Metaomic study on the ecophysiological cascade underlaying seasonal N2O emissions
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Nitrospira Sp. Microthrix Nitrosomonas Sp. Candidatus Accumulibacter Phosphatis
SUBMITTER: 
Martin Pabst
LAB HEAD: Martin Pabst
PROVIDER: PXD051095 | Pride | 2025-02-21
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| MP_NR21072023_S10_180_DDA01.raw | Raw | |||
| MP_NR21072023_S10_180_DDA02.raw | Raw | |||
| MP_NR21072023_S11_180_DDA01.raw | Raw | |||
| MP_NR21072023_S11_180_DDA02.raw | Raw | |||
| MP_NR21072023_S12_180_DDA01.raw | Raw |
Items per page: 5 1 - 5 of 27 |
Similar Datasets
Project description:Effluent from geoduck clam larval rearing tanks at two different pH (8.2 and 7.1) was collected at 4 time points (Days 1, 5, 8, and 12) over 12 days in a shellfish hatchery in Washington state, USA. The water was filtered to 0.2 microns to retain the bacterial fraction.
2021-04-21 | PXD020692 | Pride
Project description:The majority of potent greenhouse gas nitrous oxide (N2O) emissions originate from microbially mediated reactions. The enzyme N2O reductase is the only known biological N2O sink and has evolved in two phylogenetically distinct lineages (clades I and II). Clade II is of particular interest for biotechnology as it is often associated with non-denitrifying N2O reducers. In this study, Laureni et al. investigated the environmental conditions that select for clade II. To do so, we enriched two N2O-respiring communities at low dilution rates, under both electron donor (acetate) and electron acceptor (N2O) limitations, in order to assess the impact of substrate affinity and N2O cytotoxicity on community assembly. We used a combination of genome-resolved metagenomics and shotgun metaproteomics to identify the taxonomy and metabolic potential of the steady-state community members. Corresponding author: Michele Laureni, contact: m.laureni@tudelft.nl
2025-01-18 | PXD047071 | Pride
Project description:A metabolomics and whole cell lysate shotgun proteomics study was performed to investigate the glycolytic modes in Ca. Accumulibacter phosphatis.
2024-10-28 | PXD048326 | Pride
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:Anaerobic digestion (AD) is a core technology in management of urban organic wastes, converting a fraction of the organic carbon to methane and the residual digestate, the biorest, have a great potential to become a major organic fertilizer for agricultural soils in the future. At the same time, mitigation of N2O-emissions from the agricultural soils is needed to reduce the climate forcing by food production. Our goal was therefore to enrich for N2O reducing bacteria in AD digestates prior to fertilization, and in this way provide an avenue for large-scale and low-cost cultivation of strongly N2O reducing bacteria which can be directly introduced to agricultural soils in large enough volumes to alter the fate of nitrogen in the soils. Gas kinetics and meta-omics (metagenomics and metaproteomics) analyses of the N2O enriched digestates identified populations of N2O respiring organisms that grew by harvesting fermentation intermediates of the methanogenic consortium.
2022-02-16 | PXD022030 | Pride
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: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:Nitrosomonas europaeais 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 ofN. europaeato 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 NH3to nitrite, depending on dilution rate and Na2CO3concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to NH3-limited cultures. Rates of N2O production increased 2.5- 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) up to 4.4% (0.2 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 (cbbgene 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 thatN. europaeaadapts physiologically during IC-limited steady state growth, which leads to uncoupling of NH3oxidation from growth and increased N2O production. Transcriptome responses of N. europaea in 60 mM NH4+ to suboptimum levels of carbonate (1.0 mM and 0.2 mM) in continuous steady-state culture in a bioreactor.
2016-03-28 | E-GEOD-70988 | biostudies-arrayexpress
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