The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there remains a gap in comprehending how drought stress influences the co-occurring network patterns within these compartments and their ecological functional potentials. To address this gap, a pot experiment was conducted with two treatments: continuous flooding as a control and drought treatment. Bulk soil, rhizosphere, and endosphere samples were collected and subjected to high-throughput sequencing and bioinformatics analysis. The results revealed that drought stress significantly reduced the rice biomass but increased the Shannon diversity index in both the rhizosphere and endosphere bacterial communities with no observable effect on richness across compartments. Additionally, drought treatment markedly altered the community structure and bacterial assemblages in these compartments, resulting in the specific enrichment of Actinobacteriota, Gemmatimonadetes, and Patescibacteria, while Bacteroidetes and Firmicutes were depleted in the rhizosphere and endosphere. Furthermore, drought heightened the complexity of the co-occurring networks and the proportions of positive links across all sampling compartments; this effect was accompanied by an increase in the number of connectors in the bulk soil and rhizosphere, as well as module hubs in the rhizosphere. Functional potential prediction indicated that drought stress significantly altered multiple potential ecological functions across all sampling compartments, particularly enriching functions related to the oxidation of sulfur, manganese, and hydrogen in the bulk soil, while functions associated with iron oxidation were significantly depleted in the rhizosphere. Overall, our results demonstrate that under drought stress, rice may specifically enrich certain bacterial taxa and enhance their positive interactions within its root system to improve adaptation.

Tetrastigma hemsleyanum is a valuable medicinal plant whose dryland cultivation typically yields 30–35% lower flavonoid concentration than forest understory systems due to soil and microbial deficiencies. We investigated whether biochar amendment could bridge this quality gap through rhizosphere microecological regulation. Using a split-plot pot experiment with in situ soils from a bamboo forest and a vegetable field, we applied biochar at 2%. Biochar in bamboo forest (MBBC) achieved the highest flavonoid concentrations, exceeding unamended forest and vegetable controls by 22% and 35%, respectively. Biochar effects were habitat-specific. In acidic forest soils (pH 4.95), it raised the pH to 5.61, while in vegetable fields, it boosted leucine aminopeptidase by 159%. Partial least squares path modeling revealed biochar exerted its effects indirectly (indirect effect = 0.88), with soil extracellular enzymes mediating between soil conditions and plant biosynthetic enzymes (PAL, CHS, CHI). Fungal composition was positively associated with biosynthesis (β = 1.68, p < 0.01), particularly Mortierellomycetes, whereas bacterial diversity unexpectedly exhibited a significant negative correlation with it (β = −0.79, p < 0.05). Biochar disrupted Eurotiomycetes dominance in forest soils (from 85% to 39%), creating functionally diverse niches that were associated with enhanced flavonoid accumulation. These findings demonstrate biochar functions as an ecological niche regulator, providing a sustainable strategy for high-quality medicinal plant production in non-native habitats.