Sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA268784 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12818432.fastq.gz | Fastqsanger.gz | |||
| SRR12818433.fastq.gz | Fastqsanger.gz | |||
| SRR12818434.fastq.gz | Fastqsanger.gz | |||
| SRR12818435.fastq.gz | Fastqsanger.gz | |||
| SRR12818436.fastq.gz | Fastqsanger.gz |
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Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | 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.
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Project description:The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.
2016-02-22 | GSE77866 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | biostudies-arrayexpress
Project description:To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
2018-05-01 | GSE98512 | GEO
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
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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:Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
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Project description:Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.
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