Dataset Open Access

Effects of plant diversity and community age on soil microbial communities

Schmid, Marc W; von Moorsel, SJ; Hahl, T; De Luca, E; Wagg, C; Niklaus, PA; Schmid, B

This record contains supplementary information for the article "Effects of plant diversity and community age on soil microbial communities".

SI_tab_1_annotation.ods: Taxonomic annotations of the operational taxonomic unit (OTU) identified in the study.

SI_tab_2_counts.ods: Number of reads per OTU and sample.

SI_tab_3_enrichment.ods: The table contains all phyla tested for enrichment/depletion in sets of differentially abundant OTUs. "Contrast" indicates the differential expression contrast. "Observed" corresponds to the number of OTUs annotated with a given phyla in the set of differentially abundant OTUs. "Expected" gives the number of OTUs which would be expected to be annotated with a given phyla if the test set were randomly sampled from the reference set. Note: in the previous versions, this table was based on another differential abundance analysis (with DESeq2, the analysis wasn't published).

SI_tab_4_anova_indices_legumes.ods: Analysis of variance of microbial richness (number of OTUs), effective richness (exp(Shannon Index)) and Pielou’s evenness. Contrasts among soil-legacy treatments and their interactions are indented. isMonoculture: a contrast to compare plant monocultures to plant species mixtures, logSR: log2 of plant species richness, hasLegumes: contrast for presence/absence of legumes, SL: soil legacy, AGE: new soil compared to the two other soils, INO: inoculated compared to native soil, PA: plant community age.

SI_tab_5_permanova_unifrac_grasses.ods: Multivariate analysis of variance of dissimilarities between microbial communities. Contrasts among soil-legacy treatments and their interactions are indented. MS refers to the mean squares of the dissimilarity measure (Unifrac distances). isMonoculture: a contrast to compare plant monocultures to plant species mixtures, logSR: log2 of plant species richness, hasGrass: contrast for presence/absence of grasses, SL: soil legacy, AGE: new soil compared to the two other soils, INO: inoculated compared to native soil, PA: plant community age.

SI_tab_6_permanova_legumes.ods: Top: As S5, but with Manhattan distances of log2(x+1) transformed sequence counts instead of unifrac distances. Bottom: As S5 but with legumes instead of grasses.

SI_tab_7_soilChemistry_grasses.ods: Analysis of variance of soil chemistry. isMonoculture: a contrast to compare plant monocultures to plant species mixtures, logSR: log2 of plant species richness, hasGrasses: contrast for presence/absence of grasses, SL: soil legacy, AGE: new soil compared to the two other soils, INO: inoculated compared to native soil, PA: plant community age.

SI_file_1_16S_otu_sequences.fa.gz: 16S-OTUs sequences in fasta format, gz compressed.

SI_file_2_ITS_otu_sequences.fa.gz: ITS-OTUs sequences in fasta format, gz compressed.

 

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SI_file_1_16s_otu_sequences.fa.gz
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SI_file_2_ITS_otu_sequences.fa.gz
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SI_tab_1_annotation.ods
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SI_tab_2_counts.ods
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SI_tab_3_enrichment.ods
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SI_tab_4_anova_indices_legumes.ods
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SI_tab_5_permanova_unifrac_grasses.ods
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SI_tab_6_permanova_legumes.ods
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SI_tab_7_soilChemistry_grasses.ods
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