Tracking Fungal Community Responses to Maize Plants by DNA- and RNA-Based Pyrosequencing
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{"title"=>"Tracking Fungal Community Responses to Maize Plants by DNA- and RNA-Based Pyrosequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Eiko E.", "last_name"=>"Kuramae", "scopus_author_id"=>"6508244589"}, {"first_name"=>"Erik", "last_name"=>"Verbruggen", "scopus_author_id"=>"36948737900"}, {"first_name"=>"Remy", "last_name"=>"Hillekens", "scopus_author_id"=>"55448266400"}, {"first_name"=>"Mattias", "last_name"=>"de Hollander", "scopus_author_id"=>"24166120100"}, {"first_name"=>"Wilfred F M", "last_name"=>"Röling", "scopus_author_id"=>"6701615227"}, {"first_name"=>"Marcel G A", "last_name"=>"van der Heijden", "scopus_author_id"=>"56464821900"}, {"first_name"=>"George A.", "last_name"=>"Kowalchuk", "scopus_author_id"=>"7003778501"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23875012", "sgr"=>"84880426918", "doi"=>"10.1371/journal.pone.0069973", "scopus"=>"2-s2.0-84880426918", "pui"=>"369379017", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"1d06bd47-a465-35ba-8261-b4dc5fcb2b7b", "abstract"=>"We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age) in pots associated with four maize cultivars, including two genetically modified (GM) cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA). The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most \"active\" fungi (as recovered via RNA). Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production). Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.", "link"=>"http://www.mendeley.com/research/tracking-fungal-community-responses-maize-plants-dna-rnabased-pyrosequencing", "reader_count"=>55, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Librarian"=>2, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>8, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>1, "Librarian"=>2, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>8, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>36, "Neuroscience"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>8}}, "reader_count_by_country"=>{"United States"=>2, "Brazil"=>1, "Chile"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1121958"], "description"=>"(1)<p>Operational Taxonomic Unit.</p>(2)<p>The values are mean of replicates (n = 2–3).</p>(3)<p>Values with the same letters were not significantly (ns) different (<i>P</i><0.05); *<i>P</i><0.05Significant comparisons at p<0.05.</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "sequences", "richness", "dna", "rna", "soils", "cultivars", "respective", "genetically", "modified", "lines", "sampling", "times"], "article_id"=>747934, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimators_of_sequences_diversity_evenness_richness_and_coverage_given_by_environmental_DNA_and_RNA_in_soils_with_two_maize_cultivars_M_8202_8202_Monumental_D_8202_8202_DKC3420_and_their_respective_genetically_modified_lines_M_GM_8202_8202_event_MON810_D/747934", "title"=>"Estimators of sequences diversity, evenness, richness and coverage given by environmental DNA and RNA in soils with two maize cultivars (M = Monumental; D = DKC3420) and their respective genetically modified lines (M-GM = event MON810; D-GM = DKC3421YG) at different sampling times (t1 = 47 days; t2 = 104 days) after sowing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121954"], "description"=>"<p>Relative abundance of different fungal phyla recovered from environmental DNA and RNA in soils with two maize cultivars (M = Monumental; D = DKC 3420) and their respective genetically modified lines (M-GM = event MON810; D-GM = DKC 3421YG) at two different sampling times (t1 = 47 days; t2 = 104 days) of plant age.</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "abundance", "fungal", "phyla", "recovered", "dna", "rna", "soils", "cultivars", "respective", "genetically", "modified", "lines", "sampling", "times"], "article_id"=>747931, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.g004", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_different_fungal_phyla_recovered_from_environmental_DNA_and_RNA_in_soils_with_two_maize_cultivars_M_8202_8202_Monumental_D_8202_8202_DKC_3420_and_their_respective_genetically_modified_lines_M_GM_8202_8202_event_MON810_D_GM_8202_8202/747931", "title"=>"Relative abundance of different fungal phyla recovered from environmental DNA and RNA in soils with two maize cultivars (M = Monumental; D = DKC 3420) and their respective genetically modified lines (M-GM = event MON810; D-GM = DKC 3421YG) at two different sampling times (t1 = 47 days; t2 = 104 days) of plant age.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121953"], "description"=>"<p>NMDS analysis based on relative abundance of fungal OTUs based on environmental DNA and RNA both at sampling times t1-47 days and t2-104 days of plant age.</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "abundance", "fungal", "otus", "dna", "rna", "sampling", "times", "t1-47", "days", "t2-104"], "article_id"=>747930, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.g003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_NMDS_analysis_based_on_relative_abundance_of_fungal_OTUs_based_on_environmental_DNA_and_RNA_both_at_sampling_times_t1_47_days_and_t2_104_days_of_plant_age_/747930", "title"=>"NMDS analysis based on relative abundance of fungal OTUs based on environmental DNA and RNA both at sampling times t1-47 days and t2-104 days of plant age.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121957"], "description"=>"<p>Numbers are mean of replicates.</p><p>Non-Parametric MANOVA (NPMANOVA) test between samples based on Bray-Curtis distance measure. Significance levels: ns: <i>P</i>>0.05;</p>**<p><i>P</i><0.005;</p>***<p><i>P</i><0.0005.</p><p>Relative abundances lower than 0.1% is not shown.</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "abundance", "fungal", "groups", "pyrosequencing", "dna", "rna", "soils", "cultivars", "respective", "genetically", "modified", "lines", "sampling", "times"], "article_id"=>747933, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.t003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_soil_fungal_groups_based_on_pyrosequencing_analysis_of_environmental_DNA_and_RNA_in_soils_with_two_maize_cultivars_and_their_respective_genetically_modified_lines_at_different_sampling_times_t1_8202_8202_47_days_t2_8202_8202_104_day/747933", "title"=>"Relative abundance (%) of soil fungal groups based on pyrosequencing analysis of environmental DNA and RNA in soils with two maize cultivars and their respective genetically modified lines at different sampling times (t1 = 47 days; t2 = 104 days) of plant age.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121956"], "description"=>"<p>Tests were performed separately for each nucleic acid type at each time point (t1 = 47 days and t2 = 105 days of plant age). Significant values are indicated in bold. The bottom part of the table represents separate PERMANOVA’s for DNA and RNA in response to the factor “sampling time”.</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "two-way", "permanova", "non-bt", "types"], "article_id"=>747932, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.t002", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_two_way_PERMANOVA_testing_the_effect_of_GM_Bt_vs_non_Bt_maize_and_cultivar_each_of_the_two_types_of_parental_cultivars_/747932", "title"=>"Results of two-way PERMANOVA testing the effect of “GM” (Bt <i>vs.</i> non-Bt maize) and “cultivar” (each of the two types of parental cultivars).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121951"], "description"=>"<p>Percentage of fungal OTUs shared between nucleic acid type (DNA; RNA) in different sampling times (t1 = 47 days; t2 = 104 days).</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "fungal", "otus", "nucleic", "sampling", "times"], "article_id"=>747929, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_fungal_OTUs_shared_between_nucleic_acid_type_DNA_RNA_in_different_sampling_times_t1_8202_8202_47_days_t2_8202_8202_104_days_/747929", "title"=>"Percentage of fungal OTUs shared between nucleic acid type (DNA; RNA) in different sampling times (t1 = 47 days; t2 = 104 days).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 02:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1121949"], "description"=>"<p>Non-metric multidimensional scaling (NMDS) analysis of presence and absence of fungal OTUs based on Jaccard-index of similarity with 95% confidence intervals shared between sampling times (t1 = 47 days; t2 = 104 days) and nucleic acid type (DNA, RNA).</p>", "links"=>[], "tags"=>["crops", "cereals", "maize", "ecology", "Community Ecology", "community structure", "Ecological risk", "Ecological environments", "Terrestrial environments", "biota", "microbial ecology", "microbiology", "Mycology", "fungi", "multidimensional", "scaling", "fungal", "otus", "jaccard-index", "intervals", "sampling", "times", "nucleic"], "article_id"=>747928, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Eiko E. Kuramae", "Erik Verbruggen", "Remy Hillekens", "Mattias de Hollander", "Wilfred F. M. Röling", "Marcel G. A. van der Heijden", "George A. Kowalchuk"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0069973.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_multidimensional_scaling_NMDS_analysis_of_presence_and_absence_of_fungal_OTUs_based_on_Jaccard_index_of_similarity_with_95_confidence_intervals_shared_between_sampling_times_t1_8202_8202_47_days_t2_8202_8202_104_days_and_nucleic_acid_type_DNA_/747928", "title"=>"Non-metric multidimensional scaling (NMDS) analysis of presence and absence of fungal OTUs based on Jaccard-index of similarity with 95% confidence intervals shared between sampling times (t1 = 47 days; t2 = 104 days) and nucleic acid type (DNA, RNA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 02:21:21"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"2", "full-text"=>"0", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

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"=>"/Biology and life sciences/Plant science", "average_usage"=>[269, 451, 577, 699, 812, 922, 1019, 1126, 1225, 1309, 1404, 1493, 1563]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[284, 475, 603, 722, 826, 928, 1026, 1129, 1225, 1310, 1390, 1468, 1549]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[298, 487, 610, 722, 827, 929, 1029, 1125, 1217, 1306, 1388, 1464, 1535]}, {"subject_area"=>"/Ecology and environmental sciences/Plant ecology", "average_usage"=>[253, 410]}]}
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