Denitrification gene abundance across environmental gradients
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28446 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. subtilis was able to rapidly remove nitrate from wastewater. In these conditions, B. subtilis overexpressed nitrogen assimilatory and respiratory genes including NasD, NasE, NarG, NarH, and NarI, which arguably accounted for the observed boost in denitrification. Next, we attempted to use the the ammonium- and nitrate-enriched wastewater samples bio-augmented with B. subtilis in the cathodic compartment of bioelectrochemical systems (BES) operated in anaerobic condition. B. subtilis only had low relative abundance in the microbial community, but bio-augmentation promoted the growth of Clostridium butyricum and C. beijerinckii, which became the dominant species. Both bio-augmentation with B. subtilis and electrical current from the cathode in the BES promoted butyrate production during fermentation of glucose. A concentration of 3.4 g/L butyrate was reached with a combination of cathodic current and bio-augmentation in ammonium-enriched wastewater. With nitrate-enriched wastewater, the BES effectively removed nitrate reaching 3.2 mg/L after 48 h. In addition, 3.9 g/L butyrate was produced. We propose that bio-augmentation of wastewater with B. subtilis in combination with bioelectrochemical processes could both boost denitrification in nitrate-containing wastewater and enable commercial production of butyrate from carbohydrate- containing wastewater, e.g. dairy industry discharges. These results suggest that B. subtilis bio-augmentation in our BES promotes simultaneous wastewater treatment and butyrate production.
2020-05-15 | GSE150480 | GEO
Project description:Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin transcriptional activators, proteins harbouring a domain of unknown function (DUF2249), and a cyanoglobin. Additionally, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.
2024-04-22 | GSE245042 | GEO
Project description:Many proteins and enzymes involved in denitrification in haloarchaea can be inferred to be located between the cytoplasmic membrane and the S-layer, based on the presence of a Tat signal sequence and the orientation of the active site that some of these enzymes have. The membrane fraction of the haloarchaeon Haloferax mediterranei (R-4), grown under anaerobic conditions in the presence of nitrate, was solubilised to identify the respiratory proteins associated or anchored to it. Using Triton X-100, CHAPS and n-Octyl-β-d-glucopyranoside at different concentrations we found the best conditions for isolating membrane proteins in micelles, in which enzymatic activity and stability were maintained. Then, they were subjected to purification using two chromatographic steps followed by the analysis of the eluents by NANO-ESI Chip-HPLC-MS/MS. The results showed that the four main enzymes of denitrification (nitrate, nitrite, nitric oxide and nitrous oxide reductases) in H. mediterranei were identified and they were co-purified thanks to the micelles made with Triton X-100 (20% w/v for membrane solubilisation and 0.2% w/v in the buffers used during purification). In addition, several accessory proteins involved in electron transfer processes during anaerobic respiration as well as proteins supporting ATP synthesis, redox balancing and oxygen sensing were detected. This is the first characterization of anaerobic membrane proteome of haloarchaea under denitrifying conditions using liquid chromatography-mass spectrometry. It provides new information for a better understanding of the anaerobic respiration in haloarchaea.
2020-12-07 | PXD022473 | Pride
Project description:Polyribosomal fractions derived from P25 mice were the starting material for IPs of the FMRP protein and associated mRNA. Therefore we wanted to determine the relative abundance of all mRNAs in the starting pool for the IP as a denominator with which to compare the IPed material. [mRNA profiling]: We prepared polyribosomes on sucrose gradients in duplicate from 2 FVB WT mice, age P25, and purified RNA from polyribosomal fractions of each of the two gradients.
2011-07-20 | E-GEOD-26742 | biostudies-arrayexpress
Project description:Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unraveled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here, we used fine-combed RNAseq in tandem with photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study combinatory effects of stress response using clustering along gradients. We describe major hubs in genetic networks underpinning stress response and acclimation in the molecular physiology of Mesotaenium. Our data suggest that lipid droplet formation, plastid and cell wall-derived signals denominate molecular programs since more than 600 million years of streptophyte evolution—before plants made their first steps on land.
2022-11-11 | PXD037847 | Pride
Project description:Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also have to survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O2 tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well-known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N2O- over NO3--reduction in bradyrhizobia is retained under carbon limitation. Here we show that starved cultures of a Bradyrhizobium strain with respiration rates 1-18% of well-fed cultures, reduced all available N2O before touching provided NO3-. These organisms, which carry out complete denitrification, have the periplasmic nitrate reductase NapA but lack the membrane-bound nitrate reductase NarG. Proteomics showed similar levels of NapA and NosZ (N2O reductase), excluding that the lack of NO3- reduction was due to low NapA abundance. Instead, this points to a metabolic-level phenomenon where the bc1 complex, which channels electrons to NosZ via cytochromes, is a much stronger competitor for electrons from the quinol pool than the NapC enzyme, which provides electrons to NapA via NapB. The results contrast the general notion that NosZ activity diminishes under carbon limitation and suggest that bradyrhizobia carrying NosZ can act as strong sinks for N2O under natural conditions, implying that this criterion should be considered in the development of biofertilizers.
2023-03-11 | PXD038844 | Pride
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
2014-07-22 | GSE59620 | GEO
Project description:Ralstonia eutropha H16 is a denitrifying microorganism able to use nitrate and nitrite as terminal electron acceptors under oxygen deprivation. To identify proteins showing an altered expression pattern in response to oxygen supply, R. eutropha cells grown aerobically and anaerobically were compared in a comprehensive proteome and transcriptome approach. Nearly 700 proteins involved in several processes including respiration, cell appendages formation, DNA and cofactor biosynthesis were found to be differentially expressed. A combination of 1D-gel-LC and conventional 2D-gel analysis of six consecutive sample points covering the entire denitrification sequence revealed a detailed view on the abundance pattern of the key proteins of denitrification. Denitrification- or anaerobiosis-induced alterations of the respiratory chain included a distinct expression pattern for multiple terminal oxidases. Alterations of the central metabolism were restricted to a few key functions including the isoenzymes for aconitase and isocitrate dehydrogenase, respectively. Although R. eutropha is a strictly respiratory bacterium, the abundance of certain fermentation enzymes was increased. This work represents a comprehensive survey of denitrification on proteomic and transcriptomic level and provides unique insight into how R. eutropha adapts its metabolism to low oxygen conditions.
2014-09-01 | PXD000888 | Pride
Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients. 12 samples were collected from two long-term polluted areas (Olkusz and Miasteczko M-EM-^ZlM-DM-^Eskie) in Southern Poland. In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised
2014-07-22 | E-GEOD-59620 | biostudies-arrayexpress
Project description:Small RNAs recently emerged as a new class of mobile instructive signals in development. Here, we investigate their mechanism of action and show that the gradients formed by mobile small RNAs generate sharply defined domains of target gene expression. By modulating the source of artificial miRNAs we show that boundary formation is an inherent property of the small RNA gradient itself. The threshold-based readout of such gradients is highly sensitive to small RNA levels at the source, allowing plasticity in the positioning of a target gene expression boundary. In addition to generating sharp expression domains of their immediate targets, the readouts of opposing small RNA gradients enable formation of stable and uniformly positioned developmental boundaries. These novel patterning properties of small RNAs are reminiscent of those of morphogens in animal systems. However, their exceptionally high specificity, direct mode of action, and the fully intrinsic nature of their gradients, distinguish mobile small RNAs from classical morphogens. Our findings present mobile small RNAs and their targets as highly portable and evolutionarily-tractable regulatory modules through which to create pattern in development and beyond.
2017-12-01 | GSE94720 | GEO