Ontology highlight
ABSTRACT:
PROVIDER: PRJNA449441 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6976370_1.fastq.gz | Fastqsanger.gz | |||
| SRR6976370_2.fastq.gz | Fastqsanger.gz | |||
| SRR6976371_1.fastq.gz | Fastqsanger.gz | |||
| SRR6976371_2.fastq.gz | Fastqsanger.gz | |||
| SRR6976372_1.fastq.gz | Fastqsanger.gz |
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Project description:Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants can be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.
2019-11-11 | PXD014605 | Pride
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.
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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.
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Project description:Microbial degradation of coumarin under methanogenic conditions
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Project description:Identification of the peptides composing the enriched multisubunit enzymes natively purified from the microbial enrichment, based on gel bands obtained by native electrophoresis. The anaerobic oxidation of alkanes is a microbial process occurring in deep-sea hydrocarbon seeps that plays a key ecological role in these exotic niches. The metabolic capacity of anaerobic ethane oxidation, involving uncharted biochemistry, was reported in two archaeal species depending on sulfate-reducing partner bacteria. This study deciphers the molecular basis of the CO2-generating steps of ethanotrophy by characterising the native archaeal enzymes isolated from a thermophilic enrichment. While other microorganisms couple these steps to ferredoxin reduction, we found that the CO-dehydrogenase and the formylmethanofuran-dehydrogenase are bound to F420-reductase modules. The crystal structures of these multi-metalloenzyme complexes revealed electronic bridges coupling C1-oxidation to F420-reduction. Accordingly, both systems exhibit robust F420-reductase activities, which are not detected in methanogenic or methanotrophic relative organisms. We speculate that the whole catabolism of these archaea is reoriented towards F420-reduction, which facilitates the electron transfer to the sulfate-reducing partner, therefore representing the driving force of ethanotrophy.
2024-09-23 | PXD054507 | Pride
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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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