Wetland soil microcosm
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75000 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To unravel complex dynamics of environmental disturbance and microbial metabolic activities, we set up laboratory microcosms to investigate the effects of SO42- and O2 alone or in combination on microbial activities and interactions, as well as the resulting fate of carbon within wetland soil. We used proteogenomics to characterize the biochemical and physiological responses of microbial communities to individual perturbations and their combined effects. Stoichiometric models were employed to deconvolute carbon exchanges among the main functional guilds. These findings can contribute to the development of mechanistic models for predicting greenhouse gas emissions from wetland ecosystems under various climate change scenarios.
2024-05-19 | PXD047453 | Pride
Project description:Wetland microbiomes play a crucial role in the global carbon cycle by modulating soil organic carbon (SOC) and greenhouse gas (GHG) emissions. Understanding how microbial communities respond to environmental changes is essential for predicting wetland carbon fluxes under future climate scenarios. Here, we investigated the biogeochemistry of a temperate lacustrine wetland across four seasons and three soil depths, integrating greenhouse gas flux measurements, porewater metabolite profiles, metagenomics, metabolomics, and metaproteomics. While seasonal shifts in GHG fluxes and porewater chemistry were evident, microbial community composition and function were primarily structured by soil depth, suggesting resilience to short-term seasonal fluctuations. Depth-correlated microbial taxa and metabolic pathways revealed distinct stratification: surface soils were enriched in metabolically versatile Gammaproteobacteria capable of oxygen and nitrate respiration, as well as methane and sulfur oxidation, whereas deeper layers favored strict anaerobic metabolism, with increasing abundances of Anaerolinea and Methanomicrobia. Metabolomics showed an enrichment of purine nucleotides and amino acids at the surface, while deeper soils accumulated amino sugars and phenolic compounds, highlighting differences in carbon processing. Metaproteomics confirmed active metabolic pathways, linking functional potential to microbial activity. By integrating multi-omics with biogeochemical measurements, this study provides a system-level view of wetland microbial function and resilience, contributing to predictive models of wetland carbon cycling under future climate change.
The work (proposal:https://doi.org/10.46936/10.25585/60000490) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2025-06-23 | MSV000098292 | MassIVE
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
2020-03-06 | GSE146427 | GEO
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:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
Project description:Investigation of mRNA expression (using HiSeq 2500) in response to treatment of Daphnia magna to pyriproxyfen, wetland water, or stormwater samples.
2022-07-26 | GSE208591 | GEO
Project description:The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of soil type, soil transplant and landuse changes on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles.
2016-02-04 | GSE77546 | GEO
Project description:This dataset contains raw files for metabolites collected from the soil and roots of four wetland plant species under non-sterile conditions, both in soil and hydroponically, during the day and night time periods.
2024-05-01 | MSV000094652 | MassIVE