R object containing taxonomic information for each OTU

This is an R object (.rds file) containing the taxonomic information for all possible OTUs detected in this dataset. These are the GreenGenes 13_8 97% reference OTUs

Arkansas 2016 and California 2014-15 R object

R object for Arkansas 2016 and California 2014-2015 Seasons in "tidy" format. That is, each variable is a column and each row corresponds to a single observation. This can be used directly with the R scripts in the github repo: https://github.com/bulksoil/LifeCycleManuscrip

OTU Table Clustered at 97% for all samples

A gzipped tab separated file. The OTU identifiers are in the column 'OTUID'. This is a matrix where each row represents one OTU and each column represents one sample (corresponding to "SampleID" in the mapping file). The data can be unzipped in the UNIX/LINUX terminal using the command 'gunzip lc_study_otu_table.tsv.gz

Organellar OTUs

R object (.rds file) containing all of the detected mitochondrial and plastid OTUs from the Greengenes 13_8 reference database

Sample Metadata

A tab separated file with information about the samples in the OTU table

California 2016 R object.

R object containing the data for the California 2016 season in "tidy" format

Rhizocompartments become more similar between field sites as a function of plant age.

<p>(A) Pairwise distances between each site within each common time point and each common compartment. The numerical values used to construct this plot can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s011" target="_blank">S11 Data</a>. (B) Mean total relative abundance of the site-specific operational taxonomic units (OTUs) within each time point. All OTUs found to be differentially abundant between sites within each common time point can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s012" target="_blank">S12 Data</a>. The numerical values used to construct panel B can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s013" target="_blank">S13 Data</a>.</p

Varieties with different developmental rates have skewed microbiota progressions.

<p>(A) The developmental stage of the tested varieties as a function of plant age. We staged each variety using descriptors previously described [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.ref024" target="_blank">24</a>]. R0 corresponds to the panicle initiation stage. It is important to note that M401 and M206 had nearly identical times to panicle initiation but afterwards diverged in time to heading. Data used to construct panel A can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s016" target="_blank">S16 Data</a>. (B) Principal coordinates analysis (PCoA) of the 2016 data indicating that root-associated compartment and plant age are major determinants of microbiota structure. The numerical values used to construct panel B can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s014" target="_blank">S14 Data</a>. (C) Linear slope estimates for the principal coordinate (PCo) 2 in panel B as a function of plant age for rhizosphere and endosphere compartments of each variety. Separate linear models were constructed for data prior to 84 days (corresponding to the sixth collection time point, the point at which all varieties had at least entered the panicle initiation stage) and for data after this time point. Letters under each point indicate statistical significance. Statistical tests were constrained to individual compartments and times of the season (prior to 84 days and after 84 days). The values used to construct panel C can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s015" target="_blank">S15 Data</a>. (D) The predicted developmental stage of the 2016 data as predicted by the stage-discriminant sparse random forest (RF) models. Developmental stage predictions used to construct panel D can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s016" target="_blank">S16 Data</a>. (E) Total relative abundance estimates for early and late colonizing stage-discriminant taxa between each cultivar and compartment. The values used to construct panel E can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s017" target="_blank">S17 Data</a>.</p

Random forest model detects taxa that are accurately predictive of plant age.

<p>(A) The result of predicting plant age using the sparse random forest (RF) models for the 2014 and 2015 season. Each point represents a predicted age value. Solid circles represent predictions from training data, while hollow points represent predictions from test data. The numerical values used to construct panel A can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s004" target="_blank">S4 Data</a>. (B) Abundance profiles for the age-discriminant operational taxonomic units (OTUs) in rhizosphere and endosphere compartments over the course of the California 2014 growing season. OTUs are ordered along the <i>y</i>-axis by timing of peak abundance. The orders of the OTUs on the <i>y</i>-axis are not shared between rhizosphere and endosphere despite both the models for each compartment sharing a subset of age-discriminant taxa. OTUs are colored by their classification as early, late, or complex colonizers over the season (see color scale in panel C). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s040" target="_blank">S3 Table</a> for order of OTUs. There were 18 OTUs with decreasing patterns, 7 OTUs with complex dynamic patters, and 60 OTUs with increasing dynamic relative abundances in the rhizosphere. In the endosphere, there were 22 OTUs with decreasing relative abundances, 7 OTUs with complex patterns, and 56 with increasing relative abundances over the season. Slope estimates used to classify OTUs as having early, late, or complex patterns can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s005" target="_blank">S5 Data</a>. (C) Mean total abundance for the age-discriminant taxa across sites and compartments. The numerical values used to construct panel C can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s007" target="_blank">S7 Data</a>.</p

The root-associated microbiota stabilizes after 8–9 weeks after germination.

<p>(A) Principal coordinates analysis (PCoA) of Bray-Curtis dissimilarity between samples colored by root compartment. The numerical values used to construct this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003862#pbio.2003862.s001" target="_blank">S1 Data</a>. (B) The same plot as in panel A but colored by the field location. (C) The same analysis as in panels A and B but now showing principal coordinate (PCo) 1 versus PCo3, and the points are colored by the age of the plants from which the samples were taken. Hollow points represent bulk soil samples. (D) Heatmaps showing mean pairwise z-scores for similarity, computed as (1 − Bray-Curtis dissimilarity), between time points in each compartment for the 2014 California samples.</p