Terrestrial mud volcanoes represent surface features of channels for subsurface methane transport and, therefore, constitute an important source of methane emission from natural environments. How microbial processes regulate methane emissions in terrestrial mud volcanoes has yet to be fully addressed. This study demonstrated the geochemical characteristics and microbial communities of four mud volcano and seep sites in two geological settings of Sicily, Italy. At sites within the accretionary wedge that exhibited higher methane and sulfate concentrations, the communities were dominated by members capable of catalyzing methane and sulfate metabolisms and organic degradation. In particular, both anaerobic and aerobic methanotrophs were abundant and their abundance distribution coincided with the geochemical transition. In contrast, the sites near Mount Etna were characterized by high fluid salinity, CO 2 , and low methane and sulfate concentrations, with communities consisting of halophilic organic degraders and sulfur metabolizers, along with a minor presence of aerobic methanotrophs. Substantial variations in community composition and geochemistry across spatial and vertical redox gradients suggest that physicochemical contexts imposed by the geology, fluid path, and source characteristics play a vital role in shaping community composition and cycling of methane, sulfur and organic carbon in Sicily mud volcanoes.
Methane hydrates are distributed throughout the South China Sea (SCS), and the total abundance of methane hydrate in the SCS is estimated to be 42.8Gt C. It has been revealed that the tectonic transition in the SCS may affect the origin of methane deposited in sediments.Because the sediment communities in the active (FWCR) and passive (FR) margins off southwestern Taiwan were shifted and diversified as burial progressed, we hypothesized that microbial differentiation would vary the fate of organic matter utilization and impact the origin of methane.In this study, we supplied 13 C-labelled methanol, methylamine, acetate, and glucose as carbon sources with slurries from three depth intervals (5, 50, and 120 mbsf) sampled from both FWCR and FR to reveal the connections between community structures and potential metabolic pathways.We found that methyl-based methanogenesis only occurred in the incubation from 5 mbsf in FR, which possessed an increased proportion of Methanococcoides spp.In contrast, the newly produced methane was not detected in other incubations.By capturing the accumulation of 13 CO 2 in other groups, we inferred that fermentation was the primary process consuming methyl compounds.Moreover, parts of methyl compounds were assimilated and accumulated in microbial biomass with rates ranging from 7.87 × 10 -5 to 2.14 × 10 -2 mg C/day and 2.85 × 10 -4 to 3.27 × 10 -4 mg C/day in incubations from FR and FWCR, respectively.By visualizing the growth form of Methanococcoides spp., we found that they usually formed aggregates with bacteria, but some aggregates were only composed of Methanococcoides spp.themselves.In the groups supplying acetate and glucose, regardless of sites and depths heterotrophs such as Fusibacter spp.and Marinobacter spp.were the dominantly enriched groups, yet their enriched proportions were distinct.Our current work demonstrates that the variable microbial communities between tectonic settings affect the degradation rates and metabolic pathways of organic matter in marine sediments.In situ methanogenesis is one of the sources of methane in the passive margin, while the source of methane in the active margin may rely on thermogenic methane from the deep reservoir.
In the northern South China Sea (SCS) we explored methane dynamics in the water column during SONNE-cruise SO266 in October/November 2018. Two depth zones contained elevated methane concentrations: the upper 400 m ( 10°C and > 20°C, respectively. Both 16S rRNA gene and pmoA amplicon analyses revealed distinct microbial and methanotrophic communities in water with temperature of 27°C, ~10°C, and 3°C. Second, we found elevated methane concentrations in 200-400 m in the FWCR-region whereas increased methane concentrations occurred in the uppermost 100 m above SSFR. The deeper plume above FWCR might be due to an intrusion of the Kuroshio water mass into SCS keeping the methane from being aerobically oxidized in the warm surface water and vented to the atmosphere. Finally, all peak methane concentrations occurred in water depth, with rather low backscatter, i.e. in water depth with less suspended matter. At the seafloor, ocean currents and long-term seepage appeared to control methane dynamics. We derived methane fluxes of 0.08-0.12 mmol m-2 d-1 from a 4.5 km2 area at FWCR and of 3.0-79.9 mmol m-2 d-1 from a 0.01 km2 area at SSFR. Repetitive sampling of the area at SSFR indicated that changing directions of ocean currents possibly affected methane concentrations and thus flux. In contrast to these seepage sites with distinct methane plumes, retrieval of drilling equipment produced no methane plume. Even gas emission triggered by seafloor drilling did not supply measureable methane concentrations after 3 hours, but caused an increase in methanotrophic activity as determined by rate measurements and molecular-biological analyses. Apparently, only long-term seepage can generate methane anomalies in the ocean.
Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selected taxa (Pisces, Crustacea, Echinoidea, and Asteroidea), which are good candidates for identification from images. Taxonomic identification ranks obtained for the images varied among these taxa (e.g., family/order for fishes, genus for echinoderms). At these ranks, imagery provided a higher taxonomic richness for hard-bottom and complex habitats, partially explained by the poor performance of trawling on these rough substrates. For the same reason, the gamma diversity of Pisces and Crustacea was also higher from images, but no difference was observed for echinoderms. On soft bottoms, physical sampling provided higher alpha and gamma diversity for fishes and crustaceans, but these differences tended to decrease for crustaceans identified to the species/morphospecies level from images. Physical sampling and imagery were selective against some taxa (e.g., according to size or behavior), therefore providing different facets of biodiversity. In addition, specimens collected at a larger scale facilitated megafauna identification from images. Based on this complementary approach, we propose a robust methodology for image-based faunal identification relying on a taxonomic framework, from collaborative work with taxonomists. An original outcome of this collaborative work is the creation of identification keys dedicated specifically to in situ images and which take into account the state of the taxonomic knowledge for the explored sites.
Abstract Identification of methane origins remains a challenging work as current diagnostic signals are often not sufficient to resolve individual formation and post‐formation processes. To address such a knowledge gap in a tectonically active and fragmented terrain, samples from mud volcanoes, gas seeps, and springs distributed along structural features onshore and offshore of Taiwan were analyzed for their isotopic compositions of methane, nitrogen, helium, dissolved inorganic carbon, CO 2 , and water. Our analyses yielded Δ 13 CH 3 D and Δ 12 CH 2 D 2 values ranging between +1.9‰ and +7.8‰ and between +3.0‰ and +19.9‰, respectively. A portion of the samples were characterized by values that represent the thermodynamic equilibrium at temperatures of 99°–260°C. These temperature estimates, together with the bulk isotopic compositions and local geothermal gradients (25°–30°C/km), suggest that methane was formed by thermal maturation of organic matter at depths of 2–9 km below the land surface and channeled upward along faults. Other samples were found to deviate from equilibrium by varying degrees. Considering the geological background, helium isotopic ratios, and nitrogen isotopologue compositions, and methanogens detected at some sites, these gases are either abiotic in origin or a mixture of microbial and thermogenic sources. Regardless of whether the equilibrium of methane isotopologues was reached, few sites hosted by sedimentary formations were characterized by mantle‐like helium signatures, indicating decoupled origins and potential degassing of helium from the relic igneous source. Overall, these results suggest the extraction of methane and other gases from multiple depths from strata fragmented by fault displacement in an active orogenic belt.
Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.
Abstract Flatfishes (Pleuronectiformes) are a species‐rich and distinct group of fishes characterized by cranial asymmetry. Flatfishes occupy a wide diversity of habitats, including the tropical deep‐sea and freshwaters, and often are small‐bodied fishes. Most scientific effort, however, has been focused on large‐bodied temperate marine species important in fisheries. Phylogenetic study of flatfishes has also long been limited in scope and focused on the placement and monophyly of flatfishes. As a result, several questions in systematic biology have persisted that molecular phylogenetic study can answer. We examine the Pleuronectoidei, the largest suborder of Pleuronectiformes with >99% of species diversity of the order, in detail with a multilocus nuclear and mitochondrial data set of 57 pleuronectoids from 13 families covering a wide range of habitats. We combine the molecular data with a morphological matrix to construct a total evidence phylogeny that places fossil flatfishes among extant lineages. Utilizing a time‐calibrated phylogeny, we examine the timing of diversification, area of origin and ancestral temperature preference of Pleuronectoidei. We find polyphyly or paraphyly of two flatfish families, the Paralichthyidae and the Rhombosoleidae, and support the creation of two additional families—Cyclopsettidae and Oncopteridae—to resolve their non‐monophyletic status. Our findings also support the distinctiveness of Paralichthodidae and refine the placement of that lineage. Despite a core fossil record in Europe, the observed recent diversity of pleuronectoids in the Indo‐West Pacific is most likely a result of the Indo‐West Pacific being the area of origin for pleuronectoids and the ancestral temperature preference of flatfishes is most likely tropical.
Abstract Widely distributed bottom simulating reflectors (BSRs) imply the potential existence of gas hydrates offshore southwestern Taiwan. To compare the distribution of methane concentrations along passive and active margins in the region, bottom waters and cored sediments were collected during four cruises from 2005 to 2006. The results reveal that sites with high methane concentrations are predominantly distributed in the active margin and site GS5 is the only site that contains very high methane concentrations in the passive margin of studied area. Anomalously high methane fluxes still can be obtained from the calculation of diffusive methane flux, although there might be some gas leakage during or after sampling procedures. The profiles of methane and sulfate concentration reveal very shallow depths of the sulfate–methane interface (SMI) at some sites. There is evidence that sulfate reduction is mainly driven by the process of anaerobic methane oxidation. Thus, sulfate fluxes can be used as a proxy for methane fluxes through the use of diffusion equations; and the results show that the fluxes are very high in offshore southwestern Taiwan. The depths of the SMI are different at sites GH6 and C; however, both methane profiles reveal parallel methane gradients below the SMI. This might be because of methane migration to surface sediments from the same reservoir with the same diffusion rates. Although BSRs are widely distributed both in the active margin and in the passive margin, most sites with high methane concentrations have been found in the active margin. Therefore, the specific tectonic settings in offshore SW Taiwan might strongly control the stability of gas hydrates, and thus affect the methane concentrations and fluxes of the sediments and sea waters. Furthermore, the carbon isotopic composition of methane shows that a biogenic gas source is dominant at shallower depth; however, some thermogenic gases might be introduced through the fracture/fault zones from deeper source in the active region of studied area.
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