Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.

      Related collections

      Most cited references 57

      • Record: found
      • Abstract: found
      • Article: not found

      Search and clustering orders of magnitude faster than BLAST.

       Robert Edgar (2010)
      Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
        Bookmark
        • Record: found
        • Abstract: found
        • Article: not found

        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.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          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.
            Bookmark

            Author and article information

            Affiliations
            [1 ] Departments of Natural Resource Sciences & Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada
            [2 ] Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
            Universita degli Studi di Milano-Bicocca, ITALY
            Author notes

            Competing Interests: Mount Polley Mine Inc provided matching funds, site access, transportation, and material assistance in completing this research project (including protective equipment, boat rental and access, SONDE water quality probes, and access to data/schematics collected by mine employees). This does not alter our adherence to PLOS ONE policies on sharing data and materials.

            [¤]

            Current address: Department of Biology, Covenant College, Lookout Mountain, Georgia, United States of America

            Contributors
            ORCID: http://orcid.org/0000-0003-0416-4128, Role: Conceptualization, Role: Data curation, Role: Formal analysis, Role: Funding acquisition, Role: Investigation, Role: Methodology, Role: Project administration, Role: Software, Role: Supervision, Role: Validation, Role: Visualization, Role: Writing – original draft, Role: Writing – review & editing
            Role: Conceptualization, Role: Formal analysis, Role: Methodology, Role: Project administration, Role: Resources, Role: Supervision, Role: Validation, Role: Writing – original draft, Role: Writing – review & editing
            Role: Data curation, Role: Investigation, Role: Methodology, Role: Project administration, Role: Resources, Role: Software, Role: Supervision, Role: Validation, Role: Writing – review & editing
            Role: Data curation, Role: Investigation, Role: Methodology, Role: Validation, Role: Visualization, Role: Writing – review & editing
            Role: Data curation, Role: Investigation, Role: Methodology, Role: Writing – review & editing
            Role: Conceptualization, Role: Writing – review & editing
            Role: Conceptualization, Role: Funding acquisition, Role: Project administration, Role: Resources, Role: Supervision, Role: Writing – original draft, Role: Writing – review & editing
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            25 April 2018
            2018
            : 13
            : 4
            29694379
            5918821
            10.1371/journal.pone.0196032
            PONE-D-17-36438
            (Editor)
            © 2018 Garris et al

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

            Counts
            Figures: 9, Tables: 1, Pages: 25
            Product
            Funding
            Funded by: funder-id http://dx.doi.org/10.13039/501100004489, Mitacs;
            Award ID: IT03863
            Award Recipient : ORCID: http://orcid.org/0000-0003-0416-4128
            Funded by: funder-id http://dx.doi.org/10.13039/501100000233, Genome British Columbia;
            Award ID: E01MTP
            Award Recipient :
            Funded by: funder-id http://dx.doi.org/10.13039/501100000233, Genome British Columbia;
            Award ID: E01MTP
            Award Recipient :
            Funded by: funder-id http://dx.doi.org/10.13039/100008762, Genome Canada;
            Award Recipient :
            Funded by: funder-id http://dx.doi.org/10.13039/100008762, Genome Canada;
            Award Recipient :
            Funded by: funder-id http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
            Award ID: EGP 462139 - 13
            Award Recipient :
            Funded by: Mount Polley Mining Corp.
            Award Recipient :
            This project was supported by a Mitacs Accelerate/Elevate Post-doctoral Fellowship for Heath Garris, where professional development seminars/training were provided with little/no input into the content of the research proposal/execution. This program was co-funded by a partner industry (Mount Polley Mining Corp) that contributed substantially to the development of the project (in the form of site access, feasibility assessment, material support, and manuscript review). Additional funding from NSERC was awarded to support an initial (pre-breach) water quality project. NSERC monitored changes in the proposed project scope by requesting reports, but did not contribute to the content of the study directly. Finally, Genome BC and Genome Canada supported the project through funding and consultation on project scope/applicability/suitability with respect to the use of genomics technologies and accomplishment of project goals, which served to improve project precisions/outcomes. Project funding web references: Mitacs ( https://www.mitacs.ca/en/impact/postdoctoral-fellows-share-program-benefits-mitacs-elevate-retreat); Genome BC ( https://www.genomecanada.ca/en/metagenomics-assess-impacts-mount-polley-mine-taillings-dam-breach-associated-ecosystems); Genome Canada ( https://www.genomecanada.ca/en/metagenomics-assess-impacts-mount-polley-mine-taillings-dam-breach-associated-ecosystems); Mount Polley Mine ( https://www.imperialmetals.com/assets/docs/mt-polley/2015-02-23_MPFN.pdf).
            Categories
            Research Article
            Earth Sciences
            Marine and Aquatic Sciences
            Bodies of Water
            Lakes
            Ecology and Environmental Sciences
            Aquatic Environments
            Freshwater Environments
            Lakes
            Earth Sciences
            Marine and Aquatic Sciences
            Aquatic Environments
            Freshwater Environments
            Lakes
            Earth Sciences
            Geology
            Petrology
            Sediment
            Earth Sciences
            Geology
            Sedimentary Geology
            Sediment
            Physical Sciences
            Chemistry
            Chemical Compounds
            Salts
            Sulfates
            Biology and Life Sciences
            Ecology
            Community Ecology
            Community Structure
            Ecology and Environmental Sciences
            Ecology
            Community Ecology
            Community Structure
            Earth Sciences
            Hydrology
            Surface Water
            Biology and Life Sciences
            Microbiology
            Medical Microbiology
            Microbiome
            Biology and Life Sciences
            Genetics
            Genomics
            Microbial Genomics
            Microbiome
            Biology and Life Sciences
            Microbiology
            Microbial Genomics
            Microbiome
            Biology and Life Sciences
            Ecology
            Ecological Metrics
            Species Diversity
            Ecology and Environmental Sciences
            Ecology
            Ecological Metrics
            Species Diversity
            Earth Sciences
            Geomorphology
            Topography
            Landforms
            Shores
            Custom metadata
            All sequence data are available at https://www.ncbi.nlm.nih.gov/, project number PRJNA433688. Metadata are available at http://www.datadryad.org/, accession DOI: https://doi.org/10.5061/dryad.d52df21.

            Uncategorized

            Comments

            Comment on this article