Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean
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ABSTRACT:
PROVIDER: PRJNA563349 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10056267_1.fastq.gz | Fastqsanger.gz | |||
| SRR10056267_2.fastq.gz | Fastqsanger.gz | |||
| SRR10056268_1.fastq.gz | Fastqsanger.gz | |||
| SRR10056268_2.fastq.gz | Fastqsanger.gz | |||
| SRR10056269_1.fastq.gz | Fastqsanger.gz |
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Project description:The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.
2021-04-30 | GSE136729 | GEO
Project description:In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2. The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies. Keywords: Growth protocol Desulfovibrio vulgaris Hildenborough was cultured at 37°C with thiosulfate as the only electron acceptor (with lactate as the electron donor) to mid-log phase. Cultures were also cultivated similarly using sulfate as the sole electron acceptor to mid-log phase. Gene expression profiles of cultures grown with thiosulfate as the electron acceptor were compared with those of the cultures grown with sulfate as the electron acceptor for dissimilatory sulfate reductiontion. Total RNA was harvested from four replicate cultures for microarray analysis. RNA extraction, purification, and labeling were performed independently on each cell sample. Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (dye swap).
2008-05-31 | E-GEOD-8072 | biostudies-arrayexpress
Project description:Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.
| S-EPMC6647121 | biostudies-literature
Project description:In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2. The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies. Keywords: Growth protocol
2008-05-31 | GSE8072 | GEO
Project description:Zero-valent sulfur (ZVS) and thiosulfate are important intermediates in the biogeochemical cycle of sulfur. The former has been proved to be existed in the cold seep and hydrothermal systems. Three thiosulfate oxidation pathways are already identified and here we found a novel one in Erythrobacter, which was the first genus in the family Erythrobacteraceae that could accumulate ZVS during thiosulfate oxidation. Erythrobacter flavus 21-3 was isolated from the sediment of clod seep. Genomic analyses showed the typical genes encoding Sox multienzyme complex were absent in the genome of E. flavus 21-3. Through proteome and genome data, we identified a three gene involved pathway of thiosulfate oxidation, including thiosulfate dehydrogenase (tsdA), thiosulfohydrolase (soxB) and sulfur dioxygenases (sdo). For the first time, genetic operating system was constructed in Erythrobacter, and mutant strains ΔtsdA, ΔsoxB, ΔsdoA, ΔsdoB and ΔsdoAB were constructed. Stoichiometry was calculated and tetrathionate and ZVS were found to be the intermediates in this novel thiosulfate oxidation pathway. The diverse and distribution of these proteins were investigated and this novel thiosulfate oxidation pathway may exist in bacteria formerly ignored the function of ZVS production. The results give a powerful evidence for a new source of biogenetic ZVS in cold seep.
2021-09-09 | PXD016502 | Pride
Project description:Malaspina Expedition 2010 bathypelagic metagenomes co-assembly
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Project description:Warming of the North Atlantic Ocean from the 1950s to 2012 is analyzed on neutral density surfaces and vertical levels in the upper 2000?m. Three reanalyses and two observational data sets are compared. The net gain of 5?×?1022?J in the upper 2000?m is roughly 30% of the global ocean warming over this period. Upper ocean heat content (OHC) is dominated in most regions by heat transport convergence without widespread changes in the potential temperature/salinity relation. The heat convergence is associated with sinking of midthermocline isopycnals, with maximum sinking occurring at potential densities ?0?=?26.4-27.3, which contain subtropical mode waters. Water masses lighter than ?0?=?27.3 accumulate heat by increasing their volume, while heavier waters lose heat by decreasing their volume. Spatially, the OHC trend is nonuniform: the low latitudes, 0-30°N are warming steadily while large multidecadal variability occurs at latitudes 30-65°N.Key pointsHeat content change dominated by heat transport convergence Due to widespread sinking trend of midthermocline isopycnals over 50+ years.
| S-EPMC4681455 | biostudies-literature
Project description:Over the past half a century, both the Indian Ocean (IO) and the North Atlantic Ocean (NA) exhibit strong warming trends like a global mean surface temperature (SST). Here, we show that not only simply as a result of increased greenhouse gases, but the IO-NA interaction through atmospheric teleconnection boosts up their warming trends. Climate model simulations demonstrate that the IO warming increases the NA SST by enhancing the longwave radiation through atmospheric teleconnection, subsequently, the warmer NA SST-induced atmospheric teleconnection leads to IO warming by reducing evaporative cooling with weakened surface winds. This two-way interaction (i.e., IO-NA warming chain) acts as positive feedback that reinforces warming over both ocean basins. The Pacific Ocean is partly involved in this warming chain as a modulator in an interdecadal timescale. These results highlight the importance of understanding ocean-basin interactions that may provide a more accurate future projection of warming.
| S-EPMC9270466 | biostudies-literature
Project description:Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. RT-qPCR provided initial evidence that SoxT1A and SoxT1B from H. denitrificans may be intricate components of the oxidation pathway and/or involved in its transcriptional regulation. Here, we extend these analyses with genome-wide mRNA-Seq data for the reference strain, comparing transcription in the absence and presence of 2 mM thiosulfate
2024-11-14 | GSE278992 | GEO
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