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.