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PubMed2025

A deep-sea hydrothermal vent worm detoxifies arsenic and sulfur by intracellular biomineralization of orpiment (As2S3).

The alvinellid worm Paralvinella hessleri is the only animal that colonizes the hottest part of deep-sea hydrothermal vents in the west pacific. We found P. hessleri accumulates exceptionally high level of toxic element arsenic (>1% of wet weight) and tolerated elevated concentrations hydrogen sulphide. Using advanced microscopy, elementary analysis, and genomics and proteomics approaches, we identified a previously unrecognized arsenic-sulfide biomineralization process in P. hessleri. Our data suggest that arsenic accumulates within epithelial cell granules, where it likely reacts with sulphide diffused inward from the hydrothermal vent fluid, resulting in the intracellular formation of orpiment (As₂S₃) minerals. In this "fighting poison with poison" manner, the highly toxic arsenic and sulphide were simultaneously detoxified in the form of orpiment minerals within the intracellular granules of the single layer of epithelial cells. This process represents a remarkable adaptation to extreme chemical environments. Our study provides new insights into understanding animals' environment adaptation mechanisms and the diversity and plasticity of biomineralization.

Animals↗

PubMed2025

Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.

Animals↗

PubMed2026

Draft genome sequence of Archaeoglobaceae strain SR50 isolated from a shallow hydrothermal vent in the caldera of Saint-Paul Island, French Southern and Antarctic Lands.

We report the draft genome sequence of SR50, the first cultivated member of the genus JdFR-22 within the Archaeoglobaceae family, which currently includes three genera with cultivated representatives. Isolated from a shallow hydrothermal vent off Saint-Paul Island, a strictly protected area, SR50 is able to grow lithoautotrophically by sulfate reduction.

Archaeoglobaceae↗

PubMed2026

Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents.

This study presents medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) from microbial mats and sediments at Hatiba Mons, a Red Sea hydrothermal system. We recovered 1,217 bacterial and archaeal MAGs across 75 phyla, dominated by Planctomycetota and Thermoproteota. Approximately 70% of these genomes likely represent previously uncharacterized taxa.

extreme environment↗

PubMed2026

Phylum-wide propionate degradation and its potential connection to poly-gamma-glutamate biosynthesis in Candidatus Cloacimonadota phylum.

The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

Propionates↗

PubMed2026

Replicating lipid micelles: a feasible precursor to the origin of life and the earliest appearance of genomes.

The most commonly accepted scenario of early Earth includes: creation of the universe around 13.8 Ga (Giga-annus; or 109 years ago); establishment of our solar system ~ 4.60 Ga; and formation of Earth ~ 4.54 Ga. The earliest life forms on our planet so far observed to have existed, are microbes that left signals of their presence in rocks ~ 3.6 Ga - suggesting that Life forms existed within the first 940 million years after Earth's formation. However, an intriguing recent publication [1] infers that the last universal common ancestor (LUCA) likely existed by 4.2 Ga, and that the inferred LUCA had a genome of at least 2.5 Mb of DNA, encoding around 2,600 proteins; this suggests that sophisticated Life might have existed within the first 340 million years after Earth was formed. The commonly accepted geological history of early Earth suggests that the turbulent Hadean Eon lasted until 4.0 Ga, with the Late Heavy Bombardment (LHB) period occurring around 4.1 to 3.8 Ga. If Earth during the Hadean exhibited a molten surface, intense volcanic activity, and constant bombardment by asteroids and comets - how were sensitive molecules (e.g., nucleic acids, proteins) able to survive? Considering the "Lipid First" hypothesis [2], we propose that replicating lipid micelles are feasible candidates for having populated much of Earth's deep hydrothermal vents and turbulent surface within the first 340 million years of Earth's existence. These lipid micelles could therefore have provided a plausible form of "protective capsules" inside which early Life's sensitive molecules were able to evolve.

Origin of Life↗

PubMed2026

A prolonged hydrothermal past at Santorini Caldera revealed by sedimentary trace metal and microbial signatures.

Hydrothermal systems in volcanic calderas are critical in signalling volcanic unrest, forming ore deposits, and sustaining chemosynthetic microorganisms. Analysis of a ~3500-year sequence of sediments collected from the Santorini caldera, Greece, during International Ocean Discovery Program (IODP) Expedition 398 reveals the behaviour of a prolonged paleo-hydrothermal system. Sediment geochemical and metagenomic data record vigorous hydrothermal activity and metal fluxes for ~1100 years, within a 2270-year window between two major eruptions. Sediment hydrothermally-derived trace metals are significantly enriched over background (~200-fold for As and Hg, and 10-50-fold for Mn, Sb, Mo, and V), with long-term metal fluxes (9 t yr-1 As, 2.5 t yr-1 Cu, 7 kg yr-1 Ag) comparable to fluxes from present-day geothermal fields in the Taupo Volcanic Zone. Metagenomic analysis identifies elevated metal resistance genes-signals of microbial adaptation to heightened hydrothermal stressors. Here we integrate geological and genomic evidence to decipher the paleoenvironmental and biogeochemical history of the past hydrothermal system at Santorini caldera.

Geologic Sediments↗

PubMed2026

Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions.

The anaerobic oxidation of methane and C2+-alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free cultures of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.

Geologic Sediments↗