Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
| Main Authors: | Bakker, Matthew G., Schlatter, Daniel C., Otto-Hanson, Lindsey, Kinkel, Linda L. |
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| Format: | info dataset |
| Terbitan: |
, 2013
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5006317 |
Daftar Isi:
- 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.
- 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