Effect of Redox Conditions on Bacterial Community Structure in Baltic Sea Sediments with Contrasting Phosphorus Fluxes
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{"title"=>"Effect of redox conditions on bacterial community structure in Baltic sea sediments with contrasting phosphorus fluxes", "type"=>"journal", "authors"=>[{"first_name"=>"Anne K.", "last_name"=>"Steenbergh", "scopus_author_id"=>"35867377200"}, {"first_name"=>"Paul L E", "last_name"=>"Bodelier", "scopus_author_id"=>"6602832669"}, {"first_name"=>"Caroline P.", "last_name"=>"Slomp", "scopus_author_id"=>"6602166464"}, {"first_name"=>"Hendrikus J.", "last_name"=>"Laanbroek", "scopus_author_id"=>"7006250571"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24667801", "doi"=>"10.1371/journal.pone.0092401", "sgr"=>"84899800144", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84899800144", "issn"=>"19326203", "pui"=>"373020661"}, "id"=>"d5b07526-932c-3154-aba2-a4028ffa02f5", "abstract"=>"<p>Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.</p>", "link"=>"http://www.mendeley.com/research/effect-redox-conditions-bacterial-community-structure-baltic-sea-sediments-contrasting-phosphorus-fl-5", "reader_count"=>28, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>7, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>9, "Earth and Planetary Sciences"=>8}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>7}}, "reader_count_by_country"=>{"Netherlands"=>1, "Mexico"=>1, "France"=>1, "Russia"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1434239", "https://ndownloader.figshare.com/files/1434241", "https://ndownloader.figshare.com/files/1434242"], "description"=>"<div><p>Phosphorus release from sediments can exacerbate the effect of eutrophication in coastal marine ecosystems. The flux of phosphorus from marine sediments to the overlying water is highly dependent on the redox conditions at the sediment-water interface. Bacteria are key players in the biological processes that release or retain phosphorus in marine sediments. To gain more insight in the role of bacteria in phosphorus release from sediments, we assessed the effect of redox conditions on the structure of bacterial communities. To do so, we incubated surface sediments from four sampling sites in the Baltic Sea under oxic and anoxic conditions and analyzed the fingerprints of the bacterial community structures in these incubations and the original sediments. This paper describes the effects of redox conditions, sampling station, and sample type (DNA, RNA, or whole-cell sample) on bacterial community structure in sediments. Redox conditions explained only 5% of the variance in community structure, and bacterial communities from contrasting redox conditions showed considerable overlap. We conclude that benthic bacterial communities cannot be classified as being typical for oxic or anoxic conditions based on community structure fingerprints. Our results suggest that the overall structure of the benthic bacterial community has only a limited impact on benthic phosphate fluxes in the Baltic Sea.</p></div>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "redox", "bacterial", "baltic", "sediments", "contrasting", "phosphorus"], "article_id"=>973549, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0092401.s001", "https://dx.doi.org/10.1371/journal.pone.0092401.s002", "https://dx.doi.org/10.1371/journal.pone.0092401.s003"], "stats"=>{"downloads"=>9, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_Redox_Conditions_on_Bacterial_Community_Structure_in_Baltic_Sea_Sediments_with_Contrasting_Phosphorus_Fluxes_/973549", "title"=>"Effect of Redox Conditions on Bacterial Community Structure in Baltic Sea Sediments with Contrasting Phosphorus Fluxes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434238"], "description"=>"<p>Significance codes: *** = 0.001, ** = 0.001<0.01.</p><p>Exbin72 dataset = dataset in which the relative intensity of DGGE bin 72 has been excluded from the FPCA analysis (see Results section).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "variance", "dataset", "exbin72"], "article_id"=>973548, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.t001", "stats"=>{"downloads"=>12, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Permutational_Analysis_of_Variance_PERMANOVA_of_the_original_dataset_and_the_exbin72_dataset_/973548", "title"=>"Permutational Analysis of Variance (PERMANOVA) of the original dataset and the exbin72 dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434233"], "description"=>"<p>The relative intensity of DGGE bin 72 of bulk DNA, whole-cell, and RNA fraction of in situ and incubated samples.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "dgge", "bin"], "article_id"=>973543, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_intensity_of_DGGE_bin_72_/973543", "title"=>"Relative intensity of DGGE bin 72.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434234"], "description"=>"<p>The percentage of total variance in this dataset explained by axis 1 and 2 is 28.6% and 17.1% for the DNA fraction, 42.3% and 16.1% for the RNA fraction, and 21.2% and 15.3% for the whole-cell fraction. The shape and fill of the symbols in the subplots are coded according to the legends.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "pca", "dgge", "fingerprints", "exbin72", "dataset", "whole-cell"], "article_id"=>973544, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g005", "stats"=>{"downloads"=>0, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correspondence_Analysis_plots_based_on_Functional_PCA_of_DGGE_fingerprints_of_the_exbin72_dataset_of_the_DNA_RNA_and_whole_cell_fraction_/973544", "title"=>"Correspondence Analysis plots based on Functional PCA of DGGE fingerprints of the exbin72 dataset of the DNA, RNA, and whole-cell fraction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434232"], "description"=>"<p>The left-hand panels represent the original dataset. The percentage of total variance in this dataset explained by axis 1 and 2 is 22.3% and 20.4%, respectively. The right-hand panels represent the exbin72 dataset (in which the abundance of bin 72, assumed to be of cyanobacterial origin, has been set to zero; see Results section); the percentage of variance explained by the axes is 28.2% and 15.1%. The symbols in the replicate plots are coded according to the legends. The dashed lines represent the three major clusters of the clustering dendrograms (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092401#pone-0092401-g001\" target=\"_blank\">Figure 1</a>), and the solid arrow in the left-hand panels the fit of bin 72 to community structure (r<sup>2</sup> = 0.58; see text and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092401#pone.0092401.s003\" target=\"_blank\">Table S2 in File S1</a>). The pH of the incubations was determined at the end of the incubation period. The in situ pH of station LF3 was not determined, and is assumed to be 7.5.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "pca", "dgge"], "article_id"=>973542, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g003", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correspondence_Analysis_plot_based_on_Functional_PCA_of_DGGE_fingerprints_/973542", "title"=>"Correspondence Analysis plot based on Functional PCA of DGGE fingerprints.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434229"], "description"=>"<p>Each vertical line of pixels represents the DGGE lane of a single sample. Lower bin numbers correspond to the top of the DGGE gel. Higher relative intensities of DGGE bins are represented with darker pixels. The clustering dendrogram shows the relation between samples. The sample fraction, sampling station, amendment and redox condition of each sample is color- coded between the dendrogram and the fingerprints (fraction: bulk DNA = white, whole-cell DNA = blue, RNA = black; station: LF1 = white, LF1.5 = yellow, LF3 = blue, LF5 = black; amendment: control = white, CNP = black, in situ = yellow; redox: oxic = white, anoxic = black, in situ = yellow).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "dgge"], "article_id"=>973539, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visual_representation_of_the_DGGE_fingerprints_/973539", "title"=>"Visual representation of the DGGE fingerprints.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434237"], "description"=>"<p>Significance codes: *** = 0.001, ** = 0.001<0.01, * = 0.01<0.05.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "variance", "exbin72", "datasets", "whole-cell", "rna"], "article_id"=>973547, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.t002", "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Permutational_Analysis_of_Variance_PERMANOVA_of_the_separate_exbin72_datasets_of_the_bulk_DNA_whole_cell_DNA_and_RNA_fraction_/973547", "title"=>"Permutational Analysis of Variance (PERMANOVA) of the separate exbin72 datasets of the bulk DNA, whole-cell DNA, and RNA fraction.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434236"], "description"=>"<p>The phylogenetic affiliation of selected DGGE bands was determined on the basis of phylogenetic tags assigned by the RDP classifier (see text). DGGE bins from which bands from separate lanes received different tags are classified as such, causing the combined phylogenetic labels of several of the categories. The abbreviation “Prot.” stands for Proteobacteria.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "abundance", "bacterial", "phyla", "classes"], "article_id"=>973546, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g006", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_bacterial_phyla_Panel_a_and_classes_Panel_b_/973546", "title"=>"Relative abundance of bacterial phyla (Panel a) and classes (Panel b).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1434227"], "description"=>"<p>Schematic overview of samples and replicates.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "community structure", "Marine ecology", "microbial ecology", "Marine biology", "microbiology", "bacteriology", "Bacterial biochemistry", "geochemistry", "Biogeochemistry", "marine and aquatic sciences", "overview", "samples"], "article_id"=>973537, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Anne K. Steenbergh", "Paul L. E. Bodelier", "Caroline P. Slomp", "Hendrikus J. Laanbroek"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092401.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_overview_of_samples_and_replicates_/973537", "title"=>"Schematic overview of samples and replicates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-25 03:20:28"}

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Relative Metric

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