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Microplastics alter composition of fungal communities in aquatic ecosystems : Fungal communities on microplastics

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      Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

      mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
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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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          Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

          Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical to assess the strengths, weaknesses, and overall suitability of these platforms for the interrogation of microbial communities. Here, we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nucleotide reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in length (i.e., V34, V4, and V45) by resequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we reprocessed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.
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            Author and article information

            Affiliations
            [1 ]Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
            [2 ]Institute for Biochemistry and Biology, Faculty of Science, Potsdam University; Potsdam Germany
            [3 ]Universidad Latina de Costa Rica, Campus San Pedro, Apdo. 10138-1000; San Jose Costa Rica
            [4 ]Environmental Microbiology Working Group; Leibniz Institute for Baltic Sea Research; Warnemünde Germany
            Journal
            Environmental Microbiology
            Environ Microbiol
            Wiley
            14622912
            November 2017
            November 2017
            October 13 2017
            : 19
            : 11
            : 4447-4459
            10.1111/1462-2920.13891
            © 2017

            http://doi.wiley.com/10.1002/tdm_license_1.1

            http://onlinelibrary.wiley.com/termsAndConditions#vor

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