Evolution and biogeography of deep-sea vent and seep invertebrates

Comparative study of integrated bio-responses in deep-sea and nearshore mussels upon abiotic condition changes: Insight into distinct regulation and adaptation

Deep-sea mussels, one of the dominant species in most deep-sea ecosystems, have long been used as model organisms to investigate the adaptations and symbiotic relationships of deep-sea macrofauna under laboratory conditions due to their ability to survive under atmospheric pressure. However, the impact of additional abiotic conditions beyond pressure, such as temperature and light, on their physiological characteristics remains unknown. In this study, deep-sea mussels (Gigantidas platifrons) from cold seep of the South China Sea, along with nearshore mussels (Mytilus coruscus) from the East China Sea, were reared in unfavorable abiotic conditions for up to 8 days. Integrated biochemical indexes including antioxidant defense, immune ability and energy metabolism were investigated in the gill and digestive gland, while cytotoxicity was determined in hemocytes of both types of mussels. The results revealed mild bio-responses in two types of mussels in the laboratory, represented by the effective antioxidant defense with constant total antioxidant capability level and malondialdehyde content. There were also disparate adaptations in deep-sea and nearshore mussels. In deep-sea mussels, significantly increased immune response and energy reservation were observed in gills, together with the elevated cytotoxicity in hemocytes, implying the more severe biological adaptation was required, mainly due to the symbiotic bacteria loss under laboratory conditions. On the contrary, insignificant biological responses were exhibited in nearshore mussels except for the increased energy consumption, indicating the trade-off strategy to use more energy to deal with potential stress. Overall, this comparative study highlights the basal bio-responses of deep-sea and nearshore mussels out of their native environments, providing evidence that short-term culture of both mussels under easily achievable laboratory conditions would not dramatically alter their biological status. This finding will assist in broadening the application of deep-sea mussels as model organism in future research regardless of the specialized research equipment.

Discovery of the first hydrothermal field along the 500-km-long Knipovich Ridge offshore Svalbard (the Jøtul field)

Oceanic spreading centers north of Iceland are characterized by ultraslow spreading rates, and related hydrothermal activity has been detected in the water column and at the seafloor along nearly all ridge segments. An exception is the 500-km-long Knipovich Ridge, from where, until now, no hydrothermal vents were known. Here we report the investigation of the first hydrothermal vent field of the Knipovich Ridge, which was discovered in July 2022 during expedition MSM109. The newly discovered hydrothermal field, named Jøtul hydrothermal field, is associated with the eastern bounding fault of the rift valley rather than with an axial volcanic ridge. Guided by physico-chemical anomalies in the water column, ROV investigations on the seafloor showed a wide variety of fluid escape sites, inactive and active mounds with abundant hydrothermal precipitates, and chemosynthetic organisms. Fluids with temperatures between 8 and 316 °C as well as precipitates were sampled at four vent sites. High methane, carbon dioxide, and ammonium concentrations, as well as high 87Sr/86Sr isotope ratios of the vent fluids indicate strong interaction between magma and sediments from the Svalbard continental margin. Such interactions are important for carbon mobilization at the seafloor and the carbon cycle in the ocean.

To live or die: "Fine-tuning" adaptation revealed by systemic analyses in symbiotic bathymodiolin mussels from diverse deep-sea extreme ecosystems

Hydrothermal vents (HVs) and cold seeps (CSs) are typical deep-sea extreme ecosystems with their own geochemical characteristics to supply the unique living conditions for local communities. Once HVs or CSs stop emission, the dramatic environmental change would pose survival risks to deep-sea organisms. Up to now, limited knowledge has been available to understand the biological responses and adaptive strategy to the extreme environments and their transition from active to extinct stage, mainly due to the technical difficulties and lack of representative organisms. In this study, bathymodiolin mussels, the dominant and successful species surviving in diverse deep-sea extreme ecosystems, were collected from active and extinct HVs (Southwest Indian Ocean) or CSs (South China Sea) via two individual cruises. The transcriptomic analysis and determination of multiple biological indexes in stress defense and metabolic systems were conducted in both gills and digestive glands of mussels, together with the metagenomic analysis of symbionts in mussels. The results revealed the ecosystem- and tissue-specific transcriptional regulation in mussels, addressing the autologous adaptations in antioxidant defense, energy utilization and key compounds (i.e. sulfur) metabolism. In detail, the successful antioxidant defense contributed to conquering the oxidative stress induced during the unavoidable metabolism of xenobiotics commonly existing in the extreme ecosystems; changes in metabolic rate functioned to handle toxic matters in different surroundings; upregulated gene expression of sulfide:quinone oxidoreductase indicated an active sulfide detoxification in mussels from HVs and active stage of HVs & CSs. Coordinately, a heterologous adaptation, characterized by the functional compensation between symbionts and mussels in energy utilization, sulfur and carbon metabolism, was also evidenced by the bacterial metagenomic analysis. Taken together, a new insight was proposed that symbiotic bathymodiolin mussels would develop a "finetuning" strategy combining the autologous and heterologous regulations to fulfill the efficient and effective adaptations for successful survival.

Spatial patterns of β-diversity under cumulative pressures in the Western Mediterranean Sea

Understanding the spatial dynamics of biodiversity is an essential issue in marine ecology and requires combining information at local and regional scales. β-diversity is an important measure of biodiversity that informs on the differences in community composition between sites and, thus, in the species turnover in the community structure. In this study, we analysed and predicted the spatial patterns of β-diversity for fishes, invertebrates and the demersal assemblage along the Iberian Mediterranean coast. We used Bayesian Bootstrap Generalized Dissimilarity Models (BBGDMs) to study the effects of environment and human pressures on the β-diversity of invertebrate, fishes and the entire demersal assemblage from 1994 to 2015 using different time windows to account for temporal variability. Then, we used these relationships to predict the spatial patterns of β-diversity in the whole Iberian Mediterranean coast. Our results highlighted that the regional spatial patterns of β-diversity were best described by bathymetry and a cumulative index of coastal impacts. We identified specific regions with the highest β-diversity in the study area, which were complementary to hotspots of species richness and presented different degree of overlapping with existent marine protected areas. Overall, our study illustrates that by modelling spatial turnover using β-diversity we can better understand and predict spatial variation of biodiversity and the effects of particular variables, providing relevant information to end-users and policy makers for designing specific spatial conservation and management strategies.

Fluid chemistry alters faunal trophodynamics but not composition on the deep-sea Capelinhos hydrothermal edifice (Lucky Strike vent field, Mid-Atlantic Ridge)

The recently discovered deep-sea Capelinhos hydrothermal edifice, ~ 1.5 km of the main Lucky Strike (LS) vent field (northern Mid-Atlantic Ridge), contrasts with the other LS edifices in having poorly-altered end-member hydrothermal fluids with low pH and chlorine, and high metal concentrations. Capelinhos unique chemistry and location offer the opportunity to test the effects of local abiotic filters on faunal community structure while avoiding the often-correlated influence of dispersal limitation and depth. In this paper, we characterize for the first time the distribution patterns of the Capelinhos faunal communities, and analyze the benthic invertebrates (> 250 µm) inhabiting diffusive-flow areas and their trophic structures (δ13C, δ15N and δ34S). We hypothesized that faunal communities would differ from those of the nearest LS vent edifices, showing an impoverished species subset due to the potential toxicity of the chemical environment. Conversely, our results show that: (1) community distribution resembles that of other LS edifices, with assemblages visually dominated by shrimps (close to high-temperature focused-fluid areas) and mussels (at low-temperature diffuse flow areas); (2) most species from diffuse flow areas are well-known LS inhabitants, including the bed-forming and chemosymbiotic mussel Bathymodiolus azoricus and (3) communities are as diverse as those of the most diverse LS edifices. On the contrary, stable isotopes suggest different trophodynamics at Capelinhos. The high δ15N and, especially, δ13C and δ34S values suggest an important role of methane oxidation (i.e., methanotrophy), rather than the sulfide oxidation (i.e., thiotrophy) that predominates at most LS edifices. Our results indicate that Capelinhos shows unique environmental conditions, trophic structure and trophodynamics, yet similar fauna, compared to other LS edifices, which suggest a great environmental and trophic plasticity of the vent faunal communities at the LS.

Fossilized giant sulfide-oxidizing bacteria from the Devonian Hollard Mound seep deposit, Morocco

The giant sulfide-oxidizing bacteria are particularly prone to preservation in the rock record, and their fossils have been identified in ancient phosphorites, cherts, and carbonates. This study reports putative spherical fossils preserved in the Devonian Hollard Mound hydrocarbon-seep deposit. Based on petrographical, mineralogical, and geochemical evidence the putative microfossils are interpreted as sulfide-oxidizing bacteria similar to the present-day genus Thiomargarita, which is also found at modern hydrocarbon seeps. The morphology, distribution, size, and occurrence of the fossilized cells show a large degree of similarity to their modern counterparts. Some of the spherical fossils adhere to worm tubes analogous to the occurrence of modern Thiomargarita on the tubes of seep-dwelling siboglinid worms. Fluorapatite crystals were identified within the fossilized cell walls, suggesting the intercellular storage of phosphorus analogous to modern Thiomargarita cells. The preservation of large sulfide-oxidizing bacteria was probably linked to changing biogeochemical processes at the Hollard Mound seep or, alternatively, may have been favored by the sulfide-oxidizing bacteria performing nitrate-dependent sulfide oxidation-a process known to induce carbonate precipitation. The presence of sulfide-oxidizing bacteria at a Devonian hydrocarbon seep highlights the similarities of past and present chemosynthesis-based ecosystems and provides valuable insight into the antiquity of biogeochemical processes and element cycling at Phanerozoic seeps.

Genetic divergence and migration patterns of a galatheoid squat lobster highlight the need for deep-sea conservation

Information on genetic divergence and migration patterns of vent- and seep-endemic macrobenthos can help delimit biogeographical provinces and provide scientific guidelines for deep-sea conservation under the growing threats of anthropogenic disturbances. Nevertheless, related studies are still scarce, impeding the informed conservation of these hotspots of deep-sea biodiversity. To bridge this knowledge gap, we conducted a population connectivity study on the galatheoid squat lobster Shinkaia crosnieri - a deep-sea foundation species widely distributed in vent and seep ecosystems in the Northwest Pacific. With the application of an interdisciplinary methodology involving population genomics and oceanographic approaches, we unveiled two semi-isolated lineages of S. crosnieri with limited and asymmetrical gene flow potentially shaped by the geographic settings, habitat types, and ocean currents - one comprising vent populations in the Okinawa Trough, with those inhabiting the southern trough area likely serving as the source; the other being the Jiaolong (JR) seep population in the South China Sea. The latter might have recently experienced a pronounced demographic contraction and exhibited genetic introgression from the Okinawa Trough lineage, potentially mediated by the intrusion of the North Pacific Intermediate Water. We then compared the biogeographic patterns between S. crosnieri and two other representative and co-occurring vent- and seep-endemic species using published data. Based on their biogeographical subdivisions and source-sink dynamics, we highlighted the southern Okinawa Trough vents and the JR seep warrant imperative conservation efforts to sustain the deep-sea biodiversity in the Northwest Pacific.

Three new species of Ascarophis van Beneden, 1871 (Nematoda: Cystidicolidae) from deep-sea hydrothermal vent fishes of the Pacific Ocean

Examinations of some deep-sea hydrothermal vent fishes from the western and eastern regions of the Pacific Ocean revealed the presence of three new species of Ascarophis van Beneden, 1871 (Nematoda: Cystidicolidae), all gastrointestinal parasites, namely: A. justinei n. sp. from Thermarces cerberus Rosenblatt & Cohen (type host) and Thermichthys hollisi Cohen, Rosemblatt & Moser (both Zoarcidae, Perciformes) and A. globuligera n. sp. from T. cerberus from the Northern East Pacific Rise, and A. monofilamentosa n. sp. from Pyrolicus manusanus Machida & Hashimoto (Zoarcidae, Perciformes) from the Manus Basin near Papua New Guinea. Specimens are described and illustrated based on light and scanning electron microscopical examinations. In addition to other morphological differences, all the three new species differ from each other by the structure of eggs: eggs bearing a lateral superficial swelling (A. globuligera n. sp.), eggs with one conspicuously long filament on one pole (A. monofilamentosa n. sp.) and eggs smooth, without any filaments or swellings (A. justinei n. sp.). The egg morphology of the two first-named species is unique within all species of Ascarophis, which indicates that all the three newly described species of Ascarophis are probably endemic to the respective hydrothermal vents as their fish hosts.

Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat

BACKGROUND

The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments.

RESULTS

The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance.

CONCLUSIONS

In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.

Difference in sulfur regulation mechanism between tube-dwelling and free-moving polychaetes sympatrically inhabiting deep-sea hydrothermal chimneys

The environment around deep sea hydrothermal vents is characterized by an abundance of sulfur compounds, including toxic hydrogen sulfide. However, numerous communities of various invertebrates are found in it. It is suggested that invertebrates in the vicinity of hydrothermal vents detoxify sulfur compounds by biosynthesis of taurine-related compounds in the body. On the other hand, the vent endemic polychaete Alvinella pompejana has spherocrystals composed of sulfur and other metals in its digestive tract. It was considered that the spherocrystals contribute to the regulation of sulfur in body fluids. Paralvinella spp. and Polynoidae. gen. sp. live sympatrically and in areas most affected by vent fluid. In this study, we focused on the digestive tract of Paralvinella spp. and Polynoidae. gen. sp. to examine whether they have spherocrystals. We also investigated the possible involvement of bacteria in the digestive tract in spherulization. Examination with a scanning electron microscope (SEM) equipped with Energy Disperse X-ray Spectroscopy (EDS) detected spherocrystals containing sulfur and iron in the digestive tract of Paralvinella spp. In contrast, such spherocrystals were not observed in that of Polynoidae. gen. sp. although sulfur is detected there by inductively coupled plasma-optical emission spectrometry (ICP-OES). Meta-16S rRNA analysis indicated that the floras of the digestive tracts of the two species were very similar, suggesting that enteric bacteria are not responsible for spherocrystal formation. Analysis of taurine-related compounds indicated that the digestive tissues of Polynoidae. gen. sp. contain a higher amount of hypotaurine and thiotaurine than those of Paralvinella spp. Therefore, the two sympatric polychaetes use different strategies for controlling sulfur, i.e., Paralvinella spp. forms spherocrystals containing elemental sulfur and iron in the digestive tract, but Polynoidae. gen. sp. accumulates taurine-related compounds instead of spherocrystals. Such differences may be related to differences in their lifestyles, i.e., burrow-dweller or free-moving, or may have been acquired phylogenetically in the evolutionary process.

High Microeukaryotic Diversity in the Cold-Seep Sediment

Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.

Insights into the Deep Phylogeny and Novel Gene Rearrangement of Mytiloidea from Complete Mitochondrial Genome

The extant marine mussels which belong to the Mytiloidea are widespread species inhabiting mostly coastal waters, with some distributed in the deep sea. To clarify the classification systems and phylogenetic relationships range from genus to family level within Mytiloidea, new sequence was used in a phylogenetic analysis including all the available Mytiloidea mitochondrial genomes. In this study, the complete mitochondrial genome of Vignadula atrata is 15,624 bp in length and contains 12 protein-coding genes (PCGs, atp8 is absent), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on 12 PCGs showed that it has a close relationship to Bathymodiolus. The analysis of gene rearrangements in the Pteriomorphia showed that the arrangements are highly variable across species, novel gene rearrangements were found within Mytiloidea. The V. atrata mitogenome was provided in detail, with notes on the sequence and a key to the species of Vignadula. This study provides a perspective on the taxonomic histories of the marine mussels and refines the unclear relationship between the origin and evolution of species in Mytiloidea within Bivalvia.

Bioaccumulation of emerging persistent organic pollutants in the deep-sea cold seep ecosystems: Evidence from chlorinated paraffin

Persistent organic pollutants (POPs) are highly toxic and can accumulate in marine organisms, causing nonnegligible harm to the global marine ecosystem. The Cold seep is an essential marine ecosystem with the critical ecological function of maintaining the deep-sea carbon cycle and buffering global climate change. However, the environmental impact of emerging POPs in the deep-sea cold seep ecosystem is unknown. Here, we investigated the potential pollution of chlorinated paraffins (CPs) and their bioaccumulation in the cold seep ecosystem. High concentrations of CPs were detected in the cold seep ecosystems, where CPs bioaccumulated by the keystone species of deep-sea mussels can be released into the surface sediment and vertically migrate into the deeper sediment. Furthermore, more toxic CPs were accumulated from transforming other CPs in the cold seep ecosystem. Our study provides the first evidence that high concentrations of POPs are bioaccumulated by deep-sea mussels in the cold seep ecosystem, causing adverse ecological effects. The discovery of CPs bioaccumulation in the deep-sea cold seep ecosystem is a crucial mechanism affecting deep-sea carbon transport and cycling. This study has important guiding significance for revealing the deep-sea carbon cycle process, addressing global climate change, and making deep-sea ecological and environmental protection policies.

Genetic population structures of common scavenging species near hydrothermal vents in the Okinawa Trough

Deep-sea mining of hydrothermal deposits off the coast of Japan is currently under consideration, and environmental baseline studies of the area are required to understand possible impacts. The aim of this study is to clarify population structures of dominant benthic megafaunal species near hydrothermal vent fields in the Okinawa Trough, using a population genetics approach. We examined dominant deep-sea scavenging species including eels, several amphipods, and a decapod and performed population genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region. Several sites were sampled within Okinawa Trough to examine intra-population diversity while two other locations 1400-2400 km away were chosen for inter-population comparisons. For synaphobranchid eels Simenchelys parasitica and Synaphobranchus kaupii, our results showed significant intra-population diversity but no inter-population genetic differentiation, suggesting strong genetic connectivity and/or large population sizes. In addition, single nucleotide polymorphism analysis also confirmed strong genetic connectivity for Simenchelys parasitica. Among scavenging amphipods, we detected seven putative species using molecular phylogenetic analysis. We evaluated population structures of the most abundant species of amphipods and a decapod species (Nematocarcinus lanceopes). Our results provide basic information on the genetic population structures of benthic megafaunal species near hydrothermal vent fields, which can be used to select candidate species for future connectivity analysis with high-resolution genetic markers and aid understanding of the potential population impacts of environmental disturbances.

Metal bioaccumulation and transfer in benthic species based on isotopic signatures of individual amino acids in South China Sea cold seep environments

Cold seeps are deep-sea 'oases' with dense and dominant coexisting populations of large mussels and tubeworms under extreme environments. Under such natural source of high metal concentrations, the present study investigated the metal bioaccumulation and transfer with trophic positions in six benthic species by the isotopic δ¹⁵N and δ¹³C signatures in the active Haima cold seep, South China Sea. Comparing the isotopic signatures of bulk-tissue and amino acids by compound-specific isotopic analysis (CSIA-AA), we found that the bulk trophic (TP_B) values in the benthos except mussels were significantly higher than those of CSIA-based TP_Glu-Phe values. The estimated CSIA-based TP_Glu-Phe values showed a relatively compressed food chain with much changeable and unique amino acid isotopic heterogeneity, followed slim tubeworms (1.20)<mussels (1.38)<clams (1.52)<brittle stars (1.82)<giant tubeworms (2.16)<shrimps (2.31). All species accumulated relatively high concentrations of Fe, Zn, Cu, and Cr, especially for Zn in clams. Pearson correlation analysis showed that most metals had no significant relationship between their bioaccumulation and trophic positions, whereas Hg showed a significantly positive bioaccumulation through trophic transfer in such a compressed food chain. Water exposure was a major metal source rather than bacterial assimilation for most metals in the cold seep higher consumers. Hyperaccumulation of specific metals in some tissues of different benthos indicated different metal overflows in the Haima cold seep (As and Ni for tubeworms, Zn and Cd for clam gills, Ag and Cu for mussel gills). This study demonstrated high metal adaptations in different species and stable isotopic characteristics of amino acid metabolism in a natural high metal source of an active deep-sea cold seep, which is important for deep-sea development and environmental protection.

Potential functions and applications of diverse microbial exopolysaccharides in marine environments

Exopolysaccharides (EPSs) from microorganisms are essential harmless natural biopolymers used in applications including medications, nutraceuticals and functional foods, cosmetics, and insecticides. Several microbes can synthesize and excrete EPSs with chemical properties and structures that make them suitable for several important applications. Microbes secrete EPSs outside their cell walls, as slime or as a "jelly" into the extracellular medium. These EPS-producing microbes are ubiquitous and can be isolated from aquatic and terrestrial environments, such as freshwater, marine water, wastewater, and soils. They have also been isolated from extreme niches like hot springs, cold waters, halophilic environments, and salt marshes. Recently, microbial EPSs have attracted interest for their applications such as environmental bio-flocculants because they are degradable and nontoxic. However, further efforts are required for the cost-effective and industrial-scale commercial production of microbial EPSs. This review focuses on the exopolysaccharides obtained from several extremophilic microorganisms, their synthesis, and manufacturing optimization for better cost and productivity. We also explored their role and applications in interactions between several organisms.

Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules

Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.

Deep-sea organisms research oriented by deep-sea technologies development

Deep-sea environment, characterized by high pressures, extremely high/low temperatures, limited photosynthesis-generated organic matter, darkness, and high levels of corrosion, is home to flourishing special ecosystems in the world. Here, we illustrate how the deep-sea equipment offers insights into the study of life in the deep sea based on the work in the past five decades. We first describe how organisms in the deep sea are studied, even though it is highly difficult to get access to such extreme environments. We then explain the role of deep-sea technologies in advancing research on the evolution of organisms in hydrothermal vents, cold seeps, seamounts, oceanic trenches, and whale falls from the following perspectives: biological diversity, mechanisms of environmental adaptation, biological evolution, and ecosystem connectivity. Finally, to better understand the function and service of deep-sea organisms, and further conserve the special creatures under anthropologic activity and climate change, we highlight the importance of innovative deep-sea technologies to promote cutting-edge research on deep-sea organisms, and note the remaining challenges and developing directions for deep-sea equipment.

Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella

Background

The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promoting local adaptation and contributing to bursts of speciation and species specialization. The tube-dwelling worms Alvinella pompejana called the Pompeii worm and its sister species A. caudata live syntopically on the hottest part of deep-sea hydrothermal chimneys along the East Pacific Rise. They are exposed to extreme thermal and chemical gradients, which vary greatly in space and time, and thus represent ideal candidates for understanding the evolutionary mechanisms at play in the vent fauna evolution.

Results

We explored genomic patterns of divergence in the early and late stages of speciation of these emblematic worms using transcriptome assemblies and the first draft genome to better understand the relative role of geographic isolation and habitat preference in their genome evolution. Analyses were conducted on allopatric populations of Alvinella pompejana (early stage of separation) and between A. pompejana and its syntopic species Alvinella caudata (late stage of speciation). We first identified divergent genomic regions and targets of selection as well as their position in the genome over collections of orthologous genes and, then, described the speciation dynamics by documenting the annotation of the most divergent and/or positively selected genes involved in the isolation process. Gene mapping clearly indicated that divergent genes associated with the early stage of speciation, although accounting for nearly 30% of genes, are highly scattered in the genome without any island of divergence and not involved in gamete recognition or mito-nuclear incompatibilities. By contrast, genomes of A. pompejana and A. caudata are clearly separated with nearly all genes (96%) exhibiting high divergence. This congealing effect however seems to be linked to habitat specialization and still allows positive selection on genes involved in gamete recognition, as a possible long-duration process of species reinforcement.

Conclusion

Our analyses highlight the non-negligible role of natural selection on both the early and late stages of speciation in the iconic thermophilic worms living on the walls of deep-sea hydrothermal chimneys. They shed light on the evolution of gene divergence during the process of speciation and species specialization over a very long period of time.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02057-y.

Adaptation and evolution of the sea anemone Alvinactis sp. to deep‐sea hydrothermal vents: A comparison using transcriptomes

Sea anemones are diverse and ecologically successful members of Anthozoa. They are often found in intertidal and shallow waters, although a few of them inhabit harsher living conditions, such as deep‐sea hydrothermal vents. Here, we sequenced the transcriptome of the vent sea anemone Alvinactis sp., which was collected from Edmond vent along the central Indian Ocean ridge at a depth of 3275 m, to explore the molecular mechanisms related to adaptation to vents. Compared with another deep‐sea anemone (Paraphelliactis xishaensis) and five shallow water sea anemones, a total of 117 positively selected genes and 46 significantly expanded gene families were found in Alvinactis sp. specifically that may be related to its vent‐specific aspect of adaptation. In addition, 127 positively selected genes and 23 significantly expanded gene families that were found in both Alvinactis sp. and P. xishaensis. Among these, vent‐specific adaptations of Alvinactis sp. may involve genetic alterations in peroxisome, ubiquitin‐mediated protein degradation, oxidative phosphorylation, and endocytosis, and its deep‐sea adaptation may involve changes in genetic information processing. Differentially expressed genes between Alvinactis sp. and the deep‐sea anemone P. xishaensis were enriched in a variety of pathways related to adaptation, such as energy metabolism, genetic information processing, endocytosis, and peroxisomes. Overall, we provided the first transcriptome of sea anemones that inhabit vents, which enriches our knowledge of deep‐sea hydrothermal vent adaptation and the diversity of sea anemones.

Effects of scale worm parasitism on interactions between the symbiotic gill microbiome and gene regulation in deep sea mussel hosts

Diverse adaptations to the challenging deep sea environment are expected to be found across all deep sea organisms. Scale worms Branchipolynoe pettiboneae are believed to adapt to the deep sea environment by parasitizing deep sea mussels; this biotic interaction is one of most known in the deep sea chemosynthetic ecosystem. However, the mechanisms underlying the effects of scale worm parasitism on hosts are unclear. Previous studies have revealed that the microbiota plays an important role in host adaptability. Here, we compared gill-microbiota, gene expression and host-microorganism interactions in a group of deep sea mussels (Gigantidas haimaensis) parasitized by scale worm (PA group) and a no parasitic control group (NPA group). The symbiotic microorganism diversity of the PA group significantly decreased than NPA group, while the relative abundance of chemoautotrophic symbiotic bacteria that provide the host with organic carbon compounds significantly increased in PA. Interestingly, RNA-seq revealed that G. haimaensis hosts responded to B. pettiboneaei parasitism through significant upregulation of protein and lipid anabolism related genes, and that this parasitism may enhance host mussel nutrient anabolism but inhibit the host’s ability to absorb nutrients, thus potentially helping the parasite obtain nutrients from the host. In an integrated analysis of the interactions between changes in the microbiota and host gene dysregulation, we found an agreement between the microbiota and transcriptomic responses to B. pettiboneaei parasitism. Together, our findings provide new insights into the effects of parasite scale worms on changes in symbiotic bacteria and gene expression in deep sea mussel hosts. We explored the potential role of host-microorganism interactions between scale worms and deep sea mussels, and revealed the mechanisms through which scale worm parasitism affects hosts in deep sea chemosynthetic ecosystem.

Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps

Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation.

IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.

Coupled Simulation of Hydrate-Bearing and Overburden Sedimentary Layers to Study Hydrate Dissociation and Methane Leakage

Methane leakage during natural gas hydrate (NGH) exploitation is one of the important challenges restricting its safe development, which necessitates further investigation. However, only a few experimental studies have been conducted to characterize the relationship between methane (CH4) leakage and NGH exploitation. The CH4 leakage mechanism and controlling factors in the hydrate dissociation process are still unclear. A coupled simulator has been developed to study the CH4 hydrate exploitation and the possible leakage of CH4. The new system overcomes the difficulty of constructing hydrate-free overlying strata and seawater in previous studies and can simulate the in situ natural environment containing hydrate reservoirs, overlying strata and overlying seawater as well. In addition, the simulator integrates the spatial distribution of temperature, pressure and electric resistance in hydrate reservoir systems, and allows for the visual monitoring of the overlying strata and the sampling of overburden gas and liquids. The effectiveness of the coupled simulations was verified through experimental testing. The coupled simulations allowed for the characterization of the CH4 leakage mechanism and can be used to develop safe strategies for NGH exploitation.

Full-Length Transcriptome Comparison Provides Novel Insights into the Molecular Basis of Adaptation to Different Ecological Niches of the Deep-Sea Hydrothermal Vent in Alvinocaridid Shrimps

The deep-sea hydrothermal vent ecosystem is one of the extreme chemoautotrophic environments. Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, and Alvinocaris longirostris Kikuchi and Ohta, 1995, are typically co-distributed and closely related alvinocaridid shrimps in hydrothermal vent areas with different ecological niches, providing an excellent model for studying the adaptive evolution mechanism of animals in the extreme deep-sea hydrothermal vent environment. The shrimp S. leurokolos lives in close proximity to the chimney vent discharging high-temperature fluid, while A. longirostris inhabits the peripheral areas of hydrothermal vents. In this study, full-length transcriptomes of S. leurokolos and A. longirostris were generated using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology. Expression analyses of the transcriptomes showed that among the top 30% of highly expressed genes of each species, more genes related to sulfide and heavy metal metabolism (sulfide: quinone oxidoreductase, SQR; persulfide dioxygenase, ETHE1; thiosulfate sulfurtransferase, TST, and ferritin, FRI) were specifically highly expressed in S. leurokolos, while genes involved in maintaining epibiotic bacteria or pathogen resistance (beta-1,3-glucan-binding protein, BGBP; endochitinase, CHIT; acidic mammalian chitinase, CHIA, and anti-lipopolysaccharide factors, ALPS) were highly expressed in A. longirostris. Gene family expansion analysis revealed that genes related to anti-oxidant metabolism (cytosolic manganese superoxide dismutase, SODM; glutathione S-transferase, GST, and glutathione peroxidase, GPX) and heat stress (heat shock cognate 70 kDa protein, HSP70 and heat shock 70 kDa protein cognate 4, HSP7D) underwent significant expansion in S. leurokolos, while CHIA and CHIT involved in pathogen resistance significantly expanded in A. longirostris. Finally, 66 positively selected genes (PSGs) were identified in the vent shrimp S. leurokolos. Most of the PSGs were involved in DNA repair, antioxidation, immune defense, and heat stress response, suggesting their function in the adaptive evolution of species inhabiting the extreme vent microhabitat. This study provides abundant genetic resources for deep-sea invertebrates, and is expected to lay the foundation for deep decipherment of the adaptive evolution mechanism of shrimps in a deep-sea chemosynthetic ecosystem based on further whole-genome comparison.

Deep-Sea Sediment and Water Simulator for Investigation of Methane Seeping and Hydrate Formation

The ubiquitous methane seeping process in the deep-sea environment could significantly influence the global methane cycle and carbon budget. Hydrate formation on the methane bubble during the seeping process is an important way for sequestrating methane during bubble migration. Uncovering the complete methane leakage process needs to reveal the methane leakage pathway and hydrate conversion mechanism. Hence, we built a deep-sea sediment and water simulator to investigate the methane seeping and hydrate formation. The simulator can mimic the deep-sea sediment and water environment with a lower sediment chamber and an upper seawater chamber. The monitoring of the bubble migration path and hydrate transformation and aggregation in the sediment chamber is realized mainly through the spatial distribution of electric resistance and temperature variations. The seawater chamber is equipped with a built-in movable camera and four external windows to observe the rising and morphological evolution of gas and hydrate bubbles. The quantitative storage and escape of CH4 gas could be realized through the measurement of multiple gas/liquid collection ports and cumulative incoming/outgoing gas volume. In addition, a movable biological liquid injection port was designed in the seawater chamber for the coupling CH4 conversion of hydrate formation and microorganism-mediated oxidation. Through the experimental test on each function of the system, the effectiveness of the device was proved. The development of this device has pioneering significance for the experimental simulation of the methane seeping process in a simulated submarine cold spring area.

In-situ Raman study on kinetics behaviors of hydrated bubble in thickening

Natural gas leakage by means of bubbles in cold seep abundantly existed on the ocean floor, causing the change of ocean ecology and the increase of atmospheric temperature. Fortunately, hydrated bubbles as a way of methane sequestration can reduce the effect on the ocean ecology and the escape of gas bubbles from the ocean floor, and are getting attention. To know the growth mode and efficiency of gas hydrate sequestration on bubble, the thickening growth kinetics of hydrated bubble was studied in present work. In-situ Raman spectroscopy was used to analyze the evolution of gas pores and mass transfer channels in the sI CH₄, sI CH₄-C₂H₆ and sII CH₄-C₂H₆ hydrate films on the hydrated bubble by the peak area ratio of Raman spectra. Three types of Raman spectra (a-, b-, and c-type), three texture structures of film (Large gas pore; Small gas pore; No gas pore) and two hydrate thickening patterns (filling of new hydrate within large gas pores; covering growth on the original hydrate lattice) were provided in the thickening of hydrated bubble. Results showed that the thickening of the hydrated bubble was a multi-stages growth, i.e., quick growth (stage I), slow growth (stage II), and no growth (stage III). The texture structures and the type and size of gas pore in hydrated bubble were critical for the kinetics growth rate of hydrated bubble in thickening. Especially, the theory of heterogeneous growth of hydrated bubble was proposed to apply the hydrate growth at the interface of two or multi- bubbles, accelerating the efficiency of carbon sequestration as the hydrated bubble. This study will provide a better theoretical basis for understanding the behaviors and efficiency of hydrated carbon sequestration on the surface of bubbles resulting from the gas leakage in the hydrate exploitation or the natural cold seep. SYNOPSIS: Hydrated bubble strongly modulates the emission of a potent greenhouse gas from the deep sea.

The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment

Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.

Influence of methane seepage on isotopic signatures in living deep-sea benthic foraminifera, 79° N

Fossil benthic foraminifera are used to trace past methane release linked to climate change. However, it is still debated whether isotopic signatures of living foraminifera from methane-charged sediments reflect incorporation of methane-derived carbon. A deeper understanding of isotopic signatures of living benthic foraminifera from methane-rich environments will help to improve reconstructions of methane release in the past and better predict the impact of future climate warming on methane seepage. Here, we present isotopic signatures (δ¹³C and δ¹⁸O) of foraminiferal calcite together with biogeochemical data from Arctic seep environments from c. 1200 m water depth, Vestnesa Ridge, 79° N, Fram Strait. Lowest δ¹³C values were recorded in shells of Melonis barleeanus, - 5.2‰ in live specimens and - 6.5‰ in empty shells, from sediments dominated by aerobic (MOx) and anaerobic oxidation of methane (AOM), respectively. Our data indicate that foraminifera actively incorporate methane-derived carbon when living in sediments with moderate seepage activity, while in sediments with high seepage activity the poisonous sulfidic environment leads to death of the foraminifera and an overgrowth of their empty shells by methane-derived authigenic carbonates. We propose that the incorporation of methane-derived carbon in living foraminifera occurs via feeding on methanotrophic bacteria and/or incorporation of ambient dissolved inorganic carbon.

Adaption to hydrogen sulfide-rich environments: Strategies for active detoxification in deep-sea symbiotic mussels, Gigantidas platifrons

The deep-sea mussel Gigantidas platifrons is a representative species that relies on nutrition provided by chemoautotrophic endosymbiotic bacteria to survive in both hydrothermal vent and methane seep environments. However, vent and seep habitats have distinct geochemical features, with vents being more harsh than seeps because of abundant toxic chemical substances, particularly hydrogen sulfide (H₂S). Until now, the adaptive strategies of G. platifrons in a heterogeneous environment and their sulfide detoxification mechanisms are still unclear. Herein, we conducted 16S rDNA sequencing and metatranscriptome sequencing of G. platifrons collected from a methane seep at Formosa Ridge in the South China Sea and a hydrothermal vent at Iheya North Knoll in the Mid-Okinawa Trough to provide a model for understanding environmental adaption and sulfide detoxification mechanisms, and a three-day laboratory controlled Na₂S stress experiment to test the transcriptomic responses under sulfide stress. The results revealed the active detoxification of sulfide in G. platifrons gills. First, epibiotic Campylobacterota bacteria were more abundant in vent mussels and contributed to environmental adaptation by active oxidation of extracellular H₂S. Notably, a key sulfide-oxidizing gene, sulfide:quinone oxidoreductase (sqr), derived from the methanotrophic endosymbiont, was significantly upregulated in vent mussels, indicating the oxidization of intracellular sulfide by the endosymbiont. In addition, transcriptomic comparison further suggested that genes involved in oxidative phosphorylation and mitochondrial sulfide oxidization pathway played important roles in the sulfide tolerance of the host mussels. Moreover, transcriptomic analysis of Na₂S stressed mussels confirmed the upregulation of oxidative phosphorylation and sulfide oxidization genes in response to sulfide exposure. Overall, this study provided a systematic transcriptional analysis of both the active bacterial community members and the host mussels, suggesting that the epibionts, endosymbionts, and mussel host collaborated on sulfide detoxification from extracellular to intracellular space to adapt to harsh H₂S-rich environments.

A g-Type Lysozyme from Deep-Sea Hydrothermal Vent Shrimp Kills Selectively Gram-Negative Bacteria

Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type (g-type). To date, no study on g-type lysozyme in crustacean has been documented. Here, we report the identification and characterization of a g-type lysozyme (named LysG1) from the shrimp inhabiting a deep-sea hydrothermal vent in Manus Basin. LysG1 possesses conserved structural features of g-type lysozymes. The recombinant LysG1 (rLysG1) exhibited no muramidase activity and killed selectively Gram-negative bacteria in a manner that depended on temperature, pH, and metal ions. rLysG1 bound target bacteria via interaction with bacterial cell wall components, notably lipopolysaccharide (LPS), and induced cellular membrane permeabilization, which eventually caused cell lysis. The endotoxin-binding capacity enabled rLysG1 to alleviate the inflammatory response induced by LPS. Mutation analysis showed that the bacterial binding and killing activities of rLysG1 required the integrity of the conserved α3 and 4 helixes of the protein. Together, these results provide the first insight into the activity and working mechanism of g-type lysozyme in crustacean and deep-sea organisms.

Characteristics of Two Crustins from Alvinocaris longirostris in Hydrothermal Vents

Crustins are widely distributed among different crustacean groups. They are characterized by a whey acidic protein (WAP) domain, and most examined Crustins show activity against Gram-positive bacteria. This study reports two Crustins, Al-crus 3 and Al-crus 7, from hydrothermal vent shrimp, Alvinocaris longirostris. Al-crus 3 and Al-crus 7 belong to Crustin Type IIa, with a similarity of about 51% at amino acid level. Antibacterial assays showed that Al-crus 3 mainly displayed activity against Gram-positive bacteria with MIC₅₀ values of 10–25 μM. However, Al-crus 7 not only displayed activity against Gram-positive bacteria but also against Gram-negative bacteria Imipenem-resistant Acinetobacter baumannii, in a sensitive manner. Notably, in the effective antibacterial spectrum, Methicillin-sensitive Staphylococcus aureus, Escherichia coli (ESBLs) and Imipenem-resistant A. baumannii were drug-resistant pathogens. Narrowing down the sequence to the WAP domain, Al-crusWAP 3 and Al-crusWAP 7 demonstrated antibacterial activities but were weak. Additionally, the effects on bacteria did not significantly change after they were maintained at room temperature for 48 h. This indicated that Al-crus 3 and Al-crus 7 were relatively stable and convenient for transportation. Altogether, this study reported two new Crustins with specific characteristics. In particular, Al-crus 7 inhibited Gram-negative imipenem-resistant A. baumannii.

Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts

The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not been well studied in marine environments. Here, we analysed the composition of the symbiont community in two deep-sea, Bathymodiolus mussel species along their known distribution range at hydrothermal vents on the Mid-Atlantic Ridge, with a focus on the hybrid zone where they interbreed. In-depth metagenomic analyses of the sulphur-oxidising symbionts of 30 mussels from the hybrid zone, at a resolution of single nucleotide polymorphism analyses of ~2500 orthologous genes, revealed that parental and hybrid mussels (F2-F4 generation) have genetically indistinguishable symbionts. While host genetics does not appear to affect symbiont composition in these mussels, redundancy analyses showed that geographic location of the mussels on the Mid-Atlantic Ridge explained most of the symbiont genetic variability compared to the other factors. We hypothesise that geographic structuring of the free-living symbiont population plays a major role in driving the composition of the microbiome in these deep-sea mussels.

Hidden historical habitat-linked population divergence and contemporary gene flow of a deep-sea patellogastropod limpet

Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.

Meiofauna and nematode community composition in a hydrothermal vent and deep-sea sediments in the Central Indian Ridge

The hydrothermal ecosystem is very unusual, yet little research has so far been conducted on meiofauna in hydrothermal zones. To identify the communities of both meiofauna and nematodes around the Onnuri Vent Field (OVF), we collected sediment from a hydrothermal zone in the OVF and deep-sea (DS) sediments (non-vent) outside the OVF. Sampling was conducted at seven stations using multiple corers on the Research Vessel ISABU in June 2018 and June-July 2019. The average densities of meiofauna ± standard deviation ranged from 21.7 ± 5.2 to 122.3 ± 45.0 individuals/10 cm². The structure of the meiofaunal community differed between the OVF and DS. The two most dominant groups of meiofauna in both environments were nematodes and harpacticoids. Statistical analyses showed significant differences in the structure of the nematode community between OVF and DS. We also found that the richness, evenness, and diversity of nematodes in the OVF were lower than those in the DS.

The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers

The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.

A Toll-like receptor identified in Gigantidas platifrons and its potential role in the immune recognition of endosymbiotic methane oxidation bacteria

Symbiosis with chemosynthetic bacteria is an important ecological strategy for the deep-sea megafaunas including mollusks, tubeworms and crustacean to obtain nutrients in hydrothermal vents and cold seeps. How the megafaunas recognize symbionts and establish the symbiosis has attracted much attention. Bathymodiolinae mussels are endemic species in both hydrothermal vents and cold seeps while the immune recognition mechanism underlying the symbiosis is not well understood due to the nonculturable symbionts. In previous study, a lipopolysaccharide (LPS) pull-down assay was conducted in Gigantidas platifrons to screen the pattern recognition receptors potentially involved in the recognition of symbiotic methane-oxidizing bacteria (MOB). Consequently, a total of 208 proteins including GpTLR13 were identified. Here the molecular structure, expression pattern and immune function of GpTLR13 were further analyzed. It was found that GpTLR13 could bind intensively with the lipid A structure of LPS through surface plasmon resonance analysis. The expression alternations of GpTLR13 transcripts during a 28-day of symbiont-depletion assay were investigated by real-time qPCR. As a result, a robust decrease of GpTLR13 transcripts was observed accompanying with the loss of symbionts, implying its participation in symbiosis. In addition, GpTLR13 transcripts were found expressed exclusively in the bacteriocytes of gills of G. platifrons by in situ hybridization. It was therefore speculated that GpTLR13 may be involved in the immune recognition of symbiotic methane-oxidizing bacteria by specifically recognizing the lipid A structure of LPS. However, the interaction between GpTLR13 and symbiotic MOB was failed to be addressed due to the nonculturable symbionts. Nevertheless, the present result has provided with a promising candidate as well as a new approach for the identification of symbiont-related genes in Bathymodiolinae mussels.

A glimpse of deep-sea adaptation in chemosynthetic holobionts: Depressurization causes DNA fragmentation and cell death of methanotrophic endosymbionts rather than their deep-sea Bathymodiolinae host

Bathymodiolinae mussels are typical species in deep-sea cold seeps and hydrothermal vents and an ideal model for investigating chemosynthetic symbiosis and the influence of high hydrostatic pressure on deep-sea organisms. Herein, the potential influence of depressurization on DNA fragmentation and cell death in Bathymodiolinae hosts and their methanotrophic symbionts were surveyed using isobaric and unpressurized samples. As a hallmark of cell death, massive DNA fragmentation was observed in methanotrophic symbionts from unpressurized Bathymodiolinae while several endonucleases and restriction enzymes were upregulated. Additionally, genes involved in DNA repair, glucose/methane metabolism as well as two-component regulatory system were also differentially expressed in depressurized symbionts. DNA fragmentation and programmed cell death, however, were rarely detected in the host bacteriocytes owing to the orchestrated upregulation of inhibitor of apoptosis genes and downregulation of caspase genes. Meanwhile, diverse host immune recognition receptors were promoted during depressurization, probably enabling the regain of symbionts. When the holobionts were subjected to a prolonged acclimation at atmospheric pressure, alternations in both the DNA fragmentation and the expression atlas of aforesaid genes were continuously observed in symbionts, demonstrating the persistent influence of depressurization. Contrarily, the host cells demonstrated certain tolerance against depressurization stress as expression level of some immune-related genes returned to the basal level in isobaric samples. Altogether, the present study illustrates the distinct stress responses of Bathymodiolinae hosts and their methanotrophic symbionts against depressurization, which could provide further insight into the deep-sea adaptation of Bathymodiolinae holobionts while highlighting the necessity of using isobaric sampling methods in deep-sea research.

The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

Specialized adaptations allow vent-endemic crabs (Xenograpsus testudinatus) to thrive under extreme environmental hypercapnia

Shallow hydrothermal vent environments are typically very warm and acidic due to the mixing of ambient seawater with volcanic gasses (> 92% CO₂) released through the seafloor making them potential ‘natural laboratories’ to study long-term adaptations to extreme hypercapnic conditions. Xenograpsus testudinatus, the shallow hydrothermal vent crab, is the sole metazoan inhabitant endemic to vents surrounding Kueishantao Island, Taiwan, where it inhabits waters that are generally pH 6.50 with maximum acidities reported as pH 5.50. This study assessed the acid–base regulatory capacity and the compensatory response of X. testudinatus to investigate its remarkable physiological adaptations. Hemolymph parameters (pH, [HCO₃⁻], \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text{P}}_{{{\text{CO}}_{2} }}$$\end{document}PCO2, [NH₄⁺], and major ion compositions) and the whole animal’s rates of oxygen consumption and ammonia excretion were measured throughout a 14-day acclimation to pH 6.5 and 5.5. Data revealed that vent crabs are exceptionally strong acid–base regulators capable of maintaining homeostatic pH against extreme hypercapnia (pH 5.50, 24.6 kPa \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text{P}}_{{{\text{CO}}_{2} }}$$\end{document}PCO2) via HCO₃⁻/Cl⁻ exchange, retention and utilization of extracellular ammonia. Intact crabs as well as their isolated perfused gills maintained \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text{P}}_{{{\text{CO}}_{2} }}$$\end{document}PCO2tensions below environmental levels suggesting the gills can excrete CO₂ against a hemolymph-directed \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text{P}}_{{{\text{CO}}_{2} }}$$\end{document}PCO2 gradient. These specialized physiological mechanisms may be amongst the adaptations required by vent-endemic animals surviving in extreme conditions.

De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

Identification and characterization of endosymbiosis-related immune genes in deep-sea mussels Gigantidas platifrons

Deep-sea mussels of the subfamily Bathymodiolinae are common and numerically dominant species widely distributed in cold seeps and hydrothermal vents. During long-time evolution, deep-sea mussels have evolved to be well adapted to the local environment of cold seeps and hydrothermal vents by various ways, especially by establishing endosymbiosis with chemotrophic bacteria. However, biological processes underlying the establishment and maintenance of symbiosis between host mussels and symbionts are largely unclear. In the present study, Gigantidas platifrons genes possibly involved in the symbiosis with methane oxidation symbionts were identified and characterized by Lipopolysaccharide (LPS) pull-down and in situ hybridization. Five immune related proteins including Toll-like receptor 2 (TLR2), integrin, vacuolar sorting protein (VSP), matrix metalloproteinase 1 (MMP1), and leucine-rich repeat (LRR-1) were identified by LPS pull-down assay. These five proteins were all conserved in either molecular sequences or functional domains and known to be key molecules in host immune recognition, phagocytosis, and lysosome-mediated digestion. Furthermore, in situ hybridization of LRR-1, TLR2 and VSP genes was conducted to investigate their expression patterns in gill tissues of G. platifrons. Consequently, LRR-1, TLR2, and VSP genes were found expressed exclusively in the bacteriocytes of G. platifrons. Therefore, it was suggested that TLR2, integrin, VSP, MMP1, and LRR-1 might be crucial molecules in the symbiosis between G. platifrons and methane oxidation bacteria by participating in symbiosis-related immune processes.

Phylogeny, biogeography and systematics of Pacific vent, methane seep, and whale-fall Parougia (Dorvilleidae : Annelida), with eight new species

Dorvilleidae is a diverse group of annelids found in many marine environments and also commonly associated with chemosynthetic habitats. One dorvilleid genus, Parougia, currently has 11 described species, of which two are found at vents or seeps: Parougia wolfi and Parougia oregonensis. Eight new Parougia species are recognised and described in this study from collections in the Pacific Ocean, all from whale-falls, hydrothermal vents, or methane seeps at ~600-m depth or greater. The specimens were studied using morphology and phylogenetic analyses of DNA sequences from mitochondrial (cytochrome c oxidase subunit I, 16S rRNA, and cytochrome b) and nuclear (18S rRNA and histone 3) genes. Six sympatric Parougia spp. were found at Hydrate Ridge, Oregon, while three of the Parougia species occurred at different types of chemosynthetic habitats. Two new species were found over wide geographical and bathymetric ranges. Another dorvilleid genus, Ophryotrocha, has previously been highlighted as diversifying in the deep-sea environment. Our results document the hitherto unknown diversity of another dorvilleid genus, Parougia, at various chemosynthetic environments. http://zoobank.org/urn:lsid:zoobank.org:pub:EC7EBBEA-2FB5-43D6-BE53-1A468B541A5C

Divergence history and hydrothermal vent adaptation of decapod crustaceans: A mitogenomic perspective

Decapod crustaceans, such as alvinocaridid shrimps, bythograeid crabs and galatheid squat lobsters are important fauna in the hydrothermal vents and have well adapted to hydrothermal vent environments. In this study, eighteen mitochondrial genomes (mitogenomes) of hydrothermal vent decapods were used to explore the evolutionary history and their adaptation to the hydrothermal vent habitats. BI and ML algorithms produced consistent phylogeny for Decapoda. The phylogenetic relationship revealed more evolved positions for all the hydrothermal vent groups, indicating they migrated from non-vent environments, instead of the remnants of ancient hydrothermal vent species, which support the extinction/repopulation hypothesis. The divergence time estimation on the Alvinocarididae, Bythograeidae and Galatheoidea nodes are located at 75.20, 56.44 and 47.41–50.43 Ma, respectively, which refers to the Late Cretaceous origin of alvinocaridid shrimps and the Early Tertiary origin of bythograeid crabs and galatheid squat lobsters. These origin stories are thought to associate with the global deep-water anoxic/dysoxic events. Total eleven positively selected sites were detected in the mitochondrial OXPHOS genes of three lineages of hydrothermal vent decapods, suggesting a link between hydrothermal vent adaption and OXPHOS molecular biology in decapods. This study adds to the understanding of the link between mitogenome evolution and ecological adaptation to hydrothermal vent habitats in decapods.

Gene expression study in Bathymodiolus azoricus populations from three North Atlantic hydrothermal vent sites

The deep-sea hydrothermal vents are known as harsh environments, abundant in animal diversity surrounded by fluids with specific physiological and chemical composition. Bathymodiolus azoricus mussels are endemic species dwelling at hydrothermal vent sites and at distinct depth ranges. Mussels from Menez Gwen (MG), Lucky Strike (LS), Rainbow (Rb) were collected at 800 m, 1730 m and 2310 m depths respectively, along the Mid-Atlantic Ridge. Five different tissues including gill, digestive gland, mantle, adductor muscle and foot from MG, LS and Rb mussels were selected for gene expression analyses by qPCR. 30 genes were tested to investigate the level of immune and apoptotic gene expression among B. azoricus populations. Statistical analyses confirmed tissue-specific gene expression differences among the five tissues. The digestive gland tissue showed a higher transcriptional activity characterized by an up-regulation of gene activities, contrary to what was assessed in the adductor muscle tissue. Five categories included recognition, signaling, transcription, effector and apoptotic genes were analyzed in this study. The majority of genes differed in levels of expression between MG/LS and LS/Rb in the digestive gland. Our findings suggest that gene expression profiles are inherent to the tissue analyzed, thus implying an immune tissue-specificity controlling defense responses across B. azoricus mussel body as a whole.

An LRR-domain containing protein identified in Bathymodiolus platifrons serves as intracellular recognition receptor for the endosymbiotic methane-oxidation bacteria

As domain species in seep and vent ecosystem, Bathymodioline mussels has been regarded as a model organism in investigating deep sea chemosymbiosis. However, mechanisms underlying their symbiosis with chemosynthetic bacteria, especially how the host recognizes symbionts, have remained largely unsolved. In the present study, a modified pull-down assay was conducted using enriched symbiotic methane-oxidation bacteria as bait and gill proteins of Bathymodiolus platifrons as a target to isolate pattern recognition receptors involved in the immune recognition of symbionts. As a result, a total of 47 proteins including BpLRR-1 were identified from the pull-down assay. It was found that complete cDNA sequence of BpLRR-1 contained an open reading frame of 1479 bp and could encode a protein of 492 amino acid residues with no signal peptide or transmembrane region but eight LRR motif and two EFh motif. The binding patterns of BpLRR-1 against microbial associated molecular patterns were subsequently investigated by surface plasmon resonance analysis and LPS pull-down assay. Consequently, BpLRR-1 was found with high binding affinity with LPS and suggested as a key molecule in recognizing symbionts. Besides, transcripts of BpLRR-1 were found decreased significantly during symbiont depletion assay yet increased rigorously during symbionts or nonsymbiotic Vibrio alginolyticus challenge, further demonstrating its participation in the chemosynthetic symbiosis. Collectively, these results suggest that BpLRR-1 could serve as an intracellular recognition receptor for the endosymbionts, providing new hints for understanding the immune recognition in symbiosis of B. platifrons.

The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids

The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, “G(A)_nT” motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.

Resource partitioning among brachiopods and bivalves at ancient hydrocarbon seeps: A hypothesis

Brachiopods were thought to have dominated deep-sea hydrothermal vents and hydrocarbon seeps for most of the Paleozoic and Mesozoic, and were believed to have been outcompeted and replaced by chemosymbiotic bivalves during the Late Cretaceous. But recent findings of bivalve-rich seep deposits of Paleozoic and Mesozoic age have questioned this paradigm. By tabulating the generic diversity of the dominant brachiopod and bivalve clades–dimerelloid brachiopods and chemosymbiotic bivalves–from hydrocarbon seeps through the Phanerozoic, we show that their evolutionary trajectories are largely unrelated to one another, indicating that they have not been competing for the same resources. We hypothesize that the dimerelloid brachiopods generally preferred seeps with abundant hydrocarbons in the bottom waters above the seep, such as oil seeps or methane seeps with diffusive seepage, whereas seeps with strong, advective fluid flow and hence abundant hydrogen sulfide were less favorable for them. At methane seeps typified by diffusive seepage and oil seeps, oxidation of hydrocarbons in the bottom water by chemotrophic bacteria enhances the growth of bacterioplankton, on which the brachiopods could have filter fed. Whereas chemosymbiotic bivalves mostly relied on sulfide-oxidizing symbionts for nutrition, for the brachiopods aerobic bacterial oxidation of methane and other hydrocarbons played a more prominent role. The availability of geofuels (i.e. the reduced chemical compounds used in chemosynthesis such as hydrogen sulfide, methane, and other hydrocarbons) at seeps is mostly governed by fluid flow rates, geological setting, and marine sulfate concentrations. Thus rather than competition, we suggest that geofuel type and availability controlled the distribution of brachiopods and bivalves at hydrocarbon seeps through the Phanerozoic.