Ratoon rice is a unique cropping system that utilizes the regenerative capacity of rice tillers to achieve one sowing with two harvests in a single growing season, thus exhibiting great yield potential. However, the ratooning ability is often constrained by impaired root function after the first harvest. In this study, we established an integrated nutrient management (INM) strategy to enhance root growth and function, thereby improving nutrient use efficiency and yield. Compared with farmers' conventional management (FCM), INM increased annual total yield by 7.8% and 13.9% and enhanced ratooning ability by 20.7% and 19.0% in 2024 and 2025, respectively. INM consistently maintained higher root biomass in both main and ratoon crops: by 26.9% and 54.0% in 2024, and by 44.8% and 26.0% in 2025. Root biomass was significantly and positively correlated with brown rice weight across both seasons, and was positively associated with ratooning ability. INM also promoted early root establishment after transplanting, increasing the white-root number by 105.7%, 175.0%, and 484.8% at 3, 5, and 14 days after transplanting (DAT), respectively. Meanwhile, the xylem sap exudation rate and root triphenyl tetrazolium chloride (TTC) reduction activity were increased by 37.4% and 64.5% relative to FCM. In the 2024 ratoon season, INM improved nutrient use efficiency, with partial factor productivity (PFP) of nitrogen (PFPN), phosphorus (PFPP), and potassium (PFPK) increased by 371.0%, 59.3%, and 91.1%, respectively. Gene Set Enrichment Analysis (GSEA) revealed significant enrichment of gene sets involved in root growth, development, nutrient acquisition, and assimilation under INM, providing molecular evidence for root-mediated nutrient synergy. In summary, INM enhances root growth and function, promotes nutrient uptake and utilization, and consequently improves yield. These results offer a practical management strategy supported by physiological and transcriptomic evidence for boosting ratoon rice production via root-mediated nutrient synergies.

Shade stress severely constrains soybean yield in soybean-maize intercropping systems, yet the intensity threshold triggering shade avoidance responses and the underlying hormonal mechanisms remain elusive. Here, through two-year field experiments, we demonstrate that shading coverage rate exceeding 80% is the critical threshold initiating shade avoidance, increasing plant height by 16-61%. The seventh internode is the initial responsive site where epidermal cells elongate by 69.86% longitudinally, while radial growth is broadly suppressed (cell area reduced by approximately 41%). Furthermore, integrated hormonal profiling and gene expression analyses demonstrate that shade promotes active gibberellin (GA) accumulation via dual metabolic reprogramming: upregulating biosynthetic genes GmGA20ox1 and GmGA3ox1 and downregulating catabolic genes GmGA2ox-7a and GmGA2ox-7b, leading to a 56.87% increase in GA1 content. Notably, exogenous GA fully mimics the shade-induced phenotype, with genotype sensitivity ranking BX10 > BD2 > W82, indicating that GA plays a central role in mediating the shade response. Yield analysis shows that shade inhibits soybean biomass accumulation and grain yield and preferentially suppresses reproductive rather than vegetative growth, reducing effective pod number and seeds per plant by ~50% whereas 100-seed weight only decreases by 6.55%. Together, these findings reveal that shade modulates GA homeostasis via "enhanced biosynthesis and suppressed catabolism" to remodel internodes, providing a theoretical basis for shade-tolerant soybean breeding and optimizing intercropping systems.

Anthocyanins are important pigment of blood orange (Citrus sinensis). While nutrient availability is known to affect fruit pigmentation, the specific role of mineral elements and their underlying mechanisms remain largely unclear. Our filed experiment in two blood orange orchards at the same site but with different fertilizer recipes resulted in distinct variations in anthocyanin content in the fruit peel. This study identified magnesium (Mg) as the primary influencing factor, accounting for up to 25% of the positive variance in peel anthocyanin accumulation. Transcriptomic analysis combined with exogenous Mg treatments revealed significantly differential expression of key structural genes involved in anthocyanin biosynthesis, including CsDFR and CsANS. Furthermore, the expression of the nutrient-responsive transcription factor CsbZIP53 exhibited a dose-dependent response to Mg concentrations. In vivo quantitative analyses of tobacco leaves and blood orange peel demonstrated that Mg promotes the expression of CsbZIP53. Overexpressing CsbZIP53 in citrus leaves upregulated the expression of genes involved in anthocyanin biosynthesis and increased the relative accumulation of anthocyanin aglycones. Dual-luciferase reporter assays and electrophoretic mobility shift assay revealed that CsbZIP53 activates the transcription of CsDFR and CsANS, achieved by specifically recognizing and binding to the G-box motifs within the promoters of these target genes. Taken together, we propose a model whereby Mg upregulated CsbZIP53, which subsequently targets might bind to the G-box regions of target gene promoters to upregulate anthocyanin biosynthetic genes. From the perspective of application and practice, we recommend the supplementing Mg fertilizers from the fruit expansion stage through to maturity, to improve fruit coloration and overall quality of blood orange fruits.

Phosphorus (P) is an essential yet frequently deficient plant nutrient. Optimizing P distribution and recycling between tissues is vital for improving P utilization efficiency (PUE). Yet, the mechanisms underlying the transport and re-translocation of P within plants remain unclear. Here, wide-ranging natural diversity in seed P allocation and positive correlations among yield traits were found using 190 soybean accessions in field trials. Among them, the P-efficient genotype BX10 outperformed BD2 in assessments of PUE that were largely explained through differences in P redistribution from pods to seeds under low P stress. Pods of BX10 were therefore subjected to transcriptome analysis, and GmVPE1 was identified as a vacuolar Pi transporter to investigate further. Importantly, significant DNA polymorphism in GmVPE1 promoter regions was remarkably associated with seed weight among soybean accessions grown on P-deficient soils. Further analyses suggested that mRNA abundance of GmVPE1 in haplotype 2 (Hap) is significantly higher than that GmVPE1Hap1. GmVPE1 was highly upregulated by P deficiency and preferentially expressed in pods, seeds, and seed coats, which was consistent with GUS staining using transgenic soybean plants carrying pGmVPE1Hap2::GUS. Near-isogenic lines carrying the GmVPE1Hap2 allele, along with stable transgenic soybeans overexpressing GmVPE1 in a GmVPE1Hap1 background, had increases in PUE, more seed setting, and greater yields in both greenhouse and field trials than control plants. In summary, natural variation among GmVPE1 alleles determines genetic expression and subsequent P re-translocation phenotypes, which impacts PUE and yield, and thereby makes this an important genetic resource for soybean molecular breeding.

Pleasant aroma is a distinctive character of Wuyi Rock tea, but its optimization through agricultural practices remains largely unexplored. Here, we conducted a two-year field trials in the core-region of Wuyi Rock tea production area with organic or chemical fertilizer. The results indicated that organic fertilizer significantly improves soil fertility, as indicated by increased pH and organic matter. GC-MS analysis showed that organic fertilizer obviously affects the aroma metabolites in tea leaves, with the levels of 1-Hexanol (C6H14O), 2-Ethyl-1-hexanol (C8H18O), (E,E)-2,4-Heptadienal (C7H10O), E-Nerolidol (C15H26O) and 3-octen-2-one (C8H14O) increasing by 56.55%, 104.44%, 64.39%, 64.10% and 48.10%, respectively, compared to chemical fertilizer, thereby improving its aroma quality. The correlation analysis and PLS-PM model combined with the results from ionomics and metabolomics, further elucidated that soil fertility significantly impacted the mineral nutrients in tea leaves, thereby regulating the content of volatile metabolites. Altogether, the research findings provide practical fertilizer usage guidelines for tea farmers, helping to improve the aroma quality and overall market value of tea.

Legume plants commonly associate with both arbuscular mycorrhizal (AM) fungi and rhizobia and thus enhance the acquisition of phosphorus (P) and nitrogen (N) nutrition. Inoculation with AM fungi can promote nodulation and N2 fixation of legume plants; however, the underlying mechanisms remain poorly understood. Here, root exudates collected from AM-colonised soybean plants showed greater accumulation of the specific flavonoids (daidzein and genistein) and phenolic acids (benzoic acid and p-Hydroxybenzoic acid), and significantly promoted nodulation. Furthermore, the exudates from AM-colonised roots and the derived specific flavonoids and phenolic acids effectively increased rhizobial growth, chemotaxis, biofilm formation. Addition of the specific synthetic root exudates enhanced nodulation and N2 fixation, and expression of the core nodulation genes in soybean. Overexpression of a phenylalanine ammonia-lyase gene, GmPAL2.4 markedly upregulated the expression of the genes related to the biosynthesis of daidzein, genistein, benzoic acid, and p-Hydroxybenzoic acid, and increased accumulation of these specific flavonoids and phenolic acids in the transgenic plants, thus enhancing nodulation and N2 fixation. In summary, we demonstrated a crucial role of specific flavonoids and phenolic acids induced by AM symbiosis in promoting rhizobium-host symbiosis. This offers a pathway for improving symbiotic efficiency through the use of specific synthetic compounds.

Synthetic microbial communities (SynComs) are a promising tool for making full use of the beneficial functions imparted by whole bacterial consortia. However, the complexity of reconstructed SynComs often limits their application in sustainable agriculture. Furthermore, inter-strain interactions are often neglected during SynCom construction. Here, we propose a strategy for constructing a simplified and functional SynCom (sfSynCom) by using elite helper strains that significantly improve the beneficial functions of the core symbiotic strain, here Bradyrhizobium elkanii BXYD3, to sustain the growth of soybean (Glycine max). We first identified helper strains that significantly promote nodulation and nitrogen fixation in soybean mediated by BXYD3. Two of these helper strains assigned to the Pantoea taxon produce acyl homoserine lactones, which significantly enhanced the colonization and infection of soybean by BXYD3. Finally, we constructed a sfSynCom from these core and helper strains. This sfSynCom based on the core-helper strategy was more effective at promoting nodulation than inoculation with BXYD3 alone and achieved effects comparable to those of a complex elite SynCom previously constructed on the basis of potential beneficial functions between microbes and plants alone. Our results suggest that considering interactions between strains as well as those between strains and the host plant might allow construction of sfSynComs.

Microbiota-mediated nutrient turnover in the rhizosphere determines nutrient bioavailability, thereby enhancing nutrient uptake, utilization, and ultimately crop productivity. Consequently, elucidating the functional core microbiota in rhizosphere nutrient turnover is of critical importance. In this study, we leveraged soybean germplasm core collections to investigate the tripartite relationship among host genotype, core microbiota and nutrient availability, with a focus on delineating the pivotal role of core microbiota in nutrient turnover. Our results suggest that phylogenetic variation significantly shape root-associated microbial communities and rhizosphere nutrient availability, explaining 11.75 % and 2.07 % of total variances, respectively. Core microbiota analysis identified 29 phylogenetic conserved core amplicon sequence variants (ASVs), the majority of which exhibited significant correlated with nutrient availability. Notably, three key core ASVs-ASV13, ASV14 and ASV12, positively correlated with alkali-hydrolyzed nitrogen, available phosphorus, and soil organic matter, respectively. These taxa were subsequently incorporated into a Bradyrhizobium-based synthetic bacterial community (SynCom) to validate their functional roles. Further experiments confirmed that core microbiota-driven nutrient turnover directly facilitates host plant, as evidenced by SynCom inoculation assays. Collectively, this study establishes that phylogenetically conserved core microbiota critically regulate nutrient turnover and acquisition efficiency in the rhizosphere. These insights advance our understanding the ecological function of core microbiota in the rhizosphere and provide a framework for harnessing the beneficial traits in sustainable agriculture.

Auxin is the most important phytohormone, regulating root growth and development in plants. ARFs function as central regulators in auxin signaling in model plants, and the functions of ARF activators have been widely investigated, while the functions of ARF repressors remain elusive. In this study, we investigated the family of GmARFs in soybean through a genome-wide expression pattern and functional study of roots highly expressing ARFs. In total, we identified 59 GmARF members in the soybean genome. GmARFs harbor canonical B3 DNA-binding (B3), ARF (Aux rep), and PB1 functional protein domains. We identified two potential repressor genes, GmARF9b (Glyma.03G070500) and GmARF2a (Glyma.05G200800), which are specifically or highly expressed in the roots. Histochemical staining suggested that both genes are primarily expressed in the stele, root tips, and lateral root primordia. Subcellular localization analysis showed they were mainly localized in the nucleus. Overexpression of GmARF9b and GmARF2a significantly inhibited root growth using a transgenic hairy root assay. Root section analysis further suggested that GmARF9b and GmARF2a negatively regulated cortical cell layers and the longitudinal cell length of roots, thereby modulating root growth. Overall, this study has preliminarily identified two GmARFs that inhibit root growth in soybean. This discovery has deepened our understanding of the functions of ARFs in root development and has provided guidance for breeding crop roots with improved nutrient use efficiency.

The establishment of nitrogen fixing microbiota is essential for associative nitrogen fixation in cereal crops. This opinion proposes three potential strategies to increase associative nitrogen fixation in cereal crops.

Lignification of juice sacs is a primary contributor to reductions in fruit quality, with impacts on taste and economic value of pomelo (Citrus grandis). To date, information on the regulation of fruit lignification remains fragmentary. In this study, we first analyzed the relationship between lignification and nutrient status of pomelo juice sacs, which revealed a significant positive correlation between nitrate (NO3-) concentration and lignin concentration, with over 60% of lignin accumulation explained by NO3- levels in three models of machine learning-based regression. Results from field trails in 11 pomelo orchards, as well as in pear fruits and soybean roots exposed to low or high NO3- supplies, further demonstrated that nitrate plays an important role in lignification. Transcriptomic analysis further showed that pomelo laccases (CgLACs) were more intensively up-regulated upon addition of NO3- than any of the genes encoding one of the other 12 enzymes involved in lignin biosynthesis. Among the nine identified CgLACs, CgLAC3 was the most significantly up-regulated CgLAC in high nitrate treated plants. Over-expressing CgLAC3 increased lignin concentrations in both pomelo albedo and soybean hairy roots. Taken together, we conclude that nitrate modulates fruit lignification in pomelo through regulation of CgLAC3 expression, which suggests that NO3--N fertilization may affect fruit lignification, and thereby can be managed to improve fruit quality.

Soil legacy effects, especially soil bacterial legacy effects, influence growth, fitness and nutrient acquisition in sequential cropping systems. To date, mechanisms underlying soil bacterial legacy influences on subsequent crops remain largely unknown. In this study, we employed soybean monoculture (S), corn monoculture (C), and soybean/corn intercropping (SC) to study soil legacy effects on the growth and nutrient acquisition of wheat. In these tests, S, C and SC drove establishment of distinctive soil bacterial communities, with higher abundances of Actinobacteria and Proteobacteria taxa observed in SC plots than in S and C treatments. Variation among soil bacterial communities was associated with functional shifts in nitrogen cycling in SC treatment compared to other treatments(C and Control). Soil legacy effects in turn may contribute to growth, nutrient acquisition and grain production in wheat crops planted in rotations. Pot assay suggest that soil microorganism of SC treatment significantly increased the plant height of wheat by 15.1 % and 18.7 %, the shoot biomass by 50.7 % and 62.7 %, the nitrogen content by 76.0 % and 94.9 %, the phosphorus content by 80.3 % and 75.9 %, and the potassium content by 64.0 % and 83.7 % by compared with C and S. Actinobacteria taxa collections further promote nutrient acquisition of wheat. Taken together, our observations from field plots and manipulation of specific bacterial taxa revealed novel soil bacterial legacy effects of previously reared crops on subsequent crops. These new insights open avenues for using soil legacy effects for positive impacts in crop rotation systems.

Levulinic acid, a hydrolysis product of lignocellulose, can be metabolized into important compounds in the field of medicine and pesticides by engineered strains of Saccharomyces cerevisiae. Levulinic acid, as an intermediate product widely found in the conversion process of lignocellulosic biomass, has multiple applications. However, its toxicity to Saccharomyces cerevisiae reduces its conversion efficiency, so screening Saccharomyces cerevisiae genes that can tolerate levulinic acid becomes the key. By creating a whole-genome knockout library and bioinformatics analysis, this study used the phenotypic characteristics of cells as the basis for screening and found the HMX1 gene that is highly sensitive to levulinic acid in the oxidative stress pathway. After knocking out HMX1 and treating with levulinic acid, the omics data of the strain revealed that multiple affected pathways, especially the expression of 14 genes related to the cell wall and membrane system, were significantly downregulated. The levels of acetyl-CoA and riboflavin decreased by 1.02-fold and 1.44-fold, respectively, while the content of pantothenic acid increased. These findings indicate that the cell wall-membrane system, as well as the metabolism of acetyl-CoA and riboflavin, are important in improving the resistance of Saccharomyces cerevisiae to levulinic acid. They provide theoretical support for enhancing the tolerance of microorganisms to levulinic acid, which is significant for optimizing the conversion process of lignocellulosic biomass to levulinic acid.

Phosphorus (P) is one of the three macronutrients for plants. Because of its low mobility and high fixation in soils, low P availability is a worldwide constraint for crop productivity. Molecular biology provides great opportunities to improve P efficiency in plants. However, transgenic plants cannot be commercialized before integrating all the knowledge on bottlenecks for improving P efficiency of crops/pastures. This review intends to summarize the main strategies of bioengineering to improve P efficiency of crops/pastures, including conventional and molecular assisted breeding, identification and application of key genes for biotech plants. It highlights recent advances in the understanding of improving P efficiency through the integration of bioengineering with P fertilization and cultivation management.

Phosphate (Pi) availability is well known to regulate plant root growth. However, it remains largely unknown how flavonoid synthesis participates in affecting plant root growth in response to Pi starvation. In the study, the crystal structure of a plant protein phosphatase, GmHAD1-2, was dissected using X-ray crystallography for the first time. It was revealed that GmHAD1-2 contained a modified Rossmannoid class of α/β folds with three layered α/β sandwich. Transcripts of GmHAD1-2 were increased by Pi starvation in soybean roots, especially in lateral root tips. GmHAD1-2 suppression or overexpression significantly influenced soybean lateral root length and number, as well as phosphorus (P) content. Furthermore, GmHAD1-2 was found to interact with a chalcone reductase, GmCHR1. Suppression of GmHAD1-2 significantly changed the flavonoid biosynthesis pathway in soybean roots. Taken together, the results highlight that GmHAD1-2 can regulate soybean root growth by influencing flavonoid metabolism.

Obtaining consistent multi-view images of litchis is crucial for various litchi-related studies, such as data augmentation and 3D reconstruction. This paper proposes a two-stage model that integrates the Mask2Former semantic segmentation network with the Wonder3D multi-view generation network. This integration aims to accurately segment and extract litchis from complex backgrounds and generate consistent multi-view images of previously unseen litchis. In the first stage, the Mask2Former model is utilized to predict litchi masks, enabling the extraction of litchis from complex backgrounds. To further enhance the accuracy of litchi branch extraction, we propose a novel method that combines the predicted masks with morphological operations and the HSV color space. This approach ensures accurate extraction of litchi branches even when the semantic segmentation model’s prediction accuracy is not high. In the second stage, the segmented and extracted litchi images are passed as input into the Wonder3D network to generate multi-view of the litchis. After comparing different semantic segmentation and multi-view synthesis networks, the Mask2Former and Wonder3D networks demonstrated the best performance. The Mask2Former network achieved a mean Intersection over Union (mIoU) of 79.79% and a mean pixel accuracy (mPA) of 85.82%. The Wonder3D network achieved a peak signal-to-noise ratio (PSNR) of 18.89 dB, a structural similarity index (SSIM) of 0.8199, and a learned perceptual image patch similarity (LPIPS) of 0.114. Combining the Mask2Former model with the Wonder3D network resulted in an increase in PSNR and SSIM scores by 0.21 dB and 0.0121, respectively, and a decrease in LPIPS by 0.064 compared to using the Wonder3D model alone. Therefore, the proposed two-stage model effectively achieves automatic extraction and multi-view generation of litchis with high accuracy.

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.

Increasing global demand for food presents a significant challenge to maintaining soil health and sustainable production of agricultural crops. As plant root-associated microbial fitness is greatly impacted by community growth, development, and nutrient acquisition, the cultivation of functional assembly of root-associated microbes may provide solutions for achieving food security while maintaining healthy soils. Here, we propose a four-part strategy to promote soil health and agricultural productivity by partnering crops with root-associated microbes.

In arbuscular mycorrhizal (AM) symbiosis, sugars in root cortical cells could be exported as glucose or sucrose into peri-arbuscular space for use by AM fungi. However, no sugar transporter has been identified to be involved in sucrose export. An AM-inducible SWEET transporter, GmSWEET6, was functionally characterised in soybean, and its role in AM symbiosis was investigated via transgenic plants. The expression of GmSWEET6 was enhanced by inoculation with the cooperative fungal strain in both leaves and roots. Heterologous expression in a yeast mutant showed that GmSWEET6 mainly transported sucrose. Transgenic plants overexpressing GmSWEET6 increased sucrose concentration in root exudates. Overexpression or knockdown of GmSWEET6 decreased plant dry weight, P content, and sugar concentrations in non-mycorrhizal plants, which were partly recovered in mycorrhizal plants. Intriguingly, overexpression of GmSWEET6 increased root P content and decreased the percentage of degraded arbuscules, while knockdown of GmSWEET6 increased root sugar concentrations in RNAi2 plants and the percentage of degraded arbuscules in RNAi1 plants compared with wild-type plants when inoculated with AM fungi. These results in combination with subcellular localisation of GmSWEET6 to peri-arbuscular membranes strongly suggest that GmSWEET6 is required for AM symbiosis by mediating sucrose efflux towards fungi.

大豆与根瘤菌的共生固氮是农业生态系统中主要的氮来源之一,研究其互作机制意义重大,但是由于根瘤菌个体小,转化难,目前尚缺乏高效、稳定标记根瘤菌的方法,限制了其在互利共生方面的研究.为开发用于大豆与慢生根瘤菌互作研究的根瘤菌标记方法,本研究通过改造原始载体pMG103,构建高效表达tdTomato、GUS、LUC的标记载体,以高效固氮的慢生根瘤菌株系Bradyrhizobium elkanii BXYD3为试验菌株,采用电击转化法进行标记.利用显微镜、GUS染液、化学成像仪观察标记的B.elkaniiBXYD3根瘤菌在大豆不同时期不同部位的定殖情况.结果表明:成功获得了 tdTomato、GUS及LUC标记的慢生根瘤菌转化菌株,携带不同标记的慢生根瘤菌株B.elkanii BXYD3能在大豆根表及根瘤内稳定定殖,并且可满足不同试验需求.本研究建立了较为稳定的表达多种标记蛋白的载体,且能较好地应用于慢生根瘤菌株系中,为直观研究大豆与慢生根瘤菌的互作提供有效的方法参考.