Procrustes analyses reveal structural differences between sampling
strategies
When we ran Procrustes analyses on bacterial and fungal groups using
presence/absence data, we saw significant differences between sampling
strategies for all groups except for AMF (Table 3). When considering the
relative abundances of all SVs, as opposed to basing analyses on
presence/absence, as we did above, the two sampling strategies still
recovered significantly different microbial communities in root bacteria
and in non-AM root fungi (Figure 4, Table 3). For FFE, the two sampling
strategies produced slightly more correlated community structures, but
the similarity was weak (Table 3). This is likely because some plants
had very similar FFE communities, while others had completely different
FFE communities (Supporting Information, Fig. S3). Only AMF communities
were consistently similar between sampling strategies when considering
SV abundance.