Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA191610 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Transcriptional profiling of methanotrophic bacteria (pmoA gene) in methane oxidation biocover soil by depth
2013-09-28 | GSE51235 | GEO
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning. We conducted in situ warming experiments for three years using open-top chambers (OTCs) at one sub-Antarctic (Falkland Islands, 52ºS) and two Antarctic locations (Signy and Anchorage Islands, 60ºS and 67ºS respectively) (see Supplementary Fig. 1 for a map). OTCs increased annual soil temperature by an average of 0.8°C (at a depth of 5 cm), resulting in 8-43% increase in positive-degree days annually and a decrease in freeze-thaw cycle frequency by an average of 15 cycles per year (8). At each location, we included densely vegetated and bare fell-field soils in the experimental design for a total of six environments. Densely vegetated and bare environments represent two contrasting environments for Antarctic soil microorganisms, with large differences in terms of C and N inputs to soils. Massively parallel pyrosequencing (Roche 454 GS FLX Titanium) of 16S rRNA gene amplicons was used to follow bacterial diversity and community composition [GenBank Accession Numbers: HM641909-HM744649], and functional gene microarrays (GeoChip 2.0)(11) were used to assess changes in functional gene distribution. Bacterial and fungal communities were also quantified using real-time PCR.
2010-12-30 | E-GEOD-22825 | biostudies-arrayexpress
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning.
2010-12-30 | GSE22825 | GEO
Project description:Arabidopsis plants were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.07-1.08) under a 16 h light/8 h dark regimen (40 ± 10 ?mol photons/m2/s) at 22 C.Dehydration treatment: The 3-week-old plants were grown for 2 or 3 days without watering. To obtain accurate results, we carefully raised single plants in Petri dishes, each containing an equal amount of soil. Soil moisture contents were calculated from soil dry weight. Untreated; the soil moisture content was 84.3%. Under dehydration, on the second day, the soil moisture content was 51.1%. Under dehydration, on the third day, the moisture content was 11.6%.
2009-08-07 | E-MEXP-2174 | biostudies-arrayexpress
Project description:The effects of two years' winter warming on the overall fungal functional gene structure in Alaskan tundra soil were studies by the GeoChip 4.2 Resuts showed that two years' winter warming changed the overall fungal functional gene structure in Alaskan tundra soil.
2019-03-07 | GSE127899 | GEO
Project description:Transcriptional profiling of methanotrophic bacteria (pmoA gene) in methane oxidation biocover soil by depth Three-different depth condition in methane oxidation biocover soil: top, middle and botton layer soil: genomic DNA extract. Three replicate per array.
2013-09-28 | E-GEOD-51235 | biostudies-arrayexpress
Project description:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant
2020-12-31 | GSE135153 | GEO