Synthetic cloud microbial community
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA986488 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metatranscriptomics of a synthetic denitrifying microbial community under high-salinity conditions
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Project description:<p>Microorganisms maintain metabolic activity in clouds, with recognized impacts on chemical reactivity by contributing to the processing of small organic compounds, radicals and their precursors. However, the conditions in clouds can be highly contrasted (temperature, light, etc), and it remains unknown how these influences microbial metabolism. Here we explored the functioning of microorganisms exposed to typical cloud water conditions through transcriptomics and metabolomics. Mixed cell suspensions of representative microbial isolates from cloud water, composed of a strain of basidiomycetous fungi (Dioszegia hungarica) and three strains of bacteria (Rhodococcus enclensis, Pseudomonas syringae and P. graminis) were prepared in artificial cloud water, and exposed to combined contrasted conditions of temperature (5 vs 17 °C), oxidants (0 vs 250 µM H2O2) and light (dark vs artificial solar light) to mimic cloud conditions during winter night (WN) and summer day (SD). Differential metabolomics and transcriptomics allowed to highlight 25 differently abundant metabolites and 218 differentially expressed genes (DEGs) between these conditions of incubation. In SD: the fungi overexpressed genes of the mitochondrial oxidative phosphorylation chain, fatty acids biosynthesis and succinate assimilation enzymes. the detection by LC-MS of 3 acylcarnitines supports the occurrence of fatty acid transports into the mitochondrion, related with energy production or possibly hydrogen peroxide scavenging. In bacteria, DEGs encoding components of ROS scavenging systems were predominant. In WN: in the yeast, DEGs encoding chaperones, proteins of the ribosome and proteasome were overexpressed, suggesting high protein turnover. For bacteria, protein rescue processes targeting oxidation-sensitive sulphur containing proteins were more expressed, and DL-methionine sulfoxide was detected. Half of the identified bacterial DEG colocalised in 17 clusters suggesting coordinated gene expression. This study demonstrates that eukaryotes and prokaryotes may engage in distinct strategies to survive in clouds depending on environmental conditions.</p>
2026-02-12 | MTBLS12281 | MetaboLights
Project description:To explore the ecological basis for multiple bacteria species coexistence, we set up three bacteria (Ruegeria pomeroyi DSS-3, Vibrio hepatarius HF70, and Thalassospira sp. HF15), either in monoculture or in co-cultures (in all combinations) for a 8 day growth-dilution cycles. At ~15h of day 4 (P4) and day 8 (P8) of growth-dilution cycles, we examined transcriptomic responses of these bacteria. Differential gene expressions were used to generate hypothesis about ecological and physiological responses of one in the presence of another/other bacteria.
2022-08-01 | GSE199797 | GEO
Project description:High-salinity nitrate removal by a synthetic microbial community derived from marine plastic biofilms
| PRJNA1403737 | ENA
Project description:Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods can be complementary in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.
2022-12-13 | PXD036445 | Pride
Project description:Transcriptome of a Synthetic Microbial Community
| PRJNA821508 | ENA