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

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          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.

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          Most cited references 57

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          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.
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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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                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
                © 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.

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