Similar Datasets
Project description:We report here the RNA seq results of sRNA enriched Paracoccus denitrificans grown under three different N2O levels (high N2O reffered to as CuL/ low N2O reffered to as CuH/ Low N2O aerobic reffered to as CuH O2)
2016-11-16 | GSE85362 | GEO
Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 ± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 ± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 µmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287
2020-01-07 | GSE142805 | GEO
Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 ± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 ± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 µmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287
2020-01-07 | GSE142804 | GEO
Project description:Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities to profile microbial gene transcript in agricultural soils with low and high flux of N2O. A total of 96 genes displayed expression that differed significantly between low and high N2O emitting soils. Creation and validation of an cDNA microarray from environmental microbial mRNA, to use as a monitoring tool for microbial gene expression Microbial expression profiles comparing two high N2O-emitting sites (3 soil replicates and microarrays each) and two low N2O-emitting sites (3 soil replicates and microarray each) from sugarcane site in Mackay, Australia
2010-08-05 | E-GEOD-23422 | biostudies-arrayexpress
Project description:Mitigation of N2O-emissions from soils is needed to reduce climate forcing by food production. Inoculating soils with N2O-reducing bacteria would be effective, but costly and impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production may provide a low-cost and widely applicable solution. Firstly, we show that indigenous N2O-reducing bacteria in digestates grow to high levels during anaerobic enrichment under N2O. Gas kinetics and meta-omic analysis show that the N2O respiring organisms, recovered as metagenome-assembled genomes (MAGs) grow by harvesting fermentation intermediates of the methanogenic consortium. Three digestate-derived denitrifying bacteria were obtained through isolation, one of which matched the recovered MAG of a dominant Dechloromonas-affiliated N2O reducer. While the identified N2O-reducers encoded genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O-sinks in the current system. Secondly, moving towards practical application, we show that these isolates grow by aerobic respiration in digestates, and that fertilization with these enriched digestates reduces N2O emissions. This shows that the ongoing implementation of biogas production in agriculture opens a new avenue for cheap and effective reduction of N2O emissions from food production.
2022-02-16 | PXD023233 | Pride
Project description:Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities to profile microbial gene transcript in agricultural soils with low and high flux of N2O. A total of 96 genes displayed expression that differed significantly between low and high N2O emitting soils. Creation and validation of an cDNA microarray from environmental microbial mRNA, to use as a monitoring tool for microbial gene expression
2010-08-05 | GSE23422 | GEO
Project description:Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2), and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to replete (> 5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on dilution rate and Na2CO3 concentration. IC limitation resulted in a 1.5-fold increase in cellular maintenance energy requirements compared to NH3-limited cultures. Rates of N2O production increased 2- and 6.3 fold under the two IC-limited conditions increasing the percentage of oxidized NH3-N being transformed to N2O-N from 0.5% (replete) to 4.4% (0.25 mM Na2CO3). Transcriptome analysis showed differential expression (p ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits, and increased expression of genes involved in C1 metabolism including RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924-0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady state growth, which leads to uncoupling of NH3 oxidation from growth and increased N2O production.
2016-03-28 | GSE70988 | GEO
Project description:Bradyrhizobia are common members of soil microbiomes and known as N2-fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2O. Inoculation with compatible rhizobia is often needed for optimal N2-fixation, but the choice of inoculant may have consequences for N2O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2O. The N2O-reducing isolates had strong preference for N2O- over NO3--reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3- reductase) and Nos (N2O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3- reductase (Nar), reduced N2O and NO3- simultaneously. We propose that the control at the metabolic level, favoring N2O reduction over NO3- reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
2021-09-27 | PXD023200 | Pride