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      Geological processes mediate a microbial dispersal loop in the deep biosphere

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          Abstract

          The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.

          Abstract

          Abstract

          Subsurface microbial dispersal facilitated by geological processes circulates living biomass in and out of the deep biosphere.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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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

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: ResourcesRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: InvestigationRole: ResourcesRole: Visualization
                Role: Investigation
                Role: Formal analysisRole: MethodologyRole: Software
                Role: ConceptualizationRole: MethodologyRole: ValidationRole: Writing - review & editing
                Role: ConceptualizationRole: MethodologyRole: SoftwareRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing - review & editing
                Role: Investigation
                Role: Investigation
                Role: InvestigationRole: Validation
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Investigation
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: InvestigationRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                August 2022
                26 August 2022
                : 8
                : 34
                : eabn3485
                Affiliations
                [ 1 ]Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada.
                [ 2 ]Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada.
                [ 3 ]Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada.
                [ 4 ]Department of Biological Sciences, Idaho State University, Pocatello, USA.
                [ 5 ]Applied Petroleum Technology, Calgary, Canada.
                Author notes
                [* ]Corresponding author. Email: daniel.gittins@ 123456ucalgary.ca
                [†]

                Present address: Athabasca University, Athabasca, Canada.

                [‡]

                Present address: Queen Mary University of London, London, UK.

                Author information
                https://orcid.org/0000-0002-7227-1120
                https://orcid.org/0000-0001-8039-8546
                https://orcid.org/0000-0002-0051-0890
                https://orcid.org/0000-0001-7086-2237
                https://orcid.org/0000-0003-0240-2655
                https://orcid.org/0000-0002-1109-3797
                https://orcid.org/0000-0001-6892-0936
                https://orcid.org/0000-0002-8353-9313
                https://orcid.org/0000-0003-3530-5560
                https://orcid.org/0000-0003-3249-970X
                https://orcid.org/0000-0003-0944-4153
                https://orcid.org/0000-0002-6319-6536
                https://orcid.org/0000-0002-8691-8116
                Article
                abn3485
                10.1126/sciadv.abn3485
                9417182
                36026445
                e14a7d27-d234-4032-b507-ae7ad064186d
                Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 19 November 2021
                : 13 July 2022
                Funding
                Funded by: MITACS Accelerate Fellowship;
                Funded by: Genome Canada Genomics Applications Partnership Program grant facilitated by Genome Atlantic and Genome Alberta;
                Funded by: Canada Foundation for Innovation grant for instrumentation;
                Award ID: CFI-JELF 33752
                Funded by: Campus Alberta Innovates Program Chair;
                Categories
                Research Article
                Earth, Environmental, Ecological, and Space Sciences
                SciAdv r-articles
                Microbiology
                Molecular Biology
                Microbiology
                Custom metadata
                Nicole Falcasantos

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