Activated sludge metagenome
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ABSTRACT:
PROVIDER: PRJNA1056786 | ENA |
REPOSITORIES: ENA
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Project description:Study on effective nitrogen recovery from high-yield Cyanophycin in algal-bacterial sludge
| PRJNA1056309 | ENA
Project description:Landfill leachate water is often treated in a biological processing step. In most cases a stable operation of the industrial scale plants is controlled by sum parameters such as process relevant ion concentrations, dry matter concentration and dissolved oxygen concentration. A deeper understanding of the current status of the individual cell or the biocoenosis would help to understand malfunctions or the reason for inefficient plant performance. In a simple batch experimental setup, samples of two different conditions have been generated to unravel bacterial proteome changes in response to medium term lack of oxygen supply and landfill leachate addition. The first condition was an activated sludge sample condition from an industrial scale landfill leachate treatment plant with the process stages of nitrification and denitrification. After 45 days without aeration and with addition of leachate and carbon sources as fed batch, the second sample (condition 2) was taken. A comprehensive LC-MS/MS based protemic screen was performed aiming for the identification and quantification of waste water specific bacteria proteomes. To this end, a novel combination of two protein extraction methods has been established meeting the requirements for LC-MS/MS anaylsis. Around 600 proteins were identified of which 90 % were quantified in at least 3 replicates. Numerous essential proteins to maintain the cell redox homeostasis are overexpressed in the condition 1 which was aerated with oxygen and stressed by the ultrafiltration compared to condition 2, which was not aerated in a lab experiment. In addition, heat and cold shock proteins and two proteins related to the apoptosis of organisms (spermidine/putrescine transport system and apoptosis-inducing factor) were identified.
2022-02-23 | PXD011917 | Pride
Project description:The light-organ symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri offers the opportunity to decipher the hour-by-hour events that occur during the natural colonization of an animal's epithelial surface by its microbial partners. To determine the genetic basis of these events, a glass-slide microarray was used to characterize the light-organ transcriptome of juvenile squid in response to the initiation of symbiosis. Patterns of gene expression were compared between animals not exposed to the symbiont, exposed to the wild-type symbiont, or exposed to a mutant symbiont defective in either of two key characters of this association: bacterial luminescence or autoinducer (AI) production. Hundreds of genes were differentially regulated as a result of symbiosis initiation, and a hierarchy existed in the magnitude of the host's response to three symbiont features: bacterial presence > luminescence > AI production. Putative host receptors for bacterial surface molecules known to induce squid development are up-regulated by symbiont light production, suggesting that bioluminescence plays a key role in preparing the host for bacteria-induced development. Further, because the transcriptional response of tissues exposed to AI in the natural context (i.e., with the symbionts) differed from that to AI alone, the presence of the bacteria potentiates the role of quorum signals in symbiosis. Comparison of these microarray data with those from other symbioses, such as germ-free/conventionalized mice and zebrafish, revealed a set of shared genes that may represent a core set of ancient host responses conserved throughout animal evolution.
2008-11-10 | GSE13533 | GEO
Project description:Activated sludge bacterial and archeal communities from Konstanz, Germany to study Microbial Dark Matter (Phase II) - J533_phenol metaG metagenome
| PRJNA364546 | ENA
Project description:The light-organ symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri offers the opportunity to decipher the hour-by-hour events that occur during the natural colonization of an animal's epithelial surface by its microbial partners. To determine the genetic basis of these events, a glass-slide microarray was used to characterize the light-organ transcriptome of juvenile squid in response to the initiation of symbiosis. Patterns of gene expression were compared between animals not exposed to the symbiont, exposed to the wild-type symbiont, or exposed to a mutant symbiont defective in either of two key characters of this association: bacterial luminescence or autoinducer (AI) production. Hundreds of genes were differentially regulated as a result of symbiosis initiation, and a hierarchy existed in the magnitude of the host's response to three symbiont features: bacterial presence > luminescence > AI production. Putative host receptors for bacterial surface molecules known to induce squid development are up-regulated by symbiont light production, suggesting that bioluminescence plays a key role in preparing the host for bacteria-induced development. Further, because the transcriptional response of tissues exposed to AI in the natural context (i.e., with the symbionts) differed from that to AI alone, the presence of the bacteria potentiates the role of quorum signals in symbiosis. Comparison of these microarray data with those from other symbioses, such as germ-free/conventionalized mice and zebrafish, revealed a set of shared genes that may represent a core set of ancient host responses conserved throughout animal evolution. Six experimental treatments of juvenile animals were performed for the microarray matrix: uncolonized (Apo); uncolonized, but supplemented with AI (Apo + AI); colonized by wild-type V. fischeri (wild type); colonized by a mutant defective in luciferase synthesis (luxA); colonized by a mutant defective in AI synthesis (luxI); and, colonized by the luxI mutant, but supplemented with AI (luxI + AI). At 18 h postinoculation, animals were anesthetized in 2% ethanol in HOSW, and the light organs were removed into RNAlater (Ambion Biosystems).
2008-11-10 | E-GEOD-13533 | 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: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:Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge on the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark‑light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy null mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark‑light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light‑induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.
2023-10-12 | GSE245047 | GEO