Richness and evenness between sampling strategies
Contrary to our predictions, richness differed only for root bacteria
where homogenizing before subsampling resulted in slightly more SVs
recovered than homogenizing after subsampling (Supporting Information,
Table S2 and Fig. S1). Evenness did not differ for any microbial group.
In addition, neither sampling strategy produced saturated species
accumulation curves for any microbial community sampled, although AMF
sampling approached saturation (Supporting Information, Fig. S2). This
indicated inadequate sampling to characterize site richness, due to
species turnover among plants. However, sequencing effort curves did
saturate for all groups, indicating that sequencing depth was not a
limiting factor in estimating the richness in individual samples (Figure
2).
The most abundant SVs, (those occurring in at least half of our samples
and recovered by both sampling strategies), represented only a small
proportion of the microbial communities recovered. This included 5.5%
of all AMF SVs (Glomus, Clairoideoglomus ), while just 0.7 % of
total bacterial SVs (Bacillus, unknown bacteria) and 0.9% non-AM
fungal SVs (Nectriaceae, Plectosphaerella, Tetracladium ), fit
these criteria. Foliar fungi were the most SV-rich group
(Figure 3), and only 0.8% of total SVs (Mycosphaerella ) occurred
in at least half of all samples and were recovered by both sampling
strategies.