Ontology highlight
ABSTRACT:
PROVIDER: PRJNA987419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25052441_1.fastq.gz | Fastqsanger.gz | |||
| SRR25052441_2.fastq.gz | Fastqsanger.gz | |||
| SRR25052442_1.fastq.gz | Fastqsanger.gz | |||
| SRR25052442_2.fastq.gz | Fastqsanger.gz | |||
| SRR25052443_1.fastq.gz | Fastqsanger.gz |
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Project description:This study explores the use of short settling times as a strategy to enhance microbial selection and prevent bulking induced by nutrient shortage in an aerobic dynamic feeding (ADF) process using mixed microbial cultures (MMCs) for polyhydroxyalkanoate (PHA) production from fermentation digestate. A 5.0-L aerobic reactor was operated under three conditions: Long Settling (LS, 30 minutes), Short Settling (SS, 10 minutes), and Short Settling under Nutrient Shortage (SS-NS, 10 minutes with reduced nutrient load). Short settling significantly improved biomass settleability, reducing the Sludge Volume Index (SVI) from 126 to 25 mL g⁻¹, and promoted the formation of dense flocs enriched in PHA-accumulating bacteria, as confirmed by transmission electron microscopy. Process kinetics revealed enhanced substrate uptake rates and improved storage yields under SS conditions, despite an elevated C/P ratio. Notably, nutrient shortage conditions were inadvertently reached by the proliferation of Polytoma mirum in the feeding tank. Although Polytoma mirum did not affect VFA composition, its presence significantly reduced nitrogen and phosphorus concentrations. These nutrient shortage conditions were maintained for at least 30 days until the system began to exhibit stress, as demonstrated by an increased SVI (178.6 mL g⁻¹). Microbial community analyses indicated marked shifts: the eukaryotic assemblage transitioned from sessile to motile ciliates under SS, while bacterial diversity within the PHA‐accumulating fraction remained high, with key taxa such as Sphaerotilus and Neomegalonema becoming more prevalent under phosphorus-limited conditions. Overall, short settling not only improved microbial selection but also prevented bulking by retaining well-aggregated biomass, thereby mitigating nutrient shortage conditions.
2025-07-24 | GSE303499 | GEO
Project description:This study explores the use of short settling times as a strategy to enhance microbial selection and prevent bulking induced by nutrient shortage in an aerobic dynamic feeding (ADF) process using mixed microbial cultures (MMCs) for polyhydroxyalkanoate (PHA) production from fermentation digestate. A 5.0-L aerobic reactor was operated under three conditions: Long Settling (LS, 30 minutes), Short Settling (SS, 10 minutes), and Short Settling under Nutrient Shortage (SS-NS, 10 minutes with reduced nutrient load). Short settling significantly improved biomass settleability, reducing the Sludge Volume Index (SVI) from 126 to 25 mL g⁻¹, and promoted the formation of dense flocs enriched in PHA-accumulating bacteria, as confirmed by transmission electron microscopy. Process kinetics revealed enhanced substrate uptake rates and improved storage yields under SS conditions, despite an elevated C/P ratio. Notably, nutrient shortage conditions were inadvertently reached by the proliferation of Polytoma mirum in the feeding tank. Although Polytoma mirum did not affect VFA composition, its presence significantly reduced nitrogen and phosphorus concentrations. These nutrient shortage conditions were maintained for at least 30 days until the system began to exhibit stress, as demonstrated by an increased SVI (178.6 mL g⁻¹). Microbial community analyses indicated marked shifts: the eukaryotic assemblage transitioned from sessile to motile ciliates under SS, while bacterial diversity within the PHA‐accumulating fraction remained high, with key taxa such as Sphaerotilus and Neomegalonema becoming more prevalent under phosphorus-limited conditions. Overall, short settling not only improved microbial selection but also prevented bulking by retaining well-aggregated biomass, thereby mitigating nutrient shortage conditions.
2025-07-24 | GSE303497 | GEO
Project description:This study explores the use of short settling times as a strategy to enhance microbial selection and prevent bulking induced by nutrient shortage in an aerobic dynamic feeding (ADF) process using mixed microbial cultures (MMCs) for polyhydroxyalkanoate (PHA) production from fermentation digestate. A 5.0-L aerobic reactor was operated under three conditions: Long Settling (LS, 30 minutes), Short Settling (SS, 10 minutes), and Short Settling under Nutrient Shortage (SS-NS, 10 minutes with reduced nutrient load). Short settling significantly improved biomass settleability, reducing the Sludge Volume Index (SVI) from 126 to 25 mL g⁻¹, and promoted the formation of dense flocs enriched in PHA-accumulating bacteria, as confirmed by transmission electron microscopy. Process kinetics revealed enhanced substrate uptake rates and improved storage yields under SS conditions, despite an elevated C/P ratio. Notably, nutrient shortage conditions were inadvertently reached by the proliferation of Polytoma mirum in the feeding tank. Although Polytoma mirum did not affect VFA composition, its presence significantly reduced nitrogen and phosphorus concentrations. These nutrient shortage conditions were maintained for at least 30 days until the system began to exhibit stress, as demonstrated by an increased SVI (178.6 mL g⁻¹). Microbial community analyses indicated marked shifts: the eukaryotic assemblage transitioned from sessile to motile ciliates under SS, while bacterial diversity within the PHA‐accumulating fraction remained high, with key taxa such as Sphaerotilus and Neomegalonema becoming more prevalent under phosphorus-limited conditions. Overall, short settling not only improved microbial selection but also prevented bulking by retaining well-aggregated biomass, thereby mitigating nutrient shortage conditions.
2025-07-24 | GSE303500 | GEO
Project description:The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
2005-11-26 | GSE3681 | GEO
Project description:Proteomic analysis for mouse kidney proteins enriched with E4-PHA lectin
2025-09-02 | PXD055469 | JPOST Repository
Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The deletion of (R)-3-hydroxydecanoyl-ACP:CoA transacylase (PhaG), which connects de novo FA and PHA synthesis pathways, while causing further 1.8-fold decrease in PHA content, did not abolish PHA accumulation. Further proteome analysis revealed quinoprotein alcohol dehydrogeanses PedE and PedH as potential monomer suppliers, but when these were deleted PHA level remained at 2.2 – 14.8 % CDW depending on the fatty acid used, and whether nitrogen limitation was applied. To identify the other non-specific dehydrogenases supply monomers for PHA synthesis, we analysed the proteome of the sextuple mutant under nitrogen limiting and non-limiting conditions.
2023-05-10 | PXD037937 | Pride
Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The proteomes of the WT, phaJ1phaJ4 and phaJ1maoCphaJ4 strains in MSM medium with octanoate under nitrogen limited condition were detected. In addition, we found that the deletion of PhaJ1 in P. putida KT2440 has a negative impact on the PHA accumulation in cells cultivated on glucose with nitrogen limitation conditions. It seems PhaJ1 also mediates the synthesis of PHA when glucose was used as the carbon and energy source. To investigate the role of PhaJ1 in PHA accumulation with glucose, the proteomes of P. putida KT2440 wild type, phaJ1, phaJ1phaJ4 and phaJ1maoCphaJ4 mutant growing on glucose were detected and compared.
2023-05-10 | PXD037932 | Pride
Project description:Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures. To maximize PHA production, mixed microbial cultures may be enriched for PHA-producing bacteria with a high storage capacity through the imposition of cyclic, aerobic feast-famine conditions in a sequencing batch reactor (SBR). Though enrichment SBRs have been extensively investigated a bulk solutions-level, little evidence at the proteome level is available to describe the observed SBR behavior to guide future SBR optimization strategies. As such, the purpose of this investigation was to characterize proteome dynamics of a mixed microbial culture in an SBR operated under aerobic feast-famine conditions using fermented dairy manure as the feedstock for PHA production. At the beginning of the SBR cycle, excess PHA precursors were provided to the mixed microbial culture (i.e., feast), after which followed a long duration devoid of exogenous substrate (i.e., famine). Two-dimensional electrophoresis was used to separate protein mixtures during a complete SBR cycle, and proteins of interest were identified.
2017-01-31 | PXD003126 | Pride