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Different sampling strategies yield different microbial communities
The sampling strategies compared in this study (homogenizing tissue before subsampling and homogenizing tissue after subsampling) are common methods found in the literature for characterizing plant-associated microbial communities14,23,26,29. Procrustes analyses and community overlap between sampling strategies demonstrated that different strategies can capture disparate microbial communities within plants, with the extent of these differences depending on the community targeted and plant tissue type sampled. In FFE as well as bacterial and non-AM fungal communities in roots, subsamples from the same plant resulted in completely different sets of species recovered, illustrating the severe undersampling that is inherent to each of these strategies. With these sampling strategies, we are undoubtedly sacrificing power and accuracy to characterize the subtler aspects of plant microbiome interactions, despite often seeing community differences across landscapes, treatments or seasons.
Richness was higher when homogenizing before subsampling for bacteria only, despite differences observed in composition for all groups. It is perhaps surprising that homogenizing plant tissues before subsampling did not recover more species than homogenizing after subsampling for fungi as well, because with the former approach, more plant tissue is initially represented. Indeed, a previous study showed that sample pooling or homogenizing before subsampling resulted in a higher richness of soil fungi compared to equally sized individual samples50. In Song et al. (2015)50 they also found that multiple individual subsamples, rather than the single homogenized subsample, resulted in higher richness. This may suggest that the scale at which we are physically able to break down the particle size of plant tissues, as opposed to soil, is not always fine enough to sufficiently homogenize the fungi within. Because of this, plant-associated microbial communities may require a greater sampling effort than soil microbes. Additionally, the removal of low-abundant SVs did not result in differences in richness between the two sampling strategies for any microbial group, suggesting that neither strategy is better at capturing rare species. Although this study was performed only on milkweed plants, we believe that these results are applicable to other plant species as well. The richness reported here is similar to other studies of plant-associated microbes (e.g.51,52), indicating that differences in subsamples were not due to extreme richness of milkweed-associated microbes.
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 thousands42,53, global estimates of fungal species in general range in the millions54,55. A recent global estimate of bacterial richness suggests similar scales56. 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 (Fig. 4, Supplementary Fig. S3), 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.
Rare SVs contribute to variation among subsamples
Our results show that low abundant, rare SVs largely contributed to the differences seen between sampling strategies. Even AMF communities, which were already similar, increased in overlap by 50% between strategies after low abundant SVs (represented by  More