Two ecological rules behind randomness in microbiome associated with pepper (Capsicum annuum) root

Abstract

Background and aims

The plant root exhibits significant heterogeneity, which deeply affects the associated microbial communities, but the spatial heterogeneity of microbiome associated with root is often overlooked.

Methods

Using the mini-rhizobox approach, 16S rRNA profiling and bioinformatics analyses, we analyzed an extensive dataset of 2,185 samples to decipher the mechanisms governing the assembly of the bacterial community associated with pepper roots.

Results

Our results revealed high spatial variability in bacterial communities of individual pepper root. Stochastic processes were identified as the primary drivers of bacterial community assembly at adjacent points, particularly in secondary roots, whereas deterministic processes exerted more influence in main roots and their junctions with secondary roots. Correspondingly, only 22.3% of commonly occurring ASVs followed skewed Gaussian distributions along root depth. These findings highlight randomness in bacterial community along roots. Nonetheless, bacterial richness, as indicated by the log₁₀ transformation of detected ASVs, showed a strong negative correlation with the dominance rate (R² = 0.994), emphasizing the significance of community composition over richness for advancing sustainable agriculture. Additionally, a distance-decay relationship was observed, with increasing divergence between the main and secondary roots. Both cooperative and antagonistic interactions among microbial taxa are highly context-dependent, identifying Sphingomonas and Pseudomonas as the most cooperative and antagonistic genera, respectively.

Conclusions

Microbial communities associated with plant roots are assembled primarily by stochastic processes, involving a few commonly occurring and more rarely occurring species, and are governed by two new novel rules: species richness and dominance rates, as well as a medium-strength distance-decay relationship.