Bioreactor metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA291553 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2136643.fastq.gz | Fastqsanger.gz |
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Project description:The Staphylococcus aureus strain Newman uses the dithiol-containing repressor CstR to sense sulfide stress via reactive sulfur species (RSS), allowing transcription of a mitochondrial-like sulfide oxidation system, the core of which is genetically linked to methicillin resistance determinants in MRSA strains. The cytoplasm maintains an excess of reduced relative to oxidized low molecular weight (LMW) thiols that are protective against oxidative stress and transition metal (Zn, Cd and Cu) toxicity, buffering these ions to low “free” concentrations via formation of coordination complexes. We hypothesize that unregulated H2S perturbs the LMW thiol pool by generating RSS; these, in turn, react with CstR cysteines (C31, C60), induce cst derepression, and are cleared by cst-encoded enzymes. These results show that sulfide stress induces the cst operon and a zinc starvation response, represses cysteine biosynthesis, and generally represses genes that are induced by acute oxidative stress; in addition, strong repression of the expression of staphylococcal virulence factors is observed in the ∆cstR strain.
2017-06-19 | GSE99432 | GEO
Project description:Beller, H. R., T. E. Letain, A. Chakicherla, S. R. Kane, T. C. Legler, and M. A. Coleman. 2006. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic vs. denitrifying conditions. Journal of Bacteriology 188:7005-7015. Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends. Keywords: bacterial metabolism
2006-10-06 | GSE5256 | GEO
Project description:Competition among nitrate reducing bacteria (NRB) and sulfate reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater and sediment, and therefore may play important roles in competitive interactions. Here, using Intrasporangium calvum C5 as a model NRB, we performed comparative transcriptomic and metabolomic analyses to demonstrate that the reduced sulfur compounds cysteine and sulfide differentially inhibit respiratory growth on nitrate, and that inhibition by each can be selectively relieved by a specific carbon source. These findings provide mechanistic insights into the interplay and stratification of NRBs and SRBs in diverse environments.
2020-10-01 | GSE158822 | GEO
Project description:There is a great need for setting novel measurable attributes at the cell physiological level in a scalable biopharmaceutical production process to be able to predict the process outcomes and improve process understanding. In a biologic production process, changes in culture environment due to several factors such as shear and bubble induced damage from gas sparging and agitation are known to occur. There is a gap in the knowledge of cellular response due to varying bioreactor environment itself during the course of cell culture, from lag-phase to log-phase to stationary-phase in culture. With the emergence of micro-arrays as tools for exploring cell physiological changes, it opens the possibility for studying the effect of bioreactor culture environment itself on the cell substrate. Such information could be eventually used to designate gene transcripts as biomarkers for cell status in a controlled bioreactor system. A model 5L bench-scale bubble aerated and impeller agitated bioreactor system was used to study gene expression profiles of a hybridoma cell line during the time-course of batch culture. Gene expression profiles that were variable from early-to-late in batch culture, as well as invariant gene profiles were summarized using microarray findings. Typical cellular functions studied were oxidative stress response, DNA damage response, apoptosis, antioxidant activity, cellular metabolism, and protein folding. These findings were also verified with a more rigorous semi-quantitative RT-PCR technique. The results of this study suggest that under predefined bioreactor culture conditions, significant gene changes from lag to log to stationary phase could be identified, which could then be used to track the culture state. We ran consecutive 5L bioreactor runs, each with an independent vial thaw, to achieve multiple biological replicates per time-point. Bioreactors were sampled approximately every 12 hours for RNA extraction. For the 5L bioreactors, microarray samples were run for day 1 (n=2), day 2 (n=2), day 3 (n=3), and day 3.5 (n=3). Here 2 or 3 of the three biological replicates run for each time-point were included in the analysis, based on >70% genes found. We define early exponential as day 1, peak exponential as day 2 and day 3 and late stationary as day 3.5.
2012-10-01 | E-GEOD-33062 | biostudies-arrayexpress
Project description:There is a great need for setting novel measurable attributes at the cell physiological level in a scalable biopharmaceutical production process to be able to predict the process outcomes and improve process understanding. In a biologic production process, changes in culture environment due to several factors such as shear and bubble induced damage from gas sparging and agitation are known to occur. There is a gap in the knowledge of cellular response due to varying bioreactor environment itself during the course of cell culture, from lag-phase to log-phase to stationary-phase in culture. With the emergence of micro-arrays as tools for exploring cell physiological changes, it opens the possibility for studying the effect of bioreactor culture environment itself on the cell substrate. Such information could be eventually used to designate gene transcripts as biomarkers for cell status in a controlled bioreactor system. A model 5L bench-scale bubble aerated and impeller agitated bioreactor system was used to study gene expression profiles of a hybridoma cell line during the time-course of batch culture. Gene expression profiles that were variable from early-to-late in batch culture, as well as invariant gene profiles were summarized using microarray findings. Typical cellular functions studied were oxidative stress response, DNA damage response, apoptosis, antioxidant activity, cellular metabolism, and protein folding. These findings were also verified with a more rigorous semi-quantitative RT-PCR technique. The results of this study suggest that under predefined bioreactor culture conditions, significant gene changes from lag to log to stationary phase could be identified, which could then be used to track the culture state.
2012-10-01 | GSE33062 | GEO
Project description:Enhanced biological phosphorus removal bioreactor Metagenome
| PRJNA259882 | ENA
Project description:Bacteria in an anaerobic bioreactor for Sb removal
| PRJDB18237 | ENA
Project description:Bacteria in an anaerobic bioreactor for Sb removal
| PRJDB18121 | ENA
Project description:Anaerobic ammonium-oxidising (anammox) bacteria, members of the ‘Candidatus Brocadiaceae’ family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-bound compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic- and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbour multiple copies of ammonium-, nitrite- and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite- and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells under ammonium-limitation showed that three of the seven ammonium transporter genes and one of the six nitrite transporter genes were significantly upregulated, while another ammonium and nitrite transporter gene were downregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.
2020-06-05 | GSE148825 | GEO