DOI: 10.5061/dryad.7535k
title: Data from: Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors

description: Nitrogen (N) deposition in many areas of the world is over an order of
 magnitude greater than it would be in absence of human activity. We ask
 how abiotic (N) and biotic (plant host and neighborhood) effects interact
 to influence root-associated bacterial (RAB) community assembly. Using 454
 pyrosequencing, we examined RAB communities from two dominant alpine
 tundra plants, Geum rossii and Deschampsia cespitosa, under control, N
 addition and D. cespitosa removal treatments, implemented in a factorial
 design. We hypothesized that host would have the strongest effect on RAB
 assembly, followed by N, then neighbor effects. The most dominant phyla
 were Proteobacteria (mostly Gammaproteobacteria), Actinobacteria,
 Bacteroidetes and Acidobacteria. We found RAB communities were host
 specific, with only 17% overlap in operational taxonomic units. Host
 effects on composition were over twice as strong as N effects.
 D. cespitosa RAB diversity declined with N, while G. rossii RAB did not.
 D. cespitosa removal did not influence G. rossii RAB community
 composition, but G. rossii RAB diversity declined with N only when
 D. cespitosa was absent. We conclude that RAB of both hosts are sensitive
 to N enrichment, and RAB response to N is influenced by host identity and
 plant neighborhood.
description: NiwotB_all_denoisedAll 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)NiwotB_all_map2Mapping file that corresponds with fasta file (NiwotB_all_denoised.fna)nG6XN_nchl_filtered_sorted_hostOTU 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.raref_nG6XN_nchl_filtered_sorted_host_L7This 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.raref_nG6XN_nchl_filtered_sorted_host.txtread.qiime.tableThis 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.raref_nG6XN_nchl_filtered_sorted_host_L6This 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.raref_nG6XN_nchl_filtered_sorted_host_L5This 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.raref_nG6XN_nchl_filtered_sorted_host_L4This 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.raref_nG6XN_nchl_filtered_sorted_host_L3This 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.raref_nG6XN_nchl_filtered_sorted_host_L2This 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.PD_whole_treephylogenetic diversity calculated for 100 rarefactions (202 sequences) of each sample.observed_species_L7OTU richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.observed_species_L6genus richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.observed_species_L5family richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.observed_species_L4order richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.observed_species_L3class richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.observed_species_L2phylum richness calculated for each of 100 rarefactions (to 202 sequences) performed on each sample.simpson_L7OTU diversity calculated by Simpson's diversity index in QIIME.simpson_L6Genus diversity calculated by Simpson's diversity index in QIIME.simpson_L5Family diversity calculated by Simpson's diversity index in QIIME.simpson_L4Order diversity calculated using Simpson's Diversity index in QIIMEsimpson_L3Class diversity calculated using Simpson's Diversity index in QIIMEsimpson_L2Phylum diversity calculated using Simpson's Diversity index in QIIMEeven_L2Phylum evenness, calculated using Simpson's evenness, calculated for each of 100 rarefactions (202 sequences) for each sample.even_L3Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.even_L4Order evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.even_L5Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.even_L6Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.even_L7Class evenness, calculated using Simpson's Evenness, calculated for each of 100 rarefaction tables (202 sequences) performed on each sample.weighted_unifrac_nchl_filtered_sorted_hostWeighted unifrac table built in QIIME from unrarefied OTU table (chloroplasts removed) to use for dbRDA.otu_anova_G vs D_NeffectR 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.otu_anova_NxhostR 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.otu_anova_remxNR 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.pie_chartsR code: Build pie charts for each host x treatment combination to see relative abundance of each phylumalphaR code: statistical analysis (ANOVA) on collated alpha diversity metrics (phylogenetic diversity, richness, simpson's evenness, and simpson's diversity) calculated for 100 rarefaction tables.dbRDA_bactR code: dbRDA and ordination plots, performed on weighted unifrac table derived from unrarefied OTU table.READMEREADME file, explains all other files