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ABSTRACT:
PROVIDER: PRJNA901067 | ENA |
REPOSITORIES: ENA
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Project description:The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths.
2013-09-12 | GSE50787 | GEO
Project description:The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-09-12 | E-GEOD-50787 | biostudies-arrayexpress
Project description:Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. Great progress has been made in the discovery of novel antibiotics to counteract E. coli pathogens. However, this huge progress has been undercut by the evolution of bacteria in the way of drug resistance. Enrofloxacin is one of the most efficient antibiotics against E. coli pathogens and there is considerable evidence that documents how this microorganism is becoming more resistant to this antibiotic and is developing multidrug resistance. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. For a comprehensive investigation about antibiotic resistance mechanisms, an E. coli isolate from urinary tract infection (UTI) was induced to grow under a concentration of 10 µg/ml of enrofloxacin. Proteins represent the main contributors to the mechanisms involved in antibiotic resistance in bacteria. Their abundance profile provides reliable information about the mechanisms involved in this process. Three biological replicates of control and resistant isolate have been analyzed both through 2D DIGE and shotgun proteomics. In our case, prior to perform the proteomics analysis, the screening with MS profiling of control and resistant isolates was performed highlighting the differences among strains and successfully clustering experimental strains according to PC analysis (PCA). The results clearly demonstrate differential profiles in peptide expression among clusters and between isolate and reference strain. According to these preliminary results, the protein profile of the resistant group was compared with the one of its sensitive counterpart by a proteomic analysis based on 2D-DIGE to separate proteins combined to MALDI MS analysis and database search to identify differentially expressed proteins. This analysis showed the modulation of 19 proteins between the two conditions. At the same time, another comparative proteomics investigation was also carried out by free-label nLC-MSE. This method has allowed the qualitative and quantitative analysis of total protein extracts of the two groups for the simultaneous screening of a larger number of proteins. A total of 57 differentially expressed proteins were identified and a comprehensive study on the proteins associated with enrofloxacin resistance was carried out. We classified these modulated proteins by their molecular functions and pathways where they are principally involved. This approach allowed to highlight some pathways that can be involved in an increased antibiotic resistance. Two major mechanisms were discovered. The first one was related to the stabilization of DNA structure through the up-regulation of Dsp protein. The second one was the downregulation of outer membrane protein W in order to reduce the membrane permeability to enrofloxacin. Discovered differentilally expressed proteins are principally involved in antibiotic resistance and linked to the oxidative stress response, to DNA protection and in membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. The proteins differentially expressed could represent putative targets for the development of new strategies to counteract drug and multidrug resistance.
2015-06-05 | PXD002000 | Pride
Project description:Anaerobic ammonium-oxidising (anammox) bacteria, members of the ‘Candidatus Brocadiaceae’ family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-bound compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic- and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbour multiple copies of ammonium-, nitrite- and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite- and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells under ammonium-limitation showed that three of the seven ammonium transporter genes and one of the six nitrite transporter genes were significantly upregulated, while another ammonium and nitrite transporter gene were downregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.
2020-06-05 | GSE148825 | GEO
Project description:The use of some antibiotics, including florfenicol and enrofloxacin, is allowed in aquaculture in China. Accordingly, to better address the concerns and questions associated with the impact of administered enrofloxacin and florfenicol to grass carp, here we investigated the transcriptome of the intestine of C. idella treated with these oral antibiotics. The aim of this study was to provide an in-depth evaluation of the antibiotic-induced patterns and dynamics of the microbiota grass carp and the potential mechanism involved.
2022-08-08 | E-MTAB-12058 | biostudies-arrayexpress
Project description:Four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were tested to investigate the stimulation and inhibition effects of ferrous iron on anammox bacterial activity. RNAs were extracted from the cultures, and the synthesized cDNAs by reverse transcription were used to carry out GeoChip analysis, by which the functional communities and expression level differences in functional genes under different Fe(II) concentrations conditions were obtained, and the response of anammox bacteria to Fe(II) stimulation and inhibition are speculated.
2020-08-28 | GSE120704 | GEO