Nitrosomonas europaea expression analysis of biofilm growth and biofilms exposed to phenol and toluene
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ABSTRACT:
ORGANISM(S): Nitrosomonas europaea Nitrosomonas europaea ATCC 19718
PROVIDER: GSE22646 | GEO | 2010/07/20
SECONDARY ACCESSION(S): PRJNA128031
REPOSITORIES: GEO
Similar Datasets
Project description:The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate. The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms. Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene. These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms. Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea. Four sample groups of N. europaea cells were used in this study, with biological triplicates of each group. Groups were: Control (untreated) biofilms, phenol-exposed biofilms, toluene-exposed biofilms, and exponentially growing suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors containing 4 independent growth channels and subject to 2 hour inhibition tests. During each experiment, 2 biofilm channels served as control with no inhibitor present and the other 2 biofilm channels were exposed to either 60 uM phenol or 100 uM toluene. Nitrite production was monitored throughout the experiment, and the given concentrations of phenol and toluene resulted in 50% inhibition of ammonia oxidation by the biofilms. Suspended cells were grown in batch reactors. Three 4-plex NimbleGen microarray chips were used, and each chip contained one sample from each experimental group. QC of samples was determined by spectrophotometric methods and using Agilent bioanalyzer traces to determine purity and integrity of RNA and cDNA. A sample tracking report was used to verify the correct hybridization of each sample to the intended array.
2010-07-20 | E-GEOD-22646 | biostudies-arrayexpress
Project description:Nitrosomonas europaea expression analysis of biofilm growth and biofilms exposed to phenol and toluene
| PRJNA128031 | ENA
Project description:The effects of the aromatic hydrocarbons benzene and toluene on Nitrosomonas europaea, a nitrifying bacterium that plays an important role in the removal of nitrogen from wastewater treatment plants, were studied in batch reactors. Exposure to 20 M toluene and 40 M benzene resulted in a 50% reduction in nitrifying activity after 1 h. However, Affymetrix microarray experiments detected no significant changes in gene expression in toluene exposed cells. Cells exposed to benzene were found to up-regulate a gene cluster (NE 1545 - NE 1551). This gene cluster appears to be involved with fatty-acid metabolism, lipid and membrane protein biosynthesis. TEM experiments reveal that cells exposed to benzene decrease the thickness of their membrane and the membrane becomes more structured. Keywords: stress response, benzene, toluene
2008-02-13 | GSE10507 | GEO
Project description:Investigation of the whole genome gene expression level changes relative to exponential phase growth in Nitrosomonas europaea ATCC19718 after 12 hours ammonia starvation, 144 hours ammonia starvation, and 20 minutes following ammonia addition to starved cells. The ammonia monooxygenase of chemolithotrophic ammonia oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2). Several AOB, including N. europaea, also posess a divergent monocistronic copy of amoC (amoC3) of unknown function. Previous work suggested a possible functional role for amoC3 in N. europaea during recovery from extended ammonia starvation as part of the σE- stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC3 is part of a general post-starvation cellular response system in N. europaea. We also found that amoC3 is required for efficient exit from prolonged ammonia starvation, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon also plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress responsive subunit capable of maintaining ammonia oxidation activity under stress conditions. A twelve chip study using total RNA recovered from four timepoints for each of three biological replicates of wild-type cultures of Nitrosomonas europaea ATCC 19718. Total RNA was obtained from each biological culture replicate during exponential growth, following 12 hours ammonia starvation, 144 hours ammonia starvations, and 20 minutes following ammonia addition to starved cells.
2012-08-02 | E-GEOD-35122 | biostudies-arrayexpress
Project description:Investigation of the whole genome gene expression level changes relative to exponential phase growth in Nitrosomonas europaea ATCC19718 after 12 hours ammonia starvation, 144 hours ammonia starvation, and 20 minutes following ammonia addition to starved cells. The ammonia monooxygenase of chemolithotrophic ammonia oxidizing bacteria (AOB) catalyzes the first step in ammonia oxidation by converting ammonia to hydroxylamine. The monooxygenase of Nitrosomonas europaea is encoded by two nearly identical operon copies (amoCAB1,2). Several AOB, including N. europaea, also posess a divergent monocistronic copy of amoC (amoC3) of unknown function. Previous work suggested a possible functional role for amoC3 in N. europaea during recovery from extended ammonia starvation as part of the σE- stress response regulon during the recovery of N. europaea from extended ammonia starvation, thus indicating its importance during the exit of cells from starvation. We here used global transcription analysis to show that expression of amoC3 is part of a general post-starvation cellular response system in N. europaea. We also found that amoC3 is required for efficient exit from prolonged ammonia starvation, as deleting this gene impaired growth at elevated temperatures and recovery following starvation under high oxygen tensions. Deletion of the σ32 global stress response regulator demonstrated that the heat shock regulon also plays a significant role in mediating the recovery of N. europaea from starvation. These findings provide the first described phenotype associated with the divergent AmoC3 subunit which appears to function as a stress responsive subunit capable of maintaining ammonia oxidation activity under stress conditions.
2012-08-03 | GSE35122 | GEO
Project description:Pure cultures of ammonia oxidizing bacterium, Nitrosomonas europaea, are exposed to cyanide in pseudo-steady state batch reactor in presence of ammonia. Nitrosomonas europaea are generally regarded as the most sensitive organism to various inhibitors commonly encountered in the wastewater treatment plants (WWTP). To find stress genes of Nitrosomonas europaea to cyanide known as inhibitor of respiratory process, whole-genome transcript response to cyanide was determined in this research using microarray and qRT-PCR. When 1 uM NaCN inhibits nitrification about 50 %, transcript levels of 35 genes were increased while transcript levels of 29 genes were decreased, showing more than 2-fold in total 2460 genes. moeZ (NE2353), homologue with rhodanases related to detoxification of CN-, showed 7-fold up regulation and gene cluster including moeZ also showed significant up regulation. Keywords: cyanide, stress response, moeZ
2008-06-21 | GSE10664 | GEO
Project description:Pure cultures of ammonia oxidizing bacterium, Nitrosomonas europaea, are exposed to cyanide in pseudo-steady state batch reactor in presence of ammonia. Nitrosomonas europaea are generally regarded as the most sensitive organism to various inhibitors commonly encountered in the wastewater treatment plants (WWTP). To find stress genes of Nitrosomonas europaea to cyanide known as inhibitor of respiratory process, whole-genome transcript response to cyanide was determined in this research using microarray and qRT-PCR. When 1 uM NaCN inhibits nitrification about 50 %, transcript levels of 35 genes were increased while transcript levels of 29 genes were decreased, showing more than 2-fold in total 2460 genes. moeZ (NE2353), homologue with rhodanases related to detoxification of CN-, showed 7-fold up regulation and gene cluster including moeZ also showed significant up regulation. Keywords: cyanide, stress response, moeZ The 1 uM NaCN caused more than 50 % inhibition in physiological response for 1 hour incubation. Transcriptional levels of the cells inhibited by cyanide were compared with the cells under control condition.
2010-05-26 | E-GEOD-10664 | biostudies-arrayexpress
Project description:Nitrosomonas europaea is a Gram-negative obligate chemolithoautotroph that derives energy for growth through oxidation of ammonia and participates in the process of nitrification in global nitrogen cycling. The physiological, proteomic, and transcriptional responses of N. europaea to zinc stress were studied. The nitrite production rate and ammonia-dependent oxygen uptake rate of the cells exposed to 3.4 uM ZnCl2 decreased about 61 % and 69 % within 30 minutes, respectively. Two proteins were notably up regulated in zinc treatment and the mRNA levels of their encoding genes started to increase by one hour after the addition of zinc. A total of 27 genes were up regulated and 30 genes were down regulated. Up-regulated genes included mercury resistance genes (merACDPT), inorganic ion transport genes, oxidative stress genes, toxin-antitoxin genes (TA) and two-component signal transduction systems genes. The merACDPT was the highest up regulated operon (46-fold). Down-regulated genes included the RuBisCO operon (cbbO), carbohydrate transporter (mrsA and mnxG) and amino acid transporter. Keywords: zinc, stress response, global transcription, mercury resistance genes, inorganic ion transport genes, oxidative stress genes
2007-10-24 | GSE7552 | GEO
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida KT2440 and DOT-T1E in the presence of toluene with the aim to study in more detail the mechanisms involved in toluene response in a toluene-sensitive and a toluene-tolerant strains.
2017-06-04 | GSE86321 | GEO
Project description:Pseudomonas putida S12 is exceptionally tolerant to various organic solvents. To obtain further insight in this bacterium’s primary defence mechanisms towards these potentially harmful substances, we studied its genome wide transcriptional response to sudden addition of toluene. Global gene expression profiles were monitored for 30 minutes after toluene addition. During toluene exposure, high oxygen-affinity cytochrome c oxidase is specifically expressed to provide for an adequate proton gradient supporting solvent efflux mechanisms. Concomitantly, the glyoxylate bypass route was up-regulated, to repair an apparent toluene stress-induced redox imbalance. A knock-out mutant of trgI, a recently identified toluene-repressed gene, was investigated in order to identify TrgI function. Remarkably, upon addition of toluene the number of differentially expressed genes initially was much lower in the trgI-mutant than in the wild-type strain. This suggested that after deletion of trgI cells were better prepared for sudden organic solvent stress. Before, as well as after, addition of toluene many genes of highly diverse functions were differentially expressed in trgI-mutant cells as compared to wild-type cells. This led to the hypothesis that TrgI may not only be involved in the modulation of solvent-elicited responses but in addition may affect basal expression levels of large groups of genes.
2015-01-09 | GSE64791 | GEO