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.

#### alpha diversity code

R code that tests for relationships between alpha diversity measures and treatment. Inputs are collated alpha diversity files produced in QIIME.

alpha.R

#### NiwotDGF map

Environmental mapping file, providing treatment, plot, DNA dilution, and sequencing run information for each sample.

NiwotDGF_map3.csv

#### NMDS code

R 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.R

#### ANOVA code, N effects per host

R code to test individual taxa for correlation with N in each host

otu_anova_N_isolated_host.R

#### ANOVA code, Nxhost

R code to test individual taxa for correlation with N or host, or interactions between the two.

otu_anova_Nxhost.R

#### ANOVA code, remxN

R code to test individual taxa for correlation with treatment or treatment interactions in single host

otu_anova_remxN.R

#### rarefaction plot code

R code to build alpha rarefaction plots (collated alpha rarefaction table produced in Qiime from taxa x SampleID tables)

rarefaction.R

#### RDA code

R code for RDA ordination and permutation tests

RDA.R

#### SE of OTU and seq counts

R code to calculate standard error of sequence and OTU counts for each host

SE otus seqs.R

#### OTU and sequence counts

file 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.csv

#### rarefied OTU table L2

Rarefied 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.csv

#### rarefied OTU table L3

Rarefied 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.csv

#### rarefied OTU table L4

Rarefied 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.csv

#### rarefied OTU table L5

Rarefied 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.csv

#### rarefied OTU table L6

Rarefied 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.csv

#### rarefied OTU table L7

Rarefied 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.csv

#### Unrarefied OTU table L7

Unrarefied 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.csv

#### Unrarefied OTU table L6

Unrarefied genus x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).

reduced_nosingletons_sorted_host_L6.csv

#### Unrarefied OTU table L5

Unrarefied family x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).

reduced_nosingletons_sorted_host_L5.csv

#### Unrarefied OTU table L4

Unrarefied order x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).

reduced_nosingletons_sorted_host_L4.csv

#### Unrarefied OTU table L3

Unrarefied class x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).

reduced_nosingletons_sorted_host_L3.csv

#### Unrarefied OTU table L2

Unrarefied phylum x sampleID tables (there are 6 tables for 6 taxonomic levels, species through phylum).

reduced_nosingletons_sorted_host_L2.csv

#### raw sequences

raw sequence file, fasta format

NiwotDG08F.fna

#### quality file

quality score file

NiwotDG08F.qual

#### observed_species_L2

Phylum richness calculated for 100 rarefaction plots

#### observed_species_L3

Class richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

#### observed_species_L4

Order richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

#### observed_species_L5

Family richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

#### observed_species_L6

Genus richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

#### observed_species_L7

OTU richness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

#### simpson_evenness_L2

Phylum evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L2.csv

#### simpson_evenness_L3

Class evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L3.csv

#### simpson_evenness_L4

Order evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L4.csv

#### simpson_evenness_L5

Family evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L5.csv

#### simpson_evenness_L6

Genus evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L6.csv

#### simpson_evenness_L7

Species evenness calculated for 100 rarefaction plots (there are 6 tables for 6 taxonomic levels, species through phylum. L7=species, L2=phylum)

simpson_e_L7.csv

#### simpson_diversity_L2

Phylum 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.csv

#### simpson_diversity_L3

Class 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.csv

#### simpson_diversity_L4

Order 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.csv

#### simpson_diversity_L5

Family 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.csv

#### simpson_diversity_L6

Genus 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.csv

#### simpson_diversity_L7

OTU 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.csv

#### READ ME

file explaining sample ID codes, and contents of each data and code file uploaded to Dryad