The scaly-foot snail (Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents. Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred ∼66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U α chain-like (H2-Aal) genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes. Our study provides new insights into deep-sea snail genomes and valuable resources for further studies.

At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 10⁵ cells/ml to 10⁷ cells/ml;carbon dioxide fixation capacity with the δ13C_VPDB in the biomass increased from −27.42‰ to 3460.06‰; the thiosulfate-oxidizing ability with produced SO₄²⁻ increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.

Introduction: Hydrothermal vents, rich in heavy metals, provided a unique niche for heavy metal resistant microbes. However, knowledge about copper resistant microbes in deep sea hydrothermal vents is still limited.Methods: The copper-resistant bacteria were isolated from deep-sea hydrothermal vent samples and conducted thorough physical, phylogenetic, and genomic analyses to elucidate their copper resistance capability and related genes.Results: Twelve highly copper-resistant bacteria (up to 6-10 mM) were isolated from deep sea hydrothermal fields They were affiliated with the Pseudoalteromonas (4), Marinobacter (3), Halomonas (2), Psychrobacter (1), and Pseudomonas (1) genus in the α-Proteobacteria, and the Sphingomonas (1) genus in the β-Proteobacteria. The presence of copper in the medium obviously induced the amount of polysaccharides and proteins in the crude extracellular polymeric substances (EPS) produced by Halomonas sp. CuT 3-1, Pseudoalteromonas sp. CuT 4-3 and Marinobacter metalliresistant CuT 6, which could absorb 40 to 50 mg•g⁻¹ copper. We further described a novel species, Marinobacter metalliresistant sp. nov. CuT 6^T, which exhibited a higher copper resistance and encoded more heavy metal resistance-related genes than other Marinobacter species.Discussion: It revealed that the copper resistance capability exhibited by these strains in hydrothermal fields is likely attributed to the production of exopolymeric substances, such as polysaccharides and proteins, as well as active transport or efflux mechanisms for heavy metals.

An anaerobic, Gram-positive, rod-shaped, motile and spore-forming bacterium, designated strain ZCY20-5^T, was isolated from pit clay of Chinese strong-aroma type Baijiu (Chinese liquor). Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain ZCY20-5^T belonged to the genus Caproicibacterium , family Oscillospiracheae, but it showed low similarity to the type species Caproicibacterium amylolyticum LBM18003^T (98.00 %) and Caproicibacterium lactatifermentans LBM19010^T (95.67 %). In anaerobic yeast extract medium, growth was observed at 20–45 °C (optimum, 35–40 °C), at pH 4.0–9.0 (optimum, pH 6.5–7.0) and with 0.0–2.0 % NaCl (w/v). The predominant fatty acids were C_16 : 0, C_14 : 0, C₁₃ 3-OH and C₁₆ 3-OH, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three phospholipids of unknown structure containing glucosamine and two unidentified phospholipids. Strain ZCY20-5^T exhibited an 81.32 % pairwise average nucleotide identity value, a 78.98 % average amino acid identity value and a 22.30 % digital DNA–DNA hybridization value compared to its closest relative C. amylolyticum LBM18003^T. Based on morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, strain ZCY20-5^T represents a novel species of Caproicibacterium , and the type strain is ZCY20-5^T (=MCCC 1A19399^T=KCTC 25590^T).

The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341^T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341^T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341^T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.

A thermophilic, anaerobic, iron-reducing bacterium strain JL129W03T (=KCTC 15905T=MCCC 1A14213T) was isolated from a sulfide sample collected from the Daxi hydrothermal field (60.5° E, 6.4° N, 2919 m depth) on the Carlsberg Ridge, northwest Indian Ocean. Cells grew at 55–75 °C(optimum, 70 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and at NaCl concentrations of 1.5–4.5 % (w/v; optimum 3.0 %). Under optimal growth conditions, the generation time was around 85 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, carbohydrates, organic acids and one amino acid. It was anaerobic and facultatively dependent on elemental sulphur and various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulphate, thiosulfate or nitrate. The G+C content of its genomic DNA was 34.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that its closest relative was Thermosipho atlanticus DV1140T with 95.81 % 16S rRNA sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Thermosipho , for which the name Thermosipho ferrireducens sp. nov. is proposed. The type strain is strain JL129W03T (=KCTC 15905T;=MCCC 1A14213T).