Ontology highlight
ABSTRACT:
PROVIDER: PRJNA935956 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23559000_1.fastq.gz | Fastqsanger.gz | |||
| SRR23559000_2.fastq.gz | Fastqsanger.gz | |||
| SRR23559001_1.fastq.gz | Fastqsanger.gz | |||
| SRR23559001_2.fastq.gz | Fastqsanger.gz | |||
| SRR23559002_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.
2009-07-01 | GSE13910 | GEO
Project description:Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrients availability or temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to ammonium or nitrogen starvation. We found that Synechococcus has a specific response to nanomolar nitrate concentration that differs to the response showed under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentration of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural field.
2022-07-11 | PXD031142 | Pride
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner. In this series four conditions have been analyzed. These are moderate copper shock for Synechococcus sp. WH8102 and CC9311 (pCu 11.1 and pCu 10.1, respectively), and high copper shock for WH8102 and CC9311 (pCu 10.1 and pCu 9.1, respectively). For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a non-copper-shocked sample labeled with the other Cy dye. There are six or eight slides per condition, each with two biological replicates. There are three or four technical replicates for each biological replicate including at least one flip-dye comparison. Each slide contains six replicate spots per gene.
2010-05-17 | E-GEOD-13910 | biostudies-arrayexpress
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:Proteins secreted by marine cyanobacterium Synechococcus under phosphorus stress is largely uncharacterized. This dataset characterizes the exoproteins for both an open ocean (WH8102) and coastal (WH5701) Synechococcus strain and were collected as part of the study "Dissolved organic phosphorus bond-class utilization by Synechococcus". Study Abstract: Dissolved organic phosphorus (DOP) contains compounds with phosphoester (P-O-C), phosphoanhydride (P-O-P), and phosphorus-carbon (P-C) bonds. Despite DOP’s importance as a nutritional source for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by cultures of an open ocean and a coastal ocean Synechococcus strain. Both strains exhibited comparable growth rates when provided phosphate, short-chain and long-chain polyphosphate (P-O-P), adenosine 5’-triphosphate (P-O-C and P-O-P), and glucose-6-phosphate (P-O-C) as the phosphorus source. However, growth rates on phosphomonoester adenosine 5’-monophosphate (P-O-C) and phosphodiester bis(4-methylumbelliferyl) phosphate (C-O-P-O-C) varied between strains, and neither strain grew on selected phosphonates. Consistent with the growth measurements, both strains preferentially hydrolyzed 3-polyphosphate, followed by adenosine 5’-triphosphate, and then adenosine 5’-monophosphate. The strains’ exoproteome contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5’-triphosphate under phosphate deficiency, suggests active mineralization of short-chain polyphosphate by Synechococcus’ exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity towards short-chain polyphosphate, with varying affinities between the two strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition, thereby expanding our understanding of microbially-mediated DOP cycling in marine ecosystems.
2024-07-15 | PXD051991 | Pride
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:Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation (ChIP) sequencing. We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts. We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription. RNA Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 RNA polymerase ChIP Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 Tiling Microarray of the cyanobacterium Synechococcus elongatus PCC 7942
2011-05-16 | E-GEOD-29264 | biostudies-arrayexpress
Project description:Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using 15N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more by the higher organic matter addition, and the fraction of nitrogen loss attributed to anammox slightly reduced. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community as determined using a nirS microarray, indicating the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.
2015-01-30 | GSE65430 | GEO
Project description:we investigated molecular response of an oceanic Synechococcus strain WH 8102 grown on two nitrogen sources (nitrate and urea) under present (25°C) and predicted future (28°C) temperature conditions using an IBT-based quantitative proteomic approach.
2019-08-19 | PXD011884 | Pride