Early tomato rhizosphere assembly reveals inoculum-constrained succession with increasing diversity and phylogenetic clustering

Abstract

ABSTRACT The rhizosphere microbiome, one of the most diverse and metabolically active microbial ecosystems known, plays fundamental roles in plant health and productivity. However, the ecological dynamics between germination and the establishment of the first true leaves remain poorly understood. This developmental window is characterized by rapid seedling development and root expansion. Here, we investigated rhizosphere bacterial community assembly during the first four weeks of tomato development by sampling communities arising from seven distinct natural soil inocula twice weekly to obtain fine-scale temporal resolution. Culturable bacterial load, richness, evenness and phylogenetic diversity all increased significantly during plant development, indicating progressive increases in rhizosphere ecosystem complexity. In addition, the identity of the initial microbial community significantly affected culturable bacterial load and was associated with differences in plant growth. Although temporal effects on rhizosphere bacterial community composition were significant, assembly trajectories remained strongly constrained by the initial inoculum. Temporal analysis nevertheless revealed significant taxonomic turnover despite limited global compositional restructuring. In particular, the relative abundances of Proteobacteria and Pseudomonadaceae decreased over time, whereas those of Actinobacteria, Acidobacteria and Streptomycetaceae increased. However, communities did not become progressively more similar or divergent over time. Altogether, our results indicate that early rhizosphere bacterial community assembly involves rapid ecological succession within inoculum-constrained compositional trajectories, with a progressive decline in the relative abundance of early copiotrophic Proteobacteria accompanying the emergence of more diverse and phylogenetically structured communities. These findings highlight the importance of early seedling development for understanding rhizosphere bacterial community assembly and the influence of initial microbial communities on subsequent assembly trajectories.

The authors' abstract, as published at the source. Rhizosphere, 2026 · DOI ↗