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      In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

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          Abstract

          Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in situ life detection and sequencing in the field in soils over laying ice wedges in polygonal permafrost terrain on Axel Heiberg Island, located in the Canadian high Arctic (79°26′N), an analog to the polygonal permafrost terrain observed on Mars. The life detection methods used here include (1) the cryo-iPlate for culturing microorganisms using diffusion of in situ nutrients into semi-solid media (2) a Microbial Activity Microassay (MAM) plate (BIOLOG Ecoplate) for detecting viable extant microorganisms through a colourimetric assay, and (3) the Oxford Nanopore MinION for nucleic acid detection and sequencing of environmental samples and the products of MAM plate and cryo-iPlate. We obtained 39 microbial isolates using the cryo-iPlate, which included several putatively novel strains based on the 16S rRNA gene, including a Pedobacter sp. (96% closest similarity in GenBank) which we partially genome sequenced using the MinION. The MAM plate successfully identified an active community capable of L-serine metabolism, which was used for metagenomic sequencing with the MinION to identify the active and enriched community. A metagenome on environmental ice wedge soil samples was completed, with base calling and uplink/downlink carried out via satellite internet. Validation of MinION sequencing using the Illumina MiSeq platform was consistent with the results obtained with the MinION. The instrumentation and technology utilized here is pre-existing, low cost, low mass, low volume, and offers the prospect of equipping micro-rovers and micro-penetrators with aggressive astrobiological capabilities. Since potentially habitable astrobiology targets have been identified (RSLs on Mars, near subsurface water ice on Mars, the plumes and oceans of Europa and Enceladus), future astrobiology missions will certainly target these areas and there is a need for direct life detection instrumentation.

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          A habitable fluvio-lacustrine environment at Yellowknife Bay, Gale crater, Mars.

          The Curiosity rover discovered fine-grained sedimentary rocks, which are inferred to represent an ancient lake and preserve evidence of an environment that would have been suited to support a martian biosphere founded on chemolithoautotrophy. This aqueous environment was characterized by neutral pH, low salinity, and variable redox states of both iron and sulfur species. Carbon, hydrogen, oxygen, sulfur, nitrogen, and phosphorus were measured directly as key biogenic elements; by inference, phosphorus is assumed to have been available. The environment probably had a minimum duration of hundreds to tens of thousands of years. These results highlight the biological viability of fluvial-lacustrine environments in the post-Noachian history of Mars.
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            Cassini ion and neutral mass spectrometer: Enceladus plume composition and structure.

            The Cassini spacecraft passed within 168.2 kilometers of the surface above the southern hemisphere at 19:55:22 universal time coordinated on 14 July 2005 during its closest approach to Enceladus. Before and after this time, a substantial atmospheric plume and coma were observed, detectable in the Ion and Neutral Mass Spectrometer (INMS) data set out to a distance of over 4000 kilometers from Enceladus. INMS data indicate that the atmospheric plume and coma are dominated by water, with significant amounts of carbon dioxide, an unidentified species with a mass-to-charge ratio of 28 daltons (either carbon monoxide or molecular nitrogen), and methane. Trace quantities (<1%) of acetylene and propane also appear to be present. Ammonia is present at a level that does not exceed 0.5%. The radial and angular distributions of the gas density near the closest approach, as well as other independent evidence, suggest a significant contribution to the plume from a source centered near the south polar cap, as distinct from a separately measured more uniform and possibly global source observed on the outbound leg of the flyby.
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              One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

              Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
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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
                20 December 2017
                2017
                : 8
                Affiliations
                [1] 1Department of Natural Resource Sciences, McGill University , Ste. Anne-de-Bellevue, QC, Canada
                [2] 2Bigelow Laboratory for Ocean Sciences , East Boothbay, ME, United States
                Author notes

                Edited by: Karen Olsson-Francis, Open University, United Kingdom

                Reviewed by: Richard Allen White III, Washington State University, United States; Alfonso Benítez-Páez, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Spain

                *Correspondence: J. Goordial jacqueline.goordial@ 123456mail.mcgill.ca

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

                Article
                10.3389/fmicb.2017.02594
                5742409
                692c3ffc-5334-499f-a969-cc076daac0a4
                Copyright © 2017 Goordial, Altshuler, Hindson, Chan-Yam, Marcolefas and Whyte.

                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) or licensor 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: 5, Tables: 2, Equations: 0, References: 52, Pages: 14, Words: 9757
                Funding
                Funded by: Natural Sciences and Engineering Research Council of Canada 10.13039/501100000038
                Award ID: RGPIN-298520-2012
                Award ID: RGPNS 305490-201
                Funded by: Canadian Space Agency 10.13039/501100000016
                Award ID: CSA FAST 15FASTA18
                Award ID: CSA MSR 15EXPMICRO
                Categories
                Microbiology
                Original Research

                Microbiology & Virology

                life detection, astrobiology, nanopore minion, polar microbiology, permafrost

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