A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere.
TL;DR: A microbial community from marine plastic debris is obtained and the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source is analysed, and the mechanisms involved in PET degradation are characterised by two bacterial isolates from the plastisphere.
Abstract: Background Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. Results We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. Conclusions Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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27 Feb 2015
TL;DR: This study confirms the indicated occurrence of potentially pathogenic Vibrio bacteria on marine microplastics and highlights the urgent need for detailed biogeographical analyses of marinemicroplastics.
Abstract: The qualitative and quantitative composition of biofilms on microplastic surfaces is widely unknown. A previous study (Zettler et al., 2013; EST) reports the presence of potentially pathogenic bacteria (Vibrio spp.) on floating microplastic particles. Hence microplastics could function as vectors for the dispersal of microorganisms to new habitats. Several Vibrio species are serious human pathogens. Contact with contaminated water and consumption of raw seafood are the main infection factors for Vibrio associated diseases. On research cruises to the North- and Baltic Sea, microplastic particles were collected and subjected to APW (alkaline peptone water) enrichment. Growth on selective CHROMagar™ Vibrio and further identification of isolates by MALDI-TOF (matrix assisted laser desorption/ionization time-of-flight) clearly indicate the presence of potentially pathogenic Vibrio spp. on microplastics. Our results highlight the urgent need for detailed microbiological analyses of floating microplastic particles in the future.
376 citations
01 Nov 2018
TL;DR: It was hypothesized that the microbial biofilm composition varies distinctly between different substrates, and characteristic and discriminatory taxa of significantly different biofilm communities were identified, indicating their specificity to a given substrate.
Abstract: To understand the ecological impacts of the “Plastisphere”, those microbes need to be identified that preferentially colonize and interact with synthetic polymer surfaces, as opposed to general surface colonizers. It was hypothesized that the microbial biofilm composition varies distinctly between different substrates. A long-term incubation experiment was conducted (15month) with nine different synthetic polymer films as substrate as well as glass using a natural seawater flow-through system. To identify colonizing microorganisms, 16S and 18SrRNA gene tag sequencing was performed. The microbial biofilms of these diverse artificial surfaces were visualized via scanning electron microscopy. Biofilm communities attached to synthetic polymers are distinct from glass associated biofilms; apparently a more general marine biofilm core community serves as shared core among all synthetic polymers rather than a specific synthetic polymer community. Nevertheless, characteristic and discriminatory taxa of significantly different biofilm communities were identified, indicating their specificity to a given substrate.
85 citations
TL;DR: The circular economy is a fine idea and has been around a long time, but has it made any real difference? The amount of plastic in circulation keeps getting bigger and bigger as mentioned in this paper .
44 citations
TL;DR: In this article , the authors summarize the studies related to microorganisms in the plastisphere in recent years and describe the microbial species in the Plastisphere, mainly including bacteria, fungi, and autotrophs.
Abstract: The pollution of plastic waste has become an increasingly serious environmental crisis. Recently, plastic has been detected in various kinds of environments, even in human tissues, which is an increasing threat to the ecosystems and humans. In the ocean, the plastic waste is eventually fragmentized into microplastics (MPs) under the disruption of physical and chemical processes. MPs are colonized by microbial communities such as fungi, diatoms, and bacteria, which form biofilms on the surface of the plastic called "plastisphere". In this review, we summarize the studies related to microorganisms in the plastisphere in recent years and describe the microbial species in the plastisphere, mainly including bacteria, fungi, and autotrophs. Secondly, we explore the interactions between MPs and the plastisphere. The depth of MPs in the ocean and the nutrients in the surrounding seawater can have a great impact on the community structure of microorganisms in the plastisphere. Finally, we discuss the types of MP-degrading bacteria in the ocean, and use the "seed bank" theory to speculate on the potential sources of MP-degrading microorganisms. Challenges and future research prospects are also discussed.
32 citations
TL;DR: A review of the plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophics, predators, and pathogens) can be found in this paper .
Abstract: It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.
17 citations
References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
88,255 citations
"A multi-OMIC characterisation of bi..." refers methods in this paper
...For Bacillus sp. BHET2, the genome annotations by Prokka and BlastKOALA (Blast, Basic Local Alignment Search Tool; KEGG, Kyoto Encyclopedia of Genes and Genomes; KOALA, KEGG Orthology And Links Annotation) [52] as well as subsequent local BLAST searches with known terephthalic acid and protocatechuate degradation proteins did not reveal any proteins with significant homology....
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...For local Blast searches, all matches with above 90% identity were initially kept and these were then further filtered to keep only those with above 95, 97 or 99% identity, depending on the comparison being made....
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...Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences....
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...Assembled genomes were annotated using Prokka [100] and Blast KEGG Orthology and Links Annotation (BlastKOALA) [52] (Table S4)....
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...Global distribution of our isolates in marine plastispheres and planktonic samples In order to determine the distribution of the two isolates, several searches were carried out: (i) local Blast [101] searches using the 16S rRNA gene of each isolate against the community succession amplicon sequencing data; (ii) local Blast searches using the 16S rRNA gene of each isolate against the 16S rRNA gene amplicon sequencing data from all marine plastisphere samples included in our recent plastisphere meta-analysis [33], i.e. 124,319 ASVs in 1185 samples; (iii) local Blast searches using the 16S rRNA gene of each isolate against 16S rRNA fragments from the Tara oceans metagenomes (mitags) [43–45] and (iv) MetaQUAST [102, 103] to determine the coverage for each of the isolates’ genomes within the assembled Tara metagenomes [43–45], downloaded from [104]....
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TL;DR: A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Abstract: Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.
12,489 citations
"A multi-OMIC characterisation of bi..." refers methods in this paper
...[19], an alignment of known PET hydrolases (Table S5) was constructed using the Clustal Omega programme [95] on the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBLEBI) multiple sequence alignment server [96]....
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TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
Abstract: Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
12,340 citations
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.
Abstract: UNLABELLED: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. AVAILABILITY AND IMPLEMENTATION: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/.
10,432 citations
01 Jan 1991
10,143 citations
"A multi-OMIC characterisation of bi..." refers methods in this paper
...carried out by partial sequencing of the 16S rRNA gene (GATC BioTech, Germany) using primers 27F and 1492R [99] after DNA extraction using the DNeasy Plant Mini Kit (Qiagen) with modifications (as above) and purification using the QIAquick PCR purification kit (Qiagen)....
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