Steering root-associated microbiomes via direct and soil legacy effects of neighbors

Root-associated microbiomes are widely assumed to be primarily shaped by the host plant. However, other co-occurring plants can also influence the composition of this microbiome. This can be either directly, by stimulating or suppressing microbial recruitment of the focal plant, or indirectly, through soil legacies that shape the microbial pool encountered by the focal plant during establishment. The relative importance of these neighbor effects shaping the focal plant microbiome and the consequences for focal plant growth remain poorly known. Here, we challenge the paradigm that the host plant identity is the main driver of root-associated bacterial and fungal communities.

Under experimental conditions, we show that the influence of the host plant on root-associated microbiomes is dramatically reduced in the presence of neighbors and their soil legacies. Remarkably, root-associated bacterial communities were primarily shaped by co-occurring neighbor plants, while fungal communities were mainly determined by soil legacies from previously grown plants. Furthermore, culturable microbial communities (NatComs) isolated from the roots of focal plants differed greatly depending on neighbor identity and soil legacies. Inoculating new focal plants with these communities caused strong responses in growth that varied greatly depending on the history of these isolated communities, highlighting the importance of neighbor effects. Finally, we show that metabolites produced by these microbial communities are one mechanistic pathway through which neighbors influence plant growth.

Our results stress the often-overlooked ecological and functional importance of both direct and indirect effects of neighbor plants in shaping root-associated microbiomes. By integrating neighbor effects with host identity, this work provides a starting point for understanding how neighboring plants contribute to shaping plant communities, with potential implications for sustainable agriculture. Video Abstract.