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.
Plant data: sterilized field soil treatments
Plant 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 fruits
a_final.txt
Plant data: microbial community treatments
Plant 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 fruits
b_final.txt
Key to soil sample IDs
Soil 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 collection
SMDsoils.txt
16S gene copy number estimates
16S gene copy number estimates for OTUs generated using corrected bioinformatics pipeline. OTUs with no available estimates were assigned the mean copy number of 2.7175
soil_otu_CN_v2.txt
soil 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.txt
soil OTU table
Unrarefied 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.txt
OTU taxonomy
Contains taxonomic designations for OTUs
OMD_v2.txt