Combinatorial community coalescence in early tomato assembly reveals a rhizosphere attractor in composition and abundance architecture

Abstract

The rhizosphere microbiome plays fundamental roles in plant health and productivity, yet the ecological rules governing microbiome assembly remain poorly understood. Here, we investigated early rhizosphere community assembly in tomato using a replicated combinatorial community coalescence framework, in which seven distinct natural bacterial communities were inoculated individually and in all possible pairwise and triplet combinations. Single-inoculum communities clustered according to inoculum identity, indicating a strong effect of source community composition on assembly trajectories. However, when all communities were analyzed jointly, samples formed a continuous compositional landscape with no clear evidence of discrete community states. Despite major differences in source community composition, rhizosphere communities consistently converged toward a highly similar uneven rank-abundance structure, with two ASVs accounting for 50% and a median of nineteen ASVs for 90% of total abundance. While assembly was dominated by a very small number of Pseudomonas ASVs, limited evidence of alternative dominant states was observed. Increasing inoculum complexity did not increase stochasticity but instead promoted stronger convergence toward a global rhizosphere compositional centroid. Moreover, dominance hierarchies emerging from community coalescence closely mirrored the distance of source communities to this centroid. The two most dominant communities originated from orchard soils, suggesting that historical contingency and prior adaptation to horticultural crop rhizospheres may influence competitive success. Together, these results are consistent with the existence of a canonical rhizosphere attractor in composition and abundance architecture, with patterns consistent with assembly occurring under a limited number of dominant ecological niches imposed by the tomato rhizosphere.