Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas
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{"title"=>"Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas", "type"=>"journal", "authors"=>[{"first_name"=>"Belén", "last_name"=>"Carbonetto", "scopus_author_id"=>"56233385600"}, {"first_name"=>"Nicolás", "last_name"=>"Rascovan", "scopus_author_id"=>"26423986300"}, {"first_name"=>"Roberto", "last_name"=>"Álvarez", "scopus_author_id"=>"7202902994"}, {"first_name"=>"Alejandro", "last_name"=>"Mentaberry", "scopus_author_id"=>"6701811764"}, {"first_name"=>"Martin P.", "last_name"=>"Vázquez", "scopus_author_id"=>"7401539904"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84903398796", "pmid"=>"24923965", "doi"=>"10.1371/journal.pone.0099949", "pui"=>"373399164", "isbn"=>"1932-6203", "arxiv"=>"1703.07747", "sgr"=>"84903398796"}, "id"=>"f93503b3-101f-3179-a5b7-95db5f0439e1", "abstract"=>"Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.", "link"=>"http://www.mendeley.com/research/structure-composition-metagenomic-profile-soil-microbiomes-associated-agricultural-land-tillage-syst", "reader_count"=>133, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>11, "Researcher"=>28, "Student > Ph. D. Student"=>42, "Student > Postgraduate"=>4, "Student > Master"=>23, "Other"=>2, "Student > Bachelor"=>10, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>11, "Researcher"=>28, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1533295"], "description"=>"<p>Standard error ellipses show 95% confidence areas. Circles represent samples from “La Estrella”, crosses represent “Criadero Klein” samples and triangles represent “La Negrita” samples.</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "metagenomic", "euclidean", "matrices", "cog", "categories", "pampa"], "article_id"=>1056180, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g003", "stats"=>{"downloads"=>5, "page_views"=>66, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plot_of_metagenomic_data_based_on_Euclidean_distance_matrices_of_COG_categories_of_Pampa_production_field_soil_microbiomes_/1056180", "title"=>"PCoA plot of metagenomic data based on Euclidean distance matrices of COG categories of Pampa production field soil microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533288"], "description"=>"<p>A) PCoA of cultivated and non-cultivated soil microbiomes. All sub-samples are plotted. Standard error ellipses show 95% confidence areas. B) PCoA biplot of soil properties that best explained variation in community structure. Correlations were calculated using BIOENV on average data of each sampled site (Mantel r = 0.6107, p≤0.05). Circles represent samples from “La Estrella”, crosses represent “Criadero Klein” samples and triangles represent “La Negrita” samples.</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "pampa", "microbiomes", "weighted", "unifrac"], "article_id"=>1056177, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g001", "stats"=>{"downloads"=>8, "page_views"=>195, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plots_of_Pampa_production_field_soil_microbiomes_based_on_97_similarity_Weighted_Unifrac_distance_matrices_/1056177", "title"=>"PCoA plots of Pampa production field soil microbiomes based on 97% similarity Weighted Unifrac distance matrices.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533353", "https://ndownloader.figshare.com/files/1533354", "https://ndownloader.figshare.com/files/1533355", "https://ndownloader.figshare.com/files/1533356", "https://ndownloader.figshare.com/files/1533357"], "description"=>"<div><p>Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla <i>Verrucomicrobia, Plactomycetes, Actinobacteria</i>, and <i>Chloroflexi</i> were more abundant in non cultivated soils while <i>Gemmatimonadetes, Nitrospirae</i> and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.</p></div>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "metagenomic", "microbiomes", "tillage", "systems", "argentine"], "article_id"=>1056209, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0099949.s001", "https://dx.doi.org/10.1371/journal.pone.0099949.s002", "https://dx.doi.org/10.1371/journal.pone.0099949.s003", "https://dx.doi.org/10.1371/journal.pone.0099949.s004", "https://dx.doi.org/10.1371/journal.pone.0099949.s005"], "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_Composition_and_Metagenomic_Profile_of_Soil_Microbiomes_Associated_to_Agricultural_Land_Use_and_Tillage_Systems_in_Argentine_Pampas_/1056209", "title"=>"Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533319"], "description"=>"<p>CA: conventional tillage; NT: no-tillage. Bars represent ±1 standard erro. (*)indicate significant differences (p≤0.05).</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "abundances", "cog", "categories", "microbiomes", "tillage", "systems"], "article_id"=>1056188, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g007", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundances_of_COG_categories_in_soil_microbiomes_of_tillage_systems_comparison_experiment_in_Balcarce_/1056188", "title"=>"Relative abundances of COG categories in soil microbiomes of tillage systems comparison experiment in Balcarce.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533316"], "description"=>"<p>CA: conventional tillage; NT: no-tillage. Bars represent ±1 standard error. (*) indicate significant differences (p≤0.05).</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "abundances", "taxonomic", "groups", "nt", "ct"], "article_id"=>1056185, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_relative_abundances_of_taxonomic_groups_in_NT_and_CT_soils_/1056185", "title"=>"Comparison of relative abundances of taxonomic groups in NT and CT soils.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533301"], "description"=>"<p>Bars represent ±1 standard error. (*) indicate significant differences (p≤0.05).</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "abundances", "cog", "categories", "pampas"], "article_id"=>1056183, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g004", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundances_of_COG_categories_in_Pampas_production_field_soil_microbiomes_/1056183", "title"=>"Relative abundances of COG categories in Pampas production field soil microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533315"], "description"=>"<p>A) CA: conventional tillage; NT: no-tillage. All sub-samples are plotted. Standard error ellipses show 95% confidence areas. B) PCoA biplot, nitrate was the variable that best explained variation in community structure. Correlations were calculated using BIONEV on average data of each experimental plot (Mantel r = 0.7721, p≤0.01).</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "balcarce", "microbiomes", "weighted", "unifrac"], "article_id"=>1056184, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g005", "stats"=>{"downloads"=>2, "page_views"=>195, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plots_of_Balcarce_experimental_field_soil_microbiomes_based_on_97_similarity_Weighted_Unifrac_distance_matrices_/1056184", "title"=>"PCoA plots of Balcarce experimental field soil microbiomes based on 97% similarity Weighted Unifrac distance matrices.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1533294"], "description"=>"<p>Bars represent ± 1 standard error. (*) indicate significant differences (p≤0.05).</p>", "links"=>[], "tags"=>["agriculture", "Agroecology", "ecology", "biodiversity", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Microbial physiology", "Microbial metabolism", "abundances", "taxonomic", "groups", "pampa"], "article_id"=>1056179, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Belén Carbonetto", "Nicolas Rascovan", "Roberto Álvarez", "Alejandro Mentaberry", "Martin P. Vazquez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099949.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundances_of_taxonomic_groups_in_Pampa_production_field_soil_microbiomes_/1056179", "title"=>"Relative abundances of taxonomic groups in Pampa production field soil microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-12 03:32:57"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"19", "full-text"=>"21", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"25", "full-text"=>"23", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
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  • {"unique-ip"=>"29", "full-text"=>"40", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"31", "full-text"=>"32", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"15", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
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  • {"unique-ip"=>"25", "full-text"=>"31", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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