Microbial diversity should inform sampling effort
The higher congruency that we saw between sampling strategies for AMF
compared to other microbial communities may be due to the differences in
their local and global estimated richness. While the global number of
AMF species has been estimated in the hundreds to low thousands (Öpiket al ., 2013, Davison et al ., 2015), global estimates of
fungal species in general range in the millions (Hawksworth 2001;
Hawksworth and Lücking 2017). A recent global estimate of bacterial
richness suggests similar scales (Louca et al., 2019). In this
study specifically, AMF had the lowest total SV richness and the
greatest similarity between sampling strategies, while foliar fungal
endophytes had the highest SV richness, and the lowest overlap of SVs
between strategies. Since the amount of tissue sampled was equal for all
microbial communities, the sampling effort was likely much higher for
AMF (relative to the whole AMF community), than it was for bacteria and
non-AM fungi. Consequently, with each sample we are likely sampling a
much larger proportion of true AMF species richness.
Even though the estimated total community richness was highest for
foliar fungi, the average estimated richness per individual plant was
highest for AMF. This suggests that similar AMF SVs re-occurred across
all plants with low species turnover. On the other hand, fungi in leaves
had lower average richness per plant (Figure 4, Supporting Information
Fig. 3), but the highest total richness, meaning that there was higher
turnover of FFE species among plants sampled. These results may be a
direct reflection of the overall community richness of the different
microbial groups as well as their ability to spread and co-occur within
plants. Based on these patterns, more individual plants and a greater
sampling effort within individuals are likely needed to characterize FFE
communities compared to AMF communities.