Plastic degradation by marine bacteria
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ABSTRACT:
PROVIDER: PRJEB36649 | ENA |
REPOSITORIES: ENA
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Project description:To characterize the taxonomic and functional diversity of biofilms on plastics in marine environments, plastic pellets (PE and PS, ø 3mm) and wooden pellets (as organic control) were incubated at three stations: at the Baltic Sea coast in Heiligendamm (coast), in a dead branch of the river Warnow in Warnemünde (inlet), and in the Warnow estuary (estuary). After two weeks of incubation, all pellets were frozen for subsequent metagenome sequencing and metaproteomic analysis. Biofilm communities in the samples were compared on multiple levels: a) between the two plastic materials, b) between the individual incubation sites, and c) between the plastic materials and the wooden control. Using a semiquantitative approach, we established metaproteome profiles, which reflect the dominant taxonomic groups as well as abundant metabolic functions in the respective samples.
2021-11-01 | PXD012062 | Pride
Project description:Polyethylene terephthalate (PET) and polyethylene (PE) are prominent polymer materials that comprise a significant portion of commercial plastic waste. Their durability and slow degradation rate have resulted in significant accumulation of plastic on Earth. In a recent study, macrotranscriptomic profiling of a reconstituted marine bacterial community identified 10 putative enzymes capable of directly acting on PE or PET (PEases or PETases). Among these enzymes, three recombinant proteins were reported to possess PE degradation activity. To select potential plastic degrading enzyme candidates for protein engineering efforts, we expressed and purified eight out of the 10 candidates, excluding two due to poor expression and/or solubility. Notably, several candidate proteins displayed significant esterase activity on p-nitrophenyl butyrate and exhibited unexpected thermostability despite their marine origin. Additionally, we observed dose- and time-dependent hydrolytic activity on the PET trimer substrate. Structural analysis and mutagenesis of a candidate protein confirmed the presence of catalytic triad residues, classifying it as an esterase. Furthermore, we elucidated the structural importance of the two disulfide bonds. Through point mutation experiments, we observed an enhanced hydrolytic activity of a selected enzyme candidate on PET nanoparticles. Our findings challenge the classification of the enzymes directly acting on PE and highlight the significance and complexity of validating PE degradation enzymes identified through metagenomic analysis.
| S-EPMC11270687 | biostudies-literature
Project description:Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria (MHB), using largely uncharacterized mechanisms. In Zobellia galactanivorans, we discovered and characterized the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, providing a model system for carrageenan utilization by MHB. We further demonstrate that carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and several distal genes. The genetic structure of the carrageenan utilization system is well conserved in marine Bacteroidetes, but modified in other MHB phyla. The core system is completed by additional functions which can be assumed by non-orthologous genes in different species. This complex genetic structure is due to multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.
2017-12-06 | GSE101142 | GEO
Project description:Biodegradable plastics are one possible solution for reducing plastic waste, yet the mechanisms and organisms involved in their degradation in the aquatic environment remain understudied. In this study, we have enriched a microbial community from North Sea water and sediment, capable of growing on the polyester poly(butylene succinate). This culture was grown on two other biodegradable polyesters, polycaprolactone and ecovio® FT (a PBAT-based blended biodegradable plastic), and the differences between community structure and activity on these three polymers were determined by metagenomics and metaproteomics. We have seen that the plastic supplied drives the community structure and activity. Setups growing on ecovio® FT were more diverse, yet showed the lowest degradation, while poly(butylene succinate) and polycaprolactone resulted in a less diverse community but much higher degradation efficiencies. The dominating species were Alcanivorax sp., Thalassobius sp., or Pseudomonas sp., depending on the polymer supplied. Furthermore, we have observed that Gammaproteobacteria were more abundant and active within the biofilm and Alphaproteobacteria within the free-living fraction of the enrichments. Two of the three PETase-like enzymes isolated were expressed as tandems (Ple -tan1 &Ple – tan2) and all three were produced by Pseudomonas sp. Of those, Ple-tan1 was most active on all three substrates and also the most thermostable. Overall, we could show that all three plastics investigated can be mineralized by bacteria naturally occurring within the marine environment and characterize some of the enzymes involved in the degradation process.
2023-11-22 | PXD038098 | Pride
Project description:Distinct Microbial Communities Degrade Cellulose Diacetate Plastics in the Coastal Ocean
| PRJNA938436 | ENA
Project description:The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment. These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms. Ultimately, these data suggest that marine fungi could be as important in oceanic ecosystems as they are in freshwater environments.
2020-07-14 | GSE117831 | GEO
Project description:The presence of plastic and microplastic within the oceans as well as in marine flora and fauna have caused a multitude of problems which have been topic of numerous investigations for many years. However, their impact on human health remains largely unknown. Such plastic and microplastic particles have been detected in blood and placenta, underlining their ability to enter the human body. Plastics also contain other compounds, such as plasticizers, antioxidants, or dyes, whose impact on human health is currently being studied. Critical enzymes within the metabolism of endogenous molecules, especially of xenobiotics, are the cytochrome P450 monooxygenases (CYPs). Although their importance in maintaining cellular balance has been confirmed, their interactions with plastics and related products are poorly understood. In this study, the possible relationship between different plastic-related compounds and CYP3A4 as one of the most important CYPs was analyzed using hepatic cells overexpressing this enzyme. Beginning with virtual compound screening and molecular docking of more than 1,000 plastic-related compounds, several candidates were identified to interact with CYP3A4. In a second step, RNA-sequencing was used to study in detail the transcriptome-wide gene expression levels affected by the selected compounds. The results showed that three candidate molecules (2,2'-methylene bis(6-tert-butyl-4-methylphenol, 1,1-bis(3,5-di-tert-butyl-2-hydroxyphenyl)ethane, and 2,2'-methylene bis(6-cyclohexyl-4-methylphenol) had an excellent binding affinity to CYP3A4 in silico as well as cytotoxic effects and interactions with several metabolic pathways in vitro. We identified common pathways influenced by all three selected plastic-related compounds. In particular, the suppression of pathways related to mitosis and ‘DNA-templated DNA replication’. Furthermore, several mis-regulated metabolic and inflammation-related pathways were identified, suggesting the induction of hepatotoxicity at different levels. These findings imply that these compounds may cause problems in the liver, which could subsequently affect the entire organism.
2024-01-24 | GSE237739 | GEO
Project description:Collection of marine microorganisms that degradate biodegradable plastics
| PRJDB17481 | ENA
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.
2020-09-25 | PXD018391 | Pride
Project description:Marine plastic biofragmentation Raw sequence reads
| PRJNA1105387 | ENA