Prokaryotic environmental samples
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR008490.fastq.gz | Fastqsanger.gz | |||
| DRR008491.fastq.gz | Fastqsanger.gz | |||
| DRR008492.fastq.gz | Fastqsanger.gz | |||
| DRR008493.fastq.gz | Fastqsanger.gz | |||
| DRR008494.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:<p>Particulate organic matter (fecal pellets) from zooplankton has been demonstrated to be important nutrient sources for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12-16 h of incubation. We measured bulk dissolved organic carbon, dissolved free amino acids via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16s rDNA amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.</p>
2020-11-27 | MTBLS1822 | MetaboLights
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:Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing
| PRJDB1909 | ENA
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.
2008-06-25 | GSE11837 | GEO
Project description:Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, especially in marine sediments due to their complex matrix. Few studies have been conducted on improving protein extraction methods from marine sediments. To establish an effective protein extraction workflow for clay-rich sediments, we compared, combined and improved several protein extraction methods. The presented workflow includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis via ultra-sonication, and the electro-elution and simultaneous fractionation of proteins. Using this workflow, we were able to recover 100% of the previously added Escherichia coli proteins from the sediment.
2025-05-12 | PXD054260 | 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: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. 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.
2015-01-30 | E-GEOD-65430 | biostudies-arrayexpress
Project description:Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank. The plating method offered the advantages of capturing the targeted hydrocarbonoclastic microorganisms, counting them and providing cultures for further study. However, this technique could not capture more than a total of 15 different prokaryotic taxa. Those taxa belonged predominantly to the genera Alcanivorax, Pseudoxanthomonas, Bosea, Halomonas, and Marinobacter. The individual isolates in culture consumed between 19 and 50% of the available crude oil in 10 days. Although the culture-independent approach revealed much more microbial diversity, it was not problem-free. The subdivision primers exhibited satisfactory specificity, but they failed to capture all the available taxa. The universal bacterial primer pair ignored Actinobacteria altogether, although the primer pair specific for Actinobacteria captured many of them, for example, the genera Geodermatophilus, Streptomyces, Mycobacterium, Pontimonas, Rhodococcus, Blastococcus, Kocuria, and many others. Because most researchers worldwide use universal primers for PCR, this finding should be considered critically to avoid misleading interpretations.
| S-EPMC5635167 | biostudies-literature