Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure
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{"title"=>"Linking geology and microbiology: Inactive pockmarks affect sediment microbial community structure", "type"=>"journal", "authors"=>[{"first_name"=>"Thomas H.A.", "last_name"=>"Haverkamp", "scopus_author_id"=>"55916849800"}, {"first_name"=>"Øyvind", "last_name"=>"Hammer", "scopus_author_id"=>"25624260900"}, {"first_name"=>"Kjetill S.", "last_name"=>"Jakobsen", "scopus_author_id"=>"7005413513"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24475066", "doi"=>"10.1371/journal.pone.0085990", "pui"=>"373030982", "issn"=>"19326203", "sgr"=>"84899810908", "scopus"=>"2-s2.0-84899810908"}, "id"=>"348d70e9-7d03-32ac-b261-35d41b66b16c", "abstract"=>"Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.", "link"=>"http://www.mendeley.com/research/linking-geology-microbiology-inactive-pockmarks-affect-sediment-microbial-community-structure", "reader_count"=>24, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"Norway"=>1, "United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1360000"], "description"=>"<p>The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "abundances", "otu"], "article_id"=>912768, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g006", "stats"=>{"downloads"=>3, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylum_level_abundances_of_representative_OTU_sequences_/912768", "title"=>"Phylum level abundances of representative OTU sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1360001"], "description"=>"<p>Diversity estimators are average values calculated on standardized counts based on the smallest sample with permutations (n = 1000). Standard deviations were omitted for clarity, but can be found in Table S4 in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085990#pone.0085990.s001\" target=\"_blank\">File S1</a>.</p>$<p>OTUs<sup>97</sup>: operational taxonomic units at the 97% sequences similarity cut-off.</p>*<p>Distance metrics were calculated after standardization of all samples to the smallest sample (RDC40 = 2071) and bootstrapped (n = 1000).</p>#<p>Non-Parametric Shannon.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "estimators", "oslofjord", "samples"], "article_id"=>912769, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.t003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_estimators_for_the_Oslofjord_sediment_samples_after_removal_of_unique_sequences_/912769", "title"=>"Diversity estimators for the Oslofjord sediment samples after removal of unique sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1360002"], "description"=>"$<p>The value here is the average of the back calculation for both measurements.</p>#<p>Flouride ions were only measured with a 100x dilution. So it is 1 single measurement.</p>*<p>nd: not determined.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "variables"], "article_id"=>912770, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_a_selection_of_chemical_variables_measured_per_sample_/912770", "title"=>"Overview of a selection of chemical variables measured per sample.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1360003"], "description"=>"*<p>Diameter and depth of the pockmarks was determined via the methods described in Webb et al., 2009.</p>#<p>Distances were calculated based on the geographical coordinates. Distances between all sites can be found in Table S1 in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085990#pone.0085990.s001\" target=\"_blank\">File S1</a>.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "oslofjord", "sampling"], "article_id"=>912771, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Description_of_Oslofjord_sampling_sites_/912771", "title"=>"Description of Oslofjord sampling sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1360004"], "description"=>"<p>Minimum relative abundance as calculated by Metastats >0.001. Text in bold indicates OTUs overrepresented in pockmarks. Classifications are at the order level or higher taxonomical levels.</p>*<p>Order level classification indicated when identified.</p>#<p>Abbreviation: env.samples : environmental samples.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "otus", "abundances", "40", "cm", "pockmark"], "article_id"=>912772, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.t004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Metastats_results_of_OTUs_with_significantly_different_abundances_between_the_40_cm_pockmark_and_reference_sediment_samples_/912772", "title"=>"Metastats results of OTUs with significantly different abundances between the 40 cm pockmark and reference sediment samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1360007", "https://ndownloader.figshare.com/files/1360009", "https://ndownloader.figshare.com/files/1360010", "https://ndownloader.figshare.com/files/1360012", "https://ndownloader.figshare.com/files/1360013"], "description"=>"<div><p>Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.</p></div>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "geology", "inactive", "pockmarks", "microbial"], "article_id"=>912774, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085990.s001", "https://dx.doi.org/10.1371/journal.pone.0085990.s002", "https://dx.doi.org/10.1371/journal.pone.0085990.s003", "https://dx.doi.org/10.1371/journal.pone.0085990.s004", "https://dx.doi.org/10.1371/journal.pone.0085990.s005"], "stats"=>{"downloads"=>34, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linking_Geology_and_Microbiology_Inactive_Pockmarks_Affect_Sediment_Microbial_Community_Structure_/912774", "title"=>"Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1359995"], "description"=>"<p>The red crosses indicate the sampling sites and the sampling site designation is given. The map was generated with the <a href=\"http://www.mareano.no\" target=\"_blank\">www.mareano.no</a> website.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "sampling"], "article_id"=>912763, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bathymetric_map_of_the_sampling_area_in_the_Oslofjord_/912763", "title"=>"Bathymetric map of the sampling area in the Oslofjord.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1359996"], "description"=>"<p>A) Rarefaction curves with singletons included. B) Rarefaction curves with singletons excluded. The sample coloration descriptions are indicated in the figure. Samples are grouped color wise based on location (pockmark vs. reference sediments) and depth (4 cm vs. 40 cm).</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "curves", "16s", "rrna", "sequences"], "article_id"=>912764, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_curves_of_16S_rRNA_sequences_at_the_97_sequence_similarity_cut_off_/912764", "title"=>"Rarefaction curves of 16S rRNA sequences at the 97% sequence similarity cut-off.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1359997"], "description"=>"<p><b>A)</b> Rank abundance curves for all samples at the 97% sequence similarity cut-off. Black depicts the rank abundance curve for all OTUs in all samples. Red indicates the rank abundance curve for the 28 OTUs shared across all samples. In grey the rank abundance curves are plotted for the individual samples <b>B)</b> Venn diagram showing the number of OTUs shared between each of the four groups: Pockmark 0–4 cm (PM04), Pockmark 40 cm (PM40), Reference site 0–4 cm (R04) and Reference site 40 cm (R40).</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "otus"], "article_id"=>912765, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g003", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shared_OTUs_between_all_samples_/912765", "title"=>"Shared OTUs between all samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1359998"], "description"=>"<p>The amount of variation explained for each axis is indicated in percentages. Samples are grouped color wise based on location (pockmark vs. reference sediments) and depth (4 cm vs. 40 cm) in the figure.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "coordinates", "ordination", "weighted", "unifrac"], "article_id"=>912766, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g004", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_Coordinates_Analysis_ordination_using_weighted_Unifrac_distances_/912766", "title"=>"Principal Coordinates Analysis ordination using weighted Unifrac distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1359999"], "description"=>"<p>Two-dimensional CCA ordination of the samples using one constrained axis (CCA 1) and an unconstrained axis (CA 1). The constraining factor was Total Carbon. Eigenvalue for both axes are indicated beside each axis. Environmental parameters that significantly (p<0.01) correlated with the ordination were fitted using the envfit command (Vegan package). Abbreviations: total nitrogen (TN), total carbon (TC), total organic carbon (TOC).</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "Biogeochemistry", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "marine and aquatic sciences", "Marine geology", "sediment", "bacterial", "communities", "oslofjord", "sediments", "constrained", "correspondence"], "article_id"=>912767, "categories"=>["Biological Sciences"], "users"=>["Thomas H. A. Haverkamp", "Øyvind Hammer", "Kjetill S. Jakobsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085990.g005", "stats"=>{"downloads"=>1, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationships_between_bacterial_communities_of_Oslofjord_sediments_using_constrained_correspondence_analysis_/912767", "title"=>"Relationships between bacterial communities of Oslofjord sediments using constrained correspondence analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-24 02:53:26"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Earth sciences/Geography", "average_usage"=>[310]}, {"subject_area"=>"/Earth sciences/Hydrology", "average_usage"=>[272]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[320]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[313]}]}
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