Author Contributions
LB, YL and BL conceived the study. LB, YL and BL collected samples. LB
processed samples, analyzed data and wrote the manuscript with input and
edits provided by YL and BL.
Figures :
Figure 1. Description of the two common strategies used to
subsample plant-associated microbial communities.
Figure 2. Sequence rarefaction curves for each sampling
strategy (homogenizing after subsampling and homogenizing before
subsampling) for A) bacteria in roots, B) Arbuscular mycorrhizal (AM)
fungi in roots, C) All non-AM fungi in roots and D) foliar fungal
endophytes, in Asclepias speciosa plants. Vertical lines
represent the depth(s) at which each group was rarefied.
Figure 3 . Venn Diagram showing the overlap of sequence variants
(SVs) recovered from milkweed plants at a single site, when subsampling
microbial communities using two different strategies.
Figure 4. Procrustes plots comparing two different subsampling
strategies used to characterize A.) root bacteria, B.) AMF, C.) non-AM
root fungi, and D.) foliar fungi colonizing milkweed plants. Plots are
based on non-metric multidimensional scaling of Bray-Curtis distance
matrices of Hellinger transformed relative abundances.
M2 values represent the sum of squared deviations
between sample pairs, where lower values indicate a better fit between
matrices.
Figure 5. Species accumulation curves for foliar fungal
endophytes colonizing milkweed (Asclepias speciosa ). Each curve
represents the SVs recovered from a single plant through additional
extractions of bulk material (6 leaves per plant divided into
~250 mg extractions.)
Figure 6. Nonmetric multi-dimensional scaling based on
Bray-Curtis distances of foliar fungal endophytes in milkweed plants.
Panel A represents the seasonal variation in foliar endophytic fungi
when analyzing just one extraction rep per plant (leaf discs). Panel B
represents the variation among plants when analyzing multiple
extractions from each plant in September. The zoomed in panel highlights
the less pronounced, but significant clustering among individual plants
2, 5, 12, 13 and 14.