Distinct rhizosphere effect on active and total bacterial communities in paddy soils

Rhizosphere microbes are critical for plant health and biogeochemical cycles. Understanding the diversity of active microorganisms in the rhizosphere is key to enhancing plant growth and productivity. We examined rhizosphere bacterial communities of rice by comparison of the 16S ribosomal subunit amplicons generated from both the total (DNA-based, 16S rRNA gene) and the active (RNA-based, 16S rRNA) soil microbiota. Analysis based on the 16S rRNA gene showed a higher microbial diversity, but with little change in bacterial populations across the growth stages of the plant. Analysis of 16S rRNA recovered much less diversity, demonstrating that much of the 16S signal was derived from free DNA, dead or inactive cells. The rRNA analysis showed a stable microbial population present in the rhizosphere, and this was distinct from that in the bulk soil, which was also stable across the growth period. Root exudates (e.g., acetate, lactate, oxalate and succinate), which are major components contributing to the rhizosphere effect, appeared to shape the bacterial community, with some taxa (e.g., Oxobacter, Lachnospiraceae, Coprococcus and α-Proteobacteria) being enhanced in the rhizosphere. Soil compartments (rhizosphere vs. bulk) had a greater effect on the bacterial communities than did the plant phenological stages, especially at the rRNA level. These results suggest that the rhizosphere effect plays a key role in structuring the bacterial communities in rhizosphere soils with a distinct effect on active and total bacterial communities.