Nitrogen fixation in legume roots: Soybeans and other legumes form symbiotic relationships with nitrogen-fixing bacteria in root nodules, thus ensuring the plant a ready supply of the necessary nutrient. Wang et al . worked out the signaling pathways that integrate above-ground light with below-ground root nodulation. Two mobile regulators move from shoot to root in response to light and, together, they form a signaling module in the root that induces the expression of nodulation factors. Thus, when the shoot sees enough light to support photosynthetic productivity, the root gets the signal to ramp up nitrogen fixation. —PJH

Intercropping triggers coordinated changes in gene expression and metabolite accumulation across sugarcane roots, stems, and leaves, leading to higher crop yields—an effect that has drawn growing attention. Yet, how this transcriptional and metabolic interplay precisely enhances productivity remains poorly understood, limiting insight into intercropping’s yield-promoting mechanisms. This research explored the relationships between sugarcane, its metabolites, and transcriptomes through field trials integrated with multi-omics analysis. Data from the field showed clear differences in gene expression and metabolite patterns between monoculture and intercropped sugarcane. Plants under intercropping displayed stronger differential gene expression, greater metabolite diversity, and shifts in physiological traits. Metabolite variation was closely linked to gene regulation and network complexity, which in turn affected key agricultural characteristics including plant height, stem thickness, and sugar content. Follow-up experiments confirmed that applying zinc—a element boosted by intercropping—improved growth in monoculture sugarcane and modified its hormonal composition. These results highlight the important role of coordinated transcriptome-metabolite activity in intercropping systems. The study provides valuable perspectives for making intensive farming more economical and sustainable, supporting efforts to raise crop output and improve ecosystem functions.

The symbiotic relationship between soybean and rhizobia facilitates nodulation and nitrogen fixation, providing a sustainable nutrient supply for increasing crop yields and reducing chemical fertilizer use. However, comparative studies on the conservation and strain-specificity of host gene expression regulated by different rhizobial strains remain limited. Here, we performed a comparative analysis between the previously isolated strain, Bradyrhizobium ottawaense Bott 59, and the model strain, Bradyrhizobium diazoefficiens USDA 110. Symbiotic phenotypes were evaluated after inoculation, and a root transcriptomic analysis was conducted at 3 dpi to assess early molecular responses. At 21 dpi, Bott 59-inoculated plants outperformed plants inoculated with USDA 110 in nodule number, nitrogenase activity, and biomass. Transcriptomic analysis revealed conserved host responses to both rhizobial strains, including NIN-mediated signaling, AON signaling, and the biosynthesis of phenylpropanoids and brassinosteroids. Further analysis revealed that Bott 59 specifically induced the expression of genes involved in isoflavonoid and flavonoid biosynthesis, including those encoding I2H, and HI4OMT. Moreover, Bott 59 triggered more pronounced transcriptional reprogramming in auxin, cytokinin, and jasmonic acid signaling pathways, along with differential expression of a broader set of transcription factor genes. Collectively, this study systematically unravels the conserved and strain-specific transcriptional regulatory events underlying host–rhizobium interactions. Our findings provide valuable theoretical insights and transcriptomic resources for further dissecting the molecular mechanisms of symbiotic nitrogen fixation (SNF), as well as for the targeted genetic improvement of crop nodulation and nitrogen fixation efficiency.

Cytokinin (CK) is a central regulator of plant development, yet its roles cannot be understood fully without considering how CK signaling was assembled during evolution and redeployed in different physiological contexts. In this review, we examine how prokaryotic two-component modules were elaborated into the land–plant CK system and how this system now integrates biosynthesis, transport, receptor selectivity, and feedback control to shape developmental and symbiotic outcomes. We argue that three recurring interpretive dimensions are especially useful for organizing current evidence: compartmentalized CK pools, context-dependent decoding of local CK availability, and the coupling of local CK responses to whole-plant nutrient status. These dimensions help organize current observations on why CK effects in arbuscular mycorrhiza (AM) are often conditional and readout-dependent, whereas evidence from legume–rhizobium symbiosis supports a more direct role for CK in cortical competence, nodule organogenesis, and autoregulation of nodulation. Rather than treating CK as a generic positive regulator of symbiosis, we propose that it functions as a spatially partitioned and nutritionally gated integrator whose outputs depend on cell type, developmental stage, transport route, and resource context. We conclude by highlighting key mechanistic gaps—particularly in transporter-resolved CK partitioning and systemic integration—and by outlining experimentally testable priorities for translating CK biology into crop improvement.