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      Distinct microbial communities degrade cellulose diacetate bioplastics in the coastal ocean

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          ABSTRACT

          Cellulose diacetate (CDA) is a bio-based plastic widely used in consumer products. CDA is a promising alternative to conventional thermoplastics due to its susceptibility to biodegradation in various environments. Despite widespread evidence for the degradation of CDA, relatively little is known about the microorganisms that drive degradation, particularly in the ocean. Recently, we documented the biodegradation of CDA-based materials (i.e., fabric, film, and foam) in a continuous-flow natural seawater mesocosm on the timescales of months, as indicated by mass loss, enzyme activity, and respiration to carbon dioxide. These findings paved the way for the present study aimed at identifying key microbial taxa implicated in CDA degradation. Analysis based on 16S rRNA gene amplicon sequencing of bacteria and archaea revealed that material type, incubation time, material morphology (e.g., fabric vs film), and plasticizer content significantly influenced the microbial community structure. Differential abundance analysis revealed that bacterial taxa affiliated with the families of Arenicellaceae, Cellvibrionaceae, Methyloligellaceae, Micavibrionaceae, Puniceicoccaceae, Spirosomaceae, and Thermoanaerobaculaceae, and the order of Pseudomonadales potentially initiated the degradation (i.e., deacetylation) of CDA fabric and film. These taxa were notably distinct from CDA-degrading microbes reported in non-seawater environments. Collectively, the findings lend further support for CDA as a promising next-generation, high-utility, and low-environmental persistence bioplastic material.

          IMPORTANCE

          Cellulose diacetate (CDA) is a promising alternative to conventional plastics due to its versatility in manufacturing and low environmental persistence. Previously, our group demonstrated that CDA is susceptible to biodegradation in the ocean on timescales of months. In this study, we report the composition of microorganisms driving CDA degradation in the coastal ocean. We found that the coastal ocean harbors distinct bacterial taxa implicated in CDA degradation and these taxa have not been previously identified in prior CDA degradation studies, indicating an unexplored diversity of CDA-degrading bacteria in the ocean. Moreover, the shape of the plastic article (e.g., a fabric, film, or foam) and plasticizer in the plastic matrix selected for different microbial communities. Our findings pave the way for future studies to identify the specific species and enzymes that drive CDA degradation in the marine environment, ultimately yielding a more predictive understanding of CDA biodegradation across space and time.

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          Most cited references69

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Investigation
                Role: Data curationRole: Formal analysisRole: MethodologyRole: Writing – review and editing
                Role: Funding acquisitionRole: MethodologyRole: Writing – review and editing
                Role: Writing – review and editing
                Role: Writing – review and editing
                Role: Writing – review and editing
                Role: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review and editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review and editing
                Role: Editor
                Journal
                Appl Environ Microbiol
                Appl Environ Microbiol
                aem
                Applied and Environmental Microbiology
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0099-2240
                1098-5336
                December 2023
                06 December 2023
                06 December 2023
                : 89
                : 12
                : e01651-23
                Affiliations
                [1 ]Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution; , Woods Hole, Massachusetts, USA
                [2 ]Eastman Chemical Company; , Kingsport, Tennessee, USA
                Georgia Institute of Technology; , Atlanta, Georgia, USA
                Author notes
                Address correspondence to Yanchen Sun, yanchen.sun@ 123456whoi.edu
                Address correspondence to Collin P. Ward, cward@ 123456whoi.edu

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0003-1265-2738
                https://orcid.org/0000-0002-4249-2977
                https://orcid.org/0000-0003-2979-0280
                Article
                01651-23 aem.01651-23
                10.1128/aem.01651-23
                10734458
                38054734
                7dcf0221-e711-4303-a1a6-29c23ff7ab0c
                Copyright © 2023 Sun et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 18 September 2023
                : 23 October 2023
                Page count
                supplementary-material: 2, authors: 10, Figures: 4, References: 70, Pages: 14, Words: 7920
                Funding
                Funded by: Eastman Chemical Company (ECC);
                Award Recipient :
                Funded by: Eastman Chemical Company (ECC);
                Award Recipient :
                Funded by: Woods Hole Oceanographic Institution (WHOI);
                Award Recipient :
                Funded by: Woods Hole Oceanographic Institution (WHOI);
                Award Recipient :
                Categories
                Environmental Microbiology
                environmental-microbiology, Environmental Microbiology
                Custom metadata
                December 2023

                Microbiology & Virology
                cellulose diacetate,plastic pollution,bioplastics,biodegradation,microbial communities,16s rrna gene amplicon sequencing

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