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

• Main Authors: Dean, Sarah L., Farrer, Emily C., Porras-Alfaro, Andrea, Suding, Katharine N., Sinsabaugh, Robert L.
• Format: Dataset
• Language: English
• Published: Dryad 2014
• Subjects: Deschampsia cespitosa; root; Geum rossii; alpine tundra; Tundra
• Online Access: https://dx.doi.org/10.5061/dryad.7535k; https://datadryad.org/stash/dataset/doi:10.5061/dryad.7535k

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 ... : 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 ...