Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling

Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.

Microplastic Contamination of a Benthic Ecosystem in a Hydrothermal Vent

Plastic contamination is a global pervasive issue, extending from coastal areas and open oceans to polar regions and even the deep sea. Microplastic (MP) contamination in hydrothermal vents, which are known for their high biodiversity even under extreme conditions, has remained largely unexplored. Here, we present, for the first time, MP pollution in a deep-sea hydrothermal vent at one of the biodiversity hotspots─the Central Indian Ridge. Not only the environment (seawater: 2.08 ± 1.04 MPs/L, surface sediments: 0.57 ± 0.19 MP/g) but also all six major benthic species investigated were polluted by MPs. MPs mainly consisted of polypropylene, polyethylene terephthalate, and polystyrene fragments ≤100 μm and were characterized as being either transparent or white in color. Remarkably, bioaccumulation and even biomagnification of microplastics were observed in the top predators of the ecosystem, such as squat lobsters (14.25 ± 4.65 MPs/individual) and vent crabs (14.00 ± 2.16 MPs/individual), since they contained more MPs than animals at lower trophic levels (e.g., mussels and snails, 1.75-6.00 average MPs/individuals). These findings reveal MP contamination of an ecosystem in a hydrothermal vent, thereby suggesting that their accumulation and magnification can occur in top-level animals, even within remote and extreme environments.

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.

Heavy metal tolerance, and metal biosorption by exopolysaccharides produced by bacterial strains isolated from marine hydrothermal vents

The present study highlights heavy metal tolerance, EPS production, and biosorption capacity of four hydrothermal vent bacterial strains, namely Exiguobacterium aquaticum, Mammaliicoccus sciuri, Micrococcus luteus, and Jeotgalicoccus huakuii against As, Cd, Cr, Cu, Co, Pb and Ni. The biosorption assay showed high removal efficiency of As (83%) by E. aquaticum, Cd (95%) by M. sciuri, Cu (94%) by M. luteus, and Ni (89%) by J. huakuii and their produced EPS with these metals in aqueous solution were 84%, 85%, 98%, and 91%, respectively. The maximum EPS yield was attained by optimized medium composition consisting of 1% Xylose, and 1% NaCl at pH 7. In metal-amended conditions, the four bacterial strains showed induced EPS production in the initial concentrations. SEM with EDX and CLSM images showed that the growth and EPS production of bacterial strains were affected by metal ion concentrations. A phenol sulphuric acid method and BCA assay were used to identify both the carbohydrate and total protein content of four extracted EPS. A DPPH assay revealed that EPS influences free radical scavenging and has a highly enhanced synergistic effect with its antioxidant activity. FT-IR analysis of four extracted EPS showed the shifting of peaks in the functional groups of EPS before and after adsorption of metal ions. At pH 5 and after 60 min contact time metal removal efficiency and adsorption capacity increased as calculated for As, Cd, Cu, and Ni by four extracted EPS: (86%, 20 mg/g), (74%, 19 mg/g), (94%, 60 mg/g) and (89%, 32 mg/g) and (89%, 16 mg/g), (85%, 16 mg/g), (96%, 22 mg/g) and (91%, 16 mg/g), respectively. The Langmuir compared to the Freundlich model was found to better represent the adsorption by EPS providing maximum adsorption capacities for As (34.65 mg/g), Cd (52.88 mg/g), Cu (24.91 mg/g), and Ni (58.38 mg/g).

Distinct development trajectories and symbiosis modes in vent shrimps

Most animal species have a singular developmental pathway and adult ecology, but developmental plasticity is well-known in some such as honeybees where castes display profoundly different morphology and ecology. An intriguing case is the Atlantic deep-sea hydrothermal vent shrimp pair Rimicaris hybisae and R. chacei that share dominant COI haplotypes and could represent very recently diverging lineages or even morphs of the same species. Rimicaris hybisae is symbiont-reliant with a hypertrophied head chamber (in the Mid-Cayman Spreading Centre), while R. chacei is mixotrophic with a narrow head chamber (on the Mid-Atlantic Ridge). Here, we use X-ray micro-computed tomography and fluorescence in situ hybridization to show that key anatomical shifts in both occur during the juvenile-subadult transition, when R. hybisae has fully established symbiosis but not R. chacei. On the Mid-Atlantic Ridge, the diet of R. chacei has been hypothetically linked to competition with the obligatorily symbiotic congener R. exoculata, and we find anatomical evidence that R. exoculata is indeed better adapted for symbiosis. We speculate the possibility that the distinct development trajectories in R. hybisae and R. chacei may be determined by symbiont colonization at a "critical period" before subadulthood, though further genetic studies are warranted to test this hypothesis along with the true relationship between R. hybisae and R. chacei.

Characterization of an undocumented CO2 hydrothermal vent system in the Mediterranean Sea: Implications for ocean acidification forecasting

A previously undocumented shallow water hydrothermal field from Sicily (Southern Tyrrhenian Sea, Italy) is here described, based on a multidisciplinary investigation. The field, covering an area of nearly 8000 m2 and a depth from the surface to -5 m, was explored in June 2021 to characterise the main physico-chemical features of the water column, describe the bottom topography and features, and identify the main megabenthic and nektonic species. Twenty sites were investigated to characterise the carbonate system. Values of pH ranged between 7.84 and 8.04, ΩCa between 3.68 and 5.24 and ΩAr from 2.41 to 3.44. Geochemical analyses of hydrothermal gases revealed a dominance of CO2 (98.1%) together with small amounts of oxygen and reactive gases. Helium isotope ratios (R/Ra = 2.51) and δ13CCO2 suggest an inorganic origin of hydrothermal degassing of CO2 and the ascent of heat and deep-seated magmatic fluids to the surface. Visual census of fishes and megabenthos (mainly sessile organisms) allowed the identification of 64 species, four of which are protected by the SPA/BIO Protocol and two by the International Union for Conservation of Nature. The macroalgae Halopteris scoparia and Jania rubens and the sponge Sarcotragus sp. were the dominant taxa in the area, while among fishes Coris julis and Chromis chromis were the most abundant species. This preliminary investigation of San Giorgio vent field suggests that the site could be of interest and suitable for future experimental studies of ocean acidification.

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

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

Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.

Whole genome sequencing of a novel sea anemone (Actinostola sp.) from a deep-sea hydrothermal vent

Deep-sea hydrothermal vents are usually considered as extreme environments with high pressure, high temperature, scarce food, and chemical toxicity, while many local inhabitants have evolved special adaptive mechanisms for residence in this representative ecosystem. In this study, we constructed a high-quality genome assembly for a novel deep-sea anemone species (Actinostola sp.) that was resident at a depth of 2,971 m in an Edmond vent along the central Indian Ocean ridge, with a total size of 424.3 Mb and a scaffold N50 of 383 kb. The assembled genome contained 265 Mb of repetitive sequences and 20,812 protein-coding genes. Taken together, our reference genome provides a valuable genetic resource for exploring the evolution and adaptive clues of this deep-sea anemone.

Diversity, habitat endemicity and trophic ecology of the fauna of Loki's Castle vent field on the Arctic Mid-Ocean Ridge

Loki's Castle Vent Field (LCVF, 2300 m) was discovered in 2008 and represents the first black-smoker vent field discovered on the Arctic Mid-Ocean Ridge (AMOR). However, a comprehensive faunal inventory of the LCVF has not yet been published, hindering the inclusion of the Arctic in biogeographic analyses of vent fauna. There is an urgent need to understand the diversity, spatial distribution and ecosystem function of the biological communities along the AMOR, which will inform environmental impact assesments of future deep-sea mining activities in the region. Therefore, our aim with this paper is to provide a comprehensive inventory of the fauna at LCVF and present a first insight into the food web of the vent community. The fauna of LCVF has a high degree of novelty, with five new species previously described and another ten new species awaiting formal description. Most of the new species from LCVF are either hydrothermal vent specialists or have been reported from other chemosynthesis-based ecosystems. The highest taxon richness is found in the diffuse venting areas and may be promoted by the biogenic habitat generated by the foundation species Sclerolinum contortum. The isotopic signatures of the vent community of LCVF show a clear influence of chemosynthetic primary production on the foodweb. Considering the novel and specialised fauna documented in this paper, hydrothermal vents on the AMOR should be regarded as vulnerable marine ecosystems and protective measures must therefore be implemented, especially considering the potential threat from resource exploration and exploitation activities in the near future.

Deciphering the evolvement of microbial communities from hydrothermal vent sediments in a global change perspective

Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga, Desulfobacterota, Planctomycetota, Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions.

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.

Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents

Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from four geographically- and geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. The four vent fields include Axial Seamount at the Juan de Fuca Ridge, Sea Cliff and Apollo at the Gorda Ridge, all in the NE Pacific Ocean, and Piccard and Von Damm at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. At a semi-global scale, microbial eukaryotic communities at deep-sea vents were composed of similar proportions of dinoflagellates, ciliates, Rhizaria, and stramenopiles. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent-associated strains. These findings represent a census of deep-sea hydrothermal vent protistan communities. Protistan diversity, which is shaped by the hydrothermal vent environment at a local scale, ultimately influences the vent-associated microbial food web and the broader deep-sea carbon cycle.

Isolation and Characterization of a Serratia rubidaea from a Shallow Water Hydrothermal Vent

Microbial life present in the marine environment has to be able to adapt to rapidly changing and often extreme conditions. This makes these organisms a putative source of commercially interesting compounds since adaptation provides different biochemical routes from those found in their terrestrial counterparts. In this work, the goal was the identification of a marine bacterium isolated from a sample taken at a shallow water hydrothermal vent and of its red product. Genomic, lipidomic, and biochemical approaches were used simultaneously, and the bacterium was identified as Serratia rubidaea. A high-throughput screening strategy was used to assess the best physico-chemical conditions permitting both cell growth and production of the red product. The fatty acid composition of the microbial cells was studied to assess adaptation at the lipid level under stressful conditions, whilst several state-of-the-art techniques, such as DSC, FTIR, NMR, and Ultra-High Resolution Qq-Time-of-Flight mass spectrometry, were used to characterize the structure of the pigment. We hypothesize that the pigment, which could be produced by the cells up to 62 °C, is prodigiosin linked to an aliphatic compound that acts as an anchor to keep it close to the cells in the marine environment.

Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont

BACKGROUND

The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.

RESULTS

Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.

CONCLUSIONS

The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract.

Highly structured populations of deep-sea copepods associated with hydrothermal vents across the Southwest Pacific, despite contrasting life history traits

Hydrothermal vents are extreme environments, where abundant communities of copepods with contrasting life history traits co-exist along hydrothermal gradients. Here, we discuss how these traits may contribute to the observed differences in molecular diversity and population genetic structure. Samples were collected from vent locations across the globe including active ridges and back-arc basins and compared to existing deep-sea hydrothermal vent and shallow water data, covering a total of 22 vents and 3 non-vent sites. A total of 806 sequences of mtDNA from the Cox1 gene were used to reconstruct the phylogeny, haplotypic relationship and demography within vent endemic copepods (Dirivultidae, Stygiopontius spp.) and non-vent-endemic copepods (Ameiridae, Miraciidae and Laophontidae). A species complex within Stygiopontius lauensis was studied across five pacific back-arc basins at eight hydrothermal vent fields, with cryptic species being restricted to the basins they were sampled from. Copepod populations from the Lau, North Fiji and Woodlark basins are undergoing demographic expansion, possibly linked to an increase in hydrothermal activity in the last 10 kya. Highly structured populations of Amphiascus aff. varians 2 were also observed from the Lau to the Woodlark basins with populations also undergoing expansion. Less abundant harpacticoids exhibit little to no population structure and stable populations. This study suggests that similarities in genetic structure and demography may arise in vent-associated copepods despite having different life history traits. As structured meta-populations may be at risk of local extinction should major anthropogenic impacts, such as deep-sea mining, occur, we highlight the importance of incorporating a trait-based approach to investigate patterns of genetic connectivity and demography, particularly regarding area-based management tools and environmental management plans.

Pyrofollis japonicus gen. nov. sp. nov., a novel member of the family Pyrodictiaceae isolated from the Iheya North hydrothermal field

A novel hyperthermophilic, heterotrophic archaeon, strain YC29T, was isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough, Japan. Cells of strain YC29T were non-motile, irregular cocci with diameters of 1.2-3.0 µm. The strain was an obligatory fermentative anaerobe capable of growth on complex proteinaceous substrates. Growth was observed between 85 and 100 °C (optimum 90-95 °C), pH 4.9-6.4 (optimum 5.1), and in the presence of 1.4-4.0% (w/v) NaCl (optimum 3.0%). Inorganic carbon was required as a carbon source. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the family Pyrodictiaceae. The genome size was 2.02 Mbp with a G+C content of 49.4%. The maximum values for average nucleotide identity (ANI), average amino acid identity (AAI), and in silico DNA-DNA hybridization (dDDH) value of strain YC29T with relatives were 67.9% (with Pyrodictium abyssi strain AV2T), 61.1% (with Pyrodictium occultum strain PL-19T), and 33.8% (with Pyrolobus fumarii strain 1AT), respectively. Based on the phylogenetic, genomic, and phenotypic characteristics, we propose that strain YC29T represents a novel genus and species, Pyrofollis japonicus gen. nov., sp. (type strain YC29T = DSM 113394T = JCM 39171T).

Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent

Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C content and a circular plasmid comprising 38,843 nucleotides with 29.46% G + C content. In total, 3861 protein coding genes, 104 tRNA genes and 46 rRNA genes were obtained. SWIR-1 genome contains numerous genes related to sporulation and germination. Compared with the other three Tepidibacter species, SWIR-1 contained more spore germination receptor proteins. In addition, SWIR-1 contained more genes involved in chemotaxis and two-component systems than other Tepidibacter species. These results indicated that SWIR-1 has developed versatile adaptability to the Southwest Indian Ridge hydrothermal vent environment. The genome of strain SWIR-1 will be helpful for further understanding adaptive strategies used by bacteria dwelling in the deep-sea hydrothermal vent environments of different oceans.

Molecular Networking-Guided Isolation of Cyclopentapeptides from the Hydrothermal Vent Sediment Derived Fungus Aspergillus pseudoviridinutans TW58-5 and Their Anti-inflammatory Effects

Repetitive isolation of known compounds remains a major challenge in natural-product-based drug discovery. LC-MS/MS-based molecular networking has become a highly efficient strategy for the discovery of new natural products from complex mixtures. Herein, we report a molecular networking-guided isolation procedure, which resulted in the discovery of seven new cyclopentapeptides, namely, pseudoviridinutans A-F (1-7), from the marine-derived fungus Aspergillus pseudoviridinutans TW58-5. Compounds 1-7 feature a rare amino acid moiety, O,β-dimethyltyrosine, observed for the first time from a marine-derived fungus. The planar structures of 1-7 were elucidated by detailed analyses of IR, UV, HR ESI-Q-TOF MS, and 1D and 2D NMR spectroscopic data. Meanwhile, their absolute configurations were determined through a combination of Marfey's method and X-ray diffraction. Subsequent bioassay revealed the anti-inflammation potential of 1-7, especially 6, which inhibited the production of nitric oxide (NO), a vital inflammatory mediator, in LPS-induced murine macrophage RAW264.7 cells by regulating the expression level of NLRP3 and iNOS.

Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029

The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.

"One-can" strategy for the synthesis of hydrothermal biochar modified with phosphate groups and efficient removal of uranium(VI)

Significant selectivity, reasonable surface modification and increased structural porosity were three key factors to improve the competitiveness of biochar in the adsorption field. In this study, a hydrothermal bamboo-derived biochar modified with phosphate groups (HPBC) was synthesized using "one-can" strategy. BET showed that this method could effectively increase the specific surface area (137.32 m2 g-1) and simulation of wastewater experiments indicated HPBC had an excellent selectivity for U(VI) (70.35%), which was conducive to removal of U(VI) in real and complex environments. The accurate matchings of pseudo-second-order kinetic model, thermodynamic model and Langmuir isotherm showed that at 298 K, pH = 4.0, the adsorption process dominated by chemical complexation and monolayer adsorption was spontaneous, endothermic and disordered. Saturated adsorption capacity of HPBC could reach 781.02 mg g-1 within 2 h. The introduction of phosphoric acid and citric acid by "one-can" method not only provided abundant -PO4 to assist adsorption, but also activated oxygen-containing groups on the surface of the bamboo matrix. Results showed that adsorption mechanism of U(VI) by HPBC included electrostatic action and chemical complexation involving P-O, PO and ample oxygen-containing functional groups. Therefore, HPBC with high phosphorus content, outstanding adsorption performance, excellent regeneration, remarkable selectivity and green value provided a novel solution for the field of radioactive wastewater treatment.

Plausibility of the Formose Reaction in Alkaline Hydrothermal Vent Environments

Prebiotic processes required a reliable source of free energy and complex chemical mixtures that may have included sugars. The formose reaction is a potential source of those sugars. At moderate to elevated temperature and pH ranges, these sugars rapidly decay. Here it is shown that CaCO3-based chemical gardens catalyze the formose reaction to produce glucose, ribose, and other monosaccharides. These thin inorganic membranes are explored as analogs of hydrothermal vent materials-a possible place for the origin of life-and similarly exposed to very steep pH gradients. Supported by simulations of a simple reaction-diffusion model, this study shows that such gradients allow for the dynamic accumulation of sugars in specific layers of the thin membrane, effectively protecting formose sugar yields. Therefore, the formose reaction may be a plausible prebiotic reaction in alkaline hydrothermal vent environments, possibly setting the stage for an RNA world.

The lost vent gastropod species of Lothar A. Beck

Deep-sea hydrothermal vents host many endemic species adapted to these chemosynthesis-based ecosystems. The exploration of vent fields including those in the tropical Pacific is currently accelerating, due to the development of deep-sea mining for valuable minerals. Molecular evidence has shown that many vent endemic gastropod lineages include sibling species pairs in adjacent oceanic basins. While the fauna of the Manus Basin is relatively well described, many lineages in adjacent regions in North Fiji or Lau Basins are recognised as separate species, but unnamed. Valuable material from this fauna was studied by Lothar A. Beck in the 1990s, who fully drafted descriptions for these species, but did not publish them. Beck's manuscript names, prior to the present study, represented real species but nomina nuda without taxonomic validity. Here we present the descriptions of seven new species and one new genus, extracted from Beck's unpublished manuscript that was rediscovered after his death in 2020. The publication of these descriptions makes them taxonomically available and respects the scientific contributions of Beck. Providing valid descriptions of these species is critically important now to enable the recognition of species that may require conservation in the face of future environmental destruction. Symmetriapelta Beck, gen. nov. is described as new genus. Bathyacmaea nadinae Beck, sp. nov., Pyropelta ovalis Beck, sp. nov., Pseudorimula leisei Beck, sp. nov., Lepetodrilus fijiensis Beck, sp. nov., Shinkailepas conspira Beck, sp. nov., Symmetromphalus mcleani Beck, sp. nov. and Symmetriapelta wareni Beck, sp. nov. are introduced as new species.

Linking Methanogenesis in Low-Temperature Hydrothermal Vent Systems to Planetary Spectra: Methane Biosignatures on an Archean-Earth-like Exoplanet

In this work, the viability of the detection of methane produced by microbial activity in low-temperature hydrothermal vents on an Archean-Earth-like exoplanet in the habitable zone is explored via a simplified bottom-up approach using a toy model. By simulating methanogens at hydrothermal vent sites in the deep ocean, biological methane production for a range of substrate inflow rates was determined and compared to literature values. These production rates were then used, along with a range of ocean floor vent coverage fractions, to determine likely methane concentrations in the simplified atmosphere. At maximum production rates, a vent coverage of 4-15 × 10^-4 % (roughly 2000-6500 times that of modern Earth) is required to achieve 0.25% atmospheric methane. At minimum production rates, 100% vent coverage is not enough to produce 0.25% atmospheric methane. NASA's Planetary Spectrum Generator was then used to assess the detectability of methane features at various atmospheric concentrations. Even with future space-based observatory concepts (such as LUVOIR and HabEx), our results show the importance of both mirror size and distance to the observed planet. Planets with a substantial biomass of methanogens in hydrothermal vents can still lack a detectable, convincingly biological methane signature if they are beyond the scope of the chosen instrument. This work shows the value of coupling microbial ecological modeling with exoplanet science to better understand the constraints on biosignature gas production and its detectability.

Quantifying the Bioavailable Energy in an Ancient Hydrothermal Vent on Mars and a Modern Earth-Based Analog

Putative alkaline hydrothermal systems on Noachian Mars were potentially habitable environments for microorganisms. However, the types of reactions that could have fueled microbial life in such systems and the amount of energy available from them have not been quantitatively constrained. In this study, we use thermodynamic modeling to calculate which catabolic reactions could have supported ancient life in a saponite-precipitating hydrothermal vent system in the Eridania basin on Mars. To further evaluate what this could mean for microbial life, we evaluated the energy potential of an analog site in Iceland, the Strytan Hydrothermal Field. Results show that, of the 84 relevant redox reactions that were considered, the highest energy-yielding reactions in the Eridania hydrothermal system were dominated by methane formation. By contrast, Gibbs energy calculations carried out for Strytan indicate that the most energetically favorable reactions are CO₂ and O₂ reduction coupled to H₂ oxidation. In particular, our calculations indicate that an ancient hydrothermal system within the Eridania basin could have been a habitable environment for methanogens using NH₄⁺ as an electron acceptor. Differences in Gibbs energies between the two systems were largely determined by oxygen-its presence on Earth and absence on Mars. However, Strytan can serve as a useful analog for Eridania when studying methane-producing reactions that do not involve O₂.

Volcanic-associated ecosystems of the Mediterranean Sea: a systematic map and an interactive tool to support their conservation

Background

Hydrothermal vents, cold seeps, pockmarks and seamounts are widely distributed on the ocean floor. Over the last fifty years, the knowledge about these volcanic-associated marine ecosystems has notably increased, yet available information is still limited, scattered, and unsuitable to support decision-making processes for the conservation and management of the marine environment.

Methods

Here we searched the Scopus database and the platform Web of Science to collect the scientific information available for these ecosystems in the Mediterranean Sea. The collected literature and the bio-geographic and population variables extracted are provided into a systematic map as an online tool that includes an updated database searchable through a user-friendly R-shiny app.

Results

The 433 literature items with almost one thousand observations provided evidence of more than 100 different volcanic-associated marine ecosystem sites, mostly distributed in the shallow waters of the Mediterranean Sea. Less than 30% of these sites are currently included in protected or regulated areas. The updated database available in the R-shiny app is a tool that could guide the implementation of more effective protection measures for volcanic-associated marine ecosystems in the Mediterranean Sea within existing management instruments under the EU Habitats Directive. Moreover, the information provided in this study could aid policymakers in defining the priorities for the future protection measures needed to achieve the targets of the UN Agenda 2030.

The unaccounted dissolved iron (II) sink: Insights from dFe(II) concentrations in the deep Atlantic Ocean

Hydrothermal vent sites found along mid-ocean ridges are sources of numerous reduced chemical species and trace elements. To establish dissolved iron (II) (dFe(II)) variability along the Mid Atlantic Ridge (between 39.5°N and 26°N), dFe(II) concentrations were measured above six hydrothermal vent sites, as well as at stations with no active hydrothermal activity. The dFe(II) concentrations ranged from 0.00 to 0.12 nmol L^-1 (detection limit = 0.02 ± 0.02 nmol L^-1) in non-hydrothermally affected regions to values as high as 12.8 nmol L^-1 within hydrothermal plumes. Iron (II) in seawater is oxidised over a period of minutes to hours, which is on average two times faster than the time required to collect the sample from the deep ocean and its analysis in the onboard laboratory. A multiparametric equation was used to estimate the original dFe(II) concentration in the deep ocean. The in-situ temperature, pH, salinity and delay between sample collection and its analysis were considered. The results showed that dFe(II) plays a more significant role in the iron pool than previously accounted for, constituting a fraction >20 % of the dissolved iron pool, in contrast to <10 % of the iron pool formerly reported. This discrepancy is caused by Fe(II) loss during sampling when between 35 and 90 % of the dFe(II) gets oxidised. In-situ dFe(II) concentrations are therefore significantly higher than values reported in sedimentary and hydrothermal settings where Fe is added to the ocean in its reduced form. Consequently, the high dynamism of dFe(II) in hydrothermal environments masks the magnitude of dFe(II) sourced within the deep ocean.

Hydrothermal Regeneration of Ammonium as a Basin-Scale Driver of Primary Productivity

Hydrothermal vents are important targets in the search for life on other planets due to their potential to generate key catalytic surfaces and organic compounds for biogenesis. Less well studied, however, is the role of hydrothermal circulation in maintaining a biosphere beyond its origin. In this study, we explored this question with analyses of organic carbon, nitrogen abundances, and isotopic ratios from the Paleoproterozoic Zaonega Formation (2.0 Ga), NW Russia, which is composed of interbedded sedimentary and mafic igneous rocks. Previous studies have documented mobilization of hydrocarbons, likely associated with magmatic intrusions into unconsolidated sediments. The igneous bodies are extensively hydrothermally altered. Our data reveal strong nitrogen enrichments of up to 0.6 wt % in these altered igneous rocks, suggesting that the hydrothermal fluids carried ammonium concentrations in the millimolar range, which is consistent with some modern hydrothermal vents. Furthermore, large isotopic offsets of ∼10‰ between organic-bound and silicate-bound nitrogen are most parsimoniously explained by partial biological uptake of ammonium from the vent fluid. Our results, therefore, show that hydrothermal activity in ancient marine basins could provide a locally high flux of recycled nitrogen. Hydrothermal nutrient recycling may thus be an important mechanism for maintaining a large biosphere on anoxic worlds.

Comparison of polycyclic aromatic hydrocarbon accumulation in crab tissues with the ambient marine particles from shallow hydrothermal vents, northeast Taiwan

This study investigated and compared polycyclic aromatic hydrocarbons (PAHs) in crab (Xenograpsus testudinatus), suspended particulate matter, and surface sediment sampled from Kuei-shan-tao (KST) shallow water vents just offshore northeast Taiwan. The total concentrations of PAHs (t-PAHs) in suspended particles near the vents (533-685 ng g^-1 dw) were two orders of magnitude higher than the overlying sediment (3.42-6.06 ng g^-1 dw). The t-PAHs in sediment were significantly lower than those found in suspended particulate matter and all crab tissues tested, including hepatopancreas (192-1154 ng g^-1 dw), gill (221-748 ng g^-1 dw), muscle (30-174 ng g^-1 dw), and exoskeleton (22-96 ng g^-1 dw). Principal component analysis (PCA) indicated tissue-specific bioaccumulation of PAHs in crabs. The compositions of PAHs in gill, muscle, and exoskeleton were mainly low molecular weight, while the composition in the hepatopancreas included both high and low molecular weight PAHs. Highly variable but characteristic PAH congeners and concentrations in crab tissues and ambient aquatic particles reflect bioaccumulation.

Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents

The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.

Cytotoxic shornephines and asterresins from the hydrothermal vent associated fungus Aspergillus terreus CXX-158-20

A previously unreported alkaloid, bearing an undescribed 5/7/8 tricyclic heterocyclic skeleton, shornephine D, an undescribed diketomorpholine (DKM) shornephine B, two undescribed diketomorpholine derivatives shornephine C and seco-shornephine B methyl ester, an undescribed indole-isoquinoline alkaloid asterresin C, three undescribed indole alkaloids asterresins A-B and D, together with five known compounds, were isolated from the culture of hydrothermal vent associated fungus Aspergillus terreus CXX-158-20. Their structures were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, Mosher's method, 13C NMR calculation in combination with DP4+, and ECD calculations. Shornephine D and asterresin C represent two undescribed heterocyclic skeletons. Asterresin D and giluterrin exhibited cytotoxicity activities with IC50 values of 3.96 μM and 7.97 μM against A549 cell line. Asterresin D exhibited cytotoxicity activities with IC50 values of 12.36 μM and 12.48 μM against Namalwa and U266 cell lines. Asterresin A and giluterrin exhibited synergistic effect with adriamycin against MCF-7 cell line.

Combined effects of copper oxide and nickel oxide coated chitosan nanoparticles adsorbed to styrofoam resin beads on hydrothermal vent bacteria

Microplastics are potential carriers of harmful contaminants but their combined effects are largely unknown. It needs intensive monitoring in order to achieve a better understanding of metal-oxide nanoparticles and their dispersion via microplastics such as styrofoam in the aquatic environment. In the present study, an effort was made to provide a preferable perception about the toxic effects of engineered nanoparticles (NPs), namely, copper oxide (CuO NPs), nickel oxide (NiO NPs), copper oxide/chitosan (CuO/CS NPs) and nickel oxide/chitosan (NiO/CS NPs). Characterizations of synthesized NPs included their morphology (SEM and EDX), functional groups (FT-IR) and crystallinity (XRD). Their combined toxic effect after adsorption to styrofoam (SF) was monitored using the hydrothermal vent bacterium Jeotgalicoccus huakuii as a model. This was done by determining MIC (minimum inhibitory concentration) through a resazurin assay measuring ELISA, growth, biofilm inhibition and making a live and dead assay. Results revealed that at high concentrations (60 mg/10 mL) of CuO, CuO/CS NPs and 60 mg of SF adsorbed CuO and CuO/CS NPs inhibited the growth of J. huakuii. However, NPs rather than SF inhibited the growth of bacteria. The toxicity of NPs adsorbed on plain SF was found to be less compared to NPs alone. This study revealed new dimensions regarding the positive impacts of SF at low concentrations. Synthesized NPs applied separately were found to affect the growth of bacteria substantially more than if coated to SF resin beads.

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata

BACKGROUND

In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.

RESULTS

We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.

CONCLUSION

Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.

The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep-sea hydrothermal vents

The mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single-molecule real-time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element-rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion-, prophage-sequences and transposase-coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage-specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction-modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory-based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.

Biogeography and Population Divergence of Microeukaryotes Associated with Fluids and Chimneys in the Hydrothermal Vents of the Southwest Indian Ocean

Deep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, distinct biogeographical distribution patterns and impacting factors were revealed from samples in the three hydrothermal fields of the southwest Indian Ocean, where higher gene abundance of microeukaryotes appeared in chimneys. The microeukaryotes in the fluids might be explained by hydrogeochemical heterogeneity, especially that of the nitrate and silicate concentrations, while the microeukaryotes in the chimneys coated with either Fe oxides or Fe-Si oxyhydroxides might be explained by potentially different associated prokaryotic groups. Population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fluids and chimneys and deserves further exploration to gain a deeper understanding of the trophic relationships and potential ecological function of microeukaryotes in the deep-sea extreme ecosystems, especially in the complex deep-sea chemoautotrophic habitats. IMPORTANCE Deep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fields. This might be attributed to the hydrogeochemical heterogeneity of fluids and to the potentially different associated prokaryotic groups in chimneys.

Contrasted phylogeographic patterns of hydrothermal vent gastropods along South West Pacific: Woodlark Basin, a possible contact zone and/or stepping-stone

Understanding drivers of biodiversity patterns is essential to evaluate the potential impact of deep-sea mining on ecosystems resilience. While the South West Pacific forms an independent biogeographic province for hydrothermal vent fauna, different degrees of connectivity among basins were previously reported for a variety of species depending on their ability to disperse. In this study, we compared phylogeographic patterns of several vent gastropods across South West Pacific back-arc basins and the newly-discovered La Scala site on the Woodlark Ridge by analysing their genetic divergence using a barcoding approach. We focused on six genera of vent gastropods widely distributed in the region: Lepetodrilus, Symmetromphalus, Lamellomphalus, Shinkailepas, Desbruyeresia and Provanna. A wide-range sampling was conducted at different vent fields across the Futuna Volcanic Arc, the Manus, Woodlark, North Fiji, and Lau Basins, during the CHUBACARC cruise in 2019. The Cox1-based genetic structure of geographic populations was examined for each taxon to delineate putative cryptic species and assess potential barriers or contact zones between basins. Results showed contrasted phylogeographic patterns among species, even between closely related species. While some species are widely distributed across basins (i.e. Shinkailepas tollmanni, Desbruyeresia melanioides and Lamellomphalus) without evidence of strong barriers to gene flow, others are restricted to one (i.e. Shinkailepas tufari complex of cryptic species, Desbruyeresia cancellata and D. costata). Other species showed intermediate patterns of isolation with different lineages separating the Manus Basin from the Lau/North Fiji Basins (i.e. Lepetodrilus schrolli, Provanna and Symmetromphalus spp.). Individuals from the Woodlark Basin were either endemic to this area (though possibly representing intermediate OTUs between the Manus Basin and the other eastern basins populations) or, coming into contact from these basins, highlighting the stepping-stone role of the Woodlark Basin in the dispersal of the South West Pacific vent fauna. Results are discussed according to the dispersal ability of species and the geological history of the South West Pacific.

Sulfur isotopes of hydrothermal vent fossils and insights into microbial sulfur cycling within a lower Paleozoic (Ordovician-early Silurian) vent community

Symbioses between metazoans and microbes involved in sulfur cycling are integral to the ability of animals to thrive within deep-sea hydrothermal vent environments; the development of such interactions is regarded as a key adaptation in enabling animals to successfully colonize vents. Microbes often colonize the surfaces of vent animals and, remarkably, these associations can also be observed intricately preserved by pyrite in the fossil record of vent environments, stretching back to the lower Paleozoic (Ordovician-early Silurian). In non-vent environments, sulfur isotopes are often employed to investigate the metabolic strategies of both modern and fossil organisms, as certain metabolic pathways of microbes, notably sulfate reduction, can produce large sulfur isotope fractionations. However, the sulfur isotopes of vent fossils, both ancient and recently mineralized, have seldom been explored, and it is not known if the pyrite-preserved vent organisms might also preserve potential signatures of their metabolisms. Here, we use high-resolution secondary ion mass spectrometry (SIMS) to investigate the sulfur isotopes of pyrites from recently mineralized and Ordovician-early Silurian tubeworm fossils with associated microbial fossils. Our results demonstrate that pyrites containing microbial fossils consistently have significantly more negative δ³⁴ S values compared with nearby non-fossiliferous pyrites, and thus represent the first indication that the presence of microbial sulfur-cycling communities active at the time of pyrite formation influenced the sulfur isotope signatures of pyrite at hydrothermal vents. The observed depletions in δ³⁴ S are generally small in magnitude and are perhaps best explained by sulfur isotope fractionation through a combination of sulfur-cycling processes carried out by vent microbes. These results highlight the potential for using sulfur isotopes to explore biological functional relationships within fossil vent communities, and to enhance understanding of how microbial and animal life has co-evolved to colonize vents throughout geological time.

Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands

For extending the current collection of axenic cultures of planctomycetes, we describe in this study the isolation and characterisation of strain Pan265^T obtained from a red biofilm in the hydrothermal vent system close to the Lipari Islands in the Tyrrhenian Sea, north of Sicily, Italy. The strain forms light pink colonies on solid medium and grows as a viscous colloid in liquid culture, likely as the result of formation of a dense extracellular matrix observed during electron microscopy. Cells of the novel isolate are spherical, motile and divide by binary fission. Strain Pan265^T is mesophilic (temperature optimum 30-33 °C), neutrophilic (pH optimum 7.0-8.0), aerobic and heterotrophic. The strain has a genome size of 3.49 Mb and a DNA G + C content of 63.9%. Phylogenetically, the strain belongs to the family Phycisphaeraceae, order Phycisphaerales, class Phycisphaerae. Our polyphasic analysis supports the delineation of strain Pan265^T from the known genera in this family. Therefore, we conclude to assign strain Pan265^T to a novel species within a novel genus, for which we propose the name Mucisphaera calidilacus gen. nov., sp. nov. The novel species is the type species of the novel genus and is represented by strain Pan265^T (= DSM 100697^T = CECT 30425^T) as type strain.

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.

The Physiology and Biogeochemistry of SUP05

The SUP05 clade of gammaproteobacteria (Thioglobaceae) comprises both primary producers and primary consumers of organic carbon in the oceans. Host-associated autotrophs are a principal source of carbon and other nutrients for deep-sea eukaryotes at hydrothermal vents, and their free-living relatives are a primary source of organic matter in seawater at vents and in marine oxygen minimum zones. Similar to other abundant marine heterotrophs, such as SAR11 and Roseobacter, heterotrophic Thioglobaceae use the dilute pool of osmolytes produced by phytoplankton for growth, including methylated amines and sulfonates. Heterotrophic members are common throughout the ocean, and autotrophic members are abundant at hydrothermal vents and in anoxic waters; combined, they can account for more than 50% of the total bacterial community. Studies of both cultured and uncultured representatives from this diverse family are providing novel insights into the shifting biogeochemical roles of autotrophic and heterotrophic bacteria that cross oxic-anoxic boundary layers in the ocean.

Arsenic and sulfur nanoparticle synthesis mimicking environmental conditions of submarine shallow-water hydrothermal vents

Arsenic and sulfur mineralization is a natural phenomenon occurring in hydrothermal systems where parameters like temperature and organic matter (OM) can influence the mobilization of the toxic metalloid in marine environments. In the present study we analyze the influence of temperature and OM (particularly sulfur-containing additives) on As and S precipitation based on the recent discovery of As-rich nanoparticles in the hydrothermal system near the coast of the Greek island Milos. To this end, we experimentally recreate the formation of amorphous colloidal particles rich in As and S via acidification (pH 3-4) of aqueous precursors at various temperatures. At higher temperatures, we observe the formation of monodisperse particles within the first 24 h of the experiment, generating colloidal particles with diameters close to 160 nm. The S:As ratio and particle size of the synthetized particles closely correlates with values for As_xS_y particles detected in the hydrothermal system off Milos. Furthermore, organic sulfur containing additives (cysteine and glutathione, GSH) are a key factor in the process of nucleation and growth of amorphous colloidal As_xS_y particles and, together with the temperature gradient present in shallow hydrothermal vents, dictate the stabilization of As-bearing nanomaterials in the environment. Based on these findings, we present a simple model that summarizes our new insights into the formation and mobility of colloidal As in aquatic ecosystems. In this context, amorphous As_xS_y particles can present harmful effects to micro- and macro-biota not foreseen in bulk As material.

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.

microRNAs facilitate comprehensive responses of Bathymodiolinae mussel against symbiotic and nonsymbiotic bacteria stimulation

Bathymodiolinae mussels are dominant species in cold seeps and hydrothermal vents and could harbor endosymbionts in gill bacteriocytes. However, mechanisms underlying the symbiosis have remained largely undisclosed for years. In the present study, the global expression pattern of immune-related genes and miRNAs were surveyed in Gigantidas platifrons during bacterial challenges using enriched symbiotic methane oxidation bacteria MOBs or nonsymbiotic Vibrio. As a result, multiple pattern recognition receptors were found differentially expressed at 12 h and 24 h post bacteria challenges and distinctly clustered between stimulations. Dozens of immune effectors along with signal transducers were also modulated simultaneously during MOB or Vibrio challenge. A total of 459 miRNAs were identified in the gill while some were differentially expressed post MOB or nonsymbiotic bacteria challenge. A variety of immune-related genes were annotated as target genes of aforesaid differentially expressed miRNAs. As a result, biological processes including the immune recognition, lysosome activity and bacteria engulfment were suggested to be dynamically modulated by miRNAs in either symbiotic or nonsymbiotic bacteria challenge. It was suggested that G. platifrons mussels could maintain a robust immune response against invading pathogens while establishing symbiosis with chemosynthetic bacteria with the orchestra of immune-related genes and miRNAs.

Characterization of tissue-associated bacterial community of two Bathymodiolus species from the adjacent cold seep and hydrothermal vent environments

Deep-sea mussels are widely distributed in marine chemosynthetic ecosystems. Bathymodiolus platifrons and B. japonicus, occurring at both cold seeps and hydrothermal vents, have been reported to house exclusively methanotrophic symbionts in the gill. However, the comparison of microbiota associated with different tissues between these two species from two contrasting habitats is still limited. In this study, using B. platifrons and B. japonicus collected from the adjacent cold seep and hydrothermal vent environments, we sampled different tissues (gill, adductor muscle, mantle, foot, and visceral mass including the gut) to decipher the microbial community structure at the tissue scale by employing 16S rRNA gene sequencing strategy. In the gill of both seep mussels and vent mussels, the symbiont gammaproteobacterial Methylomonaceae was the predominant lineage, and methane oxidation was identified as one of the most abundant putative function. In comparison, abundant families in other tissues were Pseudomonadaceae and Enterobacteriaceae in seep mussels and vent mussels, respectively, which may get involved in element cycling. The results revealed high similarity of community structure between two mussel species from the same habitat. The gill showed distinctive bacterial community structure compared with other tissues within the same environment, while the gill communities from two environments were more similar. Remarkably structural variations of adductor muscle, mantle, foot, and visceral mass were observed between two environments. This study can extend the understanding on the characteristics of tissue-associated microbiota of deep-sea mussels from the adjacent cold seep and hydrothermal vent environments.

Biodiversity and oil degradation capacity of oil-degrading bacteria isolated from deep-sea hydrothermal sediments of the South Mid-Atlantic Ridge

Studies have reported that various hydrocarbons and hydrocarbon-degrading bacteria are found in global deep-sea hydrothermal regions. However, little is known about degradation characteristics of culturable hydrocarbon-degrading bacteria from these regions. We speculate that these bacteria can be used as resources for the bioremediation of oil pollution. In this study, six oil-degrading consortia were obtained from the hydrothermal region of the Southern Mid-Atlantic Ridge through room-temperature enrichment experiments. The dominant oil-degrading bacteria belonged to Nitratireductor, Pseudonocardia, Brevundimonas and Acinetobacter. More varieties of hydrocarbon-degrading bacteria were obtained from sediments (preserved at 4 °C) near hydrothermal vents. Most strains had the ability to degrade high molecular weight petroleum components. In addition, Pseudonocardia was shown to exhibit a high degradation ability for phytane and pristine for the first time. This study may provide new insights into the community structure and biodiversity of culturable oil-degrading bacteria in deep-sea hydrothermal regions.

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.

Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities

AbstractMicrobial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (~30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be ~7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates.