Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1115048 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29140700_1.fastq.gz | Fastqsanger.gz | |||
| SRR29140700_2.fastq.gz | Fastqsanger.gz | |||
| SRR29140701_1.fastq.gz | Fastqsanger.gz | |||
| SRR29140701_2.fastq.gz | Fastqsanger.gz | |||
| SRR29140702_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 250 |
Similar Datasets
Project description:Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate).Soils were characterized for geochemistry, Illumina sequencing was used to determine microbial taxonomic communities and GeoChips 5.0 were used to determine microbial functional genes.
2017-01-10 | GSE92233 | GEO
Project description:The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.
2017-05-24 | GSE99220 | GEO
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: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:DOM degradation incubations of prokaryote-derived DOM by Mediterranean Sea microbial communities
| PRJEB57699 | ENA
Project description:<p>Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or synergistically address different litter types. Therefore, we decomposed beech, oak, pine and grass litter from two geologically distinct sites in a lab-scale decomposition experiment. We performed a correlative network analysis on the results of direct infusion HR-MS DOM analysis and cross-validated functional predictions from 16S rRNA gene amplicon sequencing and with DOM and metaproteomic analyses. Here we show that many functions are redundantly distributed within decomposer communities and that their relative expression is rapidly optimized to address litter-specific properties. However, community changes are likely forced by antagonistic mechanisms as we identified several natural antibiotics in DOM. As a consequence, the decomposer community is specializing towards the litter source and the state of decomposition (community divergence) but showing similar litter metabolomes (metabolome convergence). Our multi-omics-based results highlight that DOM not only fuels microbial life, but it additionally holds meta-metabolomic information on the functioning of ecosystems.</p>
2024-02-14 | MTBLS1885 | MetaboLights
Project description:This experiment aimed to understand stress responses of microbial communities differing in chronic exposure to the photosynthesis inhibitor diuron, combining untargeted metatranscriptomics (RNA-seq) and dose-response design. First, river microbial communities were incubated for 5-weeks in microcosms 1/ under constant exposure to 4µg/L of diuron (stressed community) or 2/ without contamination (non-stressed community). Then, both communities were exposed for 1 hour to a gradient of diuron concentrations to investigate differences in stress responses after chronic exposure. This experimental design enabled the determination of contig response trends as well as sensitivity thresholds.
2025-04-01 | GSE201034 | GEO
Project description:Diatom-derived polyunsaturated aldehydes (PUAs) significantly influence marine bacterial dy-namics, yet the underlying proteomic mechanisms remain elusive. We employed high-resolution comparative proteomics to decipher the functional reprogramming of two bacterial communi-ties—one naturally associated with a PUA-producing diatom (N-community) and another with a non-PUA producer (I-community)—under ecologically relevant PUA exposure. While growth rates and cell densities remained unaffected, indicating an absence of acute toxicity, proteomics revealed pronounced community-specific reorganization. N-communities displayed stable, regula-tion-oriented adjustments consistent with physiological accommodation, whereas I-communities exhibited dose-dependent stress responses, shifting toward protein repair and antioxidant defense. Our findings demonstrate that PUAs trigger profound proteomic reprogramming conditioned by the communities' prior ecological history. This functional divergence provides a molecular basis for understanding bacterial fitness and succession during diatom blooms, where PUA-mediated in-teractions could act as a selective filter shaping the phycosphere's microbial landscape. Polyunsaturated aldehydes (PUA) produced by diatoms have been proposed to exert a wide range of effects on marine bacteria, from inhibitory or stress-inducing responses to neutral or potentially beneficial effects. However, the bacterial proteomic responses remain elusive. Here, we employed a high-resolution comparative proteomic approach to decipher the functional reprogramming of two distinct bacterial communities under ecologically relevant PUA exposure. One community was composed by bacteria naturally associated with a PUA-producing diatom (N- communy and, a second community associated with a non-PUA-producing diatom (I-community). Bacterial growth rates and final cell densities were not significantly affected by any treatment, indicating the absence of toxic effects even at high PUA concentrations. Dissolved organic carbon consumption did not provide evidence that PUA was the relevant carbon source. Interestingly, comparative proteomic analyses revealed pronounced community-specific reorganization in response to PUA expo-sure.Our results show that PUAs trigger a profound proteomic reprogramming rather than a simple stress response. While I-community prioritized antioxidant defense and protein repair, N-community showed a metabolic shift towards energy conservation. These findings suggest that the metabolic history of bacterial assemblages determines their success in the phycosphere, providing a molecular basis for microbial succession during diatom blooms.
2026-06-04 | PXD075100 | Pride
Project description:Microbial community responses to diverse DOM
| PRJEB105935 | ENA