Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely on plants as the “signaler” of interaction outcomes. Even with technological advancements that allow enumeration of the microbial community, it is difficult to tease apart which of the members are the important drivers. Thornier still is the issue that the majority of these investigations are from greenhouse experiments, whose environments may impose conditions that result in plant-microbe interactions that do not reflect natural dynamics. Here, we took a community assembly approach to undertake a systematic comparison of microbial communities in field and greenhouse experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses using samples from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally-occurring resident plants in the field. We asked: 1) How does root-associated fungal diversity, composition, and host-specificity compare among studies? 2) How do soil inoculation alter fungal composition in greenhouse versus field PSF experiments? 3) Are PSF outcomes driven by shifts in relative abundance of common microbial taxa shared between hosts or host-specific associations with specialist microbes?
Results/Conclusions
Root-associated fungal communities differed widely across the four study types, but shared a common core consortium that accounted for >50% of total sequences. Roots from the greenhouse and field PSF experiments had lower among-sample dispersion in community composition and higher diversity than those from naturally occurring, field-collected plants or plants from seven-year old field-planted monocultures. These results suggest that individual plants may selectively filter fungal communities over decadal scales, returning lower per-plant diversity and higher among-plant dispersion in community composition than observed in short-term inoculation studies. Fungal communities were plant-species specific across the study types. However, PSF inoculation treatments had a stronger influence on root-associated fungi than plant identity on fungal community assembly. When used to analyze the greenhouse PSF experiment, the core fungal consortium (shared amongst studies) was more strongly host-specific than peripheral taxa. This suggests that while study environments may act as strong filters for root mycobiome assembly, the key taxa that drive host-specific effects may be preserved across study types.