A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
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{"title"=>"A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees", "type"=>"journal", "authors"=>[{"first_name"=>"Migun", "last_name"=>"Shakya", "scopus_author_id"=>"55262513700"}, {"first_name"=>"Neil", "last_name"=>"Gottel", "scopus_author_id"=>"50261683500"}, {"first_name"=>"Hector", "last_name"=>"Castro", "scopus_author_id"=>"35408795400"}, {"first_name"=>"Zamin K.", "last_name"=>"Yang", "scopus_author_id"=>"7405435258"}, {"first_name"=>"Lee", "last_name"=>"Gunter", "scopus_author_id"=>"7005594936"}, {"first_name"=>"Jessy", "last_name"=>"Labbé", "scopus_author_id"=>"55125234500"}, {"first_name"=>"Wellington", "last_name"=>"Muchero", "scopus_author_id"=>"24076751600"}, {"first_name"=>"Gregory", "last_name"=>"Bonito", "scopus_author_id"=>"6507694449"}, {"first_name"=>"Rytas", "last_name"=>"Vilgalys", "scopus_author_id"=>"7003830293"}, {"first_name"=>"Gerald", "last_name"=>"Tuskan", "scopus_author_id"=>"7004609271"}, {"first_name"=>"Mircea", "last_name"=>"Podar", "scopus_author_id"=>"6602710603"}, {"first_name"=>"Christopher W.", "last_name"=>"Schadt", "scopus_author_id"=>"7801370467"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84885728619", "sgr"=>"84885728619", "pui"=>"370046385", "isbn"=>"1932-6203", "pmid"=>"24146861", "doi"=>"10.1371/journal.pone.0076382"}, "id"=>"fb331feb-04c0-3725-b365-4967d1fa8def", "abstract"=>"Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects.", "link"=>"http://www.mendeley.com/research/multifactor-analysis-fungal-bacterial-community-structure-root-microbiome-mature-populus-deltoides-t", "reader_count"=>164, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>7, "Researcher"=>48, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>5, "Student > Master"=>21, "Other"=>7, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>7, "Researcher"=>48, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>5, "Student > Master"=>21, "Other"=>7, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>16, "Environmental Science"=>18, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>110, "Chemistry"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>110}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>16}, "Environmental Science"=>{"Environmental Science"=>18}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>11, "Finland"=>1, "Mexico"=>1, "France"=>1, "Australia"=>1, "Russia"=>1, "India"=>3}, "group_count"=>11}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1239217"], "description"=>"<p>Two endosphere samples that repeatedly failed to amplify are listed as NA in the table.</p>", "links"=>[], "tags"=>["rhizosphere", "endosphere", "bacterial", "fungal", "otus", "sampled"], "article_id"=>824384, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076382.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_rhizosphere_specific_shared_and_endosphere_specific_bacterial_and_fungal_OTUs_among_all_the_sampled_trees_/824384", "title"=>"Distribution of rhizosphere specific, shared, and endosphere specific bacterial and fungal OTUs among all the sampled trees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-16 02:49:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1239215"], "description"=>"<p>Rhizosphere is represented by brown edges and endosphere by green edges. Similarly, two the watersheds are represented by orange and blue edges for Tennessee and North Carolina, respectively. The end nodes represent the two seasons of sample collection. The number at the node represents the p-values (red for insignificant, blue for significant p≤0.05) generated by comparing the unweighted UniFrac distance metrics between two conditions (left and right nodes) using the <i>adonis</i> function of vegan package in R. Phylograms represent (A) bacterial and (B) fungal communities.</p>", "links"=>[], "tags"=>["phylogram-based", "phylogenetic-based", "watersheds", "seasons", "bacterial", "fungal"], "article_id"=>824382, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076382.g003", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_phylogram_based_illustration_of_the_experimental_design_and_difference_in_phylogenetic_based_community_structure_between_rhizosphere_endosphere_watersheds_and_seasons_for_bacterial_A_and_fungal_B_communities_/824382", "title"=>"A phylogram-based illustration of the experimental design and difference in phylogenetic-based community structure between rhizosphere, endosphere, watersheds and seasons for bacterial (A) and fungal (B) communities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-16 02:49:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1239214"], "description"=>"<p>The first row of stacked bar represents the overall relative abundance across the entire data set, the second row represents endosphere vs. rhizosphere, third row represents the relative abundance in each watershed and the fourth row represents the relative abundance in May vs. September.</p>", "links"=>[], "tags"=>["bacterial", "fungal", "communities", "roots"], "article_id"=>824381, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076382.g002", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomic_distribution_of_bacterial_A_and_fungal_B_communities_from_roots_of_Populus_deltoides_/824381", "title"=>"Taxonomic distribution of bacterial (A) and fungal (B) communities from roots of <i>Populus deltoides</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-16 02:49:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1239213"], "description"=>"<p>Each symbol on the maps represents the location of each tree sampled along the river and the corresponding symbol in the phylogenetic tree represents the genotypic relationships amongst individual hosts. The size of the symbol on the branch corresponds to the number of trees in each of the three putative host clonal groups.</p>", "links"=>[], "tags"=>["locations", "caney", "tennessee", "yadkin", "carolina", "phylogenetic", "23", "individuals", "generated", "20", "sequences"], "article_id"=>824380, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076382.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_sample_locations_along_Caney_Fork_River_in_Tennessee_and_Yadkin_River_in_North_Carolina_along_with_phylogenetic_tree_for_the_23_individuals_of_P_deltoides_generated_from_20_simple_sequences_repeat_markers_/824380", "title"=>"Map of sample locations along Caney Fork River in Tennessee and Yadkin River in North Carolina along with phylogenetic tree for the 23 individuals of <i>P. deltoides</i> generated from 20 simple sequences repeat markers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-16 02:49:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1239218", "https://ndownloader.figshare.com/files/1239219", "https://ndownloader.figshare.com/files/1239220", "https://ndownloader.figshare.com/files/1239221", "https://ndownloader.figshare.com/files/1239222", "https://ndownloader.figshare.com/files/1239223", "https://ndownloader.figshare.com/files/1239224", "https://ndownloader.figshare.com/files/1239225", "https://ndownloader.figshare.com/files/1239226", "https://ndownloader.figshare.com/files/1239227", "https://ndownloader.figshare.com/files/1239228", "https://ndownloader.figshare.com/files/1239229", "https://ndownloader.figshare.com/files/1239230", "https://ndownloader.figshare.com/files/1239231", "https://ndownloader.figshare.com/files/1239232", "https://ndownloader.figshare.com/files/1239233"], "description"=>"<div><p>Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species <i>Populus deltoides</i>, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, <i>Proteobacteria</i> and <i>Ascomycota</i> were dominant in root communities (>50%) while other higher-level phylogenetic groups (<i>Chytridiomycota, Acidobacteria</i>) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that could be separated from other measured effects.</p></div>", "links"=>[], "tags"=>["multifactor", "fungal", "bacterial", "microbiome", "mature", "trees"], "article_id"=>824385, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0076382.s001", "https://dx.doi.org/10.1371/journal.pone.0076382.s002", "https://dx.doi.org/10.1371/journal.pone.0076382.s003", "https://dx.doi.org/10.1371/journal.pone.0076382.s004", "https://dx.doi.org/10.1371/journal.pone.0076382.s005", "https://dx.doi.org/10.1371/journal.pone.0076382.s006", "https://dx.doi.org/10.1371/journal.pone.0076382.s007", "https://dx.doi.org/10.1371/journal.pone.0076382.s008", "https://dx.doi.org/10.1371/journal.pone.0076382.s009", "https://dx.doi.org/10.1371/journal.pone.0076382.s010", "https://dx.doi.org/10.1371/journal.pone.0076382.s011", "https://dx.doi.org/10.1371/journal.pone.0076382.s012", "https://dx.doi.org/10.1371/journal.pone.0076382.s013", "https://dx.doi.org/10.1371/journal.pone.0076382.s014", "https://dx.doi.org/10.1371/journal.pone.0076382.s015", "https://dx.doi.org/10.1371/journal.pone.0076382.s016"], "stats"=>{"downloads"=>43, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Multifactor_Analysis_of_Fungal_and_Bacterial_Community_Structure_in_the_Root_Microbiome_of_Mature_Populus_deltoides_Trees/824385", "title"=>"A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature <i>Populus deltoides</i> Trees", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-16 02:49:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1239216"], "description"=>"<p>Each bar represents total variance partitioned into pure effect or interaction of two or all factors. Only variance proportions that were statistically significant (p≤0.05) are listed. Variables for host and soil properties were selected based on stepwise selection (forward and backward) to remove non-significant terms from the model. (A) Variance partitioning of bacterial community from endosphere and rhizosphere. (B) Variance partitioning of fungal community from endosphere and rhizosphere.</p>", "links"=>[], "tags"=>["partitioning", "bacterial", "fungal", "communities", "roots", "seasonal", "beta", "corresponding"], "article_id"=>824383, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Migun Shakya", "Neil Gottel", "Hector Castro", "Zamin K. Yang", "Lee Gunter", "Jessy Labbé", "Wellington Muchero", "Gregory Bonito", "Rytas Vilgalys", "Gerald Tuskan", "Mircea Podar", "Christopher W. Schadt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076382.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variance_partitioning_of_bacterial_and_fungal_communities_from_the_roots_of_Populus_deltoides_into_soil_properties_host_properties_spatial_host_genotype_seasonal_and_beta_diversity_of_corresponding_bacterial_or_fungal_community_/824383", "title"=>"Variance partitioning of bacterial and fungal communities from the roots of <i>Populus deltoides</i> into soil properties, host properties, spatial, host genotype, seasonal and beta diversity of corresponding bacterial or fungal community.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-16 02:49:30"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[296, 488, 620, 717, 828, 938, 1038, 1130, 1230, 1328, 1414, 1502, 1592]}, {"subject_area"=>"/Earth sciences/Atmospheric science", "average_usage"=>[287, 443, 560, 684, 777, 894, 989, 1065, 1143, 1235, 1335, 1423, 1477]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[298, 487, 610, 722, 827, 929, 1029, 1125, 1217, 1306, 1388, 1464, 1535]}]}
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