were classified as hypereutrophic lake Lake Telaga Warna, Lake Cikaret, and Lake Cilodong, located at the upper and middle watershed, are eutrophic, characterized by deeper bottom and higher Secchi depth. At the lower watershed, Lake Sunter and Lake Cincin are hypereutrophic characterized by higher nutrients (TN and TP), COD, temperature, conductivity, salinity, and TDS. The downstream area was a densely populated area that contributed high pollution from upstream and middle of Ciliwung watershed.

Multivariate analysis of the spatial species diversity of demersal fish assemblages in relation to habitat characteristics in a subtropical national park, Taiwan

To understand the spatial species diversity of demersal fish assemblages in Taijiang National Park (TJNP) of Taiwan, fishes from 44 demersal trawl hauls and environmental data were collected in the nearshore and offshore areas of TJNP from April 2016 to May 2019. In total, fishes of 47 families, 84 genera, and 113 species were recorded. The nearshore and offshore demersal fish assemblages in TJNP exhibited significant variability in species composition assessed via beta diversity. Using distance-based redundancy analysis, we demonstrated that bottom depth and substrate type were significant explanatory variables of spatial species diversity and identified three habitat types (I: shallow soft bottom; II: deeper soft bottom; III: deeper bottom with mixed sand and gravel substrates). The nearshore assemblage was characterized by type I, where Tarphops oligolepis (flounder), Trachinocephalus myops (snakefish), and Liachirus melanospilos (carpet sole) dominated in terms of abundance. The offshore assemblage was characterized by either type II or type III because differences in substrate types among sampling sites were noticeable. At the offshore sites characterized by a deeper soft bottom (type II), Johnius distinctus (croaker), Cynoglossus kopsii (shortheaded tonguesole), and Coelorinchus formosanus (Formosa grenadier) predominated. In contrast, the westernmost sampling site, characterized by type III habitat, exhibited relatively high Shannon indices, and Scorpaena miostoma (scorpionfish), Urolophus aurantiacus (sepia stingray), and Parabothus taiwanensis (lefteye flounder) predominated. Our results provide the first baseline information on the environmental characteristics and spatial species diversity of demersal fish assemblages in TJNP and have implications for biodiversity conservation in existing spatial management areas.

Lacydonia shohoensis (Annelida, Lacydoniidae) sp. nov. – a new lacydonid species from deep-sea sunken wood discovered at the Nishi-Shichito Ridge, North-western Pacific Ocean

AbstractLacydonia Marion & Bobretsky, 1875 is the sole genus in the family Lacydoniidae Bergström, 1914. We herein describe the new species of Lacydonia shohoensis sp. nov. from 2042-m deep bottoms at Shoho Seamount of the Nishi-Shichito Ridge, the Northwest Pacific Ocean. It is most similar to L. anapaulae Rizzo et al., 2016 in having a depression on the median anterior region and lacking lateral lobes on the posterior margin of prostomium whereas it is distinguished by possessing pygidium dorsally pigmented with three reddish spots and non-pigmented pygidial lateral cirri equally elongated.

New records of deep-sea ascidians (Tunicata, Ascidiacea) from the New Caledonia region.

The deep marine bottoms around New Caledonia have been explored for forty years. The Kanacono (2016) and Kanadeep (2019) campaigns organized jointly by the Musum national dHistoire naturelle (MNHN) and the Institut de Recherche pour le Dveloppement (IRD) are the complement of this investigation. They are a part of the program La Plante Revisite in New Caledonia. Among the deep sea benthos twenty two ascidian species were collected and three represent new species showing the characteristic adaptations to an abyssal life. The high diversity of the tropical deep sea benthos is enhanced by these new results. No relations are found between littoral ascidians and forms living in the bathyal or abyssal areas.

Long-term coexistence between the macroalga Caulerpa prolifera and the seagrass Cymodocea nodosa in a Mediterranean lagoon

The potential negative influence of the seaweed Caulerpa prolifera on the seagrass Cymodocea nodosa was explored in a Mediterranean coastal lagoon (Mar Menor, Spain) where the alga suddenly and rapidly spread four decades ago. An extensive field sampling was carried out across the lagoon to characterise the distribution and abundance of both macrophytes at different spatial scales, as well as sediment characteristics. Generalised linear and additive models were performed at the whole-lagoon scale, for deep and shallow bottoms, independently, to explore factors influencing C. nodosa distribution and abundance. A high-spatial-resolution macrophyte distribution map was also generated by integrating underwater imaging, direct visualisations and orthophotographs. This map showed that both macrophytes largely dominated the ecosystem but with opposing depth patterns of abundance that mainly reflected their specific light requirements. C. nodosa was dominant at shallow depths but also grew intermingled with a dense C. prolifera bed over large areas of the deep seafloor with highly anoxic muddy sediments. Models did not reveal overall negative relationships between the macrophytes, indicating that C. prolifera was not the main driver of C. nodosa distribution and abundance in this coastal lagoon. Findings highlighted the absence of a negative direct or indirect influence of C. prolifera on C. nodosa, as supported by the fact that the distributions of both macrophytes were similar to those reported in the 1980s, just a few years after C. prolifera had spread in the lagoon. We conclude, therefore, that C. prolifera is not progressively replacing C. nodosa in this ecosystem, where both species have coexisted for decades.

A review on the effective use of Artificial Intelligence for the analysis of cyclic loading on pile foundation

A competent alternative approach to the conventional modelling techniques is artificial intelligence (AI). AI is about the computer science division that creates human intelligence machines and applications. AI-based solutions are great substitute where research is not feasible to evaluate engineering design parameters and therefore contribute to substantial human-time and effort savings in experiments. AI can also speed up the decision-making process, minimize errors and improve performance. AI can also make the decision-making process faster, reduce error rates and improve computing efficiency. Reinforced pile embankment is a useful technique used in soft soil construction, because of its advantages in reducing settlement, building time, and economic efficiency. The response of deep bottoms subjected to a uniform static surcharge was considered in most of the existing research. Very few researchers have studied the cyclical load effect or the effect of variation in depth. An experimental analysis was carried out on the impact of cyclical loading at a specific area of unreinforced and reinforced embankment of differing heights. During the initial stages of cyclical loading, soil arching, regardless of the height of the embankment, was adversely affected. However, the arching of the soil started to improve somewhat by increasing the number of cycles. The magnitude of the loads transferred to piles was increased by the reinforcement layers. But for a thinner embankment, the improvement was more obvious. The main purpose of this report is to identify the AI techniques that can be used to analyze the behaviors of pile foundation undergoing cyclic loading by making models which will help in testing different kinds of failure patterns and the solutions with which these problems can be mitigated.