Bioreactor sludge metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB13306 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR358074_1.fastq.gz | Fastqsanger.gz | |||
| DRR358074_2.fastq.gz | Fastqsanger.gz | |||
| DRR358075_1.fastq.gz | Fastqsanger.gz | |||
| DRR358075_2.fastq.gz | Fastqsanger.gz | |||
| DRR358076_1.fastq.gz | Fastqsanger.gz |
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Project description:Plastics are emerging pollutants of great concern. Macroplastics degrade into microplastics and nanoplastics, which can accumulate in living organisms with still poorly known consequences. Nanoplastics being particulate pollutants, they are handled in animal organisms by scavenger cells such as macrophages, which are important players in the immune system. Polyethylene terephthalate is one of these plastics of concern, as it is widely used in food packaging where it releases nanoparticles. We have thus undertaken a study on the effects of true-to-life polyethylene terephthalate nanoparticles prepared from water bottles on macrophages. To this purpose, we used a combination of proteomics and targeted validation experiments. Proteomics showed important adaptive changes in the proteome in response to exposure to polyethylene terephthalate nanoparticles. These changes affected for example mitochondrial, cytoskeletal and lysosomal proteins, but also proteins implicated in immune functions. Validation experiments showed that many of these changes were homeostatic, with no induced oxidative stress and no gross perturbation of the mitochondrial function. However, polyethylene terephthalate nanoparticles induced endoplasmic reticulum stress and disturbed the immune functions of macrophages. We indeed observed a slight pro-inflammatory response (1.5-fold increase in TNF secretion). We also observed a decrease in the response to bacterial stimulation (1.6 decrease in IL-6 secretion). We also observed a 20 percent decrease in the expression of important proteins involved in immune responses such as TLR2, TLR7 or collectin 12, and a two-fold decrease in the production of lysozyme. This suggests that macrophages having ingested polyethylene terephthalate nanoparticles are less efficient in their immune functions.
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Project description:Although the biodegradation of biodegradable plastics in soil and compost is well-studied, there is little knowledge on the metabolic mechanisms of synthetic polymers degradation by marine microorganisms. Here, we present a multiomics study to elucidate the biodegradation mechanism of a commercial aromatic-aliphatic copolyester film by a marine microbial enrichment culture. The plastic film and each monomer can be used as sole carbon source. Our analysis showed that the consortium synergistically degrades the polymer, different degradation steps being performed by different members of the community. Analysis of gene expression and translation profiles revealed that the relevant degradation processes in the marine consortium are closely related to poly(ethylene terephthalate) biodegradation from terrestrial microbes. Although there are multiple genes and organisms with the potential to perform a degradation step, only a few of these are active during biodegradation. Our results elucidate the potential of marine microorganisms to mineralize biodegradable plastic polymers and describe the mechanisms of labor division within the community to get maximum energetic yield from a complex synthetic substrate.
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Project description:Degradation of polyurethane and polyethylene terephthalate by a Fusarium strain enriched from soil-plant systems
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Project description:We study the transcriptional reactions of bacteria interesting for biodegradation under laboratory conditions that mimic water stress. We compared the transcriptomes of cultures growing exponential phase under optimal conditions versus their responses to an osmotic shock of 30 min in exponential phase. The osmotic shock consisted in a reduction of water potential induced by salt (NaCl, solute stress) or by polyethylene glycol (PEG8000, matric stress). The stress was such that cells are not more than 20% affected in their maximum growth rate.
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Project description:We study the transcriptional reactions of bacteria interesting for biodegradation under laboratory conditions that mimic water stress. We compared the transcriptomes of cultures growing exponential phase under optimal conditions versus their responses to an osmotic shock of 30 min in exponential phase. The osmotic shock consisted in a reduction of water potential induced by salt (NaCl, solute stress) or by polyethylene glycol (PEG8000, matric stress). The stress was such that cells are not more than 20% affected in their maximum growth rate.
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Project description:Proteomes Reveal Robust Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals
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Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.
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Project description:To get further insights on the micro-nanoplastic (MNP) effects on plants, the aim of this study was to: 1) shed light on the transcriptome changes provoked by two different polyethylene terephthalate (PET) MNPs in plant roots; 2) determine their effects on key plant growth parameters in hydroponically-cultivated Arabidopsis thaliana. MNPs of transparent (Tr-PET) and blue (Bl-PET) material caused a significant reduction in root length, while only Bl-PET significantly reduced rosette area. Plant fresh and dry weight did not change, even though various OJIP-test parameters decreased in the presence of MNPs. RNA-seq data showed that Bl-PET and, especially, Tr-PET affected gene expression in comparison to controls. Tr-PET induced starch degradation and isoprenoids, while glycolysis, trehalose metabolism and fermentation were generally repressed. Tr-PET upregulated genes involved in signaling of xenobiotics, whereas Bl-PET scarcely affected root transcriptomic profile, activating few gene categories for abiotic stresses. Regarding hormones, genes involved in ABA response were repressed, while brassinosteroid-related genes were differentially regulated by Tr-PET. Both MNPs, but especially Tr-PET, upregulated major latex protein-related genes. These results allowed to gain insight into the effects of MNP contamination in plant metabolism, identifying targets for biotechnological strategies to enhance plant tolerance and phytoremediation of these xenobiotic agents.
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