DOI: 10.5061/dryad.1t6s5
title: Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

description: Plant phenology is known to depend on many different environmental
 variables, but soil microbial communities have rarely been acknowledged as
 possible drivers of flowering time. Here, we tested separately the effects
 of four naturally occurring soil microbiomes and their constituent soil
 chemistries on flowering phenology and reproductive fitness of Boechera
 stricta, a wild relative of Arabidopsis. Flowering time was sensitive to
 both microbes and the abiotic properties of different soils; varying soil
 microbiota also altered patterns of selection on flowering time. Thus,
 soil microbes potentially contribute to phenotypic plasticity of flowering
 time and to differential selection observed between habitats. We also
 describe a method to dissect the microbiome into single axes of variation
 that can help identify candidate organisms whose abundance in soil
 correlates with flowering time. This approach is broadly applicable to
 search for microbial community members that alter biological
 characteristics of interest.
description: Plant data: sterilized
 field soil treatmentsPlant pedigree
 information, phenotype data, and fitness data from greenhouse experiment
 investigating effects of 4 different sterilized field soils.
 "Block" = experimental block; "Genotype" = genotype
 code; "Subsp" = Subspecies code: W for west, E for east;
 "Treatment" = origin of sterilized field soil; "FLT" =
 flowering time (days); "elong" = elongation rate (mm/day);
 "HAF" = height at flowering (mm); "Leafper" = number
 of leaves per mm stem; "NFr" = number of
 fruitsa_final.txtPlant data: microbial community treatmentsPlant pedigree information, phenotype data, and fitness data from greenhouse experiment investigating effects of 4 different soil microbial communities. "Block" = experimental block; "Genotype" = genotype code; "Subsp" = Subspecies code: W for west, E for east; "Treatment" = origin of soil microbial community; "FLT" = flowering time (days); "elong" = elongation rate (mm/day); "HAF" = height at flowering (mm); "Leafper" = number of leaves per mm stem; "NFr" = number of fruitsb_final.txtKey to soil sample IDsSoil sample-level metadata. "SampleID" = unique identifier for soil samples (JGI notation). "Plant_ID" = unique identifier for soil samples (Duke notation). "Site" = field site of origin. "oldPlate" = plate identifier (Duke notation). "newPlate" = plate identifier (JGI notation). "Year" = year of soil collectionSMDsoils.txt16S gene copy number estimates16S gene copy number estimates for OTUs generated using corrected bioinformatics pipeline. OTUs with no available estimates were assigned the mean copy number of 2.7175soil_otu_CN_v2.txtsoil OTU table (rarefied)Soil OTU table rarefied to 40,000 reads per sample, used for all analyses in the publication (Wagner et al. 2014 Ecology Letters). This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples BEFORE rarefaction (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample after rarefaction.soil_otu_table_rare_40k_v2.txtsoil OTU tableUnrarefied soil OTU table. This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample. This file was the input leading to the rarefied dataset ('soil_otu_table_rare40k.txt') used for all downstream analyses in the publication.soil_otu_table_v2.txtOTU taxonomyContains taxonomic designations for OTUsOMD_v2.txtREADME