Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA
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{"title"=>"Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA", "type"=>"journal", "authors"=>[{"first_name"=>"Jean Pierre", "last_name"=>"Gauthier", "scopus_author_id"=>"7202654249"}, {"first_name"=>"Yannick", "last_name"=>"Outreman", "scopus_author_id"=>"56070175000"}, {"first_name"=>"Lucie", "last_name"=>"Mieuzet", "scopus_author_id"=>"6507099428"}, {"first_name"=>"Jean Christophe", "last_name"=>"Simon", "scopus_author_id"=>"56424678900"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25807173", "doi"=>"10.1371/journal.pone.0120664", "sgr"=>"84926300513", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84926300513", "issn"=>"19326203", "pui"=>"603466548"}, "id"=>"fb6a470d-4bf5-3b78-84ba-61a9256a58a5", "abstract"=>"Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.", "link"=>"http://www.mendeley.com/research/bacterial-communities-associated-hostadapted-populations-pea-aphids-revealed-deep-sequencing-16s-rib", "reader_count"=>70, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>4, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>4, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>52, "Medicine and Dentistry"=>2, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>52}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>1, "United Kingdom"=>1, "Portugal"=>1, "Spain"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1988301"], "description"=>"<p>*obligatory symbiont and **facultative symbionts.</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355571, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_16S_rDNA_reads_in_Log_10_for_the_21_bacterial_taxa_detected_in_nine_plant_specialized_biotypes_of_the_pea_aphid_Acyrthosiphon_pisum_/1355571", "title"=>"Number of 16S rDNA reads in Log(10) for the 21 bacterial taxa detected in nine plant-specialized biotypes of the pea aphid, <i>Acyrthosiphon pisum</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988305"], "description"=>"<p>Accession numbers of representative sequences of each OTU found in the different samples (74 sequences in total) are given in Supporting Information (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120664#pone.0120664.s003\" target=\"_blank\">S3 Table</a>).</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355575, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_16S_rDNA_based_on_a_Neighbor_Joining_tree_relating_bacterial_sequences_from_references_selected_in_GenBank_REF_and_from_454_amplicon_sequencing_of_populations_and_biotypes_of_the_pea_aphid_complex_/1355575", "title"=>"Phylogenetic analysis of 16S rDNA based on a Neighbor-Joining tree relating bacterial sequences from references selected in GenBank (REF) and from 454 amplicon sequencing of populations and biotypes of the pea aphid complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988306"], "description"=>"<p>Each data point represents the bacterial community identified from a single sample (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120664#pone.0120664.t001\" target=\"_blank\">Table 1</a> for dot label legends). The Bray-Curtis dissimilarity index was used to rank distances calculated using the presence-absence community data. Stress of the nMDS = 0.152.</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355576, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_MDS_ordination_plot_comparing_bacterial_communities_from_different_pea_aphid_samples_/1355576", "title"=>"Non-metric MDS ordination plot comparing bacterial communities from different pea aphid samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988307"], "description"=>"<p>Each data point represents a pairwise combination of pea aphid biotype (Mantel test, p>0.05).</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355577, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_matrix_of_Bray_Curtis_dissimilarities_between_all_pairwise_combinations_of_pea_aphid_biotypes_and_the_matrix_of_the_genetic_distance_among_these_host_adapted_aphid_populations_/1355577", "title"=>"Relationship between the matrix of Bray-Curtis dissimilarities between all pairwise combinations of pea aphid biotypes and the matrix of the genetic distance among these host-adapted aphid populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988308"], "description"=>"<p>Host plant and geographic origins of pea aphid samples examined for intra-host bacterial diversity with 16S rDNA amplicon sequencing.</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355578, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Host_plant_and_geographic_origins_of_pea_aphid_samples_examined_for_intra_host_bacterial_diversity_with_16S_rDNA_amplicon_sequencing_/1355578", "title"=>"Host plant and geographic origins of pea aphid samples examined for intra-host bacterial diversity with 16S rDNA amplicon sequencing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988309"], "description"=>"<p>Reference sequences of 16S rDNA genes from bacterial taxa associated with insect hosts (except <i>Spiroplasma</i> from <i>Citrus</i>).</p>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355579, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_sequences_of_16S_rDNA_genes_from_bacterial_taxa_associated_with_insect_hosts_except_Spiroplasma_from_Citrus_/1355579", "title"=>"Reference sequences of 16S rDNA genes from bacterial taxa associated with insect hosts (except <i>Spiroplasma</i> from <i>Citrus</i>).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-25 05:01:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1988311", "https://ndownloader.figshare.com/files/1988312", "https://ndownloader.figshare.com/files/1988313"], "description"=>"<div><p>Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, <i>Acyrthosiphon pisum</i>, is the host of heritable bacterial symbionts, including the obligate endosymbiont <i>Buchnera aphidicola</i> and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of <i>Wolbachia</i> was confirmed in <i>A</i>. <i>pisum</i> while <i>Erwinia</i> and <i>Pantoea</i>, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.</p></div>", "links"=>[], "tags"=>["Bacterial Communities Associated", "16 S sequences", "pea aphid biotypes", "pea aphid", "Operational Taxonomic Unit", "Pea Aphids Revealed", "16 S Ribosomal DNA Associations", "Facultative symbiont communities", "obligate symbionts supply aphids", "16 S rRNA genes", "pea aphid symbionts", "facultative symbionts influence", "plant specialization", "obligate endosymbiont Buchnera aphidicola", "otu"], "article_id"=>1355581, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jean-Pierre Gauthier", "Yannick Outreman", "Lucie Mieuzet", "Jean-Christophe Simon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0120664.s001", "https://dx.doi.org/10.1371/journal.pone.0120664.s002", "https://dx.doi.org/10.1371/journal.pone.0120664.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_Communities_Associated_with_Host_Adapted_Populations_of_Pea_Aphids_Revealed_by_Deep_Sequencing_of_16S_Ribosomal_DNA_/1355581", "title"=>"Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-25 05:01:07"}

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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