Is root DNA a reliable proxy to assess arbuscular mycorrhizal community structure?

Arbuscular mycorrhizal (AM) fungi are widespread plant symbionts that extensively colonize both soil and roots. Given their influence on ecosystem processes, such as plant growth, soil carbon storage, and nutrient cycling, there is great interest in understanding the drivers of their community structure. AM fungal communities are increasingly characterized by selectively amplifying their DNA from plant roots, thus assuming that AM fungal community structure within roots provides a reliable portrait of the total (i.e., soil + roots) community. Through numerical simulations, we test this assumption using published data. We show that community structure and diversity is well preserved when analyzing only a subset of the community biomass (i.e., roots or soil), provided that the community shows a typical skewed abundance distribution, with few very dominant species and a high prevalence of rare species. Given that this community structure has been shown to be common in natural AM fungal communities, the present work would suggest that characterizing AM fungal communities using only roots or soil can provide a reliable portrait of the overall community. However, we show through additional analyses that the proportion of sample biomass used for molecular methods must be over a minimal threshold to properly characterize the community. Using published molecular data sets, we validate those results, which suggest that typical molecular protocols using low amounts of biomass may strongly influence AM fungal community characterization. Finally, we also discuss other assumptions implied by the molecular analysis of AM fungal communities, and point out urgent knowledge gaps.