Data from: Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors

Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL

Date Published: August 6, 2014

DOI: http://dx.doi.org/10.5061/dryad.7535k

 

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Title NiwotB_all_denoised
Downloaded 16 times
Description All 454 sequences in fasta format. These have already been denoised, chimera checked, and quality filtered using Ampliconnoise as implemented in MacQiime (v.1.6.0)
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Title NiwotB_all_map2
Downloaded 12 times
Description Mapping file that corresponds with fasta file (NiwotB_all_denoised.fna)
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Title nG6XN_nchl_filtered_sorted_host
Downloaded 12 times
Description OTU table built in QIIME from NiwotB_all_denoised.fna. This table has had chloroplast sequences removed. Also the most shallowly sequenced sample (G6CXN) has been removed. Columns sorted by host and treatment. Unrarefied. This table was used for dbRDA. 100 rarefactions tables (in which each sample was rarefied to the most shallowly sequenced sample = 202 sequences) were also built from this table, and alpha diversity measures were conducted on each of those 100 rarefaction tables.
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Title raref_nG6XN_nchl_filtered_sorted_host_L7
Downloaded 9 times
Description This OTU table was built in QIIME from NiwotB_all_denoised.fna. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title read.qiime.table
Downloaded 107 times
Description This script is used to read any qiime table into R. It was run prior to the other R scripts, so that the files would be uploaded correctly.
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Title raref_nG6XN_nchl_filtered_sorted_host_L6
Downloaded 7 times
Description This genus table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title raref_nG6XN_nchl_filtered_sorted_host_L5
Downloaded 10 times
Description This family table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title raref_nG6XN_nchl_filtered_sorted_host_L4
Downloaded 6 times
Description This order table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title raref_nG6XN_nchl_filtered_sorted_host_L3
Downloaded 7 times
Description This class table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title raref_nG6XN_nchl_filtered_sorted_host_L2
Downloaded 5 times
Description This phylum table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
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Title PD_whole_tree
Downloaded 16 times
Description phylogenetic diversity calculated for 100 rarefactions (202 sequences) of each sample.
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Title observed_species_L7
Downloaded 13 times
Description OTU richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title observed_species_L6
Downloaded 10 times
Description genus richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title observed_species_L5
Downloaded 13 times
Description family richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title observed_species_L4
Downloaded 10 times
Description order richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title observed_species_L3
Downloaded 7 times
Description class richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title observed_species_L2
Downloaded 8 times
Description phylum richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.
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Title simpson_L7
Downloaded 9 times
Description OTU diversity calculated by Simpson's diversity index in QIIME.
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Title simpson_L6
Downloaded 9 times
Description Genus diversity calculated by Simpson's diversity index in QIIME.
Download simpson_L6.txt (59.09 Kb)
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Title simpson_L5
Downloaded 8 times
Description Family diversity calculated by Simpson's diversity index in QIIME.
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Title simpson_L4
Downloaded 9 times
Description Order diversity calculated using Simpson's Diversity index in QIIME
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Title simpson_L3
Downloaded 11 times
Description Class diversity calculated using Simpson's Diversity index in QIIME
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Title simpson_L2
Downloaded 8 times
Description Phylum diversity calculated using Simpson's Diversity index in QIIME
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Title even_L2
Downloaded 12 times
Description Phylum evenness, calculated using Simpson's evenness, calculated for each of 100 rarefactions (202 sequences) for each sample.
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Title even_L3
Downloaded 7 times
Description Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.
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Title even_L4
Downloaded 11 times
Description Order evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.
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Title even_L5
Downloaded 5 times
Description Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.
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Title even_L6
Downloaded 10 times
Description Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.
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Title even_L7
Downloaded 7 times
Description Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.
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Title weighted_unifrac_nchl_filtered_sorted_host
Downloaded 12 times
Description Weighted unifrac table built in QIIME from unrarefied OTU table (chloroplasts removed) to use for dbRDA.
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Title otu_anova_G vs D_Neffect
Downloaded 16 times
Description R code for ANOVA on individual root associated bacterial taxa in Geum rossii and Deschampsia cespitosa. Test to determine effect of nitrogen addition on abundance of any bacterial taxa. Tested in each host seperately.
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Title otu_anova_Nxhost
Downloaded 9 times
Description R code ANOVA on individual root associated bacterial taxa in Geum rossii and Deschapmsia cespitosa roots. Purpose to determine effect of host plant identity and nitrogen addition on abundance of individual bacterial taxa.
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Title otu_anova_remxN
Downloaded 12 times
Description R code for ANOVA on individual root associated bacterial taxa in Geum rossii. Test to determine whether nitrogen addition or Deschampsia cespitosa removal (principle competitor removal) had an effect on abundance of any bacterial taxa.
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Title pie_charts
Downloaded 19 times
Description R code: Build pie charts for each host x treatment combination to see relative abundance of each phylum
Download pie_charts.R (3.14 Kb)
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Title alpha
Downloaded 22 times
Description R code: statistical analysis (ANOVA) on collated alpha diversity metrics (phylogenetic diversity, richness, simpson's evenness, and simpson's diversity) calculated for 100 rarefaction tables.
Download alpha.R (14.26 Kb)
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Title dbRDA_bact
Downloaded 50 times
Description R code: dbRDA and ordination plots, performed on weighted unifrac table derived from unrarefied OTU table.
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Title README
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Description README file, explains all other files
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When using this data, please cite the original publication:

Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2014) Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors. Environmental Microbiology Reports 7(1): 102-110. http://dx.doi.org/10.1111/1758-2229.12194

Additionally, please cite the Dryad data package:

Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2014) Data from: Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7535k
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