the spatiotemporal heterogeneity in pepper rhizosphere microbiome

Despite its crucial role in plant health and nutrient dynamics, the spatial heterogeneity of the rhizosphere microbiome has often been neglected. This study employed a mini-rhizobox approach to explore the spatiotemporal variations within the rhizosphere of pepper plants, analyzing an extensive dataset of 2 185 samples. Our findings indicated that the bacterial communities predominantly consist of a few generalist species and numerous opportunists. The log10 transformation of detected ASVs exhibited a strong negative correlation with the dominance rate (R^2= 0.994). Furthermore, we observed a distinct distance-decay relationship, with increasing divergence between main and secondary roots. The consensus co-occurrence network analysis highlighted that both cooperative and antagonistic interactions among microbial taxa are highly context-dependent, identifying Sphingomonas and Pseudomonas as the most cooperative and antagonistic genera, respectively. Stochastic processes were found to be the primary drivers of bacterial communities at neighboring points, particularly in secondary roots, whereas deterministic processes dominated in main roots and their junctions with secondary roots. The Over-representative rates of dominant genera revealed the impact of treatments on bacterial proliferation, with Pseudomonas frequently over-representing in disease-suppressive soil conditions. These findings significantly advance our understanding of rhizosphere microbial ecology, elucidating the mechanisms that govern the assembly of the rhizosphere microbiome.