DOI: 10.5061/dryad.2fc8m
title: Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome

description: A conceptual model emphasizing direct host–microbe interactions has
 dominated work on host-associated microbiomes. To understand
 plant–microbiome associations, however, broader influences on microbiome
 composition and functioning must be incorporated, such as those arising
 from plant–plant and microbe–microbe interactions. We sampled soil
 microbiomes associated with target plant species (Andropogon gerardii,
 Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in
 communities varying in plant richness (1-, 4-, 8- or 16-species). We
 assessed Streptomyces antagonistic activity and analysed bacterial and
 Streptomyces populations via 454 pyrosequencing. Host plant species and
 plant richness treatments altered networks of coassociation among
 bacterial taxa, suggesting the potential for host plant effects on the
 soil microbiome to include changes in microbial interaction dynamics and,
 consequently, co-evolution. Taxa that were coassociated in the rhizosphere
 of a given host plant species often showed consistent correlations between
 operational taxonomic unit (OTU) relative abundance and Streptomyces
 antagonistic activity, in the rhizosphere of that host. However, in the
 rhizosphere of a different host plant species, the same OTUs showed no
 consistency, or a different pattern of responsiveness to such biotic
 habitat characteristics. The diversity and richness of bacterial and
 Streptomyces communities exhibited distinct relationships with biotic and
 abiotic soil characteristics. The rhizosphere soil microbiome is
 influenced by a complex and nested array of factors at varying spatial
 scales, including plant community, plant host, soil edaphics and microbial
 taxon and community characteristics.
description: Table of OTU abundances
 across samplesThis table records the
 number of sequence reads belonging to each OTU, across each of 48 samples.
 Only OTUs present in at least 50% of samples are included here. Sample
 labels provide information on host plant species sampled (digits 1-2; Ag =
 Andropogon gerardii, Ss = Schizachyrium scoparium, Lc = Lespedeza
 capitata, Lp = Lupinus perennis), the plot sampled (digits 3-5), the
 within plot replicate (digit 6), and the plant species richness to which
 that plot was originally planted (digits 7-8). OTU001 through OTU056 are
 from the Streptomyces dataset. OTU057 through OTU626 are from the total
 bacterial dataset.OTU_AbundanceTable.xlsxStreptomyces dataset - aligned, filtered, and uniqued fasta fileAlignment of de-replicated (uniqued) sequence reads from the Streptomyces dataset.Streptomyces.fastaStreptomyces - mapping file for de-replicationStreptomyces.names maps the processes of re-replicating sequence reads prior to alignment, in Mothur format. The first column shows the accession number of the read that is carried forward into the collection of 'unique' reads. In the following column, all accession numbers for identical sequence reads are listed.Streptomyces.namesRecord of sequence processing - Streptomyces datasetThis text file contains a record of the sequence processing steps that were performed on the Streptomyces dataset. Two programs were used: AmpliconNoise and Mothur.Streptomyces_SequenceProcessing.txtBacterial dataset - aligned, filtered, and uniqued fasta fileAlignment of de-replicated (uniqued) sequence reads from the bacterial dataset.Bacteria.fastaBacteria - mapping file for dereplicationBacteria.names maps the processes of de-replicating sequence reads prior to alignment, in Mothur format. The first column shows the accession number of the read that is carried forward into the collection of 'unique' reads. In the following column, all accession numbers for identical sequence reads are listed.Bacteria.namesRecord of sequence processing - Bacterial datasetThis text file contains a record of the sequence processing steps that were performed on the Streptomyces dataset. Two programs were used: AmpliconNoise and Mothur.Bacteria_SequenceProcessing.txt