Oxic effect of benthic marine fungi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB54572 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9928355_1.fastq.gz | Fastqsanger.gz | |||
| ERR9928355_2.fastq.gz | Fastqsanger.gz | |||
| ERR9935870_1.fastq.gz | Fastqsanger.gz | |||
| ERR9935870_2.fastq.gz | Fastqsanger.gz | |||
| ERR9935890_1.fastq.gz | Fastqsanger.gz |
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Project description:This SuperSeries is composed of the following subset Series: GSE15272: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "A" GSE15273: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B" GSE15274: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-1" GSE15275: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C" GSE15276: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-2" Refer to individual Series
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Project description:In order to ensure the reproducibility of the transcriptional response of Halobacterium NRC-1 to oxic/anoxic transitions, we repeated global mRNA measurements for the oxygen time series data in GSE5924, except that cultures were equilibrated to high oxygen for 12 hours prior to the start of the experiment rather than low oxygen. The results of these data suggest that there is good (~60%) reproducibility between datasets, and that Halobacterium responds robustly to oxic/anoxic transitions. Keywords: time series
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Project description:Chemosynthetic symbioses between bacteria and invertebrates occur worldwide in a wide range of marine habitats. Although they have been intensively investigated, molecular physiological studies of chemoautotrophic bacteria colonizing the surface of animals (ectosymbioses) are scarce. Stilbonematinae nematodes are the only known invertebrates capable of cultivating monocultures of thiotrophic Gammaproteobacteria on their surface. Crucially, as these nematodes migrate through the redox zone of marine sediments, the ectosymbionts directly experience drastic variations in oxygen concentration. Here, by applying an array of omics, Raman microspectroscopy and stable isotope labeling-based techniques, we investigated the effect of varying concentrations of dissolved oxygen on physiology and metabolism of Candidatus Thiosymbion oneisti, the longitudinally dividing ectosymbiont of Laxus oneistus. We show that, unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, and that carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation in addition to genes responsible for assimilating organic carbon compounds and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization genes were upregulated in oxic versus anoxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin and cofactor biosynthesis genes likely necessary to withstand its deleterious effects. Based on this first global physiological study of an uncultured, chemosynthetic ectosymbiont, we propose that, in anoxic pore water, it proliferates by utilizing nitrate to oxidize reduced sulfur compounds, whereas, when exposed to oxygen, it exploits aerobic respiration to facilitate energetically costly assimilation of carbon and nitrogen to survive oxidative stress. Both anaerobic sulfur oxidation and its decoupling from carbon fixation represent unprecedented adaptations among chemosynthetic symbionts. We postulate that Ca. T. oneisti originated from an obligate anaerobic, denitrifying sulfur-oxidizer, which, while transitioning from the free-living to the symbiotic lifestyle, evolved mechanisms to survive the oxidative stress inherent to a life attached to an animal.
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Project description:Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here, by applying omics, Raman microspectroscopy and stable isotope labeling, we investigated the effect of oxygen on the metabolism of Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation, organic carbon assimilation and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization were upregulated in oxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and fewer symbionts were detected to divide. Based on this first global physiological study of an uncultured chemosynthetic ectosymbiont, we propose that, in anoxic sediment, its proliferation is powered by anaerobic sulfur oxidation coupled to denitrification, whereas in upper layers it makes use of aerobic respiration to facilitate assimilation of carbon and nitrogen, and to survive oxidative stress. The ectosymbiont’s versatile metabolism is thus well-adapted to exploiting a highly changeable environment.
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Project description:To gain a comprehensive systems-level understanding of cellular phenotypes, it is critical to characterize the relationship between the dynamic transcriptome and proteome during environmental perturbations. Previous comparisons have shown a lack of correlation between mRNA and protein level measurements suggesting a predominant role for post-transcriptional regulation in mediating cellular environmental responses. To investigate the extent of post-transcriptional regulation, we have analyzed transcriptome and proteome level changes over a 13-hour 28-point time course during transitions between oxic and anoxic physiologies of Halobacterium. Integrated computational analyses of these data show that temporally shifting mRNA and protein profiles relative to one another significantly increases the mRNA/protein correlation. Although time lags for unrelated genes vary widely, we observe similar temporal lags between the transcription and translation of functionally related genes. In contrast, no significant temporal separation was observed within the transcript profiles. Taken together, these data suggest that while there is indeed a direct correlation between many corresponding changes at mRNA and protein levels, translational delay may be the predominant mechanism for the temporal regulation of protein abundance during physiological oxic/anoxic transitions in Halobacterium. The approach and algorithms delineated in this study provide a framework for incorporating the temporal dimension of information processing across many different layers of gene regulation. Keywords: time course
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Project description:B. cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis (CF). In the CF lung, bacteria grow to high densities within the viscous mucus that is limited in oxygen. Pseudomonas aeruginosa, the dominant pathogen in CF patients, is known to grow and survive under oxygen-limited to anaerobic conditions by using micro-oxic respiration, denitrification and fermentative pathways. In contrast, inspection of the genome sequences of available B. cenocepacia strains suggested that B. cenocepacia is an obligate aerobic and non-fermenting bacterium. In accordance with the bioinformatics analysis, we observed that B. cenocepacia H111 is able to grow with as little as 0.1% O2 but not under strictly anoxic conditions. Phenotypic analyses revealed that H111 produced larger amounts of biofilm, pellicle and proteases under micro-oxic conditions (0.5% - 5% O2, i.e. conditions that mimic those encountered in CF lung infection), and was more resistant to several antibiotics. RNA-Seq and shotgun proteomics analyses of cultures of B. cenocepacia H111 grown under micro-oxic and aerobic conditions showed up-regulation of genes involved in the synthesis of the exopolysaccharide (EPS) cepacian as well as several proteases, two isocitrate lyases and other genes potentially important for life in micro-oxia. Oxygen regulation in Burkholderia cenocepacia was investigated using RNA-Seq of cells grown under aerobic or micro-oxic conditions.
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