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      Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania

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          Abstract

          Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds. One stream was located in a watershed that previously had UOG extraction activities but was recently abandoned. We utilized high-throughput sequencing of the 16S rRNA gene to infer differences in sediment aquatic bacterial community structure between UOG+ and UOG- streams, as well as correlate bacterial community structure to physicochemical water parameters. Although overall alpha and beta diversity differences were not observed, there were a plethora of significantly enriched operational taxonomic units (OTUs) within UOG+ and UOG- samples. Our biomarker analysis revealed many of the bacterial taxa enriched in UOG+ streams can live in saline conditions, such as Rubrobacteraceae. In addition, several bacterial taxa capable of hydrocarbon degradation were also enriched in UOG+ samples, including Oceanospirillaceae. Methanotrophic taxa, such as Methylococcales, were significantly enriched as well. Several taxa that were identified as enriched in these samples were enriched in samples taken from different streams in 2014; moreover, partial least squares discriminant analysis (PLS-DA) revealed clustering between streams from the different studies based on the presence of hydraulic fracturing along the second axis. This study revealed significant differences between bacterial assemblages within stream sediments of UOG+ and UOG- streams and identified several potential biomarkers for evaluating and monitoring the response of autochthonous bacterial communities to potential hydraulic fracturing impacts.

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          Landscapes and Riverscapes: The Influence of Land Use on Stream Ecosystems

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            EMPeror: a tool for visualizing high-throughput microbial community data

            Background As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types. Findings Features of EMPeror include: ability to visualize gradients and categorical data, visualize different principal coordinates axes, present the data in the form of parallel coordinates, show taxa as well as environmental samples, dynamically adjust the size and transparency of the spheres representing the communities on a per-category basis, dynamically scale the axes according to the fraction of variance each explains, show, hide or recolor points according to arbitrary metadata including that compliant with the MIxS family of standards developed by the Genomic Standards Consortium, display jackknifed-resampled data to assess statistical confidence in clustering, perform coordinate comparisons (useful for procrustes analysis plots), and greatly reduce loading times and overall memory footprint compared with existing approaches. Additionally, ease of sharing, given EMPeror’s small output file size, enables agile collaboration by allowing users to embed these visualizations via emails or web pages without the need for extra plugins. Conclusions Here we present EMPeror, an open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3D visualizations of microbial community data, such as the widely used principal coordinates plots. EMPeror includes a rich set of controllers to modify features as a function of the metadata. By being specifically tailored to the requirements of microbial ecologists, EMPeror thus increases the speed with which insight can be gained from large microbiome datasets.
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              Impact of shale gas development on regional water quality.

              Unconventional natural gas resources offer an opportunity to access a relatively clean fossil fuel that could potentially lead to energy independence for some countries. Horizontal drilling and hydraulic fracturing make the extraction of tightly bound natural gas from shale formations economically feasible. These technologies are not free from environmental risks, however, especially those related to regional water quality, such as gas migration, contaminant transport through induced and natural fractures, wastewater discharge, and accidental spills. We review the current understanding of environmental issues associated with unconventional gas extraction. Improved understanding of the fate and transport of contaminants of concern and increased long-term monitoring and data dissemination will help manage these water-quality risks today and in the future.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                02 August 2018
                2018
                : 9
                Affiliations
                1Department of Biology, Juniata College , Huntingdon, PA, United States
                2The Bredesen Center, The University of Tennessee, Knoxville , Knoxville, TN, United States
                3Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville , Knoxville, TN, United States
                4Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN, United States
                5Freshwater Research Initiative, Susquehanna University , Selinsgrove, PA, United States
                6Department of Earth and Environmental Sciences, Susquehanna University , Selinsgrove, PA, United States
                Author notes

                Edited by: James Cotner, University of Minnesota Twin Cities, United States

                Reviewed by: Jennifer F. Biddle, University of Delaware, United States; Casey Michael Godwin, University of Michigan, United States

                *Correspondence: Regina Lamendella, lamendella@ 123456juniata.edu

                This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2018.01697
                6083035
                Copyright © 2018 Chen See, Ulrich, Nwanosike, McLimans, Tokarev, Wright, Campa, Grant, Hazen, Niles, Ressler and Lamendella.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 6, Tables: 0, Equations: 0, References: 84, Pages: 13, Words: 0
                Funding
                Funded by: Geisinger Health System Foundation 10.13039/100001126
                Funded by: Richard King Mellon Foundation 10.13039/100000915
                Funded by: Howard Hughes Medical Institute 10.13039/100000011
                Funded by: National Science Foundation 10.13039/100000001
                Award ID: DBI-124809
                Categories
                Microbiology
                Original Research

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