ETBE degrading microbes in aquifers
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ABSTRACT:
PROVIDER: PRJEB44194 | ENA |
REPOSITORIES: ENA
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Project description:Polylactic acid (PLA) is a promising biodegradable material used in various fields, such as mulching films and disposable packaging materials. Biological approaches for completely degrading biodegradable polymers can provide environmentally friendly solutions. However, to our knowledge, no studies have performed transcriptome profiling to analyze PLA-degrading genes of PLA-degrading bacteria. Therefore, this study reports for the first time an RNA sequence approach for tracing genes involved in PLA biodegradation in the PLA-degrading bacterium Brevibacillus brevis. In the interpretation results of the differentially expressed genes, the hydrolase genes mhqD and nap and the serine protease gene besA were up-regulated by a fold change of 7.97, 4.89, and 4.09, respectively. This result suggests that hydrolases play a key role in PLA biodegradation by B. brevis. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes implicated in biofilm formation were upregulated. The biodegradation of PLA starts with bacteria attaching to the surface of PLA and forming a biofilm. Therefore, it could be confirmed that the above genes were up-regulated for access to PLA and biodegradation. Our results provide transcriptome-based insights into PLA biodegradation, which pitch a better understanding of microbial biodegradation of plastics.
2025-01-16 | GSE223668 | GEO
Project description:We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.
2018-09-07 | GSE119644 | GEO
Project description:Sucralose biodegradation and the enriched degrading-consortia revealed by combining Illumina and Nanopore sequencing
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Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil. Comparative transcriptomics of Rhodococcus erythropolis PR4 grown on n-hexadecane, diesel oil, and sodium acetate.
2014-04-21 | E-GEOD-56474 | biostudies-arrayexpress
Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil.
2014-04-21 | GSE56474 | GEO
Project description:Groundwater-derived microorganisms are known to play an important role in biogeochemical C, S and N cycling. Thereby, the presence and majorly the activity of microorganisms in aquifers affect enormously the nutrient cycling. However, the diversity and their functional capability in natural aquifers are still rare and therefore a better knowledge of the core microbial communities is urgently needed. Metaproteome analysis was applied to characterize the repertoire of microbes in the depth and to identify the key drivers of major biogeochemical processes. Therefore, 1000 L water from the aquifer was sampled by filtration on 0.3 µm glass filters. After protein extraction, proteolytic cleavage and mass spectrometric analysis (Ultimate 3000 nanoRSLC coupled to Q Exactive HF instrument), 3808 protein groups (2371 proteins with ≥2 peptides) were identified from 13,204 peptides. The findings of our study have broad implications for the understanding of aquifer cycling’s which finally leads to a greatly improved understanding of the ecosystem services provided by the microbial communities present in aquifers. In the future, functional results would allow to monitor and to assess pollution effects which would beneficially assist groundwater resource management.
2016-12-23 | PXD004351 | Pride
Project description:The biodegradation of lignite (brown coal) by microorganisms has the potential for bioremediation of contaminated mining sites and to generate alternative ways to valorize lignite, such as by producing humic acids or building block chemicals. Previously, a lignite-degrading strain of Trichoderma was isolated, but the genomic and transcriptomic basis of its lignite-degrading ability remained unknown. Here we report that the sequenced genome of the T. cf. simile WF8 strain encoded for enzymes with roles in the degradation of lignite, and potentially tolerance to lignite-breakdown products. There was only a small number of annotated unique genes in the T. cf. simile WF8 genome compared to other fungi, and likely the expression of gene families shared with other fungi is a key factor in lignite biosolubilization by T. cf. simile. The transcriptomes were analyzed of T. cf. simile cultured at two time-points with the lignite-breakdown model compounds 4-phenoxybenzoic acid (which was growth inhibitory), and phenetole and 9-10-dibutoxyanthracene (neither of which inhibited growth), and showed ~20% of genes up-regulated by one or more of these compounds. The analysis highlights candidates for characterization and engineering enzyme over-expressing T. cf. simile strains with potentially improved degradation capacity, e.g., laccases and peroxidases, or tolerance and catabolism of breakdown products, e.g., cytochrome P450s, and ring cleavage dioxygenases.
2025-01-05 | GSE285891 | GEO
Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses.
2012-06-18 | GSE38296 | GEO
Project description:This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses. Transcriptomic response of phenanthrene degrading Sphingomonas sp. LH128 biofilms as a response to short-term and long-term solute (NaCl) stress was studied using genome-wide gene expression analysis. For this purpose, the strain was grown in customized continuous glass flow chambers that contain solid phenanthrene as a sole carbon source and that allow easy recovery of biofilm cells for transcriptomic and physiological analysis. A NaCl stress of 450 mM was imposed on LH128 biofilms growing on phenanthrene crystals coated on glass slides either for 4 hours (acute stress) or for 3 days (chronic stress). RNA was extracted from the biofilm and cDNA was synthesized and labeled with Cy3. Transcriptomic response in the stressed biofilms of three replicates per conditions were analyzed and compared with non-stressed
2012-06-18 | E-GEOD-38296 | biostudies-arrayexpress