Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon
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{"title"=>"Microbial communities in sunken wood are structured by wood-boring bivalves and location in a submarine canyon", "type"=>"journal", "authors"=>[{"first_name"=>"Sonja K.", "last_name"=>"Fagervold", "scopus_author_id"=>"10041331200"}, {"first_name"=>"Chiara", "last_name"=>"Romano", "scopus_author_id"=>"23019780100"}, {"first_name"=>"Dimitri", "last_name"=>"Kalenitchenko", "scopus_author_id"=>"56160160200"}, {"first_name"=>"Christian", "last_name"=>"Borowski", "scopus_author_id"=>"56001375500"}, {"first_name"=>"Amandine", "last_name"=>"Nunes-Jorge", "scopus_author_id"=>"55179465400"}, {"first_name"=>"Daniel", "last_name"=>"Martin", "scopus_author_id"=>"8071579200"}, {"first_name"=>"Pierre E.", "last_name"=>"Galand", "scopus_author_id"=>"7006606172"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84900540848", "sgr"=>"84900540848", "pui"=>"373094142", "isbn"=>"19326203 (ISSN)", "pmid"=>"7144", "doi"=>"10.1371/journal.pone.0096248"}, "id"=>"d761fc77-50e8-3b1f-a1c9-4c60919c60c9", "abstract"=>"The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of <italic>Xylophaga</italic>, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of <italic>Xylophaga</italic> spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that <italic>Xylophaga</italic> spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of <italic>Xylophaga</italic> spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.", "link"=>"http://www.mendeley.com/research/microbial-communities-sunken-wood-structured-woodboring-bivalves-location-submarine-canyon", "reader_count"=>24, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>14, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>2, "United Kingdom"=>1, "Switzerland"=>1, "Portugal"=>1, "Spain"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/1488091", "https://ndownloader.figshare.com/files/1488092", "https://ndownloader.figshare.com/files/1488093"], "description"=>"<div><p>The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of <i>Xylophaga</i>, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of <i>Xylophaga</i> spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that <i>Xylophaga</i> spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of <i>Xylophaga</i> spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.</p></div>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions", "communities", "sunken", "structured", "wood-boring", "bivalves", "submarine"], "article_id"=>1018964, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0096248.s001", "https://dx.doi.org/10.1371/journal.pone.0096248.s002", "https://dx.doi.org/10.1371/journal.pone.0096248.s003"], "stats"=>{"downloads"=>8, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microbial_Communities_in_Sunken_Wood_Are_Structured_by_Wood_Boring_Bivalves_and_Location_in_a_Submarine_Canyon_/1018964", "title"=>"Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488088"], "description"=>"<p>Venn diagram representing bacterial OTUs unique and common to the wood samples, the pellet and the <i>Xylophaga</i> gills.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions", "diagram", "bacterial", "otus", "pellet"], "article_id"=>1018961, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.g005", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_representing_bacterial_OTUs_unique_and_common_to_the_wood_samples_the_pellet_and_the_Xylophaga_gills_/1018961", "title"=>"Venn diagram representing bacterial OTUs unique and common to the wood samples, the pellet and the <i>Xylophaga</i> gills.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488086"], "description"=>"<p>Relative proportion of the most abundant bacterial phylum or class (>1% of the sequences) found in wood, pellet and gill (Bla) samples from Blanes Canyon (BC) and its adjacent open slope (OS). *  =  contained significantly less sequences than the rest of the samples (n = 263).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions", "bacterial"], "article_id"=>1018959, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.g003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_bacterial_taxa_/1018959", "title"=>"Distribution of bacterial taxa.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488087"], "description"=>"<p>Network showing associations between OTUs found in wood and pellets from wood immerged at various depths in Blanes Canyon (BC) and its adjacent open slope (OS). OTUs are represented as nodes (white circles) in the network and the size of each node is proportional to the number of sequences contained in each OTU. Lines connect the nodes that are the most correlated (MIC values>0.5). The identifying numbers of the most abundant OTUs are written in the nodes. Colors highlight associations between the OTUs that most explain the differences between groups of samples (Oak pellet, Pine pellet, BC Pine wood and OS Pine wood). OTUs that best explain differences between samples were identified by a SIMPER analysis.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions"], "article_id"=>1018960, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_OTU_network_/1018960", "title"=>"OTU network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488085"], "description"=>"<p>Dendrogram based on Bray-Curtis distance representing the similarity between bacterial communities sequenced from the wood matrix and from burrow pellets obtained from wood immerged at various depths in Blanes Canyon (BC) and its adjacent open slope (OS).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions"], "article_id"=>1018958, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_clustering_/1018958", "title"=>"Sample clustering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488081"], "description"=>"<p>Map showing the position of the experimental moorings in relation to the Blanes Canyon (BC) and its outer slope (OS), drawn using GeoMapApp (<a href=\"http://www.geomapapp.org\" target=\"_blank\">http://www.geomapapp.org</a>). Insert, cube of pine wood (8 X 8 X 8 cm) colonized by <i>Xylophaga</i> after 12 months of immersion in Blanes Canyon.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions", "sampling", "sites"], "article_id"=>1018954, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_sampling_sites_and_wood_with_Xylophaga_burrows_/1018954", "title"=>"Map of sampling sites and wood with <i>Xylophaga</i> burrows.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488090"], "description"=>"<p>Details on the locations of the traps used for pine and oak (Fagervold et al 2013) wood immersion experiments, as well as the samples taken from each trap. Abbreviations Bla 1.2, Bla 10, Bla 11 and Bla 1.1 refer to gills extractions from four <i>Xylophaga</i> sp. A individuals.</p><p>* =  Samples from Fagervold et al (2013) that were also used in this study.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions", "samples"], "article_id"=>1018963, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_different_samples_in_the_whole_experiment_/1018963", "title"=>"Overview of the different samples in the whole experiment.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-07 02:49:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1488089"], "description"=>"<p>Number of sequences and diversity of wood, pellet and gill samples from Blanes Canyon (BC) and its open slope (OS). H′: Shannon index, Chao-1: Chao true diversity estimator, Cov: coverage.</p><p>*not subsampled (n = 263).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Niche construction", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "Microbial physiology", "Microbial metabolism", "Species interactions"], "article_id"=>1018962, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Sonja K. Fagervold", "Chiara Romano", "Dimitri Kalenitchenko", "Christian Borowski", "Amandine Nunes-Jorge", "Daniel Martin", "Pierre E. Galand"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0096248.t002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alpha_diversity_/1018962", "title"=>"Alpha diversity.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-05-07 02:49:48"}

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"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Anatomy", "average_usage"=>[267]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}, {"subject_area"=>"/Biology and life sciences/Zoology", "average_usage"=>[329]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[318]}]}
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