DOI: 10.15482/usda.adc/29944829
title: Data from: Soil microbiome composition can inform management to optimize crop production

description: Data from “Soil microbiome composition can inform management to optimize crop production” include one file “PotatoSCMP”.<b>File “PotatoSCMP” includes pre-plant soil microbial and chemical properties for 423 field soils collected from 130 commercial potato fields in Minnesota and Wisconsin. General soil and management information as well as potato yield were also included. Soils were collected between 2018-2023, in late fall (November) before planting.</b>Soil microbial properties include:(1) <b>Column Y:AB</b>, log abundance of total bacteria (log16S), fungi (logITS) and two pathogens <i>Verticillium dahliae</i> (logV) and Pathogenic <i>Streptomyces</i> spp (logS). Abundance data was measured using quantitative PCR targeting bacterial 16 S rRNA, fungal ITS, thaxtomin synthetase (<i>txt</i>AB), and <i>V. dahliae</i> IGS genes.(2) <b>Column AC:AH</b>, bacterial and fungal diversities measured as Shannon index at phylum (abbreviation: P), order (O), and genus (G) level. “Bac_G_Shannon”: bacterial diversity at the genus level. “Fun_P_Shannon”: fungal diversity at the phylum level.(3) <b>Column AI:BJM</b>, relative abundance of the top ~55% most abundant bacterial (885) and fungal (706) genera for each soil sample.(4) <b>Column BJP:BJS</b>, the first two axis of the Principal Component Analysis based on Bray-Curtis dissimilarity for bacterial (B16S_pcoa1) and fungal (ITS_pcoa1) community.(2)-(4) were calculated based on the 16S and ITS sequencing data of the soil microbial communities. DNA was extracted from field soils and used in 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.Soil chemical properties include:(5) <b>Column O:X</b>, nutrient analysis on air-dried soils assessed at the A&L Great Lakes Lab (Fort Wayne, IN). Soil pH was measured in 1:1 soil/water mixture. Soil organic matter content (OM_percent) was measured with loss-on-ignition method. Concentrations of soil phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) were measured by extracting the soil with Mehlich3 and analyzed with Inductive Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES). Both absolute concentration (K_ppm) and percent base saturation (K_Sat_percent) were reported.General soil and management information include:(6) <b>Column C:H, L:N, BJN:BJO</b>· Project: a large-scale survey (SCMP), a paired fumigation study (PF).· State: Minnesota (MN) and Wisconsin (WI).· Year: year of sample collection within each project.· Fumigation: whether the field was fumigated post soil collection (Yes/No).· Region: potato growing region of the Upper Midwest. Sand or Loam.· Soil_type: Soil type based on Web Soil Survey.· Rotation length: the last year when the field was planted with potatoes.· Rotation diversity: the number of crops (including cover crops and rotation crops) in the past three years prior to the current potato year.Potato yield:(7) <b>Column I:K</b>, potato yield of the sampling location where pre-plant soil was taken. Yield was measured as gram of fresh tuber per meter of a row. Potato variety (Russet, red, yellow, white, etc.) was also included. Tubers were harvested by hand-digging three plants at each sampling location.