Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean
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ABSTRACT:
ORGANISM(S): seawater metagenome
PROVIDER: GSE136729 | GEO | 2021/04/30
REPOSITORIES: GEO
Similar Datasets
Project description:Role of thiosulfate as a source of energy in the bathypelagic North Atlantic Ocean
| PRJNA563349 | ENA
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
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: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:Cyanobacteria are photoautotrophic prokaryotes with a plant-like photosynthetic machinery. Besides being able to grow photoautotrophically, some cyanobacteria are also capable to grow photoheterotrophically, where they use reduced organic compounds as carbon source, or even completely heterotrophically by using reduced organic compounds as carbon and energy source. The well characterized cyanobacterium Synechocystis sp. PCC 6803 can grow in darkness under light-activated heterotrophic growth (LAHG) conditions by using glucose as carbon and energy source. In the present work, we combined pre-fractioning of Synechocystis cellular membranes with a global proteome and lipidome analysis, to shift the analytical focus towards the rearrangement of the internal thylakoid membrane system observed in Synechocystis cells under LAHG conditions.
2015-03-03 | PXD000980 | Pride
Project description:Metagenomic analysis of a thiosulfate-disproportionating enrichment culture
| PRJDB7139 | ENA
Project description:Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, representing geologically ancient ecosystems which are still widespread on Earth and supposedly harbor relict microbial communities. We compared metabolic features and their genomic determinants in two strains of a single natronophilic species Dethiobacter alkaliphilus, the only cultured representative of “Dethiobacteria” class within Bacillota phylum. The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultatively chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered iron reducing ability of strain AHT1T, as well as the capability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This assumption was supported by meta-analysis of publicly available Dethiobacterial metagenomes, as well as by the enrichment of a novel phylotype from a deep subsurface non-serpentinizing slightly alkaline water after its amendment with an Fe(III) mineral. Genome analysis of D. alkaliphilus strains revealed that the most probable determinants of iron and sulfur redox transformations in the organism are multiheme c-type cytochromes. Their phylogeny reconstruction showed that sulfur and thiosulfate respiration is most probably provided by evolutionary early forms of unconventional octaheme tetrathionate and sulfite reductases sharing a root with structurally similar group of OmhA/OcwA Fe(III)-reductases. Large sets of other multihemes are likely to provide Fe(III) reduction in both strains. Also, several different, yet phylogenetically related, determinants of anaerobic Fe(II) oxidation were identified in Z-1002 genome, and the oxidation process was further experimentally proven. Considering these results and phylogenetic relatedness of D. alkaliphilus’s sulfur reductases with Fe(III) reducing cytochromes, but not with archetypal bacterial sulfur/thiosulfate reductases, we suggest that sustaining high variation of multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline anaerobic environments. We further propose that sulfur-enriched soda lakes are secondary habitats for D. alkaliphilus comparing to Fe-rich serpentinites, and discuss the evolutionary traits which might occur in prokaryotes on a crucial junction of the biosphere’s history, when intensification of the sulfur cycle outweighed the global significance of the iron cycle.
2023-10-24 | PXD040929 | Pride
Project description:The metabolic versatile hyperthermophilic dissimilatory sulfate-reducing archaeon, Archaeoglobus fulgidus VC-16, both utilize carbon monoxide as energy source and is highly resistant to toxic effects of CO. This metabolic capacity was investigated by transcriptional response to growth with CO of cultures supplemented with sulfate (S-CO) or thiosulfate (T-CO), and without external electron acceptor (CO-without election acceptor ).
2015-04-30 | E-MTAB-3035 | biostudies-arrayexpress
Project description:The hydrothermal vent gammaproteobacterium Thiomicrospira crunogena inhabits an unstable environment and must endure dramatic sweeps in habitat chemistry. This sulfur chemolithoautotroph responds to changes in dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO3-2) availability with a carbon concentrating mechanism (CCM), in which whole-cell affinity for DIC, as well as the intracellular DIC concentration, increase substantially under DIC-limitation. To determine whether this CCM is regulated at the level of transcription, cells cultivated under high-DIC conditions in chemostats were resuspended in growth medium with low concentrations of DIC, and CCM development was tracked in the presence and absence of RNA polymerase inhibitor rifampicin. The induction of the CCM, as measured by silicone oil centrifugation, was hindered in the presence of rifampicin. Similar results were observed for carboxysome gene transcription and assembly, as assayed by qRT-PCR and transmission electron microscopy, respectively. Genome-wide transcription patterns, assayed via microarrays, were compared for cells grown under DIC-limitation versus ammonia limitation. In addition to carboxysome genes, two novel genes (Tcr_1019 and Tcr_1315), present in other organisms including chemolithoautotrophs, but whose function(s) have not been elucidated in any organism, were found to be upregulated under low-DIC conditions. Likewise, under ammonia limitation, in addition to the expected enhancement of ammonia transporter and PII-gene transcription, the transcription of two novel genes was measurably enhanced (Tcr_0466 and Tcr_2018). Upregulation of all four genes was verified via qRT-PCR (Tcr_1019: 4-fold; Tcr_1315: ~7-fold; Tcr_0466: >200-fold; Tcr_2018: 7-fold), suggesting novel components are part of the response to nutrient limitation by this organism. In this study Thiomicrospira crunogena cells were grown under inorganic carbon limitation and ammonia limitation (high inorganic carbon concentrations) to examine genome wide transcription responses
2012-03-04 | E-GEOD-36254 | biostudies-arrayexpress
Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.
2013-11-01 | GSE46076 | GEO