Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity
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{"title"=>"Plant invasions associated with change in root-zone microbial community structure and diversity", "type"=>"journal", "authors"=>[{"first_name"=>"Richard R.", "last_name"=>"Rodrigues", "scopus_author_id"=>"56998170200"}, {"first_name"=>"Rosana P.", "last_name"=>"Pineda", "scopus_author_id"=>"56998419500"}, {"first_name"=>"Jacob N.", "last_name"=>"Barney", "scopus_author_id"=>"9736953000"}, {"first_name"=>"Erik T.", "last_name"=>"Nilsen", "scopus_author_id"=>"7004895780"}, {"first_name"=>"John E.", "last_name"=>"Barrett", "scopus_author_id"=>"7403498714"}, {"first_name"=>"Mark A.", "last_name"=>"Williams", "scopus_author_id"=>"56583042600"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0141424", "sgr"=>"84949599504", "pui"=>"607188290", "scopus"=>"2-s2.0-84949599504", "issn"=>"19326203", "pmid"=>"26505627"}, "id"=>"5d26d95d-8973-3cef-a246-f14063c0f168", "abstract"=>"The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.", "link"=>"http://www.mendeley.com/research/plant-invasions-associated-change-rootzone-microbial-community-structure-diversity", "reader_count"=>46, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Student > Doctoral Student"=>4, "Researcher"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Student > Doctoral Student"=>4, "Researcher"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>9, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1, "Environmental Science"=>14, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>24, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>14}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2382194"], "description"=>"<p>Parameter = soil nutrition trait; Location = the three locations where each species was sampled; Invasion Status = invaded and non-invaded plots. Bolded values indicate significant (p ≤ 0.05) effects. All nutrient units are μg element g<sup>-1</sup> soil. The statistical test (Tukey HSD means separation) is between invaded and non-invaded within site.</p><p>* = p ≤ 0.05</p><p>** = p ≤ 0.01</p><p>*** = p ≤ 0.001</p><p>Mean Values (St. Dev.) and Two-Way Analysis of Variance on Soil Nutrition Parameters from Three Sites in Central Appalachian Mountains with Invaded and Non-Invaded Locations.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586811, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_Values_St_Dev_and_Two_Way_Analysis_of_Variance_on_Soil_Nutrition_Parameters_from_Three_Sites_in_Central_Appalachian_Mountains_with_Invaded_and_Non_Invaded_Locations_/1586811", "title"=>"Mean Values (St. Dev.) and Two-Way Analysis of Variance on Soil Nutrition Parameters from Three Sites in Central Appalachian Mountains with Invaded and Non-Invaded Locations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382193"], "description"=>"<p>The following experimental groups were studied: (i) location (A, M, and R); (ii) invasion status (Invasive plants (I) and Native plants (N)); and (iii) interaction of location and invasion status (Aa, AaR, Mv, MvR, Rd, and RdR).</p><p>Details of Sampling Locations.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586810, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Details_of_Sampling_Locations_/1586810", "title"=>"Details of Sampling Locations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382201"], "description"=>"<p>The hyphen (-) indicates that no taxonomic information was available for that OTU at that level. The bacterial OTU indicated with asterisk (*) was the only OTU associated with non-invaded samples in the ISA. The last two columns indicate the percentage of relative abundance of taxa in the invaded and non-invaded samples, respectively.</p><p>Genera with a Greater Relative Abundance Associated with Invasion and Determined to have a Significant Effect Based on Indicator Species Analysis (IV > 70 and p-value < 0.01).</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586818, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genera_with_a_Greater_Relative_Abundance_Associated_with_Invasion_and_Determined_to_have_a_Significant_Effect_Based_on_Indicator_Species_Analysis_IV_gt_70_and_p_value_lt_0_01_/1586818", "title"=>"Genera with a Greater Relative Abundance Associated with Invasion and Determined to have a Significant Effect Based on Indicator Species Analysis (IV > 70 and p-value < 0.01).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382196"], "description"=>"<p><sup>a</sup> The standard error (SE) of the mean is in given in parenthesis.</p><p>Turnover (Percentage) of Inorganic Nitrogen (Mean, SE<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141424#t003fn001\" target=\"_blank\"><sup>a</sup></a>) in Non-Invaded and Invaded Locations at Three Sites in Central Appalachian Mountains.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586813, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Turnover_Percentage_of_Inorganic_Nitrogen_Mean_SE_a_in_Non_Invaded_and_Invaded_Locations_at_Three_Sites_in_Central_Appalachian_Mountains_/1586813", "title"=>"Turnover (Percentage) of Inorganic Nitrogen (Mean, SE<sup>a</sup>) in Non-Invaded and Invaded Locations at Three Sites in Central Appalachian Mountains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382192"], "description"=>"<p>The taxa are arranged as per total relative abundance across all samples, with the most abundant phyla at the bottom and the least abundant phyla at the top of the y-axis. Similarly, the phylum names in the legend are arranged from the least abundant at the top to the most abundant at the bottom.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586809, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.g002", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomic_summary_of_the_relative_abundance_of_a_bacterial_and_b_fungal_phyla_in_the_invaded_and_non_invaded_sites_/1586809", "title"=>"Taxonomic summary of the relative abundance of (a) bacterial and (b) fungal phyla in the invaded and non-invaded sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382191"], "description"=>"<p>Each circle indicates a sample. Multivariate data analysis methods of adonis and ANOSIM were used to identify whether groups were significantly different.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586808, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plot_describing_a_un_weighted_and_b_weighted_Unifrac_for_bacteria_and_c_Bray_Curtis_distances_for_fungi_in_the_invaded_and_non_invaded_sites_/1586808", "title"=>"PCoA plot describing (a) un-weighted and (b) weighted Unifrac for bacteria and (c) Bray-Curtis distances for fungi in the invaded and non-invaded sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382205", "https://ndownloader.figshare.com/files/2382206", "https://ndownloader.figshare.com/files/2382207", "https://ndownloader.figshare.com/files/2382208", "https://ndownloader.figshare.com/files/2382209", "https://ndownloader.figshare.com/files/2382210"], "description"=>"<div><p>The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (<i>Microstegium vimineum</i>), another by a shrub (<i>Rhamnus davurica</i>), and the third by a tree (<i>Ailanthus altissima</i>). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to <i>Proteobacteria</i>, <i>Acidobacteria</i>, <i>Actinobacteria</i>, and <i>Ascomycota</i> increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing <i>Nitrospirae</i> phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla <i>Proteobacteria</i> increased as a result of plant invasion, but the effect associated most strongly with root-zones of <i>M</i>. <i>vimineum</i> and <i>R</i>. <i>davurica</i>. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.</p></div>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586820, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0141424.s001", "https://dx.doi.org/10.1371/journal.pone.0141424.s002", "https://dx.doi.org/10.1371/journal.pone.0141424.s003", "https://dx.doi.org/10.1371/journal.pone.0141424.s004", "https://dx.doi.org/10.1371/journal.pone.0141424.s005", "https://dx.doi.org/10.1371/journal.pone.0141424.s006"], "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plant_Invasions_Associated_with_Change_in_Root_Zone_Microbial_Community_Structure_and_Diversity_/1586820", "title"=>"Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382200"], "description"=>"<p>Bolded values indicate significant (α<0.05) effects.</p><p>Alpha Diversity Metrics for Invasion, Location, and Location x Invasion in Fungi.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586817, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alpha_Diversity_Metrics_for_Invasion_Location_and_Location_x_Invasion_in_Fungi_/1586817", "title"=>"Alpha Diversity Metrics for Invasion, Location, and Location x Invasion in Fungi.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/2382198"], "description"=>"<p>Bolded values indicate significant (α<0.05) effects.</p><p>Alpha Diversity Metrics for Invasion, Location, and Location x Invasion in Bacteria.</p>", "links"=>[], "tags"=>["Operational taxonomic units", "plant invasion", "plant Invasions Associated", "plant invasions", "qiime", "nitrogen cycling bacteria", "usa", "indicator species analysis", "16 S rRNA", "otu"], "article_id"=>1586815, "categories"=>["Uncategorised"], "users"=>["Richard R. Rodrigues", "Rosana P. Pineda", "Jacob N. Barney", "Erik T. Nilsen", "John E. Barrett", "Mark A. Williams"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0141424.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alpha_Diversity_Metrics_for_Invasion_Location_and_Location_x_Invasion_in_Bacteria_/1586815", "title"=>"Alpha Diversity Metrics for Invasion, Location, and Location x Invasion in Bacteria.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 04:09:36"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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