Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean
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{"title"=>"Comparing bacterial community composition of healthy and dark spot-affected Siderastrea sidereain Florida and the Caribbean", "type"=>"journal", "authors"=>[{"first_name"=>"Christina A.", "last_name"=>"Kellogg", "scopus_author_id"=>"7006039925"}, {"first_name"=>"Yvette M.", "last_name"=>"Piceno", "scopus_author_id"=>"6603297197"}, {"first_name"=>"Lauren M.", "last_name"=>"Tom", "scopus_author_id"=>"36629380400"}, {"first_name"=>"Todd Z.", "last_name"=>"DeSantis", "scopus_author_id"=>"6602743913"}, {"first_name"=>"Michael A.", "last_name"=>"Gray", "scopus_author_id"=>"7401584667"}, {"first_name"=>"Gary L.", "last_name"=>"Andersen", "scopus_author_id"=>"7202552651"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84907854979", "pmid"=>"25289937", "sgr"=>"84907854979", "doi"=>"10.1371/journal.pone.0108767", "issn"=>"19326203", "pui"=>"600116602"}, "id"=>"d1e13815-b19c-3745-86e5-3fb01e8d41f7", "abstract"=>"Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.", "link"=>"http://www.mendeley.com/research/comparing-bacterial-community-composition-healthy-dark-spotaffected-siderastrea-sidereain-florida-ca", "reader_count"=>44, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>11, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>11, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Venezuela"=>1, "Belgium"=>1, "Brazil"=>1, "France"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1708528"], "description"=>"<p>Samples with the prefix ‘DRTO’ were from Dry Tortugas National Park. Samples with prefix ‘VIIS’ were from Virgin Islands National Park.</p>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196798, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0108767.g004", "stats"=>{"downloads"=>6, "page_views"=>320, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_multidimensional_scaling_NMDS_diagram_of_the_bacterial_communities_from_each_sample_based_on_4_978_operational_taxonomic_units_OTUs_detected_by_the_PhyloChip_G3_microarray_/1196798", "title"=>"Non-metric multidimensional scaling (NMDS) diagram of the bacterial communities from each sample based on 4,978 operational taxonomic units (OTUs) detected by the PhyloChip G3 microarray.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 03:21:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1708524"], "description"=>"<p>Minor phyla (less than 0.5% of any sample) and unclassified sequences are collectively represented by the ‘other’ category.</p>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196795, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0108767.g002", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_diversity_of_the_major_bacterial_phyla_associated_with_Siderastrea_siderea_corals_/1196795", "title"=>"Relative diversity of the major bacterial phyla associated with <i>Siderastrea siderea</i> corals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 03:21:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1708527"], "description"=>"<p>The 21 families shown were those representing greater than 1% of at least one sample. The remaining families and unclassified sequences are collectively represented by the ‘other’ category.</p>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196797, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0108767.g003", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_diversity_within_bacterial_families_associated_with_Siderastrea_siderea_corals_/1196797", "title"=>"Relative diversity within bacterial families associated with <i>Siderastrea siderea</i> corals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 03:21:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1708522"], "description"=>"<p>Map of Florida and the Caribbean showing the two sampling locations.</p>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196793, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0108767.g001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Florida_and_the_Caribbean_showing_the_two_sampling_locations_/1196793", "title"=>"Map of Florida and the Caribbean showing the two sampling locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 03:21:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1708543", "https://ndownloader.figshare.com/files/1708545", "https://ndownloader.figshare.com/files/1708546", "https://ndownloader.figshare.com/files/1708547", "https://ndownloader.figshare.com/files/1708548"], "description"=>"<div><p>Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral <i>Siderastrea siderea</i>. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. <i>S. siderea</i> samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and <i>Vibrios</i>, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in <i>S. siderea</i> is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral <i>S. siderea</i>.</p></div>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196810, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0108767.s001", "https://dx.doi.org/10.1371/journal.pone.0108767.s002", "https://dx.doi.org/10.1371/journal.pone.0108767.s003", "https://dx.doi.org/10.1371/journal.pone.0108767.s004", "https://dx.doi.org/10.1371/journal.pone.0108767.s005"], "stats"=>{"downloads"=>9, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparing_Bacterial_Community_Composition_of_Healthy_and_Dark_Spot_Affected_Siderastrea_siderea_in_Florida_and_the_Caribbean/1196810", "title"=>"Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected <i>Siderastrea siderea</i> in Florida and the Caribbean", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-10-07 03:21:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1708529"], "description"=>"<p><i>Siderastrea siderea</i> samples processed for microarray analysis.</p>", "links"=>[], "tags"=>["spot lesions", "DSS samples", "reef degradation", "Siderastrea siderea", "Caribbean reefs", "siderea samples", "Virgin Islands National Park", "Caribbean Coral disease", "Dark Spot Syndrome", "health state", "macroscopic signs", "pathogen", "Various bacteria", "PhyloChip G 3 microarrays", "dna", "Bacterial Community Composition", "tissue", "Tissue biopsies", "Dry Tortugas National Park", "species"], "article_id"=>1196799, "categories"=>["Biological Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0108767.t001", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Siderastrea_siderea_samples_processed_for_microarray_analysis_/1196799", "title"=>"<i>Siderastrea siderea</i> samples processed for microarray analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-07 03:21:16"}

PMC Usage Stats | Further Information

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