Data from: Disease suppression is driven by microbial community properties at fine taxonomic scales

Data from “Disease suppression is driven by microbial community properties at fine taxonomic scales” includes three files “Set1”, “Set2”, and “Set3”.

File “Set1” includes two microbial community properties and two microbial functions of 120 field soils collected from 60 commercial potato fields in Minnesota and Wisconsin. Microbial community properties include:

(1) bacterial and fungal diversities measured as Inverse Simpson’s index at phylum (abbreviation: P), class (C), order (O), family (F), genus (G), species (S) and  amplicon sequence variant (ASV) operational taxonomic unit (OTU) level. This corresponds to column 11to 24. “B_P_InvSim” represents bacterial diversity at phylum level. “F_OTU_InvSim” represents fungal diversity at ASV level.

(2) the first axis of the Principal Component Analysis based on Bray-Curtis dissimilarity for bacterial (B_Axis.1) and fungal (F_Axis.1) community. This corresponds to column 25 to 26.

Both (1) and (2) were calculated based on the 16S and Internal Transcribed Spacer (ITS) sequencing data of the soil microbial communities. DNA was extracted from field soils, and used in  Polymerase chain reaction (PCR) reactions to amplify the V3-V4 region of bacterial 16S rRNA and the eukaryotic ITS2 region. PCR products were sequenced with a MiSeq 600 cycle v3 kit. Sequencing data was processed in Qiime2.

Microbial functions include:

(3) the ability of soil microbiomes to suppress the common scab disease in potato tubers. This includes “Suppressiveness_scab_sev_ST”, which represents the suppression of the severity of disease on the infected tubers. “Suppressiveness_scab_freq” represents the suppression of the frequency of the disease. Higher values indicate less disease severity/frequency in infected plants with microbiome inoculation.

(4) the ability of soil microbiomes to promote potato tuber yield. “Control_pot_tuber_yield” represents the potato tuber yield in a sterile background soil inoculated by a soil microbiome.

Functions (3) and (4) were measured with a greenhouse experiment conducted from the winter of 2019 to spring of 2020. A total of 120 field soils were collected in the fall of 2019. Each soil was inoculated into a sterile background media to introduce the soil microbiome. Potato plants were planted. The pathogen Streptomyces scabies which causes potato common scab disease was also introduced into the inoculated soils. Four months later, potato tuber yield and disease level were estimated to calculate the two functions.

File “Set2” and “Set3” includes additional microbial community properties of the 120 field soils. File “Set2” includes the genus-level diversity within each bacterial phylum of the 120 field soils. A total of 15 bacterial phyla were included. The ASV table for each phylum was extracted using the phyloseq function “subset_taxa”. The extracted ASV tables were then merged at genus level for calculation of the Inverse Simpson diversity index using the phyloseq function “tax_glom”. File “Set3” includes the relative abundance of each bacterial phylum for the 120 field soils. A total of 27 bacterial phyla were included.