Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay

Decadal ventilation and mixing of Indian Ocean waters

Endogenous phosphorus (P) release and its complex biogeochemical transformation pose ongoing challenges for effective P management in estuarine ecosystems. However, the understanding of how these processes respond to runoff regulations remains rarely constrained. This study investigated the spatiotemporal distribution of P forms in bottom water and sediment of the Liao River Estuary under anthropogenic runoff regulations characterized by low runoff in summer and normal runoff in winter. The sediment P adsorption capacity and release potential were studied through adsorption kinetics and thermodynamic experiments. Soluble reactive P (SRP) and total dissolved P (TDP) concentrations in bottom water were low in summer but increased markedly in winter (p<0.01). The average sediment total P (TP) concentrations were 495.26 mg/kg in summer and 399.62 mg/kg in winter, with higher TP levels mainly observed in the nearshore muddy areas, likely attributable to the high proportion of fine particles. Equilibrium P concentration generally exceeded the SRP concentration in bottom water under both conditions, indicating that the sediment served as a P source. The sediment P eutrophication risk index (ERI) further showed that release risk was predominantly moderate in summer, whereas it was low in winter. Both PLS-PM and correlation analysis showed that the concentrations of Fe, Al, organic matter, and the proportion of fine particles served as key determinants influencing the content of aluminum-bound P (NaOH-rP), organic P (NaOH-nrP), and calcium-bound P (HCl-P). Furthermore, elevated SRP levels combined with reduced salt in winter likely constrain P accumulation in the sediment. This study offers novel insight into the migration and transformation of P in the estuarine environment under anthropogenic runoff regulations.

Aerobic methanotrophy at ancient marine methane seeps: A synthesis

Dissolved oxygen and suspended particles regulate the benthic flux of iron from continental margins

Unraveling antibiotic fate in a highly urbanized estuary: Spatiotemporal patterns, multi-media partitioning, and contaminant prioritization.

Concentrations of dissolved manganese and particulate manganese and aluminum were determined in samples from Narragansett Bay, Rhode Island, and its surrounding rivers. Total manganese is approximately conservative, but dissolved and particulate manganese are not. Desorption may occur in the tidal rivers at low salinities. Most riverine manganese is dissolved but manganese in the bay is predominantly particulate, probably due to rapid manganese oxidation at bay water pH.The flux of dissolved manganese into bottom waters was about 2 ± 1 µg cm‒2 d‒1. Concentrations in bottom waters are high relative to surface waters.

In highly eutrophicated Tokyo Bay, anoxic, sulfide-containing bottom water is formed in warm stagnant seasons. It seems to develop especially in the northeast area where there are many large holes made by dredging to collect sand in addition to navigation channels. At such dredged sites, the seasonal variation in the rate of sulfate reduction in sediment was examined by a radiotracer method together with various environmental factors for two years and the results were compared with those obtained at a site on the natural sea floor. The rate of sulfate reduction was much higher at the dredged sites than on the natural sea floor. The dissolved oxygen concentration in bottom water and sulfate concentration in the sediment layer were lower, and the density of sulfate-reducing bacteria and acid-volatile sulfides were higher at the dredged sites than the natural floor site. However, there was no significant correlation between the sulfate reduction rate and any of the environmental factors examined (temperature, ignition loss, DO in bottom water and density of sulfate-reducing bacteria). The rate on an area basis seemed to fluctuate in a similar pattern to the change of chlorophyll a in the water column. The addition of seston mainly composed of diatoms to the sediment sample greatly stimulated sulfate reduction in contrast to the addition of lactate. Sulfate reduction at these sites might be controlled by the supply of organic substrates especially those of algal origin.

Methane seeps are chemosynthetic ecosystems in the deep-sea environment. Microbial community structures have been extensively studied in the seepage-affected sediments and investigation in the water column above the seeping sites is still lacking. In this study, prokaryotic communities in the bottom water about 50 cm from the seabed at methane seeps with various seepage intensities in Haima, South China Sea were comparatively studied by using 16S ribosomal RNA gene sequencing. These sites were assigned based on their distinct methane content levels and seafloor landscapes as the non-seepage (NS) site, low-intensity seepage (LIS) site, and high-intensity seepage (HIS) site. The abundances of the dominant phyla Proteobacteria, Bacteroidetes, and Actinobacteria differed significantly between NS and the two seepage sites (p < 0.05). Alpha diversity differed among the three sites with the HIS site showing the lowest community diversity. Principal component analysis revealed highly divergent bacterial community structures at three sites. Many environmental variables including temperature, alkalinity, pH, methane, dissolved organic carbon (DOC), and inorganic nutrients were measured. Redundancy analysis indicated that methane content is the key environmental factor driving bacterial community variation (p = 0.001). Linear discriminant analysis effect size analysis identified various differentially enriched genera at the LIS and HIS sites. Phylogenetic analysis revealed close phylogenetic relationship among the operational taxonomic units of these genera with known oil-degrading species, indicating oil seepage may occur at the Haima cold seeps. Co-occurrence networks indicated that the strength of microbial interactions was weakest at the HIS site. This study represents a comprehensive comparison of microbial profiles in the water column of cold seeps in the SCS, revealing that the seepage intensity has a strong impact on bacterial community dynamics.

Methane (CH4), the most abundant hydrocarbon gas in the atmosphere, plays an important role in global climate change. Quantifying the dissolved methane and its air-sea flux from hydrocarbon seeps is therefore of great importance. Large quantities of natural gas are emitted from the seafloor to the coastal ocean near the Lingtou Promontory, South China Sea. We quantified concentrations of methane in surface and bottom waters at 48 stations in a 56 km2 study area. High spatial variability in dissolved methane concentrations was observed in the surface mixed layer (0.5 m water depth) and bottom water (water-sediment interface), with values ranging from 2.90 nmol L−1 to 13570.02 nmol L−1 and from 4.98 nmol L−1 to 31740.02 nmol L−1, respectively. The significant difference between concentrations of dissolved methane in surface and bottom waters suggests that most of the methane emitted from the seafloor is dissolved in the water column. The dissolution of methane in seawater may result in local oxygen depletion that may lead to ecological effects. The δ13C values of dissolved methane ranging from −59.76‰ to −48.59‰ indicate a mixture of biogenic and thermogenic gas sources. The average air-sea methane flux of Yinggehai Basin was 672.57 μmol m−2 d−1, which cannot be ignored in environment assessment. Coastal regions, especially with hydrocarbon seeps in shallow waters of the continental margin, may therefore be an important source of methane to the atmosphere.

Environmental heterogeneity in cold seeps is usually reflected by different faunal aggregates. The sediment microbiome, especially the geochemical cycling-associated communities, sustains the ecosystem through chemosynthesis. To date, few studies have paid attention to the structuring and functioning of geochemical cycling-associated communities relating to environmental heterogeneity in different faunal aggregates of cold seeps. In this study, we profiled the microbial community of four faunal aggregates in the Haima cold seep, South China Sea. Through a combination of geochemical and meta-omics approaches, we have found that geochemical variables, such as sulfate and calcium, exhibited a significant variation between different aggregates, indicating changes in the methane flux. Anaerobic methanotrophic archaea (ANME), sulfate-reducing, and sulfide-oxidizing bacteria (SRB and SOB) dominated the microbial community but varied in composition among the four aggregates. The diversity of archaea and bacteria exhibited a strong correlation between sulfate, calcium, and silicate. Interspecies co-exclusion inferred by molecular ecological network analysis increased from non-seep to clam aggregates and peaked at the mussel aggregate. The networked geochemical cycling-associated species showed an obvious aggregate-specific distribution pattern. Notably, hydrocarbon oxidation and sulfate reduction by ANME and SRB produced carbonate and sulfide, driving the alkalization of the sediment environment, which may impact the microbial communities. Collectively, these results highlighted that geofluid and microbial metabolism together resulted in environmental heterogeneity, which shaped the C and S cycling-associated microbial community.

In situ detection of the fine scale heterogeneity of active cold seep environment of the Formosa Ridge, the South China Sea

Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages. IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus–host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

Detailed knowledge of the extent of post-genetic modifications affecting shallow submarine hydrocarbons fueled from the deep subsurface is fundamental for evaluating source and reservoir properties. We investigated gases from a submarine high-flux seepage site in the anoxic Eastern Black Sea in order to elucidate molecular and isotopic alterations of low-molecular-weight hydrocarbons (LMWHC) associated with upward migration through the sediment and precipitation of shallow gas hydrates. For this, near-surface sediment pressure cores and free gas venting from the seafloor were collected using autoclave technology at the Batumi seep area at 845 m water depth within the gas hydrate stability zone. Vent gas, gas from pressure core degassing, and from hydrate dissociation were strongly dominated by methane (> 99.85 mol.% of ∑[C1–C4, CO2]). Molecular ratios of LMWHC (C1/[C2 + C3] > 1000) and stable isotopic compositions of methane (δ13C = − 53.5‰ V-PDB; D/H around − 175‰ SMOW) indicated predominant microbial methane formation. C1/C2+ ratios and stable isotopic compositions of LMWHC distinguished three gas types prevailing in the seepage area. Vent gas discharged into bottom waters was depleted in methane by > 0.03 mol.% (∑[C1–C4, CO2]) relative to the other gas types and the virtual lack of 14C–CH4 indicated a negligible input of methane from degradation of fresh organic matter. Of all gas types analyzed, vent gas was least affected by molecular fractionation, thus, its origin from the deep subsurface rather than from decomposing hydrates in near-surface sediments is likely. As a result of the anaerobic oxidation of methane, LMWHC in pressure cores in top sediments included smaller methane fractions [0.03 mol.% ∑(C1–C4, CO2)] than gas released from pressure cores of more deeply buried sediments, where the fraction of methane was maximal due to its preferential incorporation in hydrate lattices. No indications for stable carbon isotopic fractionations of methane during hydrate crystallization from vent gas were found. Enrichments of 14C–CH4 (1.4 pMC) in short cores relative to lower abundances (max. 0.6 pMC) in gas from long cores and gas hydrates substantiates recent methanogenesis utilizing modern organic matter deposited in top sediments of this high-flux hydrocarbon seep area.

Abstract. Hydroelectric reservoirs bury significant amounts of organic carbon (OC) in their sediments. Many reservoirs are characterized by high sedimentation rates, low oxygen concentrations in bottom water and a high share of terrestrially derived OC, and all of these factors have been linked to a high efficiency of OC burial. However, investigations of OC burial efficiency (OCBE, i.e., the ratio between buried and deposited OC) in reservoirs are limited to a few studies, none of which include spatially resolved analyses. In this study we determined the spatial variation in OCBE in a large subtropical reservoir and related it to sediment characteristics. Our results show that the sediment accumulation rate explains up to 92 % of the spatial variability in OCBE, outweighing the effect of other variables, such as OC source and oxygen exposure time. OCBE at the pelagic sites varied from 48 to 86 % (mean 67 %) and decreased towards the dam. At the margins, OCBE was lower (9–17 %) due to the low sediment accumulation in shallow areas. Our data show that the variability in OCBE both along the rivers–dam and the margin–pelagic axes must be considered in whole-reservoir assessments. Combining these results with a spatially resolved assessment of sediment accumulation and OC burial in the studied reservoir, we estimated a spatially resolved mean OC burial efficiency of 57 %. Being the first assessment of OCBE with such a high spatial resolution in a reservoir, these results suggest that reservoirs may bury OC more efficiently than natural lakes.