Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere
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{"title"=>"Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): The role of the rare biosphere", "type"=>"journal", "authors"=>[{"first_name"=>"Noha H.", "last_name"=>"Youssef", "scopus_author_id"=>"10044729100"}, {"first_name"=>"M. B.", "last_name"=>"Couger", "scopus_author_id"=>"35799591500"}, {"first_name"=>"Mostafa S.", "last_name"=>"Elshahed", "scopus_author_id"=>"55907765000"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203", "pui"=>"359754286", "sgr"=>"77957881743", "doi"=>"10.1371/journal.pone.0012414", "scopus"=>"2-s2.0-77957881743", "pmid"=>"20865128"}, "id"=>"90f99188-283e-3dbc-be59-d59c2c31afde", "abstract"=>"<sec> <title>Background</title> <p>The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.</p> </sec><sec> <title>Methodology/Principal Findings</title> <p>We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU<sub>0.03</sub>) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.</p> </sec><sec> <title>Conclusions/Significance</title> <p>The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.</p> </sec>", "link"=>"http://www.mendeley.com/research/finescale-bacterial-beta-diversity-within-complex-ecosystem-zodletone-spring-ok-usa-role-rare-biosph", "reader_count"=>125, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>9, "Researcher"=>51, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>32, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>9, "Researcher"=>51, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>32, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>1, "Student > Bachelor"=>7, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>2, "Environmental Science"=>18, "Biochemistry, Genetics and Molecular Biology"=>6, "Mathematics"=>1, "Agricultural and Biological Sciences"=>86, "Medicine and Dentistry"=>2, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>86}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>18}}, "reader_count_by_country"=>{"Canada"=>2, "Sweden"=>2, "United States"=>8, "Denmark"=>2, "Brazil"=>1, "Mexico"=>3, "France"=>5, "Chile"=>1, "Switzerland"=>2, "Spain"=>1, "Estonia"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/833660"], "description"=>"a<p>NUNN are the non-unique non-novel members, UN are the unique novel members, UNN are the unique non-novel members, total correspond to the total rare biosphere defined at the empirical cutoff of n≤5.</p>b<p>Numbers are averages ± standard deviations of shared/unshared OTUs percentages for 4 data points (1 quad, and 3 quads) and 6 data points (2 quads). The percentages were calculated by dividing the number of shared/unshared OTUs between “x” quadrants by the total number of observed OTUs in those “x” quadrants. The number of shared OTUs between 2 quadrants also includes the number of OTUs that these 2 quadrants share with either one or two more quadrants. The number of shared OTUs between 3 quadrants also includes the number of OTUs that these 3 quadrants share with the fourth quadrant.</p>c<p>All similarity indices values are averages ± standard deviations of 6 pair wise comparisons. We only chose those similarity indices that use the relative abundance data (instead of the abundance or the presence-absence data) due to the difference in sample sizes of the 4 groups compared.</p>", "links"=>[], "tags"=>["measures", "biosphere", "sub-groups", "quadrants", "compared"], "article_id"=>504026, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.t004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Beta_diversity_measures_for_the_rare_biosphere_sub_groups_across_the_4_quadrants_compared_to_the_total_rare_biosphere_n_8804_5_/504026", "title"=>"Beta diversity measures for the rare biosphere sub-groups across the 4 quadrants compared to the total rare biosphere (n≤5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-08-26 01:07:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/415235", "https://ndownloader.figshare.com/files/415261", "https://ndownloader.figshare.com/files/415294", "https://ndownloader.figshare.com/files/415311", "https://ndownloader.figshare.com/files/415322", "https://ndownloader.figshare.com/files/415333", "https://ndownloader.figshare.com/files/415344", "https://ndownloader.figshare.com/files/415360", "https://ndownloader.figshare.com/files/415383"], "description"=>"<div><h3>Background</h3><p>The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.</p><h3>Methodology/Principal Findings</h3><p>We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU<sub>0.03</sub>) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.</p><h3>Conclusions/Significance</h3><p>The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.</p></div>", "links"=>[], "tags"=>["fine-scale", "bacterial", "beta", "biosphere"], "article_id"=>141992, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012414.s001", "https://dx.doi.org/10.1371/journal.pone.0012414.s002", "https://dx.doi.org/10.1371/journal.pone.0012414.s003", "https://dx.doi.org/10.1371/journal.pone.0012414.s004", "https://dx.doi.org/10.1371/journal.pone.0012414.s005", "https://dx.doi.org/10.1371/journal.pone.0012414.s006", "https://dx.doi.org/10.1371/journal.pone.0012414.s007", "https://dx.doi.org/10.1371/journal.pone.0012414.s008", "https://dx.doi.org/10.1371/journal.pone.0012414.s009"], "stats"=>{"downloads"=>26, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Fine_Scale_Bacterial_Beta_Diversity_within_a_Complex_Ecosystem_Zodletone_Spring_OK_USA_The_Role_of_the_Rare_Biosphere/141992", "title"=>"Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-08-26 00:33:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/833620"], "description"=>"<p>n: corresponds to the number of clones, a: corresponds to percentage abundance.</p>a<p>Total OTUs correspond to the number of OTUs identified when reads from all quadrants are combined at the specified cutoff.</p>", "links"=>[], "tags"=>["quadrant", "abundant", "definitions"], "article_id"=>503989, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.t003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_OTUs_0_03_identified_for_each_quadrant_at_each_of_the_rare_and_abundant_species_definitions_used_in_this_study_/503989", "title"=>"Number of OTUs<sub>0.03</sub> identified for each quadrant at each of the rare and abundant species definitions used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-08-26 01:06:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/833461"], "description"=>"<p>A sub-sampling approach was implemented in which 3 subsamples from quadrant 2 (sub1, sub2, and sub3) were compared to three subsamples, each from a different quadrant (Quad 1_r, Quad 3_r, and Quad 4_r). (A) The percentage unshared OTUs, and the percentage shared OTUs between 2 quadrants, and 3 quadrants for the 3 subsamples from quadrant 2 versus the 3 subsamples from quadrants 1, 3, and 4 (* denotes that the percentage shared/unshared OTUs were significantly different between the 2 groups). Error bars represent standard deviations from 3 pairs of subsamples (2 quads) and 3 subsamples (1 quad). No error bars were obtained for the single 3-quads data point. Color-coding is as follows: the 3 subsamples from quadrant 2 (black), and the 3 subsamples from quadrants 1, 3, and 4 (white). (B) Non-metric multidimensional scaling plot for the 6 subsamples studied. Pair wise Bray-Curtis similarity indices were used to construct the plot. Stress value was close to 0 and most of the variation (77.8%) was explained by 2 axes. (C) Observed and expected number of species (S<sub>obs</sub>, and S<sub>expected</sub>, respectively) and singletons for each of the quadrants studied. The numbers were used to construct theoretical Venn diagrams as described in text. (D) The percentage shared OTUs between 4 quadrants, 3 quadrants, 2 quadrants, and the percentage unshared OTUs calculated from the obtained Venn diagram for n = 1 (shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012414#pone-0012414-g002\" target=\"_blank\">Figure 2A</a>) (observed data), and the average percentages calculated from the theoretical Venn diagrams (predicted data). Error bars represent standard deviations from 4 data points for each of the observed and predicted unshared OTUs percentages (1 quad), 6 data point for the observed shared OTUs percentages and 4 data points for the predicted shared OTUs percentages between 2 quads, 4 data points for each of the observed and predicted shared OTUs percentages between 3 quads, 4 data points for the predicted shared OTUs percentages between 4 quads. No error bars were obtained for the single 4-quads observed shared OTUs percentage data point. Color-coding is as follows: Observed data (black), and predicted data (white).</p>", "links"=>[], "tags"=>["inadequate", "sampling", "observed", "beta", "zodletone"], "article_id"=>503828, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_inadequate_sampling_on_the_observed_beta_diversity_in_Zodletone_spring_/503828", "title"=>"Effect of inadequate sampling on the observed beta diversity in Zodletone spring.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-26 01:03:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/833257"], "description"=>"<p>Color-coding is as follows: quadrant 1 (yellow), quadrant 2 (red), quadrant 3 (green), and quadrant 4 (blue).</p>", "links"=>[], "tags"=>["diagrams", "otus", "quadrants", "studied", "empirical", "cutoff", "abundant", "abundance"], "article_id"=>503601, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.g002", "stats"=>{"downloads"=>1, "page_views"=>75, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagrams_showing_the_number_of_unique_and_shared_OTUs_between_the_4_quadrants_studied_for_A_empirical_cutoff_n_8202_8202_1_for_defining_rare_species_B_empirical_cutoff_n_8804_2_for_defining_rare_species_C_empirical_cutoff_n_8804_5_for_defining_rare_/503601", "title"=>"Venn diagrams showing the number of unique and shared OTUs between the 4 quadrants studied for (A) empirical cutoff (n = 1) for defining rare species, (B) empirical cutoff (n≤2) for defining rare species, (C) empirical cutoff (n≤5) for defining rare species, (D) empirical cutoff (n≤10) for defining rare species, (E) empirical cutoff (n>10) for defining abundant species, (F) empirical cutoff (% abundance ≤0.004%) for defining rare species, (G) empirical cutoff (% abundance >1%) for defining abundant species, and (H) the entire datasets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-26 01:00:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/833391"], "description"=>"<p>Pair wise Bray-Curtis similarity indices for each of the quadrants at 4 empirical rare cutoffs (n = 1 (N<sub>1</sub>), n≤2 (N<sub>2</sub>), n≤5 (N<sub>5</sub>), and n≤10 (N<sub>10</sub>)), one empirical abundant cutoff (n>10 (Ab)), as well as for the entire datasets (All) were used to construct the plot. Grey shapes show rare and abundant members from each quadrant clustering closer together with the whole quadrant. Stress value was close to 0, and most of the variation (65–95.3%) was explained by 2 axes. The addition of a third axis did not improve the model substantially.</p>", "links"=>[], "tags"=>["multidimensional", "scaling", "plots", "quadrants"], "article_id"=>503759, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_multidimensional_scaling_plots_of_the_4_quadrants_studied_/503759", "title"=>"Non-metric multidimensional scaling plots of the 4 quadrants studied.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-26 01:02:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/833535"], "description"=>"<p>Number of high quality reads and OTUs<sub>0.03</sub> identified for each of the samples (quadrants) studied.</p>", "links"=>[], "tags"=>["reads", "samples"], "article_id"=>503901, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.t001", "stats"=>{"downloads"=>0, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_high_quality_reads_and_OTUs_0_03_identified_for_each_of_the_samples_quadrants_studied_/503901", "title"=>"Number of high quality reads and OTUs<sub>0.03</sub> identified for each of the samples (quadrants) studied.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-08-26 01:05:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/833105"], "description"=>"<p>Percentage abundance is shown on the Y-axis for (A) abundant phyla with >1% abundance in each quadrant studied, (B) phyla with % abundance ranging between 0.1 and 1% in quadrant 1, (C) phyla with % abundance ranging between 0.01 and 0.1% in quadrant 1, and (D) phyla with % abundance <0.01% in quadrant 1. Color-coding is as follows: quadrant 1 (blue), quadrant 2 (red), quadrant 3 (green), and quadrant 4 (purple).</p>", "links"=>[], "tags"=>["phyla", "zodletone", "sediment", "quadrants"], "article_id"=>503467, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_phyla_in_Zodletone_spring_source_sediment_for_the_4_quadrants_studied_/503467", "title"=>"Distribution of phyla in Zodletone spring source sediment for the 4 quadrants studied.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-08-26 00:57:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/833584"], "description"=>"<p>*The empirical cutoff used to define rare and abundant members of the community. n: corresponds to the number of clones, a: corresponds to percentage abundance. Cutoffs n = 1, n≤2, n≤5, n≤10, a≤0.004% are rare cutoffs, while n>10, and a>1% are the abundant cutoff.</p>a<p>The phylogenetic level used to bin sequences into operational taxonomic units. OTU<sub>0.03</sub> is the 97% cutoff for defining species.</p>b<p>All similarity indices values are averages ± standard deviations of all possible (6) pair wise comparisons.</p>", "links"=>[], "tags"=>["quantitative", "indices", "abundant", "members", "empirical", "totals", "phylum"], "article_id"=>503944, "categories"=>["Marine Biology", "Ecology", "Microbiology"], "users"=>["Noha H. Youssef", "M. B. Couger", "Mostafa S. Elshahed"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012414.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Qualitative_and_quantitative_similarity_indices_at_the_species_level_for_the_rare_and_abundant_members_of_the_community_defined_at_specific_empirical_cutoffs_as_well_as_for_the_totals_at_both_the_phylum_and_the_species_levels_/503944", "title"=>"Qualitative and quantitative similarity indices at the species level for the rare and abundant members of the community (defined at specific empirical cutoffs) as well as for the totals at both the phylum and the species levels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-08-26 01:05:44"}

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Relative Metric

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