Illumina Amplicon Sequencing of 16S rRNA Tag Reveals Bacterial Community Development in the Rhizosphere of Apple Nurseries at a Replant Disease Site and a New Planting Site
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{"title"=>"Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site", "type"=>"journal", "authors"=>[{"first_name"=>"Jian", "last_name"=>"Sun", "scopus_author_id"=>"56198441100"}, {"first_name"=>"Qiang", "last_name"=>"Zhang", "scopus_author_id"=>"55624487702"}, {"first_name"=>"Jia", "last_name"=>"Zhou", "scopus_author_id"=>"56065889400"}, {"first_name"=>"Qinping", "last_name"=>"Wei", "scopus_author_id"=>"7201692918"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25360786", "sgr"=>"84910009572", "doi"=>"10.1371/journal.pone.0111744", "scopus"=>"2-s2.0-84910009572", "pui"=>"600407214", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"203d3701-31fb-3d2f-9407-18b7807f16fc", "abstract"=>"We used a next-generation, Illumina-based sequencing approach to characterize the bacterial community development of apple rhizosphere soil in a replant site (RePlant) and a new planting site (NewPlant) in Beijing. Dwarfing apple nurseries of 'Fuji'/SH6/Pingyitiancha trees were planted in the spring of 2013. Before planting, soil from the apple rhizosphere of the replant site (ReSoil) and from the new planting site (NewSoil) was sampled for analysis on the Illumina MiSeq platform. In late September, the rhizosphere soil from both sites was resampled (RePlant and NewPlant). More than 16,000 valid reads were obtained for each replicate, and the community was composed of five dominant groups (Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria). The bacterial diversity decreased after apple planting. Principal component analyses revealed that the rhizosphere samples were significantly different among treatments. Apple nursery planting showed a large impact on the soil bacterial community, and the community development was significantly different between the replanted and newly planted soils. Verrucomicrobia were less abundant in RePlant soil, while Pseudomonas and Lysobacter were increased in RePlant compared with ReSoil and NewPlant. Both RePlant and ReSoil showed relatively higher invertase and cellulase activities than NewPlant and NewSoil, but only NewPlant soil showed higher urease activity, and this soil also had the higher plant growth. Our experimental results suggest that planting apple nurseries has a significant impact on soil bacterial community development at both replant and new planting sites, and planting on new site resulted in significantly higher soil urease activity and a different bacterial community composition.", "link"=>"http://www.mendeley.com/research/illumina-amplicon-sequencing-16s-rrna-tag-reveals-bacterial-community-development-rhizosphere-apple", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>17, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>17, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>42, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>42}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>4}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "Mexico"=>1, "United Kingdom"=>1, "Australia"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1774041"], "description"=>"<p>Relative read abundance of different bacterial phyla within the different communities. Sequences that could not be classified into any known group were labeled “Other”.</p>", "links"=>[], "tags"=>["New Planting Site", "Illumina MiSeq platform", "Replant Disease Site", "apple rhizosphere soil", "16 S rRNA Tag", "replant", "soil urease activity", "apple nurseries", "community development", "Bacterial Community Development", "NewPlant", "Illumina amplicon sequencing", "replant site", "Principal component analyses"], "article_id"=>1224597, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jian Sun", "Qiang Zhang", "Jia Zhou", "Qinping Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111744.g002", "stats"=>{"downloads"=>2, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_bacterial_communities_at_the_phylum_level_/1224597", "title"=>"Comparison of the bacterial communities at the phylum level.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-31 02:55:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1774043"], "description"=>"<p>“DW” means dry weight. Averages of replicates ± standard error; means followed by different letters are significantly different at <i>P</i><0.05.</p><p>NA: not applicable.</p><p>The invertase, urease and cellulase activity of soil of different treatments and plant growth mass of <i>RePlant</i> and <i>NewPlant</i>.</p>", "links"=>[], "tags"=>["New Planting Site", "Illumina MiSeq platform", "Replant Disease Site", "apple rhizosphere soil", "16 S rRNA Tag", "replant", "soil urease activity", "apple nurseries", "community development", "Bacterial Community Development", "NewPlant", "Illumina amplicon sequencing", "replant site", "Principal component analyses"], "article_id"=>1224599, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jian Sun", "Qiang Zhang", "Jia Zhou", "Qinping Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111744.t001", "stats"=>{"downloads"=>6, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_invertase_urease_and_cellulase_activity_of_soil_of_different_treatments_and_plant_growth_mass_of_RePlant_and_NewPlant_/1224599", "title"=>"The invertase, urease and cellulase activity of soil of different treatments and plant growth mass of <i>RePlant</i> and <i>NewPlant</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-31 02:55:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1774044"], "description"=>"<p>Averages of replicates ± standard error; means followed by different letters are significantly different at <i>P</i><0.05.</p><p>Comparison of the estimated operational taxonomic unit (OTU) richness, diversity indexes and Pielous evenness of the 16S rRNA gene libraries for clustering at 97% identity as obtained from the pyrosequencing analysis.</p>", "links"=>[], "tags"=>["New Planting Site", "Illumina MiSeq platform", "Replant Disease Site", "apple rhizosphere soil", "16 S rRNA Tag", "replant", "soil urease activity", "apple nurseries", "community development", "Bacterial Community Development", "NewPlant", "Illumina amplicon sequencing", "replant site", "Principal component analyses"], "article_id"=>1224600, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jian Sun", "Qiang Zhang", "Jia Zhou", "Qinping Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111744.t002", "stats"=>{"downloads"=>2, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_estimated_operational_taxonomic_unit_OTU_richness_diversity_indexes_and_Pielous_evenness_of_the_16S_rRNA_gene_libraries_for_clustering_at_97_identity_as_obtained_from_the_pyrosequencing_analysis_/1224600", "title"=>"Comparison of the estimated operational taxonomic unit (OTU) richness, diversity indexes and Pielous evenness of the 16S rRNA gene libraries for clustering at 97% identity as obtained from the pyrosequencing analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-31 02:55:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1774042"], "description"=>"<p>Principal components (PCs) 1 and 2 explained 34.2% and 24.8% of the variance, respectively.</p>", "links"=>[], "tags"=>["New Planting Site", "Illumina MiSeq platform", "Replant Disease Site", "apple rhizosphere soil", "16 S rRNA Tag", "replant", "soil urease activity", "apple nurseries", "community development", "Bacterial Community Development", "NewPlant", "Illumina amplicon sequencing", "replant site", "Principal component analyses"], "article_id"=>1224598, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jian Sun", "Qiang Zhang", "Jia Zhou", "Qinping Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111744.g003", "stats"=>{"downloads"=>7, "page_views"=>437, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_component_analysis_PCA_on_the_relative_abundance_of_bacterial_genera_using_Canoco_4_5_/1224598", "title"=>"Principal component analysis (PCA) on the relative abundance of bacterial genera using Canoco 4.5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-31 02:55:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1774039"], "description"=>"<p>Average value of 3 replicates and error bar were showed.</p>", "links"=>[], "tags"=>["New Planting Site", "Illumina MiSeq platform", "Replant Disease Site", "apple rhizosphere soil", "16 S rRNA Tag", "replant", "soil urease activity", "apple nurseries", "community development", "Bacterial Community Development", "NewPlant", "Illumina amplicon sequencing", "replant site", "Principal component analyses"], "article_id"=>1224595, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Jian Sun", "Qiang Zhang", "Jia Zhou", "Qinping Wei"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0111744.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_on_species_abundance_data_/1224595", "title"=>"Rarefaction on species-abundance data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-31 02:55:49"}

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