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.