Sludge from the batch reactor used in the removal of ibuprofen in denitrifying condition
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ABSTRACT:
PROVIDER: PRJNA759422 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15696890_1.fastq.gz | Fastqsanger.gz | |||
| SRR15696890_2.fastq.gz | Fastqsanger.gz | |||
| SRR15696891_1.fastq.gz | Fastqsanger.gz | |||
| SRR15696891_2.fastq.gz | Fastqsanger.gz | |||
| SRR15696892_1.fastq.gz | Fastqsanger.gz |
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Project description:Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale sequencing batch reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8-8.0, respectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high NH3-N (1.9-10 mg NH3-N/L) and low nitrite (3-8 mg TNN/L) are required conditions during the whole SBR cycle. Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase ?-subunit (amoA) gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the "Ca. Brocadia fulgida" type, able to grow in presence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS) gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus Nitrobacter was detected.
| S-EPMC3912432 | biostudies-literature
Project description:Ibuprofen is one of the most commonly detected pharmaceuticals in wastewater effluent; however the effects of ibuprofen on aquatic organisms are poorly understood. This study presents the transcriptome-wide response of the inland silverside, Menidia beryllina, to chronic 14 d exposures to ibuprofen.
2015-09-01 | GSE64967 | GEO
Project description:Transcriptional profiling of small intestinal explants cultured in the absence or in the presence of Ibuprofen (100 µM). Two-condition experiment, control intestinal explants vs Ibuprofen intestinal explants
2019-01-07 | GSE108369 | GEO
Project description:Ibuprofen is one of the most commonly detected pharmaceuticals in wastewater effluent; however the effects of ibuprofen on aquatic organisms are poorly understood. This study presents the transcriptome-wide response of the inland silverside, Menidia beryllina, to chronic 14 d exposures to ibuprofen. Twenty-four samples were run on twenty-four arrays, there were six replicates for each of three ibuprofen exposure concentrations and a control group.
2015-09-01 | E-GEOD-64967 | biostudies-arrayexpress
Project description:Microarray is a powerful technique that has been used extensively for genome-wide gene expression analysis. Several different microarray technologies are available, but lack of standardization makes it challenging to compare and integrate data from different platforms. Furthermore, batch related biases within datasets are common, but are often not tackled prior to the data analysis, potentially affecting the end results. In the current study, a set of 234 breast cancer samples were analyzed on two different microarray platforms. The aim was to compare and evaluate the reproducibility and accuracy of gene expression measurements obtained from our in-house 29K array platform with data from Agilent SurePrint G3 microarray platform. The 29K dataset contained known batch-effects associated with the fabrication procedure. We here demonstrate how the use of ComBat batch adjustments method can unmask true biological signals by successfully overcoming systematic technical variations caused by differences between fabrication batches and microarray platforms. Paired correlation analysis revealed a high level of consistency between data obtained from the 29K gene expression platform and Agilent SurePrint G3 platform, which could be further improved by ComBat batch adjustment. Particularly high-variance genes were found to be highly reproducibly expressed across platforms. Furthermore, high concordance rates were observed both for prediction of estrogen receptor status and intrinsic molecular breast cancer subtype classification, two clinical important parameters. In conclusion, the current study emphasizes the importance of utilizing proper batch adjustment methods to reduce systematically technical bias when comparing and integrating data from different fabrication batches and microarray platforms.
2015-06-01 | GSE54275 | GEO
Project description:Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered “generalist” and “specialist” archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 11-29% of the abundant NRE archetypes. Archetypes found in a particular site, “specialists”, were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+. A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2S, respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among denitrifying communities and supports the essential role of individual community members in overall ecosystem function.
2017-05-02 | GSE98190 | GEO
Project description:Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3(-)-N could be removed or reduced, some amount of NO2(-)-N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.
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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:Denitrifying activated sludge Metagenome
| PRJNA464171 | ENA
Project description:Complex and high levels of various pollutants in high-strength wastewaters hinder efficient and stable biological nutrient removal. In this study, the changes in pollutant removal performance and microbial community structure in a laboratory-scale anaerobic/aerobic sequencing batch reactor (SBR) treating simulated pre-fermented high-strength wastewater were investigated under different influent loading conditions. The results showed that when the influent chemical oxygen demand (COD), total nitrogen (TN), and orthophosphate (PO43--P) concentrations in the SBR increased to 983, 56, and 20 mg/L, respectively, the COD removal efficiency was maintained above 85%, the TN removal efficiency was 64.5%, and the PO43--P removal efficiency increased from 78.3% to 97.5%. Partial nitrification with simultaneous accumulation of ammonia (NH4+-N) and nitrite (NO2--N) was observed, which may be related to the effect of high influent load on ammonia- and nitrite-oxidising bacteria. The biological phosphorus removal activity was higher when propionate was used as the carbon source instead of acetate. The relative abundance of glycogen accumulating organisms (GAOs) increased significantly with the increase in organic load, while Tetrasphaera was the consistently dominant polyphosphate accumulating organism (PAO) in the reactor. Under high organic loading conditions, there was no significant PAO-GAO competition in the reactor, thus the phosphorus removal performance was not affected.
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