Terrestrial plants can influence the growth and health of adjacent plants through interspecific interaction. Here, the mechanisms of interspecific plant interaction on microbial function and nutrient utilization in the plant-soil interface (non-rhizosphere soil, rhizosphere soil, and root) were studied by soybean- and potato-poplar intercropping. First, metagenomics showed that soybean- and potato-poplar intercropping influenced the composition and co-occurrence networks of microbial communities in different ecological niches, with higher stability of the microbial community in soybean intercropping. Second, the gene abundance related to carbon metabolism, nitrogen cycling, phosphorus cycling, and sulfur cycling was increased at the poplar-soil interface in soybean intercropping. Moreover, soybean intercropping increased soil nutrient content and enzymatic activity. It showed higher metabolic potential in nutrient metabolism and transportation. Third, functional microorganisms that influenced nutrient cycling and transportation in different intercropping have been identified, namely Acidobacteria , Sphingomonas , Gemmatimonadaceae , Alphaproteobacteria , and Bradyrhizobium . Therefore, intercropping can construct microbial communities to alter metabolic functions and improve nutrient cycling and absorption. Interspecific plant interactions to influence the microbiome were revealed, opening up a new way for the precise regulation of plant microbiome. IMPORTANCE: Poplar has the characteristics of wide distribution, strong adaptability, and fast growth, which is an ideal tree species for timber forest. In this study, metagenomics and elemental analysis were used to comprehensively reveal the effects of interspecific plant interactions on microbial communities and functions in different ecological niches. It can provide a theoretical basis for the development and application of the precise management model in poplar.

Microbial remediation technology has the characteristics of high efficiency and environmental protection, which has attracted attention. However, there is complexity in the microorganism-soil–plant system. The effects of microbial agents on soil nutrients, plant quality, rhizosphere, and endophytic microorganisms are still unclear. Here, we demonstrate the application of Bacillus megaterium NCT-2 as a multifunctional agent that concurrently addresses salinization-driven nutrient imbalances and reshapes keystone microbial taxa to restore soil–plant homeostasis. The results showed that NCT-2 agent improved the soil nutrients, reduced the loss of nitrogen and sulfur, increased the content of available phosphorus, and decreased the electrical conductivity. The agent increased the number of bacteria and fungi in the soil. Meanwhile, NCT-2 agent improved the vegetable quality and yield. Specifically, the NCT-2 agent significantly increased the aboveground fresh weight, underground fresh weight, total flavonoids, antioxidant enzyme activity, ascorbic acid, Cu, Zn, Fe, P, and K in lettuce, while significantly reduced nitrate. The chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll were significantly increased by the agent. Critically, high-throughput sequencing revealed NCT-2-driven enrichment of stress-resilient taxa (e.g., Firmicutes, Acidobacteria) and functional synergists (e.g., Acetobacter), which correlated with soil nutrient fluxes and plant antioxidant capacity. By decoupling the interplay between microbial community restructuring and systemic remediation outcomes, this work establishes a novel framework for leveraging keystone taxa to optimize salinized agroecosystems.

While irrigation and fertilization are basic cultivation practices in poplar plantations on a global scale, the impact of these practices on the environment is not well understood. Here, we demonstrate that water-urea addition and water-compound fertilizer addition differentially impact soil ecosystems. We report that water-fertilizer addition did not significantly alter taxonomic diversity indices, but it did drive significant shifts in microbial community composition, reflected by changes in the relative abundance of specific taxa and their functional profiles. Water-urea addition reduced Proteobacteria and Actinobacteria in non-rhizosphere soils while increasing Acidobacteria and Chloroflexi. In contrast, water-compound fertilizer additions increased Proteobacteria and Actinobacteria dominance in rhizosphere soils. Water-fertilizer addition changed microbial composition and functional gene abundance linked to nitrogen and sulfur cycling. Water-urea treatment enriched denitrification genes and dissimilatory nitrate reduction genes ( napABC ) in rhizosphere soil, while water-compound fertilizer treatment enhanced nitrification ( amoABC , HAO ) and denitrification gene abundance in both soils. For sulfur (S) cycling, water-urea treatment favored thiosulfate oxidation genes, whereas water-compound fertilizer treatment increased assimilatory sulfate reduction genes. Multi-omics integration linked these microbial dynamics to metabolic reshaping—water-urea increased lipid and secondary metabolites in rhizosphere soils, while water-compound fertilizer additions elevated amino acid-associated metabolites in non-rhizosphere soils. Crucially, water-compound fertilizer addition reduced the gene abundance for the conversion of N ₂ O to N ₂ ( nosZ ) and altered sulfur partitioning, whereas water-urea addition elevated soil NO ₃ ⁻ and NH ₄ ⁺ but depleted available K. These results highlight trade-offs between nutrient management and microbial-mediated environmental potential, guiding optimized irrigation-fertilizer strategies for sustainable poplar silviculture. IMPORTANCE: Combined irrigation and fertilizer application affect microbial community composition, and soil nitrogen and sulfur cycles (by regulating microbial composition and the abundance of genes related to nitrogen and sulfur cycles). Water-urea reduced Proteobacteria, increased Acidobacteria, and enriched denitrification genes, elevating soil NO ₃ ⁻ /NH ₄ ⁺ . Water-compound fertilizer boosted Proteobacteria and nitrification genes. Water-urea increased rhizosphere lipids/secondary metabolites; compound fertilizer elevated non-rhizosphere amino acids. These trade-offs between nutrient gains and environmental risks guide optimized poplar plantation management.

Introduction: Salinity is a major abiotic stress threatening global agriculture. While some microorganisms are known to ameliorate soil salinity and promote plant growth, the underlying mechanisms, particularly for Priestia megaterium (formerly Bacillus megaterium ), remain less explored. Methods: Here, we investigated the efficacy and mechanism of P. megaterium NCT-2 in improving secondary saline soil by elemental analysis, 15N tracing, gene knockout and transcriptomics. Results: Our results demonstrated that the NCT-2 agent significantly reduced the content of key salt ions, notably NO₃ ⁻ , Cl ⁻ , and Na ⁺ in soil. Through a combination of biochemical assays, isotope tracing, and gene knockout techniques, we identified that the aerobic assimilation pathway is the primary route for nitrate metabolism in NCT-2, with the nasC and nasD genes being crucial for this process. Furthermore, transcriptomic analysis under salt stress revealed that NCT-2 employs a multi-faceted tolerance strategy, which includes enhancing sporulation, activating antioxidant defenses (e.g., CAT, SOD), assembling flagella, and forming vesicles. Concurrently, the strain upregulates central carbon metabolism (TCA cycle, glycolysis) and amino acid synthesis to fuel these adaptive responses. Discussion: This study provides a comprehensive theoretical foundation for using P. megaterium NCT-2 in environmental remediation and identifies key genetic targets for enhancing microbial salt tolerance.

Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition. Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization. Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video