DOI: 10.5061/dryad.5p414
title: Data from: Assembly and ecological function of the root microbiome across angiosperm plant species

description: Across plants and animals, host-associated microbial communities play
 fundamental roles in host nutrition, development, and immunity. The
 factors that shape host–microbiome interactions are poorly understood, yet
 essential for understanding the evolution and ecology of these symbioses.
 Plant roots assemble two distinct microbial compartments from surrounding
 soil: the rhizosphere (microbes surrounding roots) and the endosphere
 (microbes within roots). Root-associated microbes were key for the
 evolution of land plants and underlie fundamental ecosystem processes.
 However, it is largely unknown how plant evolution has shaped root
 microbial communities, and in turn, how these microbes affect plant
 ecology, such as the ability to mitigate biotic and abiotic stressors.
 Here we show that variation among 30 angiosperm species, which have
 diverged for up to 140 million years, affects root bacterial diversity and
 composition. Greater similarity in root microbiomes between hosts leads to
 negative effects on plant performance through soil feedback, with specific
 microbial taxa in the endosphere and rhizosphere potentially affecting
 competitive interactions among plant species. Drought also shifts the
 composition of root microbiomes, most notably by increasing the relative
 abundance of the Actinobacteria. However, this drought response varies
 across host plant species, and host-specific changes in the relative
 abundance of endosphere Streptomyces are associated with host drought
 tolerance. Our results emphasize the causes of variation in root
 microbiomes and their ecological importance for plant performance in
 response to biotic and abiotic stressors.
description: Bacterial ASV
 phylogenyPhylogenetic tree of all
 bacterial ASVs (based on DADA2 generated ASVs). PASTA
 (doi:10.1089/cmb.2014.0156) was used to generate
 phylogeny.16S_Root_Microbiome.trePhylogeny of host plant speciesPhylogenetic tree of host plant species. We downloaded accessions of 3 genes (2 plastid and 1 nuclear) for each of our plant species from GenBank: ribulose-bisphosphate carboxylase (rbcL); maturase K (matK); and internal transcribed spacer (ITS) adjacent to the 5.8S ribosomal RNA gene. We aligned sequences in MEGA v. 6.0 using MUSCLE with default parameters, followed by manually checking alignments. We used BEAST v. 2.1.3 to build a Bayesian phylogenetic tree. For each locus we implemented a standard general time-reversible model (GTR + I + Γ) and an uncorrelated lognormal clock (UCLN) to determine the rate of nucleotide change.Host_plant_species.treASV taxonomic assignmentsTaxonomy assignments of each ASV generated from DADA2 using the RDP training set and the RDP classifier (implemented in DADA2; See SI Appendix, Materials and Methods). Saved as an RDS file to be read into R.Root_microbiome_RDP_taxa.rdsHost plant phenotypic traitsThe mean and standard error of phenotypic traits measured for each host plant species. AGB = aboveground biomass; BGB = belowground biomass; RL = root length; RA = root angle; WATER = leaf % water content; SLA = specific leaf area; RHD = root hair density; SRL = specific root length. See SI Appendix Materials and Methods for more detail.PGLS_host_traits.csvASV tableCount table for ASVs generated from DADA2 from raw MiSeq reads. Rows are individual samples and columns are individual ASVs. This table underlies nearly all analyses. Can be loaded into R using read.RDS(). Generate phyloseq() object using the meta data, bacterial phylogeny, and bacterial taxonomy provided here.Root_microbiome_seqtab.rdsSample metadataMetadata associated with each individual sample. Community: E (endosphere); R (rhizosphere); S (bulk soil); RT (rhizosphere toothpick); ET (endosphere toothpick); MOCK (mock community); PAO (pure culture of Psuedomonas aeruginosa); WATER (negative control). Species: refers to the host plant species (see host plant trait data for key to species' codes); code 600 (bare soil); code 700 (toothpick); code ST (not analyzed in this experiment). Replicate: refers to experimental blocking ID. Run - refers to individual MiSeq sequencing run. Treatment - refers to watering treatment (well-watered or drought).meta.data.csvHost plant phenotypic distanceMatrix of phenotypic distance between host plant species. To create a metric of phenotypic distance we normally standardized species’ mean trait values and calculated the multi-trait Euclidean distance between species.Host_plant_phenotypic_distance.csvHost plant drought biomassBiomass data associated with individual plants in the watering manipulation experiment. Species - refers to host plant species (see phenotypic trait data for key to species code). Block - refers to experimental block. Root weight - weight of standardized root sample used for microbiome characterization (mg). AGB - aboveground biomass (mg); BGB - belowground biomass (mg). Note, not all individuals in this dataset used in the analysis.Host_plant_drought_biomass.csvPlant soil feedback (PSF) between host plant speciesSee SI Appendix Materials and Methods for a description of the PSF experiment. Focal species - host plant species that served as the focal plant in the PSF experiment. Soil C Species - host plant species that served as the soil conditioning plant in the PSF experiment. Contrast - pair of focal and soil conditioning plant species. Biomass ratio - plant soil feedback measured using total biomass. AGB ratio - plant soil feedback measured using only aboveground biomass. BGB ratio - plant soil feedback measured using only belowground biomass. Mean Gen Dist X - patristic (phylogenetic) distance between focal and soil conditioning host plant species. Mean Fun Dist X - phenotypic distance between focal and soil condition host plant species. Endo Wu W - the average weighted UniFrac distance between endosphere compartments of focal and soil conditioning host plant species. Rhizo Wu W - the average weighted UniFrac distance between endosphere compartments of focal and soil conditioning host plant species. Endo Uu W - the average unweighted UniFrac distance between endosphere compartments of focal and soil conditioning host plant species. Rhizo Uu W - the average unweighted UniFrac distance between endosphere compartments of focal and soil conditioning host plant species.Host_plant_PSF.csvRoot microbiome R scriptCode used for all bioinformatic and analytical steps.Publication.Code.Root.Microbiome.Fitzpatrick.RSRP128025SRP128025 at the NCBI Sequence Read Archive contains raw MiSeq reads for each individual sample. Note that not all samples were analyzed in: Assembly and ecological function of the root microbiome across angiosperm plant species, Fitzpatrick, Connor, Copeland, Julia, Wang, Pauline W., Guttman, David S., Kotanen, Peter M., Johnson, Marc T. J.