Root exudates serve a vital function in recruiting beneficial phosphate-solubilizing bacteria (PSB), thereby enhancing plant adaptation to phosphorus (P) deficiency. The C2H2-type zinc finger transcription factor STOP1 (sensitive to proton rhizotoxicity 1) regulates root organic acid (OA) exudation in plants. However, the impact of STOP1-regulated root OA exudation on rhizosphere microbial composition remains unexplored. This study revealed enhanced vegetation properties of soybean with higher P content in P-rich soils, while rhizosphere organic acid concentrations were elevated in P-poor soils. The soybean genotype YC03-3 in P-deficient soils specifically recruited three PSB in acid soils: Gammaproteobacteria_Incertae_Sedis, KF_JG30_C25, and Solirubrobacterales. These PSB abundances correlated positively with rhizosphere oxalate and citrate concentrations. Under P-sufficient conditions, GmSTOP1-3 overexpression in soybean plants increased oxalate and citrate exudation compared to YCO3-3 wild type (WT), leading to preferential colonization by the same three PSB species naturally present in P-deficient WT rhizosphere. The population dynamics of these PSB demonstrated strong positive correlations with the abundance of key genes involved in P cycling, particularly those governing acid/alkaline phosphatase activities and organic-P mineralization. Given the phosphate starvation-enhanced expression pattern of GmSTOP1-3, the findings indicate that specific PSB recruitment for organic-P remobilization in soybean rhizosphere depends on GmSTOP1-3-mediated oxalate and citrate exudation in P-deficient acid soils. This research establishes GmSTOP1-3 as a crucial regulator of rhizosphere microbiome assembly and P-acquisition efficiency in acid soils.

Maize/soybean intercropping systems are commonly used in developing countries, but few studies have been performed to elucidate the differences in nutrient efficiency and rhizosphere microbiome, especially when maize is intercropped with different soybean varieties. In this study, field experiments were conducted to compare the growth and yield of two soybean (Glycine max) varieties, BD2 and YC03-3, and one maize (Zea mays) variety, Huazhen, in mono-cropped and intercropped cultures. The plant biomass and N content of both crops in BD2/maize intercropping were significantly improved compared to their monoculture, but no such effects were observed in the plants of YC03-3/maize intercropping. The yield of BD2 intercropped with maize exhibited a 37.5% increment above that of BD2 in monoculture. Moreover, 19.2–29.1% longer root length of maize and 19.0–39.4% larger root volume of BD2 were observed in BD2/maize intercropping than in monoculture, but no growth advantage was observed in YC03-3/maize intercropping. Maize showed root avoidance when intercropped with BD2, but space competition when intercropped with YC03-3. 16S rRNA amplicon sequencing showed that compared with the monoculture system, rhizobacteria community composition in BD2/maize intercropping changed more significantly than that of the YC03-3/maize intercropping system. In BD2/maize intercropping, most of the rhizobacteria community biomarker bacteria of BD2 were positively correlated with plant biomass, as well as plant P and N content. Maize tended to recruit Rhizobiales and Proteobacteria, which showed positive correlation with plant biomass and N content, respectively, as well as soil available N. In conclusion, soybean varieties determined the advantages of maize/soybean intercropping through root–root interactions and modification of rhizobacteria communities. Our insight emphasizes a linkage between root traits and the rhizobacteria community, which shows the importance of optimizing intercropping systems by selection of appropriate crop varieties.

Nitrogen (N) and phosphorus (P) are two essential mineral nutrients for plant growth, which are required in relative high amount in plants. Plants have evolved a series of strategies for coordinately acquiring and utilizing N and P. However, physiological and molecular mechanisms underlying of N and P interactions remain largely unclear in soybean (Glycine max). In this study, interactions of N and P were demonstrated in soybean as reflected by significant increases of phosphate (Pi) concentration in both leaves and roots by N deficiency under Pi sufficient conditions. A total of four nitrogen limitation adaptation (NLA), encoding RING-type E3 ubiquitin ligase were subsequently identified in soybean genome. Among them, transcription of GmNLA1-1 and GmNLA1-3 was decreased in soybean by N starvation under Pi sufficient conditions, not for GmNLA1-2. Suppression of all three GmNLA1 members was able to increase Pi concentration regardless of the P and N availability in the growth medium, but decrease fresh weight under normal conditions in soybean hairy roots. However, comparted to changes in control lines at two N levels, N deficiency only resulted in a relatively higher increase of Pi concentration in GmNLA1-1 or GmNLA1-3 suppression lines, strongly indicating that GmNLA1-1 and GmNLA1-3 might regulate P homeostasis in soybean response to N starvation. Taken together, our result suggest that redundant and diverse functions present in GmNLA1 members for soybean coordinate responses to P and N availability, which mediate P homeostasis.