Ontology highlight
ABSTRACT:
PROVIDER: PRJNA415134 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6195070_1.fastq.gz | Fastqsanger.gz | |||
| SRR6195070_2.fastq.gz | Fastqsanger.gz | |||
| SRR6195080_1.fastq.gz | Fastqsanger.gz | |||
| SRR6195080_2.fastq.gz | Fastqsanger.gz | |||
| SRR6195090_1.fastq.gz | Fastqsanger.gz |
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Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
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Project description:At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition and in situ protein expression of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea).
2018-04-27 | PXD009105 | Pride
Project description:Shewanella algae C6G3 can conduct dissimilative nitrate reduction into ammonium and MnIV reduction. This bacteria have the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. This property may explain NO2/3- accumulation observed in some anaerobic zones of marine sediments. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources and with MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. Furthermore, comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of identical and non-limiting concentration of ammonium in both culture conditions. Regulators ntrB/nrtC, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine dependent genes were over-expressed. In nitrate condition, genes involved in synthesis of several amino acids were over expressed. Among the genes associated with the stress response, Kat E was highly expressed particularly under manganese condition
2018-12-31 | GSE109146 | GEO
Project description:Iron-sulfur minerals such as pyrite are found in many marine benthic habitats. At deep-sea hydrothermal vent sites they occur as massive sulfide chimneys. Hydrothermal chimneys formed by mineral precipitation from reduced vent fluids upon mixing with cold oxygenated sea water. While microorganisms inhabiting actively venting chimneys and utilizing reduced compounds dissolved in the fluids for energy generation are well studied, only little is known about the microorganisms inhabiting inactive sulfide chimneys. We performed a comprehensive meta-proteogenomic analysis combined with radiometric dating to investigate the diversity and function of microbial communities found on inactive sulfide chimneys of different ages from the Manus Basin (SW Pacific). Our study sheds light on potential lifestyles and ecological niches of yet poorly described bacterial clades dominating inactive chimney communities.
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Project description:<p>Mass spectrometry imaging (MSI) in sedimentary archives can produce records of molecular proxies at μm-scale resolution. For example, in annually varved sediments of the Santa Barbara Basin, such a fine resolution allows deciphering sub-annual distributions of archaeal tetraether lipids, haptophyte-derived alkenones and sterols. Herein, we reported the establishment of an untargeted data processing workflow aimed at dissecting the MSI datasets and extracting information beyond that obtained by targeted analysis of known molecular proxies. The combination of MSI and the untargeted workflow not only increases the spatial resolution for molecular stratigraphy but also dramatically broadens the number and diversity of molecular signals evaluated, enabling us to discover unique molecular signatures imprinted by various biogeochemical processes. We applied the proposed workflow to two MSI datasets that were both measured on the uppermost ∼10 cm of the Santa Barbara Basin sediments while covering different mass ranges. Two matrices of 18625 x 293 and 18963 x 323 (number of spectra x number of peaks) were, respectively, extracted after peak alignment using bin-wise kernel density estimation and subsequent peak picking by peak prominence filtering combined with geochemical context-based filtering. Feature extraction by non-negative matrix factorization revealed in total 15 stable molecular clusters with distinct spatial distributions in the sediments. Each cluster typically comprised several to dozens of compounds, with the majority of compounds in each cluster likely belonging to similar chemical taxonomies. Some of these clusters can be linked to specific biogeochemical processes. For example, chlorin-like compounds are possibly related to diatom production, alkenones are related to coccolithophorid production, and steranes and long-chain fatty acids likely represent terrigenous input. Supervised learning from these data mining results further extracted molecular signatures with proxy potential that appear to be linked to specific environmental conditions inferred from historical oceanographic data. However, generalizability to other sedimentary settings will require further investigation.</p>
2022-08-15 | MTBLS4609 | MetaboLights
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
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