Microbial integration of plastics in the circular economy
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PROVIDER: PRJEB48193 | ENA |
REPOSITORIES: ENA
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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: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:Degradation capacity of silk proteins by microorganisms
2023-01-16 | PXD039506 |
Project description:Since the invention over a hundred years ago, plastics have been used in many applications, and they are involved in every aspect of our lives. The extensive usage of plastics results in a tremendous amount of waste, which has become a severe burden on the environment. Several degradation approaches exist in nature to cope with ever-increasing plastic waste. Among these approaches, biodegradation by microorganisms has emerged as a natural way, which is favored by many environmentally conscious societies. To facilitate the study on biodegradation of plastics, we developed an online resource, Plastics Microbial Biodegradation Database (PMBD), to gather and present the information about microbial biodegradation of plastics. In this database, 949 microorganisms-plastics relationships and 79 genes involved in the biodegradation of plastics were manually collected and confirmed through literature searching. In addition, more than 8000 automatically annotated enzyme sequences, which were predicted to be involved in the plastics biodegradation, were extracted from the TrEMBL section of the UniProt database. The PMBD database is presented with a website at http://pmbd.genome-mining.cn/home. Data may be accessed through browsing or searching. Also included on the website are a sequence alignment tool and a function prediction tool.
| S-EPMC6859810 | biostudies-literature
Project description:Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.
| S-EPMC6752018 | biostudies-literature
Project description:Plastic associated Fungi show shared and unique taxa between the surface waters of the Western South Atlantic and the Antarctic Peninsula.
| PRJEB35146 | ENA
Project description:Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides since they produce a vast variety of glycoside hydrolases. The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharide or glycans. This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares and microarrays were directly synthetized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, previously characterized by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.
2016-12-01 | GSE80173 | GEO
Project description:Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1M-bM-^@M-^SF3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the M-bM-^@M-^\plasticsM-bM-^@M-^] or M-bM-^@M-^\lower dose plasticsM-bM-^@M-^] mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures. Methylated sperm DNA was isolated from rats ancestrally exposed to plastics (Bip). Three independent samples from the treatment group were obtained. Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays (Bip1/Cip1, Bip2/Cip2, and Bip3/Cip3), resulting in three arrays for the treatment.
2014-07-22 | E-GEOD-59555 | biostudies-arrayexpress
Project description:Effect of certain microorganisms on mouse gut microbial communities in aged group.
2021-09-24 | GSE180087 | GEO
Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation. Fifteen refuse samples with five landfill depths and ages (6m/2a, 12m/4a, 18m/6a, 24m/8a and 30m/10a) were collected from a sanitary landfill in Beijing, China. Three replicates in every landfill depth and age
2016-06-15 | E-GEOD-68712 | biostudies-arrayexpress