Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome
Publication Date
June 16, 2014
Journal
PLOS ONE
Authors
Max E. Winston, Jarrad Hampton Marcell, Iratxe Zarraonaindia, Sarah M. Owens, et al
Volume
9
Issue
6
Pages
e99641
DOI
https://dx.plos.org/10.1371/journal.pone.0099641
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0099641
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24932479
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059704
Europe PMC
http://europepmc.org/abstract/MED/24932479
Web of Science
000337738600051
Scopus
84903292583
Mendeley
http://www.mendeley.com/research/understanding-cultivarspecificity-soil-determinants-cannabis-microbiome
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Mendeley | Further Information

{"title"=>"Understanding cultivar-specificity and soil determinants of the Cannabis microbiome", "type"=>"journal", "authors"=>[{"first_name"=>"Max E.", "last_name"=>"Winston", "scopus_author_id"=>"55357538000"}, {"first_name"=>"Jarrad", "last_name"=>"Hampton-Marcell", "scopus_author_id"=>"57195913053"}, {"first_name"=>"Iratxe", "last_name"=>"Zarraonaindia", "scopus_author_id"=>"35323554900"}, {"first_name"=>"Sarah M.", "last_name"=>"Owens", "scopus_author_id"=>"55066334100"}, {"first_name"=>"Corrie S.", "last_name"=>"Moreau", "scopus_author_id"=>"15035968100"}, {"first_name"=>"Jack A.", "last_name"=>"Gilbert", "scopus_author_id"=>"7401452139"}, {"first_name"=>"Josh", "last_name"=>"Hartsel", "scopus_author_id"=>"24341072300"}, {"first_name"=>"Suzanne J.", "last_name"=>"Kennedy", "scopus_author_id"=>"55257808800"}, {"first_name"=>"S. M.", "last_name"=>"Gibbons", "scopus_author_id"=>"32867609000"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"373394672", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0099641", "scopus"=>"2-s2.0-84903292583", "pmid"=>"24932479", "sgr"=>"84903292583"}, "id"=>"17163b51-6ccd-3f09-94d7-1d7d940084ce", "abstract"=>"Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. The influence of soil type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.", "link"=>"http://www.mendeley.com/research/understanding-cultivarspecificity-soil-determinants-cannabis-microbiome", "reader_count"=>92, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>22, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>25, "Student > Postgraduate"=>2, "Student > Master"=>16, "Other"=>4, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>22, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>25, "Student > Postgraduate"=>2, "Student > Master"=>16, "Other"=>4, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>3, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>13, "Mathematics"=>1, "Agricultural and Biological Sciences"=>67, "Neuroscience"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>67}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"United States"=>6, "Mexico"=>1, "Slovenia"=>1, "Australia"=>1, "Chile"=>1}, "group_count"=>7}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1536594"], "description"=>"<p>Physical composition and tested edaphic factors for five soil types from both experiments. Abbreviations for Soil ID are: MB indicates Mo-Bio soil, OC indicates Orange County soil, number indicates experiment (1 =  first experiment, 2 =  second experiment), and final letter abbreviations detail the associated cultivar with the bulk soil. B =  Burmese, SD =  Sour Diesel, BK =  Bookoo Kush.</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "physicochemical"], "article_id"=>1058811, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Soil_Physicochemical_Data_/1058811", "title"=>"Soil Physicochemical Data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536593"], "description"=>"<p>Results of both unweighted (g-test) and weighted (ANOVA) analyses using FDR multiple test correction.</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "otus"], "article_id"=>1058810, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_significant_OTUs_for_soil_type_sample_type_and_strain_/1058810", "title"=>"Number of significant OTUs for soil type, sample type, and strain.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536588"], "description"=>"<p>Size of circles proportional to the log of the total abundance, taxonomic groups are all phylum-level, except for Proteobacteria, which is by class.</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "bacterial", "taxonomic", "groups", "types"], "article_id"=>1058805, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g004", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ternary_plot_of_distribution_of_bacterial_taxonomic_groups_among_sample_types_in_the_second_experiment_/1058805", "title"=>"Ternary plot of distribution of bacterial taxonomic groups among sample types in the second experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536587"], "description"=>"<p>Plots for unweighted analysis are based on unweighted UniFrac distance, and demonstrate relationship between soil type (A), sample type (B), strain (C), and the major PC axes (PC 1 = 13.27% variance, PC 2 = 10.15% variance, PC 3 = 6.15% variance). Plots for weighted analysis are based on weighted UniFrac distances, and demonstrate relationship between soil type (D) sample type (E), strain (F), and the major PC axes (PC 1 = 37.69% variance, PC 2 = 13.95% variance, PC 3 = 11.07% variance). Abbreviations for strains are denoted by B (Burmese), BK (BooKoo Kush), D (Sour Diesel), MW (Mauie Wowie) and WW (White Widow). Abbreviations for soil type are denoted by MB1 (Mo-Bio soil from the first experiment), MB2 (Mo-Bio soil from the second experiment) and OC (Orange County soil).</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "microbial", "pooled", "experiments", "unweighted", "weighted"], "article_id"=>1058804, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plots_of_microbial_community_similarity_in_pooled_experiments_for_unweighted_analysis_A_8211_C_and_weighted_analysis_D_8211_F_/1058804", "title"=>"PCoA plots of microbial community similarity in pooled experiments for unweighted analysis (A–C) and weighted analysis (D–F).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536584"], "description"=>"<p>Plots for unweighted analysis are based on unweighted UniFrac distance, and demonstrate relationship between sample type (A), strain (B), and the major PC axes (PC 1 = 26.46% variance, PC 2 = 7.36% variance). Plots for weighted analysis are based on weighted UniFrac distances, and demonstrate relationship between sample type (C), strain (D), and the major PC axes (PC 1 = 62.98% variance, PC 2 = 15.43% variance). Abbreviations for strains are denoted by B (Burmese), BK (BooKoo Kush), and D (Sour Diesel).</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "microbial", "unweighted", "weighted"], "article_id"=>1058801, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g001", "stats"=>{"downloads"=>5, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plots_of_microbial_community_similarity_in_first_experiment_for_unweighted_analysis_A_8211_B_and_weighted_analysis_C_8211_D_/1058801", "title"=>"PCoA plots of microbial community similarity in first experiment for unweighted analysis (A–B) and weighted analysis (C–D).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536595"], "description"=>"<div><p>Understanding microbial partnerships with the medicinally and economically important crop <i>Cannabis</i> has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, <i>Cannabis</i> presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct <i>Cannabis</i> cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. The influence of soil type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community <i>composition</i> across sample types is determined mainly by soil type, while community <i>structure</i> within endorhiza samples is determined mainly by host cultivar.</p></div>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "cultivar-specificity", "determinants", "microbiome"], "article_id"=>1058812, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Understanding_Cultivar_Specificity_and_Soil_Determinants_of_the_Cannabis_Microbiome/1058812", "title"=>"Understanding Cultivar-Specificity and Soil Determinants of the <i>Cannabis</i> Microbiome", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536592"], "description"=>"<p>MB  =  Mo-Bio soil, OC  =  Orange County soil. Note the significant differences between alpha diversity in the bulk soil and rhizosphere but negligible differences between endorhiza alpha diversity between soil types.</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "alpha", "types"], "article_id"=>1058809, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g006", "stats"=>{"downloads"=>2, "page_views"=>80, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plots_of_alpha_diversity_observed_species_for_endorhiza_rhizosphere_and_bulk_soil_from_two_separate_soil_types_in_the_second_eperiment_/1058809", "title"=>"Box plots of alpha diversity (observed species) for endorhiza, rhizosphere, and bulk soil from two separate soil types in the second eperiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536590"], "description"=>"<p>Initials (i.e. B vs. C) stand for comparisons of beta-distances for samples within groups (R =  rhizosphere, C =  <i>Cannabis</i> endorhiza, B =  bulk soil).</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "beta-diversity", "distances", "communities", "weighted", "unweighted"], "article_id"=>1058807, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g005", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plots_of_beta_diversity_distances_between_communities_for_both_weighted_and_unweighted_analyses_/1058807", "title"=>"Box plots of beta-diversity distances between communities for both weighted and unweighted analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1536585"], "description"=>"<p>Plots for unweighted analysis are based on unweighted UniFrac distances, and demonstrate relationship between soil type (A), sample type (B), strain (C), and the major PC axes (PC 1 = 32.06% variance, PC 2 = 11.34% variance, PC 3 = 5.67% variance). Plots for weighted analysis are based on weighted UniFrac distances, and demonstrate relationship between soil type (D), sample type (E), strain (F), and the major PC axes (PC 1 = 34.51% variance, PC 2 = 25.41% variance, PC 3 = 19.31% variance). Note that PC 1 in the unweighted analysis is dominated by variation in soil type (A), but PC 1 in weighted analysis is dominated by strain (F). Grey points (Fig. 2c, 2f) represent bulk soil samples that aren't associated with either strain. Abbreviations for strains are denoted by MW (Mauie Wowie) and WW (White Widow), and abbreviations for soil type are denoted by MB (Mo-Bio soil) and OC (Orange County soil).</p>", "links"=>[], "tags"=>["agriculture", "crops", "cell biology", "Plant cell biology", "ecology", "Plant ecology", "Plant-environment interactions", "microbial ecology", "genetics", "genomics", "metagenomics", "microbiology", "Plant microbiology", "Plant science", "microbial", "unweighted", "weighted"], "article_id"=>1058802, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Max E. Winston", "Jarrad Hampton-Marcell", "Iratxe Zarraonaindia", "Sarah M. Owens", "Corrie S. Moreau", "Jack A. Gilbert", "Josh Hartsel", "Suzanne J. Kennedy", "S. M. Gibbons"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099641.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_plots_of_microbial_community_similarity_in_second_experiment_for_unweighted_analysis_A_8211_C_and_weighted_analysis_D_8211_F_/1058802", "title"=>"PCoA plots of microbial community similarity in second experiment for unweighted analysis (A–C) and weighted analysis (D–F).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-16 03:25:17"}

PMC Usage Stats | Further Information

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