Introduction: Soybean root rot, a devastating soil-borne disease, severely limits global soybean yield and quality. Traditional control measures cause environmental pollution and have regional limitations. Root-associated microbiomes are vital for plant health, but most studies use relative abundance sequencing that distorts actual microbial quantities. This study used absolute quantitative high-throughput sequencing to clarify soil chemical properties and bacterial community assembly in healthy and diseased soybeans, laying a theoretical foundation for microbiome-based root rot management. Methods: Samples were collected from bulk soil, and the endosphere, rhizoplane, rhizosphere of healthy and diseased soybeans in black soil fields of Heilongjiang. Soil chemical properties, including pH, soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK), were determined. Absolute quantitative sequencing of bacterial 16S rRNA V4–V5 region was performed, combined with qPCR for absolute abundance calibration. Bioinformatics analyses included α/β diversity, co-occurrence network, community assembly (βNTI & RCbray), random forest and correlation analysis to identify key taxa and their relationships with environmental factors. Results: Root rot significantly reduced rhizosphere SOC (by 29.13%), TN (8.57%), AN (24.18%), AP (18.86%), while increased AK (12.82%) and pH. However, the contents of certain bacterial taxa at the genus levels showed significant differences in both absolute and relative abundances. The bacterial co-occurrence network indicate that the interaction in the healthy soybean (H) group was more complex than that in the diseased soybean (S) group. Specifically, 1 module hub and 21 connectors were identified in the H group, whereas 55 connectors were detected in the S group. Community assembly in both the H and S groups was governed by deterministic processes, with homogeneous selection primarily observed in the S group. Random forest and correlation heatmap analyses revealed ASV115 ( Candidatus Koribacter ) in H group was positively correlated with SOC, pH and AN; ASV16 ( Streptomyces ), ASV42 ( Agrobacterium ) and ASV46 ( Mesorhizobium ) were keystones in S group. Discussion: Root rot destroyed rhizosphere nutrient balance and reshaped bacterial community structure, reducing network complexity. Absolute quantification effectively compensated for the defects of relative abundance, accurately reflecting community changes. These findings clarify the microecological mechanism of soybean root rot, supporting the development of biocontrol strategies targeting rhizosphere microbiome for sustainable soybean production.

Microbial-enhanced oil recovery (MEOR) is a promising technology for oilfield development. To improve MEOR efficiency, two functional strains—Bacillus mucilaginosus ZZ-8 and Bacillus amyloliquefaciens ZZ-11—were isolated and purified. The growth characteristics, biosurfactant production, and crude oil emulsification performance of these strains were systematically evaluated through single-strain cultures and a co-culture system (ZZ-8: ZZ-11 = 1:1). The results demonstrated that the co-culture system exhibited superior growth and functional performance compared to monocultures. The cell-free supernatant significantly reduced oil–water interfacial tension, decreasing the contact angle from 53.56 ± 1.3° to 28.78 ± 0.82°, thereby enhancing crude oil detachment from rock surfaces and improving oil displacement efficiency. Gas chromatography (GC) analysis further confirmed the co-culture system’s pronounced degradation of long-chain alkanes (C17–C35). In oil sand washing experiments, the 1:1 mixed-strain fermentation broth achieved a crude oil elution rate of 84.39%, representing an 89.80% increase over uninoculated medium. This study not only validates the synergistic effect of the B. mucilaginosus–B. amyloliquefaciens co-culture system in enhancing oil recovery but also provides a theoretical foundation and innovative strategy for its practical application in MEOR technology.