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.

数据集“疾病抑制由微生物群落特性在精细分类尺度驱动”包含三个文件：“Set1”、“Set2”和“Set3”。其中，“Set1”文件包含来自明尼苏达州和威斯康星州60个商业马铃薯田的120个田间土壤样本的两种微生物群落特性和两种微生物功能。微生物群落特性包括：（1）以门（缩写：P）、纲（C）、目（O）、科（F）、属（G）、种（S）和扩增子序列变异（ASV）操作分类单元（OTU）水平测量的细菌和真菌多样性，以逆辛普森指数表示。这对应于第11至24列。“B_P_InvSim”代表门水平的细菌多样性，“F_OTU_InvSim”代表ASV水平的真菌多样性。（2）基于Bray-Curtis距离的主成分分析的第一轴，分别针对细菌（B_Axis.1）和真菌（F_Axis.1）群落。这对应于第25至26列。以上两点均基于土壤微生物群落的16S和内部转录间隔区（ITS）测序数据计算得出。DNA从田间土壤中提取，用于聚合酶链反应（PCR）反应以扩增细菌16S rRNA的V3-V4区域和真核生物ITS2区域。PCR产物使用MiSeq 600周期v3试剂盒进行测序。测序数据在Qiime2中进行处理。微生物功能包括：（3）土壤微生物群落抑制马铃薯块茎上常见晚疫病的能力。这包括“Suppressiveness_scab_sev_ST”，代表对感染块茎上疾病严重程度的抑制。“Suppressiveness_scab_freq”代表对疾病频率的抑制。更高的值表示在接种微生物群落的感染植物中疾病严重程度/频率较低。“Control_pot_tuber_yield”代表由土壤微生物群落接种的灭菌背景土壤中的马铃薯块茎产量。功能（3）和（4）通过2019年冬季至2020年春季进行的温室实验进行测量。2019年秋季共收集了120个田间土壤样本。每个土壤样本接种到灭菌背景培养基中，以引入土壤微生物群落。种植马铃薯植物，并将引起马铃薯晚疫病的病原体Streptomyces scabies引入接种土壤。四个月后，估计马铃薯块茎产量和疾病水平，以计算两个功能。文件“Set2”和“Set3”包含120个田间土壤的额外微生物群落特性。文件“Set2”包含120个田间土壤中每个细菌门内的属水平多样性。共包含15个细菌门。使用phyloseq函数“subset_taxa”提取每个门的ASV表，然后使用phyloseq函数“tax_glom”合并提取的ASV表，以计算逆辛普森多样性指数。文件“Set3”包含120个田间土壤中每个细菌门的相对丰度。共包含27个细菌门。