Rice rhizosphere microbiome is more diverse but less variable along environmental gradients compared to bulk soil

Despite the importance of the rice rhizosphere microbiota for soil functions and crop productivity, little is known about the differences in the diversity, structure, and functions of these communities compared to surrounding bulk soils and these effects on a broad scale.

We compared archaeal and bacterial community diversity, structure and functions in the rice rhizosphere versus bulk soils from 50 sites across 900 km in eastern China, and explored their interkingdom interactions and keystone taxa.

The rhizosphere microbiome had higher α-diversity, lower β-diversity and weaker edaphic distance-decay patterns than bulk microbiome, indicating a homeostatic effects of rice roots. Compared with the bulk interkingdom networks, the rhizosphere networks had more links between archaea and bacteria, higher complexity and stability. The keystone taxa in the rhizosphere were shifted towards sulfate-reducing, iron-reducing, and carbon-degrading microbes, potentially offering benefits to the host plants. Microbial community assembly in bulk and rhizosphere soils was largely stochastic at the community level, but with deterministic for specific finer taxonomic taxa (e.g. Haliangium) in the rhizosphere. Functional predictions revealed that the rhizosphere was enriched in genes for carbon, sulfur, and iron metabolism, in contrast to reduced nitrogen metabolism genes.

Rice root-driven selection of specialized microbial taxa promotes higher α-diversity and a more stable microbial community, characterized by intensive functionality in iron reduction and nutrient cycling beyond nitrogen metabolism. These findings deepen our understanding of microbial distribution patterns in rice rhizosphere under semi-aquatic, low-oxygen conditions and may offer new insights into sustainable cropland management.