Ontology highlight
ABSTRACT:
PROVIDER: PRJNA992270 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
| PRJEB41211 | ENA
Project description:Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. Sixteen samples analyzed.
2015-07-09 | E-GEOD-70539 | biostudies-arrayexpress
Project description:Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems.
2015-07-09 | GSE70539 | GEO
Project description:These are the additional files that were not already in public repositories for this manuscript. These samples are negative ionization mode, organic matter metabolomics datasets from many distinct environments, including global cropland; dryland; late Pleistocene-aged permafrost; temperate and tropical forest soils; rivers and lakes; and ocean DOM.
| MSV000095785 | MassIVE
Project description:The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.
2018-10-19 | GSE121473 | 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:<p>While irrigation and fertilization are basic cultivation practices in poplar plantations on a global scale, the impact of these practices on the environment is not well understood. Here, we demonstrate that water-urea coupling and water-compound fertilizer coupling differentially impact soil ecosystems. We report that water-fertilizer coupling did not significantly alter taxonomic diversity indices (richness, evenness), but it did drive significant shifts in microbial community composition, reflected by changes in the relative abundance of specific taxa (e.g., core phyla) and their functional profiles. Water-urea coupling reduced Proteobacteria and Actinobacteria in non-rhizosphere soils while increasing Acidobacteria and Chloroflexi. In contrast, water-compound fertilizer coupling amplified Proteobacteria and Actinobacteria dominance in rhizosphere soils. Water-fertilizer coupling reshaped microbial composition and functional gene abundance linked to nitrogen and sulfur cycling, indicating a potential shift in microbial-mediated N and S transformation processes. Water-urea treatment enriched denitrification genes and dissimilatory nitrate reduction genes (napABC) in rhizosphere soil, while water-compound fertilizer treatment enhanced nitrification (amoABC, HAO) and denitrification gene abundance in both soils. For sulfur (S) cycling, water-urea treatment favored thiosulfate oxidation genes (SOX complex), whereas water-compound fertilizer treatment increased assimilatory sulfate reduction genes. Multi-omics integration linked these microbial dynamics to metabolic reprogramming—water-urea increased lipid and secondary metabolites in rhizosphere soils, while water-compound fertilizers elevated amino acid-associated metabolites in non-rhizosphere soils.</p>
2025-06-17 | MTBLS12375 | MetaboLights
Project description:Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives.
2018-03-30 | GSE112489 | GEO
Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO