Ontology highlight
ABSTRACT:
PROVIDER: PRJNA938248 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
Project description:Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach. Whole genome DNA microarray experiments were performed using a common reference design to identify differentially expressed genes in nematodes exposed to one of three river sediments of differing pollution level. Each sample consists of the 5 “biological replicates”.
2008-06-25 | E-GEOD-11837 | biostudies-arrayexpress
Project description:N2O-reducing bacterium
| PRJDB7296 | ENA
Project description:Soil Chemistry and Microbiome Determine N2O Emission Potential in Soils Metagenome
| PRJNA678002 | ENA
Project description:N2O response of N2O-reducing chemolithoautotroph
| PRJDB15435 | ENA
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:The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc ±1.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam.
2012-10-10 | GSE41416 | GEO