DOI: 10.5061/dryad.sv33f
title: Data from: Nitrogen deposition alters plant–fungal relationships: linking belowground dynamics to aboveground vegetation change

description: Nitrogen (N) deposition rates are increasing globally due to anthropogenic
 activities. Plant community responses to N are often attributed to altered
 competitive interactions between plants, but may also be a result of
 microbial responses to N, particularly root-associated fungi (RAF), which
 are known to affect plant fitness. In response to N, Deschampsia
 cespitosa, a codominant plant in the alpine tundra at Niwot Ridge (CO),
 increases in abundance, while Geum rossii, its principal competitor,
 declines. Importantly, G. rossii declines with N even in the absence of
 its competitor. We examined whether contrasting host responses to N are
 associated with altered plant–fungal symbioses, and whether the effects of
 N are distinct from effects of altered plant competition on RAF, using 454
 pyrosequencing. Host RAF communities were distinct (only 9.4% of OTUs
 overlapped). N increased RAF diversity in G. rossii, but decreased it in
 D. cespitosa. D. cespitosa RAF communities were more responsive to N than
 G. rossii RAF communities, perhaps indicating a flexible microbial
 community aids host adaptation to nutrient enrichment. Effects of removing
 D. cespitosa were distinct from effects of N on G. rossii RAF, and D.
 cespitosa presence reversed RAF diversity response to N. The most dominant
 G. rossii RAF order, Helotiales, was the most affected by N, declining
 from 83% to 60% of sequences, perhaps indicating a loss of mutualists
 under N enrichment. These results highlight the potential importance of
 belowground microbial dynamics in plant responses to N deposition.
description: alpha diversity
 codeR
 code that tests for relationships between alpha diversity measures and
 treatment. Inputs are collated alpha diversity files produced in
 QIIME.alpha.RNiwotDGF mapEnvironmental mapping file, providing treatment, plot, DNA dilution, and sequencing run information for each sample.NiwotDGF_map3.csvNMDS codeR code to build NMDS plot of bray-curtis distance matrix describing distances between communities from each sample. Also a permutation test for correlations between treatments and community distances. Input is taxa x SampleID table produced in Qiime.NMDS.RANOVA code, N effects per hostR code to test individual taxa for correlation with N in each hostotu_anova_N_isolated_host.RANOVA code, NxhostR code to test individual taxa for correlation with N or host, or interactions between the two.otu_anova_Nxhost.RANOVA code, remxNR code to test individual taxa for correlation with treatment or treatment interactions in single hostotu_anova_remxN.Rrarefaction plot codeR code to build alpha rarefaction plots (collated alpha rarefaction table produced in Qiime from taxa x SampleID tables)rarefaction.RRDA codeR code for RDA ordination and permutation testsRDA.RSE of OTU and seq countsR code to calculate standard error of sequence and OTU counts for each hostSE otus seqs.ROTU and sequence countsfile containing sequence and OTU counts for each sample. These statistics are calculated for data that has been filtered for poor quality sequences, and seemingly contaminated samples have been removed.stats.csvrarefied OTU table L2Rarefied phyla x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into phylum.reduced_nosingles_rarefied_557_99_L2.csvrarefied OTU table L3Rarefied class x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into class.reduced_nosingles_rarefied_557_99_L3.csvrarefied OTU table L4Rarefied order x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into orders.reduced_nosingles_rarefied_557_99_L4.csvrarefied OTU table L5Rarefied family x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into family.reduced_nosingles_rarefied_557_99_L5.csvrarefied OTU table L6Rarefied genus x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample), then taxa were collapsed into genera.reduced_nosingles_rarefied_557_99_L6.csvrarefied OTU table L7Rarefied OTU x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum). OTU table was rarefied to 557 sequences (size of smallest sample).reduced_nosingles_rarefied_557_99_L7.csvUnrarefied OTU table L7Unrarefied OTU x sampleID tables (the paper includes analyses on 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum. The other tables can be constructed from this one in QIIME).reduced_nosingletons_sorted_host_L7.csvUnrarefied OTU table L6Unrarefied genus x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).reduced_nosingletons_sorted_host_L6.csvUnrarefied OTU table L5Unrarefied family x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).reduced_nosingletons_sorted_host_L5.csvUnrarefied OTU table L4Unrarefied order x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).reduced_nosingletons_sorted_host_L4.csvUnrarefied OTU table L3Unrarefied class x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).reduced_nosingletons_sorted_host_L3.csvUnrarefied OTU table L2Unrarefied phylum x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).reduced_nosingletons_sorted_host_L2.csvraw sequencesraw sequence file, fasta formatNiwotDG08F.fnaquality filequality score fileNiwotDG08F.qualobserved_species_L2Phylum richness calculated for 100 rarefaction plotsobserved_species_L3Class richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)observed_species_L4Order richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)observed_species_L5Family richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)observed_species_L6Genus richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)observed_species_L7OTU richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_evenness_L2Phylum evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L2.csvsimpson_evenness_L3Class evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L3.csvsimpson_evenness_L4Order evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L4.csvsimpson_evenness_L5Family evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L5.csvsimpson_evenness_L6Genus evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L6.csvsimpson_evenness_L7Species evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_e_L7.csvsimpson_diversity_L2Phylum level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L2.csvsimpson_diversity_L3Class level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L3.csvsimpson_diversity_L4Order level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L4.csvsimpson_diversity_L5Family level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L5.csvsimpson_diversity_L6Genus level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L6.csvsimpson_diversity_L7OTU level Simpson's diversity calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)simpson_L7.csvREAD MEfile explaining sample ID codes, and contents of each data and code file uploaded to Dryad