Denitrifier Community in the Oxygen Minimum Zone of a Subtropical Deep Reservoir
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{"title"=>"Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir", "type"=>"journal", "authors"=>[{"first_name"=>"Zheng", "last_name"=>"Yu", "scopus_author_id"=>"55514843900"}, {"first_name"=>"Jun", "last_name"=>"Yang", "scopus_author_id"=>"56183078800"}, {"first_name"=>"Lemian", "last_name"=>"Liu", "scopus_author_id"=>"54418749200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84899719906", "doi"=>"10.1371/journal.pone.0092055", "pui"=>"373007544", "issn"=>"19326203", "pmid"=>"24664112", "scopus"=>"2-s2.0-84899719906"}, "id"=>"9301f057-3071-3ea1-b46b-1c1a42864329", "abstract"=>"Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×109 copies L-1 for DNA and 4.19×108 copies L-1 for RNA), and the lowest value was nosZ gene (7.56×105 copies L-1 for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.", "link"=>"http://www.mendeley.com/research/denitrifier-community-oxygen-minimum-zone-subtropical-deep-reservoir", "reader_count"=>38, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>9, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>9, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Environmental Science"=>11, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Chemistry"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>11}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Netherlands"=>2, "Ireland"=>1, "Japan"=>1, "Mexico"=>1, "Australia"=>1, "India"=>1}, "group_count"=>4}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1432652"], "description"=>"<p>Error bars indicate standard errors of the three replicates samples with three triplicate qPCR reactions. “x” indicate undetected data from quantitative RT-PCR.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "16s", "rrna", "denitrifying", "copies", "litre", "dna", "genes", "dongzhen"], "article_id"=>972205, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_16S_rRNA_and_denitrifying_gene_copies_per_litre_water_and_RNA_DNA_ratio_of_five_genes_in_Dongzhen_Reservoir_/972205", "title"=>"Number of 16S rRNA and denitrifying gene copies per litre water and RNA: DNA ratio of five genes in Dongzhen Reservoir.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432651"], "description"=>"<p>(B) Richness estimates (ACE, Chao1) for six different clone libraries with MOTHUR at 97% similarity level.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "rarefaction", "curves", "defined", "16", "rrna", "denitrifying"], "article_id"=>972204, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Rarefaction_curves_of_OTUs_which_were_defined_at_97_sequence_similarity_for_the_16_S_rRNA_gene_and_denitrifying_gene_sequences_/972204", "title"=>"(A) Rarefaction curves of OTUs, which were defined at 97% sequence similarity for the 16 S rRNA gene and denitrifying gene sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432665", "https://ndownloader.figshare.com/files/1432666"], "description"=>"<div><p>Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the <i>narG</i> gene recorded the highest abundance among the denitrifying genes (2.76×10<sup>9</sup> copies L<sup>−1</sup> for DNA and 4.19×10<sup>8</sup> copies L<sup>−1</sup> for RNA), and the lowest value was <i>nosZ</i> gene (7.56×10<sup>5</sup> copies L<sup>−1</sup> for DNA and undetected for RNA). The RNA: DNA ratios indicated that <i>narG</i> gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the <i>narG</i> gene was dominated by <i>Albidiferax</i>, while <i>nirS</i> gene was dominated by <i>Dechloromonas</i>. The main OTU of <i>nirK</i> gene was <i>Rhodopseudomonas palustris</i>, but for <i>norB</i> and <i>nosZ</i> genes, they were <i>Bacillus</i> and <i>Bradyrhizobium</i>, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.</p></div>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "subtropical"], "article_id"=>972218, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0092055.s001", "https://dx.doi.org/10.1371/journal.pone.0092055.s002"], "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Denitrifier_Community_in_the_Oxygen_Minimum_Zone_of_a_Subtropical_Deep_Reservoir_/972218", "title"=>"Denitrifier Community in the Oxygen Minimum Zone of a Subtropical Deep Reservoir", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432660"], "description"=>"<p>Values are mean ± SE (n = 3).</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "variables", "dongzhen", "reservoir", "october"], "article_id"=>972213, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Environmental_variables_in_the_oxygen_minimum_zone_of_Dongzhen_Reservoir_in_October_2011_/972213", "title"=>"Environmental variables in the oxygen minimum zone of Dongzhen Reservoir in October 2011.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432659"], "description"=>"<p>Bacterial community compositions at phylum level and Proteobacteria at class level revealed by clone library and 454 pyrosequencing.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "compositions", "phylum", "proteobacteria", "revealed", "clone", "454"], "article_id"=>972212, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_community_compositions_at_phylum_level_and_Proteobacteria_at_class_level_revealed_by_clone_library_and_454_pyrosequencing_/972212", "title"=>"Bacterial community compositions at phylum level and Proteobacteria at class level revealed by clone library and 454 pyrosequencing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432656"], "description"=>"<p>Shown are OTUs assigned to the highest taxonomic level possible using a BLASTN in GenBank database. The circle size corresponds to the relative average abundance OTUs for each denitrifying gene.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "abundance", "denitrifying", "genes", "genus", "dongzhen"], "article_id"=>972209, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g005", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_different_denitrifying_genes_at_the_genus_or_species_level_in_Dongzhen_Reservoir_/972209", "title"=>"Relative abundance of different denitrifying genes at the genus (or species) level in Dongzhen Reservoir.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432654"], "description"=>"<p>Relative abundance of different bacterial groups from 16 S rRNA gene and five denitrifying genes based on the clone library analysis.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "abundance", "bacterial", "groups", "16", "rrna", "denitrifying", "genes", "clone"], "article_id"=>972207, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g004", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_different_bacterial_groups_from_16_S_rRNA_gene_and_five_denitrifying_genes_based_on_the_clone_library_analysis_/972207", "title"=>"Relative abundance of different bacterial groups from 16 S rRNA gene and five denitrifying genes based on the clone library analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432650"], "description"=>"<p>Genes encoding enzymes that mediate the denitrification steps include those for nitrate reductase (<i>narG</i>), nitrite reductase (<i>nirS</i>/<i>nirK</i>), nitric oxide reductase (<i>norB</i>) and nitrous oxide reductase (<i>nosZ</i>).</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "nitrogen"], "article_id"=>972203, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scheme_for_nitrogen_transformation_from_NO_3_8722_to_N_2_by_denitrification_/972203", "title"=>"Scheme for nitrogen transformation from NO<sub>3</sub><sup>−</sup> to N<sub>2</sub> by denitrification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-24 03:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1432661"], "description"=>"<p>PCR Primers used in this study.</p>", "links"=>[], "tags"=>["ecology", "Freshwater ecology", "microbial ecology", "Evolutionary biology", "population genetics", "genetics", "Gene function", "Molecular genetics", "microbiology", "Public and occupational health", "chemistry", "Analytical chemistry", "Chemical analysis", "Water analysis", "Environmental chemistry", "Water chemistry", "primers"], "article_id"=>972214, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Zheng Yu", "Jun Yang", "Lemian Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092055.t001", "stats"=>{"downloads"=>4, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_Primers_used_in_this_study_/972214", "title"=>"PCR Primers used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-24 03:18:45"}

PMC Usage Stats | Further Information

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Relative Metric

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