This README_Lankau2022.txt file was generated on 02-28-2022 by Richard Lankau GENERAL INFORMATION 1. Title of Dataset: Data from: Crop health is predicted by soil microbial diversity across phylogenetic scales 2. Author Information Corresponding Investigator Name: Richard Lankau Institution: University of Wisconsin-Madison, Madison, WI, USA Email: lankau@wisc.edu Co-investigator 1 Name: Isabelle George Institution: University of Wisconsin-Madison, Madison, WI, USA Co-investigator 2 Name: Max Miao Institution: University of Wisconsin-Madison, Madison, WI, USA 3. Date of data collection: 2017-2019 4. Geographic location of data collection: Wisconsin, USA 5. Funding sources that supported the collection of the data: Wisconsin Potato and Vegetable Growers Association 6. Recommended citation for this dataset: Lankau, R.A., Data from: Crop health is predicted by soil microbial diversity across phylogenetic scales DATA & FILE OVERVIEW 1. Description of dataset These data include 1) data on potato plant tuber yields and disease severity from a greenhouse experiment and 2) phylogenetic tree and list of taxonomic identifications for soil bacterial communities used in the greenhouse experiment 2. File List: File 1 Name: denovotree.newick File 1 Description: Phylogenetic tree made from de novo assembly of 16S sequences of bacterial Amplicon Sequence Variants File 2 Name: Lankau_et_al._Ecosphere_Supplemental_Tables.xlsx File 2 Description: Summary tables of taxa-by-taxa associations with potato crop performance for taxa defined at three levels of phylogenetic resolution File 3 Name: potatofunccladediv_forsubmission.csv File 3 Description: Potato plant performance metrics from greenhouse experiment and measures of bacterial community diversity File 4 Name: potatorar_forsubmission_tax.csv File 4 Description: List of taxonomic identification for bacterial Amplification Sequence Variants METHODOLOGICAL INFORMATION See associated article: Lankau et al. Crop health is predicted by soil microbial diversity across phylogenetic scales. Ecosphere DATA-SPECIFIC INFORMATION FOR: Lankau_et_al._Ecosphere_Supplemental_Tables.xlsx 1. Number of tables: 3 2. Number of cases/rows: variable 3. Variable List: Clade Phylogenetic Clade (either at ASV level for Table S5, at branch length of 0.4 for Table S6, or branch length of 0.1 for Table S7) SequenceCount2015 Total number of sequence reads assigned to clade in 2015 dataset Frequency2015 Number of samples in which clade was detected in 2015 dataset SequenceCount2017 Total number of sequence reads assigned to clade in 2017 dataset Frequency2017 Number of samples in which clade was detected in 2017 dataset stdB_2015L Standardized beta (regression coefficient) of model regressing tuber yield in low nutrient conditions against clade in exploratory experiment P_2015L P value of regression of tuber yield in low nutrient conditions against clade in exploratory experiment Padj_2015L P value of regression of tuber yield in low nutrient conditions against clade in exploratory experiment, false discovery rate adjustment stdB_2015H Standardized beta (regression coefficient) of model regressing tuber yield in high nutrient conditions against clade in exploratory experiment P_2015H P value of regression of tuber yield in high nutrient conditions against clade in exploratory experiment Padj_2015H P value of regression of tuber yield in high nutrient conditions against clade in exploratory experiment, false discovery rate adjustment stdB_2015CS Standardized beta (regression coefficient) of model regressing common scab symptoms against clade in exploratory experiment P_2015CS P value of regression of common scab symptoms against clade in exploratory experiment Padj_2015CS P value of regression of common scab symptoms against clade in exploratory experiment, false discovery rate adjustment stdB_2017L Standardized beta (regression coefficient) of model regressing tuber yield in low nutrient conditions against clade in confirmatory experiment P_2017L P value of regression of tuber yield in low nutrient conditions against clade in confirmatory experiment Padj_2017L P value of regression of tuber yield in low nutrient conditions against clade in confirmatory experiment, false discovery rate adjustment stdB_2017H Standardized beta (regression coefficient) of model regressing tuber yield in high nutrient conditions against clade in confirmatory experiment P_2017H P value of regression of tuber yield in high nutrient conditions against clade in confirmatory experiment Padj_2017H P value of regression of tuber yield in high nutrient conditions against clade in confirmatory experiment, false discovery rate adjustment stdB_2017CS Standardized beta (regression coefficient) of model regressing common scab symptoms against clade in confirmatory experiment P_2017CS P value of regression of common scab symptoms against clade in confirmatory experiment Padj_2017CS P value of regression of common scab symptoms against clade in confirmatory experiment, false discovery rate adjustment 4. Missing data codes: None 5. Abbreviations used: N/A; not applicable DATA-SPECIFIC INFORMATION FOR: potatofunccladediv_forsubmission.csv 1. Number of variables: 2. Number of cases/rows: 42 3. Variable List: Variable Definition FieldID Numerical identified of each potato field where microbes were sourced Experiment Exploratory experiment (2015) or confirmatory experiment (2017) - may be best to analyze separately field name Farmers field codes diffCSscore Measure of disease severity - average for three replicates of each microbial community Mean.Control.Microbe Potato tuber yield under fertilized conditions - average of three replicate pots per microbial community Mean.LowN.Microbe Potato tuber yield under unfertilized conditions - average of three replicate pots per microbial community varCtub Variance in "Control" tuber yields among the three replicate pots varNtub Variance in "LowN" tuber yields among the three replicate pots varCSscore Variance in disease severity scores among the three replicate pots invVar_Ctub inverse of varCtub invVar_Ntub inverse of varNtub invVar_Csscore inverse of varCSscore Std.Err.Mean.Control.Microbe Standard Error in "Control" tuber yields among the three replicate pots Std.Err.Mean.LowN.Microbe Standard Error in "LowN" tuber yields among the three replicate pots seCSscore Standard Error in disease severity scores among the three replicate pots claderich0.1 Richness of bacterial clades defined at the 0.1 branch unit cut-off from node cladediv0.1 Shannon-Weinder diversity of bacterial clades defined at the 0.1 branch unit cut-off from node claderich0.15 Richness of bacterial clades defined at the 0.15 branch unit cut-off from node cladediv0.15 Shannon-Weinder diversity of bacterial clades defined at the 0.15 branch unit cut-off from node claderich0.2 Richness of bacterial clades defined at the 0.2 branch unit cut-off from node cladediv0.2 Shannon-Weinder diversity of bacterial clades defined at the 0.2 branch unit cut-off from node claderich0.25 Richness of bacterial clades defined at the 0.25 branch unit cut-off from node cladediv0.25 Shannon-Weinder diversity of bacterial clades defined at the 0.25 branch unit cut-off from node claderich0.3 Richness of bacterial clades defined at the 0.3 branch unit cut-off from node cladediv0.3 Shannon-Weinder diversity of bacterial clades defined at the 0.3 branch unit cut-off from node claderich0.35 Richness of bacterial clades defined at the 0.35 branch unit cut-off from node cladediv0.35 Shannon-Weinder diversity of bacterial clades defined at the 0.35 branch unit cut-off from node claderich0.4 Richness of bacterial clades defined at the 0.4 branch unit cut-off from node cladediv0.4 Shannon-Weinder diversity of bacterial clades defined at the 0.4 branch unit cut-off from node claderich0.45 Richness of bacterial clades defined at the 0.45 branch unit cut-off from node cladediv0.45 Shannon-Weinder diversity of bacterial clades defined at the 0.45 branch unit cut-off from node claderich0.5 Richness of bacterial clades defined at the 0.5 branch unit cut-off from node cladediv0.5 Shannon-Weinder diversity of bacterial clades defined at the 0.5 branch unit cut-off from node claderich0.55 Richness of bacterial clades defined at the 0.55 branch unit cut-off from node cladediv0.55 Shannon-Weinder diversity of bacterial clades defined at the 0.55 branch unit cut-off from node claderich0.6 Richness of bacterial clades defined at the 0.6 branch unit cut-off from node cladediv0.6 Shannon-Weinder diversity of bacterial clades defined at the 0.6 branch unit cut-off from node claderich0.7 Richness of bacterial clades defined at the 0.7 branch unit cut-off from node cladediv0.7 Shannon-Weinder diversity of bacterial clades defined at the 0.7 branch unit cut-off from node claderich0.8 Richness of bacterial clades defined at the 0.8 branch unit cut-off from node cladediv0.8 Shannon-Weinder diversity of bacterial clades defined at the 0.8 branch unit cut-off from node asvrich Richness of unique bacterial amplicon sequence variants asvdiv Shannon-Weiner diversity of amplicon sequence variants PD Faiths' phylogenetic diversity