Nanoplastics-metagenomic
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA951521 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24085900_1.fastq.gz | Fastqsanger.gz | |||
| SRR24085900_2.fastq.gz | Fastqsanger.gz | |||
| SRR24085901_1.fastq.gz | Fastqsanger.gz | |||
| SRR24085901_2.fastq.gz | Fastqsanger.gz | |||
| SRR24085902_1.fastq.gz | Fastqsanger.gz |
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Project description:Nanoplastics stimulate methane production via hydrogenotrophic Methanocella spp. in waterlogged paddy soils
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Project description:Nanoplastics were generated from common consumer plastics (PET, HDPE, PS, PVC) and exposed to simulated marine weathering for up to 10 weeks. Fourier-Transform Infrared (FT-IR) spectroscopy and ζ-potentials measurements revealed continuous changes in the composition of the nanoplastics consistent with oxidation. Although the chemical composition and oxidation of the nanoplastics influenced their ability to sorb Polycyclic Aromatic Hydrocarbons (PAHs), for all investigated conditions, sorption of PAH to nanoplastics achieved effective PAH concentrations that were orders of magnitude higher than the solubility limit in water. In an intestinal membrane model, PAH-loaded nanoplastics enhanced the overall PAH transport into and across the membrane, with HDPE achieving the highest intracellular PAH concentration. RNA sequencing of cell membranes exposed to nanoplastics revealed significant transcriptional changes, including upregulation of oxidative stress and detoxification pathways (NQO1, CYP1A1, CYP1B), especially in response to PAH-loaded nanoplastics, while genes associated with basic cell functions, such as cellular migration (NCKAP5, MACROD2) and division (KIF20A) were downregulated. These findings suggest that nanoplastics can increase bioaccessibility and bioavailability of hydrophobic carcinogens and enhance cellular stress, raising concerns about the potential environmental and health impacts associated with nanoplastics as carriers of hydrophobic environmental toxins.
2025-06-20 | GSE281152 | GEO
Project description:Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance and gas consumption/production of three wild-type strains and one genetically engineered strain in two independent quadruplicate chemostat bioreactor experiments: 1) with molecular hydrogen and carbon dioxide; and 2) with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. We collected statistically reliable transcriptomics and proteomics data sets from these steady-state bioreactors, which we integrated within our genome-scale metabolic models. The implementation of an pan-model that contains combined reactions from all three microbes allowed us to perform an interspecies comparison of the complete omics data set. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways, such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach using fermentation and omics data with genome-scale modeling for the investigation of lesser studied metabolisms, and the biotechnological potential of Methanothermobacter spp. as production platform hosts.
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Project description:The objective was to evaluate the impact of nanoplastics on various niches of the microbiome in a mouse model
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Project description:Nanoplastics are produced by breakdown of plastics in environmental contamination or commercial use for cosmetics or daily expenses. Emerging evidence indicate that ingested nanoplastics with a size smaller than 100 nm have the potential to reach the brain and induces neurotoxicity. However, the potential toxicity of nanoplastics on brain are limited because of difficulties in synthesize of nanoplastics. In present study, we synthesized the fluorescent polystyrene nanoplastics (PSNPs) and examined the toxicity of PSNPs in brain in vivo and in vitro analyses by comparison to IR-813 fluorophore. Synthesized PSNPs were characterized by fluorescence imaging system, scanning electron microscopy, and Fourier-transform infrared spectroscopy. PSNPs were detected in adult mice brain by oral ingestion. In addition, a series of behavioral analyses showed that oral ingestion of PSNPs induced memory impairments. Among brain cells, PSNPs were predominantly internalized in microglia, and uptake of PSNPs induced microglial activation. In addition, the conditioned medium derived from microglia exposed to PSNPs repressed hippocampal neuronal activity. Furthermore, transcriptome analysis showed that PSNPs changed gene expressions in microglia, elevation of neuroinflammation in contrast to suppression of neurotrophic factors. These results indicated that predominant uptake of PSNPs in microglia induced elevation of neuroninflammatory responses whereas suppression of neurotrophic factors that may contribute to the cognitive impairment. Our findings indicate the toxic mechanism and potential detrimental effect of nanoplastic in brain and suggest a potential risk of cognitive impairment by exposure to nanoplastics.
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Project description:To understand molecular events of gallbladder cells during nanoplastics exposure, we performed scRNA-seq on gallbladder using 10x Genomics Chromium platform
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2023-09-01 | GSE214536 | GEO
Project description:Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments, first, with molecular hydrogen and carbon dioxide, and second, with sodium formate. In the first experiment, we found the highest methane production rate for Methanothermobacter thermautotrophicus ΔH, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Transcriptomics and proteomics data sets from these steady-state bioreactors, in combination with the implementation of a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. While the observed differences in the growth behavior cannot be fully explained, the comparison enabled us to identify crucial differences in growth-related pathways such as formate anabolism. In the second experiment, we found stable growth with a M. thermautotrophicus ΔH plasmid-carrying strain on formate with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. The results of the two studies demonstrate the advantages of an integrative approach combining fermentation and omics data with genome-scale modeling to reveal knowledge gaps of archaeal metabolisms and the biotechnological potential of Methanothermobacter spp. as production platform hosts.
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Project description:In this study, the proteins forming the protein corona on PS and PVC were investigated after 5 min, 1 h, 6 h, or 24 h incubation of the nanoplastics with human plasma. TMT-based untargeted proteomics were applied to identify the proteins forming the protein corona.
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