Baltic Sea Sediments
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA721576 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14226828_1.fastq.gz | Fastqsanger.gz | |||
| SRR14226828_2.fastq.gz | Fastqsanger.gz | |||
| SRR14226829_1.fastq.gz | Fastqsanger.gz | |||
| SRR14226829_2.fastq.gz | Fastqsanger.gz | |||
| SRR14226830_1.fastq.gz | Fastqsanger.gz |
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Project description:Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is largely unknown. We herein presented a culture-independent method to phylogenetically characterize phosphatase-expressing bacteria in sediments. We labeled whole-cell extracts of Baltic Sea sediments with an artificial phosphatase substrate and sorted phosphatase-expressing cells with a flow cytometer. Their phylogenetic affiliation was determined by Denaturing Gradient Gel Electrophoresis. The phosphatase-expressing bacterial community coarsely reflected the whole-cell bacterial community, with a similar dominance of Alphaproteobacteria.
| S-EPMC4462931 | biostudies-literature
Project description:Oxygen depletion in coastal waters may lead to release of toxic sulfide from sediments. Cable bacteria can limit sulfide release by promoting iron oxide formation in sediments. Currently, it is unknown how widespread this phenomenon is. Here, we assess the abundance, activity, and biogeochemical impact of cable bacteria at 12 Baltic Sea sites. Cable bacteria were mostly absent in sediments overlain by anoxic and sulfidic bottom waters, emphasizing their dependence on oxygen or nitrate as electron acceptors. At sites that were temporarily reoxygenated, cable bacterial densities were low. At seasonally hypoxic sites, cable bacterial densities correlated linearly with the supply of sulfide. The highest densities were observed at Gulf of Finland sites with high rates of sulfate reduction. Microelectrode profiles of sulfide, oxygen, and pH indicated low or no in situ cable bacteria activity at all sites. Reactivation occurred within 5 days upon incubation of an intact sediment core from the Gulf of Finland with aerated overlying water. We found no relationship between cable bacterial densities and macrofaunal abundances, salinity, or sediment organic carbon. Our geochemical data suggest that cable bacteria promote conversion of iron monosulfides to iron oxides in the Gulf of Finland in spring, possibly explaining why bottom waters in this highly eutrophic region rarely contain sulfide in summer.
| S-EPMC6611076 | biostudies-literature
Project description:We assessed the abundance of microplastics (0.2-5 mm) in drift line sediments from three sites in Kiel Fjord, Western Baltic Sea. The first site is intensively used by beach visitors, the second is in close proximity to a sewage plant and the third is polluted with large-sized plastic litter. Samples were split into three grain size classes (0.2-0.5, 0.5-1, 1-5 mm), washed with calcium chloride solution, and filtered at 0.2 mm. Filters were then visually inspected, and a total of 180 fragments was classified as microplastics, of which 39% were analyzed using Raman spectroscopy. At the site that is close to a sewage plant as well as at the site with intense beach use, 1.8 and 4.5 particles (fibers plus fragments) per kg of dry sediment were found, respectively, while particle abundances reached 30.2 per kg of dry sediment at the site with high litter loads. Our data suggest that the fragmentation of large plastic debris at site seems to be a relevant source for microplastics in Western Baltic Sea beach sediments.
| S-EPMC8159790 | biostudies-literature
Project description:Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 10(4) per cm(3) at the surface and decreased exponentially to 10(0) per cm(3) at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.
| S-EPMC3524260 | biostudies-literature
Project description:The study aimed to determine the level of mercury (Hg) and its labile and stable forms in the surface sediments of the Baltic Sea. The work considers the impact of current and historical sources of Hg on sediment pollution, together with the influence of different environmental parameters, including water inflows from the North Sea. Surface sediments (top 5 cm) were collected in 2016-2017 at 91 stations located in different areas of the Baltic Sea, including Belt Sea, Arkona Basin, Bornholm Basin, Gdańsk Basin, West Gotland Basin, East Gotland Basin, and the Bothnian Sea. Besides, the particulate matter suspended in the surface and near-bottom water was also collected. The analysis of total Hg concentration and individual Hg forms in collected samples was carried out using a 5-step thermodesorption method. This method allows for the identification of three labile and thus biologically available, fractions of Hg, which are mercury halides, organic Hg, mercury oxide and sulphate. Two stable fractions, mercury sulphide and residual Hg, were also determined. The highest Hg concentrations, reaching 341 ng g-1, were measured in the highly industrialised Kiel Bay, which was additionally a munition dumping site during and after World War II. High Hg level, ranging from 228 to 255 ng g-1, was also recorded in the surface sediments of the Arkona Basin, which was a result of the cumulative effect of several factors, such as deposition of Hg-rich riverine matter, favourable hydrodynamic conditions and military activities in the past. The relatively elevated Hg concentrations, varying from 60 to 264 ng g-1, were found in the Gdańsk Basin, a region under strong anthropopressure and dominated by soft sediments. The sum of labile Hg in sediments was high and averaged 67% (with the domination of organic Hg compounds), which means that a large part of Hg can be released to the water column. It was found that the water inflows from the North Sea intensify the remobilisation of Hg and its transformation into bioavailable labile forms. As a consequence, the load of Hg introduced into the trophic chain can increase. Despite the significant reduction of Hg emission into the Baltic in the last decades, surface sediments can be an important secondary Hg source in the marine ecosystem. This is especially dangerous in the case of the western Baltic Sea.
| S-EPMC8277639 | biostudies-literature
Project description:BackgroundIn anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic organic sulphur compound in the environment and an abundant methylated compound leading to methane production in anoxic sediments. However, understanding of the microbial diversity driving DMS-dependent methanogenesis is limited, and the metabolic pathways underlying this process in the environment remain unexplored. To address this, we used anoxic incubations, amplicon sequencing, genome-centric metagenomics and metatranscriptomics of brackish sediments collected along the depth profile of the Baltic Sea with varying sulphate concentrations.ResultsWe identified Methanolobus as the dominant methylotrophic methanogens in all our DMS-amended sediment incubations (61-99%) regardless of their sulphate concentrations. We also showed that the mtt and mta genes (trimethylamine- and methanol-methyltransferases) from Methanolobus were highly expressed when the sediment samples were incubated with DMS. Furthermore, we did not find mtsA and mtsB (methylsulphide-methyltransferases) in metatranscriptomes, metagenomes or in the Methanolobus MAGs, whilst mtsD and mtsF were found 2-3 orders of magnitude lower in selected samples.ConclusionsOur study demonstrated that the Methanolobus genus is likely the key player in anaerobic DMS degradation in brackish Baltic Sea sediments. This is also the first study analysing the metabolic pathways of anaerobic DMS degradation in the environment and showing that methylotrophic methane production from DMS may not require a substrate-specific methyltransferase as was previously accepted. This highlights the versatility of the key enzymes in methane production in anoxic sediments, which would have significant implications for the global greenhouse gas budget and the methane cycle. Video Abstract.
| S-EPMC10762971 | biostudies-literature