Ontology highlight
ABSTRACT:
PROVIDER: PRJNA599305 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers. 18 samples; Triplicate PHB-enriched bacterial communities recovered from activated sludge were exposed to nanoparticle (TiO2 or Ag) or AgNO3 (as a silver control) or were not exposed to an nanoparticles (control) to determine if the naoparticles affected PHB production.
2014-12-03 | E-GEOD-63781 | biostudies-arrayexpress
Project description:Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.
2014-12-03 | GSE63781 | GEO
Project description:Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. cenocepacia H111 also up-regulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen responsive genes identified a s54 consensus sequence. The mapping of the s54 regulon as well as the characterization of a s54 mutant suggests an important role of s54 not only in control of nitrogen metabolism, but also in virulence of this organism. Nitrogen limitation and s54 regulon in B. cenocepacia
2015-04-29 | E-GEOD-66328 | biostudies-arrayexpress
Project description:Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. cenocepacia H111 also up-regulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen responsive genes identified a s54 consensus sequence. The mapping of the s54 regulon as well as the characterization of a s54 mutant suggests an important role of s54 not only in control of nitrogen metabolism, but also in virulence of this organism.
2015-04-29 | GSE66328 | GEO
Project description:For many years now, Bacillus megaterium has served as a microbial industrial strain for high-level production of recombinant proteins in the g/L-scale. Nevertheless, the impact of process-related stress has only been poorly characterized so far. Taking advantage of the recent technical developments for quantifying the cell at various molecular levels, we interrogated the osmotic stress response of B. megaterium using transcriptome, proteome, metabolome and fluxome analyses. Under osmotic upshift conditions, several stress response enzymes, iron scavenging, and reactive oxygen species (ROS) fighting proteins were upregulated. The downregulation of genes of the upper part of glycolysis resulted in the activation of the pentose phosphate pathway (PPP), generating an oversupply of NADPH. The (NADH/NAD+) ratio indicating the redox state of the cell was also altered, which was partially compensated by the higher production of lactate accompanied by the reduction of acetate secretion. NADH was produced mainly within the tricarboxylic acid cycle (TCA) cycle elucidated from the higher mRNA and protein levels of enzymes involved within this pathway. This adaptation mainly focused on the massive de novo synthesis of the compatible solute proline recruiting an osmo-dependent pathway to fulfil this requirement. 13C flux analyses confirmed these findings. Giving the high flux towards acetyl-CoA and large pool of NADPH, B. megaterium cells redirected the produced acetyl-CoA to the polyhydroxybutyrate (PHB) biosynthetic pathway under non-limiting nutrient condition, amassing around 30% of the CDW as PHB. This direct relation between osmotic stress and intracellular PHB content has been evidenced for the first time, thus opening new avenues for synthesizing this valuable biopolymer using varying salt concentrations under non-limiting nutrient conditions.
2020-05-26 | PXD015605 | Pride
Project description:Polyhydroxybutyrate (PHB) is a carbon and energy storage polymer, whose accumulation under nutrient imbalances with excess carbon is a widespread phenomenon in bacteria. PhaR is a conserved transcriptional regulator found to be associated to PHB granules in several species. Although its role in modulating PHB storage and metabolism has been extensively studied across the bacterial phylogeny, a comprehensive analysis of the PhaR regulon within the context of its dual role as a metabolic sensor and regulator remains missing. To bridge this gap, we integrated co-expression network analysis with proteome profiling across multiple mutant backgrounds (lack of PhaR (AniA) and/or PHB synthesis) in the free-living state of the PHB-accumulating alphaproteobacterial root nodule symbiont Sinorhizobium meliloti. This analysis was enriched by identifying direct regulatory targets of PhaR through a regulon-centric computational multi-step search for DNA binding site motifs combined with PhaR-DNA binding and promoter-reporter assays. We confirmed that the model of accumulated PHB sequestering PhaR and thereby relieving phasin and PHB depolymerase gene repression to control cellular PHB levels also applies to S. meliloti, and showed that PhaR-mediated regulation also occurs the symbiotic state. A comprehensive picture of the impact of PHB-mediated PhaR titration on cellular functions revealed exopolysaccharide production as well as central carbon metabolism (pdh and bkd), gluconeogenesis (ppdK and pyc), entry into the TCA cycle (gltA), and the initial steps of the Entner-Doudoroff pathway (zwf, pgl and edd) as major regulatory targets, and beyond carbon metabolism several target genes of yet unknown function. Our findings highlight a pivotal role for PhaR in orchestrating carbon metabolism.
2025-09-01 | PXD061645 | Pride
Project description:Food waste is a major source of environmental pollution, as its landfills attribute to greenhouse gas emissions. This study developed a robust upcycling bioprocess that converts food waste into lactic acid through autochthonous fermentation and further produces biodegradable polymer polyhydroxybutyrate (PHB). Food can be stored without affecting its bioconversion to lactic acid, making it feasible for industrial application. Mapping autochthonous microbiota in the food waste fermentation before and after storage revealed lactic-acid-producing microorganisms dominate during the indigenous fermentation. Furthermore, through global transcriptomic and gene set enrichment analyses, it was discovered that coupling lactic acid as carbon source with ammonium sulfate as nitrogen source in Cupriavidus necator culture upregulates pathways, including PHB biosynthesis, CO2 fixation, carbon metabolism, pyruvate metabolism, and energy metabolism compared to pairing with ammonium nitrate. There was ∼90 % PHB content in the biomass. Overall, the study provides crucial insights into establishing a bioprocess for food waste repurposing.
2025-06-16 | GSE296860 | GEO
Project description:Optimization of direct cellulose fermentation by mixed bacterial culture using response surface methodology
| PRJEB43024 | ENA
Project description:Gas fermentation is emerging as an economically attractive option for the sustainable production of fuels and chemicals from gaseous waste feedstocks. Clostridium autoethanogenum can use CO and/or CO2 + H2 as its sole carbon and energy sources. Fermentation of C. autoethanogenum is currently being deployed on a commercial scale for ethanol production. Expanding the product spectrum of acetogens will enhance the economics of gas fermentation. To achieve efficient heterologous product synthesis, limitations in redox and energy metabolism must be overcome. Here, we engineered and characterised at a systems-level, a recombinant poly-3-hydroxybutyrate (PHB)-producing strain of C. autoethanogenum. Cells were grown in CO-limited steady-state chemostats on two gas mixtures, one resembling syngas (20% H2) and the other steel mill off-gas (2% H2). Results were characterised using metabolomics and transcriptomics, and then integrated using a genome-scale metabolic model reconstruction. PHB-producing cells had an increased expression of the Rnf complex, suggesting energy limitations for heterologous production. Subsequent optimisation of the bioprocess led to a 12-fold increase in the cellular PHB content. The data suggest that the cellular redox state, rather than the acetyl-CoA pool, was limiting PHB production. Integration of the data into the genome-scale metabolic model showed that ATP availability limits PHB production. Altogether, the data presented here advances the fundamental understanding of heterologous product synthesis in gas-fermenting acetogens.
2019-02-03 | GSE115837 | GEO