[Objective] To explore the control effects of Streptomyces TOR3209 and its volatile organic compounds (VOCs) on tomato Fusarium wilt and mine the differentially expressed genes related to disease resistance, thus providing effective strategies for the development of environmentally friendly biofungicides. [Methods] Strain TOR3209 suspensions of different concentrations (1.0×10¹, 1.0×10³, 1.0×10⁵, and 1.0×10⁷ CFU/mL) were co-cultured with tomato seedlings, and Fusarium equiseti was inoculated on the seedlings. The disease severity was graded. The co-culture experiment of VOCs from strain TOR3209 with tomato seedlings was conducted in a micro-greenhouse to evaluate the effect of VOCs on tomato seedlings infected by F. equiseti. Transcriptomic analysis was conducted on tomato seedlings with significant disease resistance to mine the differentially expressed genes induced by VOCs, which were then verified by RT-qPCR. [Results] The suspensions of strain TOR3209 at different concentrations all had control effects on tomato Fusarium wilt. Among them, the 1.0×10⁷ CFU/mL suspension had the best control effect (P<0.01). The biocontrol effects of different quantities of small dishes cultured with strain TOR3209 on tomato Fusarium wilt were significantly different from that of the control group. The group of 30 small dishes showed the best control effect (P<0.01). The transcriptomic analysis showed that the expression levels of disease-resistance genes encoding CXE17, LRR-RLK, F-box, TIP1-1 Aquaporin, and Peroxidase were upregulated. Fluorescence quantitative analysis indicated that co-culture of VOCs from the strain with tomato seedlings upregulated the expression levels of disease-resistance genes, indicating that the transcriptomic sequencing results were reliable. [Conclusion] The VOCs of strain TOR3209 effectively prevent and control tomato Fusarium wilt caused by F. equiseti infection by inducing the upregulated expression of disease-resistance genes in tomato seedlings. The findings lay a theoretical foundation for the research and development of biofungicides for the prevention and control of Fusarium wilt.

[Objective] Human parainfluenza virus type 3 (HPIV-3) is a key factor in global acquired respiratory infections, and there is no specific therapy available. Due to the complexity and variability of the pathogen antigen, the development of vaccines against HPIV-3 is lagging behind. It is crucial to design a novel broad-spectrum vaccine for comprehensive protection against continuously mutated wild-type strains. [Methods] To overcome the antigenic variation of the virus, we downloaded different HPIV-3 antigen proteins (F, M, N, and HN proteins) from NCBI and generated consensus sequences through sequence alignment. Furthermore, a broad-spectrum T cell epitope vaccine targeting HPIV-3 was predicted and designed via methods of reverse vaccinology. [Results] The multi-epitope vaccine (MEV) incorporated 11 cytotoxic T lymphocyte (CTL) epitopes (9-mer) and 11 helper T lymphocyte (HTL) epitopes (15-mer) from the F, M, N and HN proteins, being composed of 355 amino acid residues without adjuvant. The predicted T cell epitopes had solubility, no allergenicity, high antigenicity, and immunogenicity. The designed vaccine can effectively bind to Toll-like receptors in natural immunity, with good stability, hydrophilicity, and high population coverage. [Conclusion] The designed vaccine could be a candidate vaccine against HPIV-3 infection. We provide a novel immunoinformatics approach for vaccine design and development.

[Objective] To unravel the mechanism underlying the high-yield performance of hybrid pepper (Capsicum annuum L.) progenies and dissect parent-progeny differences across four interconnected dimensions: plant nutrient accumulation, rhizosphere soil physicochemical properties, microbial community composition, and nutrient metabolism-related functional genes. [Methods] For both parental lines and their hybrid progenies, the yields and the content of nitrogen (N), phosphorus (P), and potassium (K) in roots, fruits, and rhizosphere soil were determined, alongside rhizosphere soil physicochemical properties. High-throughput sequencing was adopted to analyze the structures of root endophytic and rhizosphere microbial communities, while metagenomic sequencing was used to quantify the abundance differences of genes associated with rhizosphere nutrient metabolism. [Results] Hybrid progenies exhibited a significant yield increase, with the highest yield increase observed in the Z3 line. All hybrids showed elevated K content in fruits, and Z3 specifically achieved transgressive accumulation of N and P in roots. A distinct turnover of the root endophytic microbial community was detected between parents and progenies. In the hybrids, functional genera including Dyella, Burkholderia-Caballeronia-Paraburkholderia, and Trichoderma were enriched, which were significantly correlated with plant nutrient uptake. In terms of rhizosphere soil properties, all hybrids had higher available phosphorus content and lower rhizosphere pH than parental lines. Notably, Z3 possessed unique advantages of high total nitrogen reserve and increased organic matter content in the rhizosphere. Additionally, the abundance of genes related to P and K metabolism was higher in hybrids than in parents, which was particularly prominent in Z3. [Conclusion] The transgressive yields of pepper hybrids is driven by the synergy among the rhizosphere environment, microbial communities, and the host plant. Specifically, hybrid progenies constructed an efficient microecosystem by enriching functional microbes (e.g., Dyella) and enhanced nutrient metabolism efficiency through increased abundance of P and K metabolism-related genes. These improvements ultimately led to the formation of nutrient utilization advantages, characterized by efficient nutrient absorption in roots and effective nutrient translocation to fruits. This study provides a novel theoretical framework for deciphering the microbial-driven mechanisms underlying parent-progeny differences in nutrient use efficiency of crops and further enriches the theory of plant-microbe-soil interactions.

Probiotic microbiota in roots can enhance nutrient uptake and stress tolerance, thereby improving plant growth. [Objective] To identify elite microbial resources from alfalfa roots. [Methods] We used eight functional bacterial strains isolated from the roots of Medicago sativa var. ‘Caoyuan No. 3’ and eight synthetic microbial communities (synthetic microbial communities, SynComs) composed of different strains for seed soaking treatments under 0, 200, and 250 mmol/L NaCl stress conditions. The germination potential (rate), radicle (embryonic shoot) length, and seed fresh weight were measured, and the effectiveness of the bacterial strains and SynComs in improving stress tolerance and growth was comprehensively evaluated via the membership function method. The effects of strains isolated from roots on alfalfa seed germination were thus evaluated. [Results] Under non-saline conditions, seed soaking had no significant impact on alfalfa seed germination. However, under salt stress, seed soaking significantly enhanced seed germination. Under 200 mmol/L and 250 mmol/L NaCl stress, MS8 was the most effective strain in promoting seed germination. Compared with the control treated with sterile water, MS8 treatment improved the germination potential by 76.67%. Compared with the control, the seeds treated with SynCom 1 exhibited increases of 113.04% to 405.41% in germination rate, significant increases of 47.87% to 56.67% in radicle length, significant increases of 19.13% to 24.01% in embryonic shoot length, and significant rises of 157.64% to 1 300.00% in fresh seed weight. [Conclusion] Under 200 mmol/L and 250 mmol/L NaCl stress, SynCom 1 was the most effective synthetic microbial community in enhancing seed germination, outperforming strain MS8. This study provides a theoretical foundation and technical support for the subsequent development of efficient functional bacterial agents to enhance the salt tolerance of alfalfa.

[Objective] To analyze the evolutionary conservation and structural characteristics of the heat shock protein GrpE from Mycoplasma bovis, elucidate its subcellular localization, and investigate its biological properties in mediating the adhesion process. [Methods] Primers were designed based on the GrpE gene sequence (GenBank accession number: CP002188.1) of Mycoplasma bovis PG45, and the prokaryotic expression vector pET-GrpE was constructed. Following gene sequencing, bioinformatics methods were employed to analyze the homology, phylogenetic relationships, physicochemical properties, and structural characteristics of GrpE. Following transformation of the recombinant plasmid and induced expression, the yielded recombinant GrpE protein was purified via nickel affinity chromatography, and then SDS-PAGE was conducted. The purified recombinant protein was used to immunize New Zealand White rabbits to generate polyclonal antibodies, with the antibody titer determined by ELISA and immunogenicity assessed via Western blotting. The subcellular localization of GrpE was examined via indirect indirect fluorescent antibody assay (IFA), ELISA, and Western blotting. The adhesion function of GrpE was validated through integrated IFA and ELISA. [Results] The prokaryotic expression vector pET-GrpE was successfully constructed in this study. Bioinformatics analysis revealed that the GrpE sequence was highly conserved in Mycoplasma bovis (with identity exceeding 95%). The encoded protein consisted of 341 amino acid residues, with no signal peptide and transmembrane domain but potential N-glycosylation and phosphorylation sites. SDS-PAGE results confirmed the successful expression of GrpE in a soluble form. Polyclonal antibodies generated via the purified recombinant protein exhibited a titer of 1:16 000. Western blotting analysis further verified the strong immunogenicity of the GrpE protein. Localization studies using IFA, ELISA, and Western blotting indicated that GrpE is distributed in both the cell membrane and the cytoplasm, with predominant distribution observed on the membrane surface. Importantly, the anti-GrpE polyclonal antiserum significantly inhibited the adhesion of Mycoplasma bovis to embryonic bovine lung (EBL) cells. Furthermore, binding assays demonstrated that the interaction between GrpE and host cell membrane proteins is dose-dependent, and this binding was inhibited by the polyclonal antibody (P<0.001). [Conclusion] GrpE is identified as a highly conserved novel adhesion of Mycoplasma bovis that directly participates in the adhesion to host cells, providing a key molecular target for elucidating the pathogenic mechanism of Mycoplasma bovis.

Hexavalent chromium [Cr(VI)] is a widespread and highly toxic heavy metal contaminant commonly found in industrial effluents from electroplating, metallurgy, and dye manufacturing. Due to its strong oxidizing nature, high solubility, and severe biological toxicity, Cr(VI) is recognized as a priority contaminant to be managed in aquatic and terrestrial environments. Although conventional treatment technologies can rapidly reduce Cr(VI) concentrations, they often entail high costs, pose risks of secondary pollution, and are susceptible to environmental fluctuations. Bioreduction of Cr(VI) has emerged as a promising alternative, offering advantages such as low energy requirements, environmental compatibility, and operational sustainability. This review provides a comprehensive overview of the core mechanisms underlying Cr(VI) bioreduction, which involve key chromate reductases, intracellular and extracellular electron transfer pathways, gene regulatory networks, and adaptive strategies of microbial communities under stress. Furthermore, we discuss the synergistic contributions of metabolic pathways, such as denitrification and sulfur cycling, to elucidate electron competition and pathway modulation in complex multi-contaminant systems. Subsequently, we analyze the effects of environmental parameters including pH, temperature, Cr concentration, and electron donor types on bioreduction efficiency. Representative studies are discussed to illustrate detoxification performance, community succession, and ecological restoration outcomes under field conditions. Finally, this review envisions future advances in microbial remediation through the application of synthetic biology to construct engineered microbial strains, the use of multi-omics technologies to elucidate metabolic pathways, and the integration of artificial intelligence (AI) with in situ sensing technologies for dynamic regulation. It further outlines a developmental framework centered on “intelligent detection-adaptive response-multifunctional coordination”, providing both a theoretical foundation and technological guidance for the in situ remediation of Cr(VI) contamination.

Chloroquine, a low-cost antimalarial agent, has garnered significant interest due to its extensive research foundation and potential anti-tumor and antiviral properties. Chloroquine exhibits broad-spectrum inhibitory effects against diverse human and animal pathogenic viruses in vitro. Its antiviral efficacy has been demonstrated against Zika virus and feline coronavirus in vivo. The primary action mechanisms of chloroquine include inhibition of viral binding to host cells and subsequent internalization, modulation of viral nucleic acid recognition pathways, blockade of autophagosome maturation, and regulation of cytokine secretion in the immune response. This review systematically summarizes the antiviral effects and mechanisms of chloroquine, providing a theoretical foundation for the future development of chloroquine and its derivatives as antivirals.

[Objective] The soil in the vegetable plantation suffered from fertility degradation, pH decrease, and heavy metal leaching, necessitating the exploration of the mechanism by which composite bacterial agents regulate the bacterial community structure, nitrogen composition, and heavy metal availability in the vegetable plantation soil. [Methods] The heavy metal-resistant bacterial strains Ralstonia Bcul-1 (R-B) and Bacillus cellulasensis Zn-B (BC-Z) were prepared with biochar as an immobilized bacterial agent and then applied to the acidic soil (pH 5.6) of a vegetable plantation under long-term tomato rotation. High-throughput sequencing of soil bacteria and the determination of soil composition were conducted to analyze the bacterial diversity, soil pH, nitrogen-carbon content, and heavy metal chemical speciation, on the basis of which the effects of the biochar composite bacterial agent on the bacterial community structure, nitrogen-carbon supply, and heavy metal activity in the soil were analyzed. [Results] Biochar immobilization facilitated the growth of exogenous bacteria R-B and BC-Z in the vegetable plantation soil contaminated with heavy metals and maintained long-term coexistence of R-B and BC-Z with the original highly resistant Bacillus (10.18%-11.88%) in the soil. Accordingly, it effectively improved the bacterial community structure, adjusted the distribution of differential bacteria (biomarkers), and restoratively increased the relative abundance of abundant bacteria (such as Streptomyces, Geopathophilus, and Nocardioids) in the soil. In addition, soil bacterial genera, partial abundant bacteria, and the exogenous bacterial strain R-B were closely related to heavy metal chemical speciation and nitrogen-carbon components. The application of biochar bacterial agents (BI+R-B, BI+BC-Z, and BI+R-B+BC-Z) increased the pH, EC, total nitrogen, nitrate nitrogen, organic matter, and total organic carbon of the soil by up to 0.41, 20.74%, 18.96%, 24.77%, 10.26%, and 21.56%, respectively, while decreasing the ammonium nitrogen residue by 13.91%, maintaining the nitrogen-carbon supply capacity of the soil. BI+R-B and BI+R-B+BC-Z reduced the content of exchangeable, reducible, and oxidizable heavy metals (Cd, Cr, Pb, Cu, and Zn) by 0.18%-12.33%, but increased the residual content of these heavy metals by 0.16%-14.59%, effectively passivating heavy metals in the soil. [Conclusion] The biochar composite bacterial agent (BI+R-B+BC-Z) improved the bacterial community structure, promoted R-B growth, increased the abundance of abundant bacteria, and maintained the long-term coexistence of exogenous bacteria R-B and BC-Z with the original highly resistant Bacillus in the vegetable plantation soil with heavy metal compound pollution. Moreover, it increased soil pH, EC, total nitrogen, nitrate nitrogen, total organic carbon, and organic matter, while reducing ammonium nitrogen residue and passivating soil heavy metals (Cd, Pb, and Cu). Therefore, it effectively regulated the bacterial community activity, exogenous bifunctional bacterial growth, nitrogen-carbon supply, pH, and heavy metal chemical speciation, with the potential to maintain the fertilizer supply capacity and control heavy metal compound pollution of vegetable plantation soil.

α-ketoglutarate is an important short-chain organic acid that is widely used in various fields such as food, medicine, cosmetics, and animal feed. However, the efficiency of producing α-ketoglutarate through biological fermentation remains to be improved, primarily due to the limitations in the synthetic capacity of microbial metabolic pathways. [Objective] To address the above issues, we developed an engineered Escherichia coli that can efficiently produce α-ketoglutarate, thereby providing theoretical support for the large-scale production of α-ketoglutarate in the future. [Methods] We employed an efficient approach combining rational and irrational modifications to overcome the constraints of endogenous metabolic pathways and enhance the biosynthesis efficiency of α-ketoglutarate. [Results] The oxidative TCA pathway was reconstructed to improve α-ketoglutarate production through expressing pyruvate carboxylase, citrate synthase, aconitase, and isocitrate dehydrogenase. The metabolic network for α-ketoglutarate biosynthesis was irrationally optimized and strengthened to enhance its biosynthesis capability by atmospheric pressure room temperature plasma mutagenesis. To improve the supply efficiency of the precursor for α-ketoglutarate biosynthesis, we reduced the dissipation of carbon flux in the pyruvate node by knocking out genes related to the accumulation of lactate, acetate, and formate. Furthermore, we knocked out the genes related to the degradation pathway of α-ketoglutarate to achieve the retention of carbon flux at α-ketoglutarate node and improve its production. Through the optimization of fermentation conditions, the fermentation in a 5 L fermenter with the engineered strain E. coli KA29 achieved the α-ketoglutarate titer, yield, and productivity of 28.7 g/L, 0.29 g/g, and 0.48 g/(L·h), respectively. [Conclusion] The research strategies mentioned above lay a foundation for the development and application of strains with high production of α-ketoglutarate and provide a reference for metabolic engineering to produce other organic acids.

[Objective] To study the phylogenetic relationship and genomic diversity of intestinal obligate commensal bacteria in different populations from various regions of Xinjiang and provide a theoretical basis for developing personalized functional probiotics for different populations. [Methods] A total of 136 strains of Bifidobacterium longum subsp. longum were isolated from mother-infant populations of Uygur and Kazak ethnic groups in Kashgar and Yili regions of Xinjiang. Comparative genomic analysis was conducted with data of the strains from other regions in China that were available in public databases. [Results] The average genome size, G+C content, and the number of coding sequences of B. longum subsp. longum were 2.38 Mb, 59.91%, and 2 160, respectively. The phylogenetic tree constructed based on core genes showed that all strains from Xinjiang belonged to four clades in the phylogenetic tree. Strains from the same ethnic group but from different geographical regions were in different clades, and there was a certain degree of overlap between geographically closer and different population-derived strains. The analysis of a larger geographical range (China) showed that B. longum subsp. longum strains and their functional genes presented obvious geographical and ethnic distribution characteristics. The analysis of COG functional genes and carbohydrate hydrolyase-related genes showed that the functional gene spectra varied greatly among strains from the same ethnic group but in different regions. The carbohydrate hydrolyase-related gene families GH13 (α-amylases) and GH43 (β-amylases) were more abundant in the strains from Kashgar region. Conversely, even strains from different ethnic groups but from geographically close regions had similar spectra of COG functional genes and carbohydrate hydrolyase-related gene families. [Conclusion] The B. longum subsp. longum strains and their functional genes from different geographical regions and ethnic groups in Xinjiang showed obvious geographical and ethnic distribution characteristics. As the geographical scale becomes large, the geographical distribution characteristics of the strains become more obvious. The relationship between the geographical distribution scale of populations and the co-evolution and specificity of strains should be verified based on larger-scale genomic data of strains.