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Marine sediments contain Earth's largest reservoir of methane, with most of this methane being produced and consumed in situ by methane-cycling archaea. While numerous studies have investigated communities of methane-cycling archaea in hydrocarbon seeps and sulfate–methane transition zones, less is known about how these archaea change from the seafloor downward throughout diffusion-dominated marine sediments. Focusing on four continental margin sites of the North Sea-Baltic Sea transition, we here investigate the in situ drivers of methane-cycling archaeal community structure and metabolism based on geochemical and stable carbon-isotopic gradients, functional gene (mcr A) copy numbers and phylogenetic compositions, and thermodynamic calculations. We observe major changes in community structure that largely follow vertical gradients in sulfate concentrations and lateral gradients in organic carbon reactivity and content. While methane-cycling archaeal communities in bioturbated and sulfatic zones are dominated by known methyl-disproportionating Methanosarcinaceae and putatively CO2-reducing Methanomicrobiaceae , the communities change toward dominance of methane-oxidizing taxa (ANME-2a-b, ANME-2c, ANME-1a-b) in sulfate–methane transition zones (SMTZs). By contrast, the underlying methanogenesis zones are dominated by the physiologically uncharacterized ANME-1d, new genus-level groups of putatively CO2-reducing Methanomicrobiaceae , and methyl-reducing Methanomassiliicoccales. Notably, mcr A copy numbers of several major taxa increase by 2 to 4 orders of magnitude from the sulfatic zone into the SMTZ or methanic zone, providing evidence of net population growth in subsurface sediment. We propose that burial-related geochemical changes cause methane-cycling archaea in continental margin sediments to go through three successional stages (sulfatic, SMTZ, methanic). Herein, the onset of each new successional stage is characterized by a period of growth- and mortality-driven turnover in the dominant taxa. [ABSTRACT FROM AUTHOR]

The isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) derived from archaea are widely used in the reconstruction of past climate and environment through proxies such as the Methane Index (MI) and TEX 86. A pre-requisite for the application of TEX 86 , which serves as a proxy for upper ocean temperature, is that the sedimentary GDGTs primarily originate from planktonic Marine Group I Thaumarchaeota. The MI is commonly used as a quality control measure for TEX 86 reconstruction to identify samples affected by methanotrophic GDGTs. Recently, the MI has also been used for the reconstruction of past methane cycling. However, the spatial variability of GDGT-based proxies and the relationship between MI and TEX 86 remain unclear. In this study, we generated a comprehensive suite of data, including gas, porewater, bulk sediment geochemistry, archaeal cell abundance, GDGTs and their derived proxies. We collected sediment cores from four study sites offshore Southwest Taiwan characterized by the absence or presence of anaerobic oxidation of methane (AOM) and differences in the depth of the sulfate-methane transition zone (SMTZ). The distance between the coring sites varied from ∼20 cm to ∼2 km. The geochemical and DNA data indicated the presence of SMTZs at depths ranging from 4 cm to 290 cm in sediments. AOM-related GDGTs were predominantly composed of GDGT-2, followed by GDGT-1, GDGT-0 and GDGT-3. Although MI values in the SMTZ could reach as high as 0.7, they did not strictly vary based on the SMTZ depth nor the methane consumption rate. This, coupled with the discrepancies in the downcore profiles of gas and porewater geochemistry compared to archaeal DNA and GDGTs, suggest that the duration of SMTZ presence could be a key factor influencing sedimentary MI values. We observed strong relationships between TEX 86 and MI at AOM sites; however, the direction of these relationships varied across different locations. Despite this, TEX 86 -derived temperatures showed good agreement between sites (<1.5 °C between sites located ∼2 km apart), and with climatology data. Consequently, our findings suggest that even in samples with high MI values above the threshold of 0.3, the bias on TEX 86 -derived temperatures may not be as significant as generally assumed. [ABSTRACT FROM AUTHOR]

Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms—denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria—remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, 15N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96–7.63 Tg N yr-1 (1.65–2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle. Little is known about nitrogen loss processes in deep-sea cold seeps. Here, the authors report that cold seeps are potential hotspots of nitrogen loss, revealing high rates and a diverse range of nitrogen loss genes across multiple microbial phyla. [ABSTRACT FROM AUTHOR]

Yeti crabs (Kiwaidae) are deep-sea hydrothermal vent and methane seep dwelling crustaceans that farm chemosynthetic microbes on their bodies. Sexual dimorphism is a common feature of decapod crustaceans, but little is known about its prevalence in species from deep-sea habitats. We address this knowledge deficit by investigating claw sexual dimorphism and symmetry in the hydrothermal-vent endemic 'Hoff crab', Kiwa tyleri. A total of 135 specimens from the East Scotia Ridge were examined, revealing mean asymmetry indices close to zero with respect to propodus length and height, albeit with a significantly larger number of marginally left-dominant individuals with respect to propodus length, possibly indicative of some task specialisation between claws, or a vestigial ancestral trait. Both male and female claws exhibit positive allometry with increasing carapace length, but males possess significantly larger claws compared with females when accounting for carapace size, exhibiting faster growing propodus length, and broader propodus heights throughout the size distribution. This marked difference is indicative of either male-male competition for mate access, sexual selection, or differential energy allocation (growth vs reproduction) between males and females, as observed in other decapod crustaceans. In contrast, a reanalysis of data for the methane seep inhabiting yeti crab Kiwa puravida revealed no significant difference in claw allometry, indicating a possible lack of similar sexual selection pressures, and highlighting potential key differences in the ecological and reproductive strategies of K. tyleri and K. puravida relating to claw function, microbial productivity and population density. Whether sex differences in claw allometry represents the norm or the exception in Kiwaidae will require the examination of other species in the family. This research enhances our understanding of the behaviour, ecology and evolution of yeti crabs, providing a basis for future studies. [ABSTRACT FROM AUTHOR]

Hesionid polychaetes are well known at hydrothermal vents, methane seeps, and unusual habitats such as whale falls. In 1985, Sirsoe grasslei was the first hesionid to be named from a hydrothermal vent. Vrijenhoekia was erected in 2008 for a closely related species from a whale fall. Further species of Sirsoe and Vrijenhoekia were described in the following decade and the genera were recovered as reciprocally monophyletic with DNA data. However, Sirsoe was made a senior synonym of Vrijenhoekia when 10 further new species from the clade were named from off the coast of Brazil. To further evaluate the status of Sirsoe and Vrijenhoekia, we present the first DNA data for the type species of Sirsoe, S. grasslei. Our results allow the reinstatement of Vrijenhoekia and emended diagnoses for Sirsoe and Vrijenhoekia. Four new species, three in Sirsoe and one in Vrijenhoekia, are also described. [ABSTRACT FROM AUTHOR]

Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems. [ABSTRACT FROM AUTHOR]

Cold seeps are areas characterised by specialized biological communities that rely on chemosynthesis for their nutrition. To date, research conducted on New Zealand's Hikurangi Margin seep communities has focused on communities at 650-1200 m water depth. Here, we characterize the macrofaunal nematode communities of New Zealand cold seeps for the first time, and at deeper (> 1200 m) seep locations (Maungaroa, Glendhu and Urutī South). There were no significant difference in nematode abundance, species richness, diversity and evenness among the seep areas, which may reflect the lack of difference in most sediment variables. However, a consistent spatial pattern in nematode abundance was observed within all the seep areas on the Hikurangi Margin: abundance was highest at or near the seep centre, decreased steeply away from the centre and was low in the periphery. These spatially consistent patterns reflect the influence of methane seepage, which appears limited to the inner 150-200 m radius of each area, on nematode abundance via input of chemosynthetic food sources. We found significant differences in nematode community structure among all three areas, with most of the heterogeneity in community structure between the shallow Urutī South area and deeper Maungaroa and Glendhu areas, and differences among nematode communities of high, medium and low abundance associated with site-specific gradients in methane seepage. Within area variability in nematode community structure was mainly correlated with food availability and sediment grain size. Consistent with previous investigations of seep nematodes, we did not find evidence of seep endemics. Although deposit feeders were generally the most abundant feeding group, there were differences in the relative abundances of different feeding groups such as microvores and epigrowth feeders among the seep areas, and as a function of distance from the centre of the seep areas. Impact on seep communities from gas hydrate extraction processes may occur via reduction or potentially cessation of free-gas methane supply to the seafloor, 'sand' production at the seafloor due to the physical degradation of the substrate structure, or alteration of the structural integrity of the seafloor substrate. Any spatial management options considered for managing these impacts should reflect the differences in benthic community structure between depths and locations on the Hikurangi Margin. [ABSTRACT FROM AUTHOR]

Borealis is a recently discovered submerged mud volcano in the Polar North Atlantic, differing from the numerous methane seepages previously identified in the region. Here we show in situ observations from a remotely operated vehicle (ROV), capturing the release of warm (11.5 °C) Neogene sediments and methane-rich fluids from a gryphon at Borealis. The surrounding seafloor within the mud volcano features extensive carbonate deposits, indicating prolonged diffuse methane migration. Sampling and imagery reveal that Borealis supports unique habitats adapted to low-oxygen conditions near methane seeps. Additionally, the irregularly shaped carbonate structures serve as a natural shelter from bottom trawling and a substratum for sessile fauna and may function as nursery grounds for threatened fish species. This discovery underscores the ecological significance of cold seep ecosystems in the Polar North Atlantic, highlighting their role in biodiversity by serving as refuges for marine species and emphasizing the need for their conservation. Borealis, a newly discovered mud volcano in the Polar North Atlantic, expels warm Neogene sediments and methane fluids. It hosts unique habitats, with carbonate structures offering refuge and nursery grounds for marine life, highlighting conservation importance. [ABSTRACT FROM AUTHOR]

Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments. In situ exposure of shallow-water mussels to deep-sea conditions induced changes in their transcriptome and microbiome, with profiles gradually aligning with those of native deep-sea mussels, highlighting the conserved interplay between evolutionary adaptations and rapid adjustments. [ABSTRACT FROM AUTHOR]

Marine hydrocarbon seeps typically harbor a relatively predictable microbiome, including anaerobic methanotrophic (ANME) archaea. Here, we sampled two cold seeps in Monterey Bay, CA – Clam Field and Extrovert Cliff – which have been known for decades but never characterized microbiologically. Many aspects of these seeps were typical of seeps worldwide, including elevated methane and sulfide concentrations, 13C-depleted dissolved inorganic carbon, and the presence of characteristic macrofauna. However, we observed atypical microbial communities: extremely few ANME sequences were detected in either 16S rRNA or mcrA gene surveys at Clam Field (< 0.1 % of total community reads), even after 6 months of incubation with methane in the laboratory, and only slightly more ANME sequences were recovered from Extrovert Cliff (< 0.3 % of total community reads). At Clam Field, a lack of ANME mcrA transcription, a lack of methane-dependent sulfate reduction, and a linear porewater methane profile were consistent with low or absent methanotrophy. Although the reason for the scarcity of ANME archaea is still unclear, we postulate that non-methane hydrocarbon release excludes anaerobic methanotrophs directly or indirectly (e.g., through competitive interactions with hydrocarbon-degrading bacteria). Our findings highlight the potential for hydrocarbon seeps without this critical biofilter and therefore greater methane emissions from sediments. [ABSTRACT FROM AUTHOR]

The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300–3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also reported for species known from Mexico, the Galápagos seamounts, Chile, and the western Pacific; as well as 16 new depth records and three new seep records for species known to occur at vents or organic falls. No single evolutionary narrative explains the patterns of biodiversity at these seeps, as even morphologically indistinguishable species can show different biogeographic affinities, biogeographic ranges, or depth ranges. The value of careful molecular taxonomy and comprehensive specimen-based regional inventories is emphasized for biodiversity research and monitoring. [ABSTRACT FROM AUTHOR]

Glauconite is an authigenic green mineral which has been studied extensively because its conditions of formation make it possible to evaluate certain parameters of the sedimentary environments where it is found. The most widespread view is that glauconite forms very slowly from a clay precursor, in environments where low sedimentation rates allow prolonged contact over time between the authigenic mineral and seawater. The latter is seen as the source of some of the chemical elements necessary for the authigenic formation of this phyllosilicate, in particular iron (Fe). Typically, for relatively shallow environments, the distal portion of continental shelves is considered the most suitable formation environment. This review article makes it possible to broaden the spectrum of environments favorable to the growth of glauconite, by identifying environments that experience very shallow deposition depths and relatively high sedimentation rates. These situations are well illustrated by the Jurassic and Cretaceous deposits of the Boulonnais coast (Pas de Calais Strait, between the English Channel and the North Sea). In particular, certain sedimentary deposits show that glauconite could have grown during very early diagenesis. It therefore appears that glauconite can form in relatively varied environments, provided that two main conditions are met: the presence of an abundance of reactive iron and weakly reducing redox conditions. The emphasis of this paper is set on contrasted situations where various sources of iron are involved in the presence of glauconite. Last, abundant-pyrite accumulations imply large supplies of iron for their formation and, as the same time, represent a considerable iron sink with regard to the marine environment.

Carbonates formed by anaerobic oxidation of methane at localized seeps have been recognized in the rock record based on a list of criteria, including anomalous deposition within detrital facies, complex petrofabrics, seep‐endemic macrofauna and 13C‐depleted isotopic signatures. While much emphasis has been placed on the latter, it is only one of several tools used for identification. This study reports on two different and rare limestone units in the forearc deposits of the Jurassic Bedford Canyon Formation in the Santa Ana Mountains, California (USA). Isolated, metre‐scale limestone pods were found to host abundant endemic Anarhynchia dimerelloid brachiopods and display diverse petrofabrics, including multiple generations of cements. However, the δ13C values of the petrofabrics ranged from −14.5 to 4.52‰ Vienna PeeDee Belemnite. These values are only slightly 13C‐depleted relative to contemporaneous seawater, thus likely recording a stronger component of oceanic dissolved inorganic carbon than hydrocarbons. Additionally, although the petrofabrics are common for seeps (primary micrite, microbialite, pelsparite, intraclastic micrite; early isopachous and botryoidal cements and yellow calcite; late‐stage void‐filling spar), the isotopic values did not follow a predicted trend of increasing δ13C with paragenetic sequence. Pelsparite δ13C values ranged from −10.65 to −7.09‰ Vienna PeeDee Belemnite while coarse spar and vein cements ranged from −11.42 to −2.44‰ Vienna PeeDee Belemnite. Olistostromes composed of brecciated pelmicrite sourced from shallow fringing‐arc environments are typical of forearc settings. Olistostromes in the Bedford Canyon Formation contain much lower δ13C values than the more classically characterized seep deposits, ranging from −21.77 to −10.78‰ Vienna PeeDee Belemnite. While the original shallow‐water source may not have a been a confined seep, the low δ13C values require the incorporation of carbon sourced from the oxidation of localized hydrocarbons. Together, these findings recommend a reconsideration of the weight placed on δ13C values as the key criterion for distinguishing seeps in the rock record. [ABSTRACT FROM AUTHOR]

Climate change disproportionately affects the Arctic, where warming is up to four times greater than the global annual average experienced in southern regions. Baffin Bay in the Canadian Arctic Archipelago is an ecologically and biologically significant area that will likely experience an increase in marine vessel traffic as a result of consistent declines in annual sea ice coverage. Along the western coast of Baffin Bay is known to be a region of active, natural hydrocarbon seeps where elevated levels of methane have been detected in previous surveys. Petroleum hydrocarbons released from the seafloor can fuel microbial production and shape the baseline microbiome. Establishing a microbial baseline is highly valuable as it contributes to a fundamental understanding of the existing microbial diversity that may be impacted in the future by anthropogenic stressors. In this study, 16S and 18S rRNA gene amplicon sequencing surveys revealed that the vertical stratification of the water column is largely driven by differences in depth, temperature, salinity, and inorganic nutrient concentrations. Chemical analysis provides further support that active petrogenic methane seepage occurs around Cape Dyer but not in areas targeted in this study. Presence of n-alkanes and toluene in association with hydrocarbon-synthesizing phytoplankton suggests biogenic production of these compounds. These findings provide a baseline for future environmental monitoring assessments to evaluate how the prokaryotic and eukaryotic microbiome may be impacted by ongoing climate change and anthropogenic stressors in western Baffin Bay. [ABSTRACT FROM AUTHOR]

The western Atlantic Ocean harbors a diverse fauna of squat lobsters, particularly in the family Munidopsidae. This study introduces Munidopsis sedna sp. nov., a species only found in the Gulf of Mexico and the first species reported to be endemic to cold seeps in the western Atlantic. Our investigation incorporates morphological analyses including micro-CT scanning evidence, multilocus molecular phylogeny, and mtDNA phylogeography, as well as ecological data derived from in situ observations and geographic distribution patterns to substantiate the recognition of the new species. Shallow molecular divergences and multiple morphological differences differentiate the new species from its closest relative, M. longimanus (A. Milne-Edwards, 1880). Additionally, we explore the potential scenario for ecological speciation within this newly identified taxon and discuss its significance in the context of conservation efforts in the Gulf of Mexico. [ABSTRACT FROM AUTHOR]

Shallow marine thrombolites from a newly discovered Lower Cretaceous cold seep in the Outer Carpathians (Poland) were analysed in order to untangle the complex sedimentological and biogeochemical processes involved in their formation and their diagenetic modifications. The studied thrombolites are made of two components: (i) microcrystalline mesoclots; and (ii) spar‐filled framework cavities. These components are dominated by calcite and show a complex spatial relationship, resulting in a heterogeneous, clotted fabric. The mesoclots exhibit digitate structures, often concentrically‐laminated, and are chiefly composed of microcrystalline material with δ13C values from −34.8 to −19.4‰ PeeDee Belemnite. Biomarkers analyses show the presence of 2, 6, 10, 15, 19‐pentamethylicosane within the mesoclots. The mesoclots host <5 mm wide microtubes filled with isopachous calcite recording even lower δ13C values (from −39.0 to −20.5‰ PeeDee Belemnite). The morphology of the mesoclots relative to their internal lamination and their geochemistry indicates that their growth was linked to anaerobic oxidation of methane while the microtubes acted as conduits for hydrocarbon‐charged fluids. The framework cavities are internally lined with framboidal pyrite, and are cemented by calcite spar with relatively high δ13C (−15.1 to −7.3‰ PeeDee Belemnite) and low δ18O values (−9.3 to −4.4‰ PeeDee Belemnite). Carbonate precipitation within the framework cavities is interpreted to have been related to bacterial sulphate reduction. U‐shaped trace fossils attributed to the ichnogenus Balanoglossites cross‐cut both mesoclots and framework cavities. The mechanisms involved in the formation and diagenesis of thrombolites at cold seeps are yet to be fully understood, and this work provides new insights on these complex biogeochemical and sedimentological processes. [ABSTRACT FROM AUTHOR]

This research quantifies the gas release rate from a natural shallow methane seep site in the Laspi Bay (Black Sea), whose origin is thermocatalytic. An adaptive single bubble identification technique was applied to analyze gas volume and release rates from passive acoustic data. Gas from the seafloor was emitted by single bubbles that occurred in clusters. The frequency of an individual bubble (830 Hz) was proportional to the bubble's radius (0.4 cm), which coincides with the optical method. The active seepage phases lasted longer than the pauses between bubble clusters. Distribution of bubble clusters and pauses duration for all seasons deviated significantly from a normal distribution. The daily and interseasonal periodicities of gas emissions were quite similar. The bubble gas flow rate ranged from 26 to 37 liters per day. Short-term water pressure fluctuations (up to a Δp of 46 mbar) caused by sea swell can impact gas flow variability. Continuous recording of hydrological parameters showed that average dissolved oxygen concentrations and salinity at the background station were slightly higher than those above the seep site. However, the data did not demonstrate significant environmental effects, such as hypoxia or submarine freshwater inflow, which was observed in other seepages areas. [ABSTRACT FROM AUTHOR]

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To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified and proposed as Paraescarpia formosa sp. nov. through morphological and phylogenetic analyses. The endosymbionts in the trunk of P. formosa analyzed by a 16S rRNA gene clone library represented only one phylotype, which belonged to the family Sedimenticolaceae in Gammaproteobacteria. In addition, the archaeal and bacterial communities in the habitat of tubeworm P. formosa were investigated by using high-phylogenetic-resolution full-length 16S rRNA gene amplicon sequencing. The results showed that anerobic methane-oxidizing archaea (ANME)-1b was most abundant and ANME-2ab was minor in a consortia of the anerobic oxidation of methane (AOM). The known sulfate-reducing bacteria (SRB) partners in AOM consortia, such as SEEP-SRB1, -SRB2, and -SRB4, Desulfococcus and Desulfobulbus, occurred in a small population (0–5.7%) at the SYER cold seep, and it was suggested that ANME-1b and ANME-2ab might be coupled with multiple SRB in AOM consortia. Besides AOM consortia, various methanogenic archaea, including Bathyarchaeota (Subgroup-8), Methanocellales, Methanomicrobiales, Methanosarcinales, Methanofastidiosales and Methanomassiliicoccales, were identified, and sulfur-oxidizing bacteria Sulfurovum and Sulfurimonas in phylum Epsilonbacteraeota were dominant. This study revealed the first investigation of microbiota in and around tubeworm P. formosa discovered at the SYER cold seep offshore southwestern Taiwan. We could gain insights into the chemosynthetic communities in the deep sea, especially regarding the cold seep ecosystems at the SCS. [ABSTRACT FROM AUTHOR]

The present proposal offers an in-depth conceptual representation of the life cycle of methane seep ecosystems, showcasing their ecological development and biogeochemical processes from beginning to end. It combines current knowledge about microbial and metazoan communities, merging environmental and geological factors into a theoretical structure. A thorough review of literature on geology, biogeochemistry, and ecology supports the conceptual representation. It details five stages: birth, youth, maturity, senescence, and extinction, with each stage explaining the respective communities and their metabolic functions. It blends ideas from various fields, providing a comprehensive perspective on methane seep ecosystems and their intricate interactions. Additionally, the manuscript points out gaps in existing knowledge and proposes future research directions, highlighting the need for quantitative models and on-site investigations to validate the theoretical model. [ABSTRACT FROM AUTHOR]

Large-scale and multi-sample datasets have revealed that microbial diversity and geographic distribution patterns are distinct across various habitats, particularly between hydrothermal vent and cold seep ecosystems. To date, our understanding of the effects of spatial and geochemical gradients on marine microbial communities remains limited. Here, we report the microbial diversity and metabolic versatility of a remote seafloor sediment ecosystem at different sites (GC-2, -4, -5, -6, -8) in the Mid-Okinawa Trough (Mid-OT) using high-throughput metagenomic sequencing technology. Desulfobacteraceae (3.1%) were detected in a high abundance at GC-2 with intense methane concentrations (353 μL/L), which showed a clear correlation with cold seeping. Whereas Candidatus Brocadiaceae (1.7%), Rhodobacteraceae (0.9%), and Rhodospirillaceae (0.7%), which are commonly involved in denitrification and sulfur oxidation, were enriched at GC-8. Concurrently investigating the potential of deep-sea microbial metabolism, we gained insights into the adaptive capabilities and metabolic mechanisms of microorganisms within seafloor environments. Utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the analysis of functional modules revealed a significant enrichment (71–74%) of genes associated with metabolic pathways. These results expand our knowledge of the relationship between microbial biodiversity and metabolic versatility in deep-sea extreme environments. [ABSTRACT FROM AUTHOR]

Cold seeps, featured by their extremely methane-rich sedimentary environments, play a significant role in the geological history and are common in marine sediments across the seafloor. Primary dolomite, possibly mediated by microorganisms, can be widely discovered in methane-rich environments. Hence, cold seeps may provide new insights into the 'dolomite problem', which has confused geologists for decades. Magnesium isotope geochemistry of seep carbonates contributes to the understanding of the dolomite formation mechanism in marine environments. In this paper, magnesium geochemical characteristics of carbonates in modern sediments are summarized, along with rare researches on magnesium isotopes of seep carbonates. Methane vigorously interacts with sulfate by anaerobic oxidation of methane at cold seeps, producing vast amounts of dissolved sulfide which can significantly promote dolomitization of seep carbonates. Compared with temperature, alkalinity, mineralogy, etc., the competition between rapid carbonate precipitation rates and aqueous ligands may be the main factor of the magnesium fractionation at cold seeps, which is controlled by the kinetic effect. The range of magnesium isotopes of seep carbonates is narrow (from -3.46‰ to -2.36‰), and an upper limit of magnesium content seems to exist. This characteristic may be a good indicator for identifying dolomitization related to anaerobic oxidation of methane. Whereas, mechanisms of magnesium isotope fractionation and dolomitization at cold seeps remain unclear, necessitating more natural samples tested, stimulated calculation and laboratory experiment. [ABSTRACT FROM AUTHOR]

Background: The deep-sea cold seep zone is characterized by high pressure, low temperature, darkness, and oligotrophy. Vesicomyidae clams are the dominant species within this environment, often forming symbiotic relationships with chemosynthetic microbes. Understanding the mechanisms by which Vesicomyidae clams adapt to the cold seep environment is significant. Acetylation modification of lysine is known to play a crucial role in various metabolic processes. Consequently, investigating the role of lysine acetylation in the adaptation of Vesicomyidae clams to deep-sea environments is worthwhile. So, a comparative study of lysine acetylation in cold seep clam Archivesica marissinica and shallow water shellfish Ruditapes philippinarum was conducted. Results: A total of 539 acetylated proteins were identified with 1634 acetylation sites. Conservative motif enrichment analysis revealed that the motifs -KacR-, -KacT-, and -KacF- were the most conserved. Subsequent gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted on significantly differentially expressed acetylated proteins. The GO enrichment analysis indicated that acetylated proteins are crucial in various biological processes, including cellular response to stimulation, and other cellular processes (p < 0.05 and false discovery rate (FDR) < 0.25). The results of KEGG enrichment analysis indicated that acetylated proteins are involved in various cellular processes, including tight junction, motor proteins, gap junction, phagosome, cGMP-PKG signaling pathways, endocytosis, glycolysis/gluconeogenesis, among others (p < 0.05 and FDR < 0.25). Notably, a high abundance of lysine acetylation was observed in the glycolysis/glycogenesis pathways, and the acetylation of glyceraldehyde 3-phosphate dehydrogenase might facilitate ATP production. Subsequent investigation into acetylation modifications associated with deep-sea adaptation revealed the specific identification of key acetylated proteins. Among these, the adaptation of cold seep clam hemoglobin and heat shock protein to high hydrostatic pressure and low temperature might involve an increase in acetylation levels. Acetylation of arginine kinase might be related to ATP production and interaction with symbiotic bacteria. Myosin heavy chain (Ama01085) has the most acetylation sites and might improve the actomyosin system stability through acetylation. Further validation is required for the acetylation modification from Vesicomyidae clams. Conclusion: A novel comparative analysis was undertaken to investigate the acetylation of lysine in Vesicomyidae clams, yielding novel insights into the regulatory role of lysine acetylation in deep-sea organisms. The findings present many potential proteins for further exploration of acetylation functions in cold seep clams and other deep-sea mollusks. [ABSTRACT FROM AUTHOR]

The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy. It is generally assumed that CO2 production is coupled to ferredoxin reduction during anaerobic alkane oxidation in archaea. Here, Lemaire et al. use biochemical and structural techniques to study native enzymes purified from an ethane-oxidising enrichment culture, showing that the enzymes deliver electrons to the F420 cofactor rather than to ferredoxin. [ABSTRACT FROM AUTHOR]

The article in the journal "Frontiers in Earth Science" explores contemporary studies on cold seeps, hydrothermal vents, mud volcanoes, and related seafloor features. These features provide insights into deep processes that are typically inaccessible to scientists. The research emphasizes multidisciplinary approaches to studying seafloor fluid emissions, highlighting the importance of geologic, physical, chemical, and biological processes in these environments. The studies cover a wide range of topics, including microbial processes, fluid dynamics, mineralization, and the role of seafloor emissions in global biogeochemical cycles. [Extracted from the article]

Background: Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota mediate the rate-limiting step of nitrification and remove the ammonia that inhibits the aerobic metabolism of methanotrophs. However, the AOA that inhabit deep-sea methane-seep surface sediments (DMS) are rarely studied. Here, we used global DMS metagenomics and metagenome-assembled genomes (MAGs) to investigate the metabolic activity, evolutionary history, and ecological contributions of AOA. Expression of AOA-specific ammonia-oxidizing gene (amoA) was examined in the sediments collected from the South China Sea (SCS) to identify their active ammonia metabolism in the DMS. Results: Our analysis indicated that AOA contribute > 75% to the composition of ammonia-utilization genes within the surface layers (above 30 cm) of global DMS. The AOA-specific ammonia-oxidizing gene was actively expressed in the DMS collected from the SCS. Phylogenomic analysis of medium-/high-quality MAGs from 18 DMS-AOA indicated that they evolved from ancestors in the barren deep-sea sediment and then expanded from the DMS to shallow water forming an amoA-NP-gamma clade-affiliated lineage. Molecular dating suggests that the DMS-AOA origination coincided with the Neoproterozoic oxidation event (NOE), which occurred ~ 800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (~ 713 mya). Comparative genomic analysis suggests that DMS-AOA exhibit higher requirement of carbon source for protein synthesis with enhanced genomic capability for osmotic regulation, motility, chemotaxis, and utilization of exogenous organic compounds, suggesting it could be more heterotrophic compared with other lineages. Conclusion: Our findings provide new insights into the evolutionary history of AOA within the Thaumarchaeota, highlighting their critical roles in nitrogen cycling in the global DMS ecosystems. EWMb7UH3jhRcWd8tHNUGyq Video Abstract [ABSTRACT FROM AUTHOR]

There is evidence from the near‐infrared observations of space missions of the presence of carbonates on the surface of several ocean worlds. However, their genesis remains unresolved. We investigate the hypothesis that these carbonates may be in the form of clathrites assuming that clathrate hydrates are stable phases in the crust and ocean of these ocean worlds. In order to support this, we studied a sample of a potential clathrite from the Hydrate Ridge cold seep (Cascadia Subduction Zone), the carbonate rock fossil of clathrate hydrates, as a terrestrial analogue. We characterised the mineralogy and texture of the sample by using a coupled confocal Raman microscope and scanning electron microscopy instrument with the aim of identifying possible geo‐ and biosignatures, which could be relevant for future missions of exploration to ocean worlds and Mars. Our results show that aragonite is the dominant mineral phase in the clathrite sample, but Mg‐calcite and dolomite were also identified. These three carbonates constitute a pattern related to clathrate hydrate formation and dissociation processes. Dolomite was defined as a biosignature of gas hydrate microbiomes because it was integrated within Mg‐calcite grains precipitated after clathrate hydrate dissociation. Nevertheless, no spectral changes were observed in Raman bands of carbonate minerals that would indicate the influence of clathrate hydrates in their genesis. We also observed that Raman band positions of the associated framboidal pyrites are a characteristic signature of the associated framboid‐like texture because its potential as biosignature may only be attributed by biochemical analysis. [ABSTRACT FROM AUTHOR]

The Pliocene cold‐seep carbonate of the Crotone Basin (South Italy) represents a key site for dimension, outcropping exposure and quality. These deposits form a large carbonate (calcite) body (350 m long, 100 m wide and 40 m thick), and are characterized by a conduit facies made of authigenic calcite interpreted as previously active gas/fluid escape pipes and by a pavement facies, depicted as the surrounding early calcite‐cemented bioclastic and siliciclastic sediments. Pavement facies are commonly colonized by chemosymbiotic and non‐chemosymbiotic macrofauna (Lucinid and Solemyid bivalves, gastropods and serpulids). The conduit microfacies is characterized by the inward accretion of dark micritic laminae alternating with whitish sparitic layers. The micritic laminae show a microbial peloidal to dendrolitic fabric, which commonly incorporates planktonic foraminifera and coprolites, whereas the crystalline layers consist of microsparitic and sparitic crusts of prismatic zoned calcite crystals. The pavement facies shows more variability, because it is typified by laminated microbial boundstones, chemosymbiotic–bivalves packstone, foraminiferal packstone/wackestone and hybrid arenites. The stratigraphic constraint coupled with the foraminiferal assemblage (planktonic taxa) suggest a deep‐water setting occasionally affected by siliciclastic sedimentary flows. The pavement facies also shows common brecciation features, suggesting the establishment of post‐depositional overpressure conditions due to the early cementation of the conduits, which triggered localized rock failure. Stable isotope analysis of the different facies reveals overall negative δ13C values (−6.8 to −37.4‰ Vienna PeeDee Belemnite), indicating the presence of a complex mixture of methane with other hydrocarbons consumed microbially via anaerobic oxidation of methane; whereas δ18O is relatively positive (0.0 to 3.4‰ Vienna PeeDee Belemnite) suggesting the possible dehydration of clay minerals and/or destabilization of gas hydrates. This study, besides helping in the definition of the migration pathways and modality of accumulation of hydrocarbon‐rich fluids, can also help in building more and more realistic models for the complex genesis of cold‐seep carbonates. [ABSTRACT FROM AUTHOR]

Active and relic marine methane‐seep sites are widely distributed globally and are distinguished by distinctive geology, biogeochemistry, and ecosystems. The discovery of methane‐seep sites in the Krishna‐Godavari (K‐G) basin has created exciting new opportunities for methane‐seep research in the Bay of Bengal. In this study, we document the occurrence of authigenic carbonates, including micro‐crystalline aragonite crust (arg‐crusts) admixed with chemosynthetic shells and high‐magnesium carbonate tubular structures (HMC‐tube), from the methane‐seep site SSD‐045/4 in the K‐G basin. The δ13C values of HMC‐tubes (−54.5 to −46.2‰) and arg‐crusts (−57.6 to −34.8‰) indicate biogenic methane as the likely carbon source. Enhanced porewater alkalinity driving carbonate precipitation may be attributed to microbial‐mediated SO₄2−‐AOM processes. Additionally, δ13C values (−35.2 ± 8‰) of the residual organic matter within the carbonates suggest a contribution of methanotrophic bacterial biomass. The δ18Ocarb values of HMC and aragonite indicate methane hydrate degassing and crystallization pathways, respectively. Pelloid‐filled burrows suggest the reworking of shallow HMC deposit by burrowing organisms, whereas the polyphase cementations (aragonite and HMC) within burrows indicate early and burial diagenetic pathways. The wide range in ΣLREE/ΣHREE ratios and Ceanom values in arg‐crusts reflect micro‐spatial variations in redox conditions, likely due to cementation occurring in both open and closed diagenetic systems. In contrast, more constrained Ceanom values and ΣLREE/ΣHREE ratios in HMC tubes suggest persistent sulfidic conditions. Overall, these findings provide insights into the pathways of carbonate formation at the K‐G basin methane‐seep site, highlighting the complex interplay of microbial processes, fluid dynamics, and diagenetic alterations. Plain Language Summary: Methane cold‐seeps are regions on the seabed where methane (CH4) gas oozes out across the sediment‐water interface into the water column. Both active and inactive seepage sites are known across the oceans. Active methane seep sites expel significant quantities of methane into the seawater which influences the oceanic methane budget as well as the carbon cycle. In contrast, the preserved authigenic carbonate deposits and chemosynthetic fauna at the relic seep sites are archives of past seepage activities. The seep ecosystem comprises a variety of chemosynthetic and non‐chemosynthetic organisms, whereas the geological features include mounds, mud volcanoes, carbonate crusts, chimneys, etc. formed due to methane expulsion processes. Here, we investigate the origin of calcium carbonate structures formed in a cold seep region off the east coast of India. The carbonate structures include tubular‐shaped high magnesian carbonates (HMC) and crusts composed of aragonite minerals. These tubes and crusts archive biological and geological processes, including past variations in methane effusion and diffusion through the sediment. Tubular structures are formed by gas flow through the sediments as chimneys and by burrowing activities of benthic organisms. On the other hand, the aragonite crusts are formed where methane flow is high across the seabed. Key Points: Relics of methanogenic high magnesian calcite tubes and aragonite crust recovered from cold seep site K‐G basin east coast of IndiaHMC precipitation is confined to sulfidic conditions in contrast to a wider redox range for aragonite precipitationReworking of unconsolidated HMC produced the pelloid rich tubular structures, whereas aragonite crust formed at high CH4 flow conditions [ABSTRACT FROM AUTHOR]

Introduction: The Aotearoa New Zealand ghost shrimp of the infraorders Axiidea and Gebiidea have never been comprehensively reviewed, with recent work uncovering a diverse regional fauna representing eight of the 14 known families. Methods: Using standard morphological and DNA sequencing tools, the family Callianopsidae is, for the first time, recorded off New Zealand, represented by a new species of Vulcanocalliax. Results: The new species was found near hydrocarbon seeps on the Hikurangi Margin, on the eastern New Zealand continental slope, and is only the second species now known in this genus. The single congener, V. arutyunovi, is only known from a mud volcano in the Gulf of Cádiz, off the Iberian Peninsula. Vulcanocalliax sp. nov. was formerly reported as an unnamed host of a new endemic New Zealand rhizocephalan barnacle Parthenopea australis and is here formally described as Vulcanocalliax beervana sp. nov. Discussion: The new species differs, e.g., in the shape of the anterior carapace margin (convexly rounded and without elevated postantennal shoulder present in V. arutyunovi), the ocular peduncle having a convex anterolateral margin (compared to a straight margin), and the uropodal exopod has a dorsomedian ridge, lacking the elevated anterior portion that is distinct in V. arutyunovi. This brings the number of described New Zealand ghost shrimp species to 18. A key to all known Callianopsidae is provided. [ABSTRACT FROM AUTHOR]

Cold seeps, where geofluids containing methane and other hydrocarbons originating from the subseafloor seeps through the sediment surface, play important roles in the elemental and energy flux between sediment and seawater. These seep sites often harbor communities of endemic animals supported by chemolithoautotrophic bacteria, either through symbiosis or feeding. Despite these animal communities being intensively studied since their discovery in the 1980's, the contribution of carbon from seep fluid to symbiotic microbes and subsequently host animals remains unclear. Here, we used natural-abundance radiocarbon to discern carbon sources: the ambient bottom water or the seeping geofluid. The 14C concentrations were measured for vesicomyid clams, a parasitic calamyzine polychaete, and a siboglinid tubeworm species from four different cold seep sites around Japan. We found most vesicomyid clams exhibiting 14C concentrations slightly lower than that of the ambient bottom water, suggesting up to 9% of C for chemolithoautotrophy originates from geofluid DIC. The different extent of fluid contribution across species may be explained by different routes to incorporate DIC and/or different DIC concentrations in the geofluid at each seep site. Stable nitrogen isotopic compositions further suggested N incorporation from geofluids in these clams, where the burrowing depth may be a key factor in determining their δ15N values. The siboglinid tubeworm showed a clear dependency for geofluid DIC, with a contribution of > 40%. Our results demonstrate the effectiveness of 14C analyses for elucidating the nutritional ecology of cold seep animals and their symbionts, as was previously shown for hydrothermal vent ecosystems. [ABSTRACT FROM AUTHOR]

As a special type of seep carbonate, the many details concerning the formation mode and mechanism of tubular seep carbonates are rarely reported. Here, new geochemical and mineralogical data regarding tubular seep carbonate (SQW-65) are reported. Sample SQW-65 had anomalously negative d13C values and positive d18Ovalues, which suggested the dissociation of gas hydrate. Additionally, almost all the sub-samples showed no Ce anomaly (Ce/Ce*average = 0.93), with obvious U enrichment (21.3< UEF <240.3), which indicates that the studied tubular seep carbonate was formed in an anoxic environment. Subsequently, the formation process of the studied tubular seep carbonate is further discussed according to the variability of mineralogical and geochemical characteristics from the rim to the core of the tubular formation. In the early stage of the studied tubular seep carbonate (periphery), owing to the influence of terrigenous components, the quartz and Ti content and Y/Ho ratio were high. However, with the formation of the periphery, the influence of terrigenous components was gradually weakened. In addition, from the rim to the core, the carbon and oxygen isotope values showed a "covariation" coupling relationship, an enrichment of U, and a reduction in total rare earth element content. This is because as the outer wall thickens and the internal fluid channel narrows, the intensity of the sulphatedriven anaerobic oxidation of methane and the associated precipitation rate of carbonate also increase. [ABSTRACT FROM AUTHOR]

Thermospores, the dormant resting stages of thermophilic bacteria, have been shown to be frequent but enigmatic components of cold marine sediments around the world. Multiple hypotheses have been proposed to explain their distribution, emphasizing their potential as model organisms for studying microbial dispersal via ocean currents. In the Arctic Ocean, the abundance and diversity of thermospores have previously been assumed to be low. However, this assessment has been based on data mainly from the western fjords of Svalbard, thus leaving most of the Arctic unexplored. Here, we expand the knowledge about the distribution of thermospores in the Arctic Ocean by investigating the abundance and diversity of thermospores in heated shelf sediments from three sites in the outer Laptev Sea. Two of the sites are located in an area with methane‐emitting cold seeps with a thermogenic source signature suggestive of an origin in a deep hydrocarbon reservoir, while the third site is a reference site not known to be impacted by seepage. We found that activity of viable thermospore populations was more prominent at one of the investigated seep sites. This finding is supported by both radiotracer growth experiments showing thermophilic, sulfate‐reducing activity triggered by heating, as well as 16S gene sequence analyses showing significantly enriched ASVs affiliated to the phylum Firmicutes following high‐temperature incubations. An enrichment of the sulfate‐reducing, endospore‐forming class Desulfotomaculia in heated samples compared to unheated samples was also observed. Furthermore, several ASVs identified at the seep site are closely related to thermospore‐producing bacteria associated with the deep biosphere, including hydrocarbon and hydrothermal systems. Based on the combined information from induced activity, estimated abundance, and phylogenetic composition using 16S rRNA gene sequencing, we propose likely source environments and dispersal vectors for thermospores in the Arctic Ocean. [ABSTRACT FROM AUTHOR]

Caudofoveata is a class of worm-like molluscs (aplacophorans) that typically have an infaunal lifestyle, burrowing in soft bottoms in a wide range of marine habitats from shallow to deep waters. Here, we describe a very large new species of caudofoveate from South China Sea methane seeps growing up to 154 mm in length: Chaetoderma shenloong sp. nov. It is the first caudofoveate to be named from a chemosynthetic ecosystem and the first aplacophoran mollusc associated with seeps. Our new species stands out from other Pacific Chaetoderma species by its large size, a wide body relative to its length, a barely sclerotised radula, and the presence of isosceles-triangular sclerites. Phylogenetic reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene placed it within a paraphyletic clade comprising Chaetodermatidae and Limifossoridae, in line with a previous phylogenetic analysis. This also revealed that C. shenloong sp. nov. is conspecific with a Chaetoderma sp. whose whole genome was recently sequenced and assembled but remained undescribed until now. The most closely related species with an available COI sequence was C. felderi, the largest caudofoveate species recorded. Our discovery suggests caudofoveates may be present in other seeps globally but so far neglected; a potential example is C. felderi from the Gulf of Mexico, where seeps are abundant but whose exact habitat remains unclear. [ABSTRACT FROM AUTHOR]

We report the first high-precision temperature measurements of individual methane seeps in the Zelenka methane seep field, achieved with an accuracy of 0.003 °C, a sensitivity of 0.001 °C, and a sampling interval of 2 seconds. This paper reviews previous Bulgarian research on underwater gas seeps, with a particular focus on the extensively studied shallow methane seep field at Zelenka, located west of Cape Kaliakra. We discuss the feasibility of temperature-based monitoring and emphasize the necessity of temperature measurements as an integral component of underwater methane seep surveillance [ABSTRACT FROM AUTHOR]

The aim of the work is to verify the hypothesis for the possibility for registration of underwater methane emissions with a drone with an RGB camera. A brief overview of research in Bulgaria related to underwater gas seeps is presented, with a focus on the best-studied area with shallow methane seeps, Zelenka, west of Cape Kaliakra. The area is covered by 1070 georeferenced images in which each individual seep is registered in 6 consecutive images captured in 15 s. Four groups of images have 30-->100 single seeps visible. Advantages of the method are the quick obtaining of detailed data for large areas, but its dependence on meteorological conditions makes it inapplicable for regular monitoring. It is one of the cheapest express methods for quick inspection of the activity of gas sources in extensive areas, and the Zelenka area is one of the most convenient in Europe for the investigation of underwater methane sources. [ABSTRACT FROM AUTHOR]

Areas of the seafloor enriched with seeping fluids host unique chemosynthetic communities, and their interactions not only linked to the presence of oil and gas resources, but directly impact global geochemical cycles. These ecosystems can be found in diverse geological settings, spanning from passive to active continental margins, and encompass environments such as mid-ocean ridges, seamounts, cold brine lakes, mud volcanoes, and carbonate pinnacles. This review aims to examine seep environments in the Western Atlantic, the Caribbean, and Colombia, with a focus on understanding: I) their nature and origin, Itheir associated seabed characteristics, III) the biological communities directly connected to them, and IV) the chemistry and flow of the emitted fluids. The review identifies the close relationship of cold seeps to various geomorphological features, including linear diapir systems, salt diapirs resulting from salt tectonics, regions of mud volcanism, and compact seafloor mounds likely associated with buried mud diapirs. However, existing data on the fauna within these environments predominantly focus on megafauna, such as vestimentiferan tubeworms (Annelida), mussels, and vesicomyid bivalves (Mollusca), overlooking the crucial role of communities of small organisms, including fungi or macrofauna. This review highlights the absence of a consistent consensus among researchers regarding the factors controlling fauna distribution and presence in seep environments. Various authors have put forth divergent factors that influence seep community structures, with some emphasizing water depth, others the geological environment, and some the relationship with geomorphological conditions and fluid emissions. These findings underscore the need for further research into environmental factors and their roles in the observed distribution, presenting a promising avenue for future investigations. [ABSTRACT FROM AUTHOR]

A cruise was conducted in the summer of 2023 from the Pearl River Estuary (PRE) to the adjacent waters of the Xisha Islands in the northern South China Sea (NSCS) to investigate the distribution, community structure, and assembly patterns of eukaryotic and prokaryotic phytoplankton using high-throughput sequencing (HTS) and microscopic observation. Dinophyta were the most abundant phylum in the eukaryotic phytoplankton community based on HTS, accounting for 92.17% of the total amplicon sequence variants (ASVs). Syndiniales was the most abundant order among eukaryotic phytoplankton, whereas Prochlorococcus was the most abundant genus within cyanobacteria. The alpha diversity showed the lowest values in the PRE area and decreased gradually with depth, while cyanobacteria exhibited higher alpha diversity indices in the PRE and at depths ranging from 75 m to 750 m. The morphological results were different from the data based on HTS. Diatoms (37 species) dominated the phytoplankton community, with an average abundance of 3.01 × 104 cells L-1, but only six species of dinoflagellate were observed. Spearman correlation analysis and redundancy analysis (RDA) showed that the distribution and community structure of phytoplankton were largely influenced by geographical location and environmental parameters in the NSCS. The neutral community model (NCM) and null model indicated that deterministic processes played a significant role in the assembly of eukaryotic phytoplankton, with heterogeneous selection and homogeneous selection accounting for 47.27 and 29.95%, respectively. However, stochastic processes (over 60%) dominated the assembly of cyanobacteria and undominated processes accounted for 63.44%. In summary, the formation of eukaryotic phytoplankton was mainly influenced by environmental factors and geographic location, but the assembly of cyanobacteria was shaped by both stochastic processes, which accounted for over 60%, and environmental selection in the NSCS. [ABSTRACT FROM AUTHOR]

Introduction: Methane seeps influence surrounding benthic communities in different ways from slight changes in benthic abundance and biomass to major altering the species composition. Materials and Methods: We studied benthic communities of 14 methane seep flares in Laptev and East Siberian seas with comparative analysis of species composition and abiotic parameters at the nearby areas not affected by methane seeps. The species diversity was comparable at seep and non-seep sites varying from 3.9 to 39.6 taxa per 100 individuals and from 4.5 to 34.8 taxa per 100 individuals, correspondingly. Results: The Laptev Slope community corresponds with the Polychaeta-community, encircling the upper continental slope area of the entire Siberian Arctic. The Lower Shelf community described in this study apparently corresponds with the Ophiocten sericeum community identified in the shelf areas of the Kara, Laptev and East Siberian seas. The Upper Shelf community is mostly inhabited by the bivalves species such as Portlandia arctica, Ennucula tenuis and Astarte montagui communities. The Estuarine community, which is the poorest by diversity but has high values of abundance and biomass is directly influenced by the Lena River runoff in terms of lower salinities and higher sedimentation rates. Discussion: Throughout the study area, the differences between the Estuarine, Upper Shelf Lower Shelf and Laptev Slope communities exceeded the differences between the seep and background non-seep areas. Several taxa demonstrated correlations with different environmental factors, including the latitude, depth, temperature, salinity, pH and methane content, not depending on the revealed benthic community. Eight taxa demonstrated correlations with the methane content measured at different sediment depths. Two siboglinids taxa demonstrated high abundances at stations with highest methane content deep in the sediment. At the Siberian shelf, our geochemical data for siboglinid habitats are the first to be published so far. [ABSTRACT FROM AUTHOR]

Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms. [ABSTRACT FROM AUTHOR]

Sea‐air methane flux was measured directly by the eddy‐covariance method across approximately 60,000 km of Arctic and Antarctic cruises during a number of summers. The Arctic Ocean (north of 60°N, between 20°W and 50°E) and Southern Ocean (south of 50°S, between 70°W and 30°E) are found to be on‐shelf sources of atmospheric methane with mean sea‐air fluxes of 9.17 ± 2.91 (SEM (standard error of the mean)) μmol m−2 d−1 and 8.98 ± 0.91 μmol m−2 d−1, respectively. Off‐shelf, this region of the Arctic Ocean is found to be a source of methane (mean flux of 2.39 ± 0.68 μmol m−2 d−1), while this region of the Southern Ocean is found to be a methane sink (mean flux of −0.77 ± 0.37 μmol m−2 d−1). The highest fluxes observed are found around west Svalbard, South Georgia, and South Shetland Islands and Bransfield Strait; areas with evidence of the presence of methane flares emanating from the seabed. Hence, this study may provide evidence of direct emission of seabed methane to the atmosphere in both the Arctic and Antarctic. Comparing with previous studies, the results of this study may indicate an increase in sea‐air flux of methane in areas with seafloor seepage over timescales of several decades. As climate change exacerbates rising water temperatures, continued monitoring of methane release from polar oceans into the future is crucial. Plain Language Summary: The amount of methane released from oceans into the atmosphere is uncertain. Most oceanic methane is stored in the seabed and can escape into the water at seafloor seeps, but the extent to which it escapes into the atmosphere remains unclear. This study uses a relatively new method, eddy‐covariance, to measure sea‐air methane fluxes during Arctic and Antarctic cruises. This is the first time this technique has been applied to sea‐air methane fluxes in both polar oceans. Our findings show that on‐shelf regions of the Arctic and Southern Oceans release methane into the atmosphere, with average fluxes of 9.17 ± 2.91 μmol m−2 d−1 and 8.98 ± 0.91 μmol m−2 d−1, respectively. We also identified areas with significant methane release in regions where methane has been found seeping into the water from the seabed. This study provides potential evidence that methane from seabed seeps may be directly emitted into the atmosphere in both the Arctic and Antarctic. Comparing with earlier studies, there is indication that the amount of methane released has increased over the last decades. As climate change drives increasing water temperatures, there is a potential for increased methane release from the seabed into the atmosphere, therefore on‐going observations of methane release from polar oceans are necessary. Key Points: Coastal regions of the Arctic Ocean and Southern Ocean are found to be sources of atmospheric methaneThe ocean releases elevated quantities of methane where seabed methane seeps have been observed in both the Arctic and Southern OceansThis study suggests a possible rise in methane release from oceanic areas with seabed seeps over last decades compared with a prior study [ABSTRACT FROM AUTHOR]

The article discusses the development and deployment of an indigenously designed low-cost underwater camera system for seabed videography in deep-sea environments, particularly focusing on cold seep ecosystems. It highlights the camera's technical specifications, cost-effectiveness, and its role in documenting marine biodiversity and ecological processes at significant depths.

Due to tectonic uplift in the Cenozoic and numerous shelf-wide glaciations during the Quaternary, -1-2.5 km of sedimentary overburden has been eroded from the Barents Sea shelf, leading to the exhumation and partial uncapping of hydrocarbon accumulations. Widespread natural gas and oil leakage from the glacially eroded middle-upper Triassic reservoir directly into the water column has been documented at the Sentralbanken high in the northern Norwegian Barents Sea. However, it remains unclear whether the hydrocarbon leakage occurs only from the middle-upper Triassic reservoir units in geological settings exceptionally conducive to hydrocarbon leakage, or if other reservoir formations contributed to the release of hydrocarbons into the water column. It is also not clear whether complete erosion of the caprock is a prerequisite for widespread liberation of natural gas and oil from glacially eroded reservoirs across Arctic continental shelves. Here we analyze multibeam echosounder data covering -5,000 km2 and a suite of high-resolution P-cable seismic lines from a range of geological structures across the northern Norwegian Barents Sea. Our analyses reveal that -21,700 natural gas seeps originate from exhumed, faulted and variably eroded structural highs bearing a range of Mesozoic reservoir formations. All investigated structural highs fuel seabed methane release hotspots with no exception. Evident from observations of seismic anomalies, fluid accumulations are pervasive in the subsurface and likely to continue fuelling seabed gas seepage into the future. We also document that gas seepage through faults piercing overburden, caprocks and reaching potential reservoir levels is pervasive at all investigated structural highs. On the Storbanken high and the Kong Karl platform, such fault-controlled seepage is more prevalent than seepage from reservoir formations subcropping below the seafloor. Using a simple parametrization approach, we estimate that seeps identified within our multibeam data coverage produce a seabed methane flux of 61 x 107 mol/yr (9,803 ton/yr), which is one to two orders of magnitude higher than other globally known submarine methane seepage provinces. Fluxes of methane from sea water to the air above the thermogenic gas seep provinces in the northern Norwegian Barents Sea remain to be determined. [ABSTRACT FROM AUTHOR]

Methane is a potent greenhouse gas that enters the marine system in large quantities at seafloor methane seeps. At a newly discovered seep site off the coast of Point Dume, CA, ~ meter‐scale carbonate chimneys host microbial communities that exhibit the highest methane‐oxidizing potential recorded to date. Here, we provide a detailed assessment of chimney geobiology through correlative mineralogical, geochemical, and microbiological studies of seven chimney samples in order to clarify the longevity and heterogeneity of these highly productive systems. U‐Th dating indicated that a methane‐driven carbonate precipitating system at Point Dume has existed for ~20 Kyr, while millimeter‐scale variations in carbon and calcium isotopic values, elemental abundances, and carbonate polymorphs revealed changes in carbon source, precipitation rates, and diagenetic processes throughout the chimneys' lifespan. Microbial community analyses revealed diverse modern communities with prominent anaerobic methanotrophs, sulfate‐reducing bacteria, and Anaerolineaceae; communities were more similar within a given chimney wall transect than in similar horizons of distinct structures. The chimneys represent long‐lived repositories of methane‐oxidizing communities and provide a window into how carbon can be transformed, sequestered, and altered over millennia at the Point Dume methane seep. [ABSTRACT FROM AUTHOR]

This article is an editorial that discusses the applications of environmental DNA (eDNA) in the aquatic ecosystem management of East Asia. eDNA is genetic material from target species that allows for the detection of species without direct observation or capturing whole organisms. The use of eDNA analysis has rapidly developed as a promising tool in various research fields, including biodiversity assessment, invasive species monitoring, and rare species conservation. The article includes six papers on eDNA research in East Asia, covering topics such as fish diversity, larval fish diversity, intracellular DNA detection, bacterial communities in deep-sea sponges, protistan community structures, and the detection of aquatic invasive species. The authors advocate for researchers to participate in the "Making eDNA FAIR" project to improve the discoverability and accessibility of eDNA data. [Extracted from the article]

Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.