Time-Series Transcriptomics Reveals Temporal Expression Patterns in Soybean (Glycine max) Roots During Symbiosis with Bradyrhizobium ottawaense HK601

Rhizobium–soybean symbiosis plays a critical role in sustainable agriculture. We isolated the slow-growing strain HK601 from the soybean cultivar ‘Heike 60’ in cold-region Heilongjiang, China, and identified it as Bradyrhizobium ottawaense by four-gene phylogeny. In pot trials, HK601 inoculation significantly promoted plant growth, effective nodule number, and total nitrogen content. HK601 also formed effective nodules on Williams 82 and 11 Heilongjiang cultivars, showing broad-spectrum nodulation. Time-series transcriptomes of symbiotic soybean roots showed 14 dpi was a key turning point in transcriptional reprogramming. Before 14 dpi, signal transduction and nodule structural development DEGs were active. After 14 dpi, DEGs related to ribosome assembly and translation declined, whereas DEGs involved in isoflavonoid biosynthesis, MAPK signaling, and defense-related pathways were transcriptionally up-regulated. This complementarity may reflect a shift from basal metabolism to symbiotic functions. The temporally cascaded activation of isoflavonoid and MAPK pathways during the mid-to-late stages may reflect a potential dual role in symbiotic signaling and defense, thereby contributing to symbiotic homeostasis. Sharp up-regulation of symbiotic marker genes (leghemoglobin and nodulins) after 14 dpi provided transcriptional evidence for the establishment of symbiotic nitrogen fixation. This study provides a promising candidate strain for cold-region soybean production and a new transcriptomic perspective on temporal host–rhizobia regulation.