Soil metagenome
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ABSTRACT:
PROVIDER: PRJNA868779 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Low buoyant density 12C DNA Metagenomic assembly
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Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.
2023-12-30 | E-MTAB-13326 | biostudies-arrayexpress
Project description:The transcriptome profiles of sporulating vs non-sporulating cells, within an isogenic culture were compared. RNA was isolated from endospore containing cells which were separated from non-spore forming cells using buoyant density gradient centrifugation within an isogenic culture (details in Veening et al, submitted).
2010-05-25 | E-GEOD-9266 | biostudies-arrayexpress
Project description:Poplar (Populus trichocarpa, clone Nisqually-1) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity. Diurnal (driven) conditions included 12L:12D light cycles and 25C/12C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (25C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (25C) and a low night temperature (12C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (25C, day; 12C, night). Light intensity and relative humidity were 700 micromol m-2s-2 and 50%, respectively. Three-month-old poplar plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual poplar plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.
2010-01-09 | E-MEXP-2509 | biostudies-arrayexpress
Project description:The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
| S-EPMC201203 | biostudies-literature
Project description:Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
| S-EPMC9670897 | biostudies-literature
Project description:While regulation of transcription, replication and cell division relies on dynamic protein binding to DNA and chromatin, it is unclear which regulatory components remain bound to compacted mitotic chromosomes. To comprehensively quantify the chromatin-associated proteome in different phases of the cell cycle, we utilized the buoyant density of DNA-protein complexes after crosslinking. This revealed variable associations for thousands of proteins to DNA including their frequent and variable phosphorylation. While epigenetic modifiers that promote transcription are lost from mitotic chromatin, repressive modifiers generally remain associated. Interestingly, while proteins involved in transcriptional elongation are evicted, most identified transcription factors are retained on mitotic chromatin to varying degrees, including core promoter binding proteins. This predicts conservation of the regulatory landscape on mitotic chromosomes, which genome-wide measurements of chromatin accessibility confirm. This work establishes a novel approach to study chromatin, provides a comprehensive catalogue of chromatin changes during the cell cycle, and reveals the degree with which the genomic regulatory landscape is maintained through mitosis.
2018-09-06 | PXD008033 | Pride
Project description:The Arecibo Observatory (AO) located in Arecibo, Puerto Rico, is the most sensitive, powerful and active planetary radar system in the world [1]. One of its principal components is the 305 m-diameter spherical reflector dish (AORD), which is exposed to high frequency electromagnetic waves. To unravel the microbial communities that inhabit this environment, soil samples from underneath the AORD were collected, DNA extracted, and sequenced using Illumina MiSeq. Taxonomic and functional profiles were generated using the MG-RAST server. The most abundant domain was Bacteria (91%), followed by Virus (8%), Archaea (0.9%) and Eukaryota (0.9%). The most abundant phylum was Proteobacteria (54%), followed by Actinobacteria (8%), Bacteroidetes (5%) and Firmicutes (4%). In terms of functions, the most abundant among the metagenome corresponded to phages, transposable elements and plasmids (16%), followed by clustering-based subsystems (11%), carbohydrates (10%), and amino acids and derivatives (9%). This is the first soil metagenomic dataset from dish antennas and radar systems, specifically, underneath the AORD. Data can be used to explore the effect of high frequency electromagnetic waves in soil microbial composition, as well as the possibility of finding bioprospects with potential biomedical and biotechnological applications.
| S-EPMC6920479 | biostudies-literature
Project description:Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.
| S-EPMC3067229 | biostudies-literature
Project description:Grassland soil wet-up metagenomes and density fractionated metagenomes
| PRJNA856348 | ENA