In natural soils, phosphorus predominantly exists in stable forms such as chelated inorganic phosphorus, resulting in low levels of available phosphorus. To cope with phosphorus limitation, woody plants typically form symbiotic associations with ectomycorrhizal fungi (ECMF) to enhance phosphorus acquisition. Studies have indicated that ECMF exhibit limited capacity to directly solubilize chelated inorganic phosphorus. However, they can recruit phosphate-solubilizing bacteria in the hyphosphere by releasing specific compounds, thereby facilitating the desorption of chelated inorganic phosphorus. Nevertheless, comprehensive reviews analyzing the role of plant-ECMF-bacteria tripartite systems in phosphorus cycling remain scarce. This article introduces the conceptual framework of plant-ECMF-bacteria tripartite systems, elucidates the physiological, biochemical, and molecular mechanisms underlying phosphorus cycling among ECMF, mycorrhiza helper bacteria, and host plants, and discusses future research directions for optimizing plant phosphorus acquisition through the tripartite systems.

Antibodies serve as critical effector molecules in mediating vaccine-induced protection. While antibody-mediated immunity has traditionally been attributed primarily to neutralization, where the fragment antigen-binding (Fab) domain blocks viral entry by preventing the interaction between viruses and host cells, accumulating evidence underscores the pivotal role of the crystallizable fragment (Fc) domain in orchestrating broader immune responses. By interacting with Fc receptors or complement receptors on effector cells such as natural killer cells, macrophages, neutrophils, and dendritic cells, the Fc domain activates multiple innate immune pathways and elicits a spectrum of non-neutralizing antiviral effector functions. These include antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), antibody-dependent complement deposition (ADCD), and complement-dependent cytotoxicity (CDC). Although the evaluation of Fc-mediated functions is more complex than the measurement of neutralizing antibody titers, the contribution of such functions to vaccine efficacy is increasingly recognized. This review provides a comprehensive overview of Fc-mediated immune effector mechanisms, highlights their critical roles in antiviral vaccine-induced protection, and summarizes recent advances in Fc function assays, with the aim of supporting the rational design and immunogenicity evaluation of next-generation viral vaccines.

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.

Chitin is the second largest renewable resource only after cellulose on Earth. Chitinases are the key enzymes for degrading chitin. Chitinases of the glycoside hydrolase family 19 (GH19) mainly exist in higher plants. In recent years, microbial GH19 chitinases have been widely discovered. This paper reviews the research progress in microbial GH19 chitinases regarding their distribution, structures, enzymatic properties, and applications and prospects the research directions in the future.

Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain, abdominal distension, and abnormal bowel movements. Its pathogenesis involves multiple factors such as imbalance of gut microbiota, immune activation, and dysfunction of the gut-brain axis. Although conventional therapies can alleviate symptoms temporarily, the limitations such as drug side effects and insufficient efficacy persistence have made microbial-targeted therapy a research hotspot. Probiotics are live microorganisms and have been proven to be beneficial to human health. Studies have shown that probiotics inhibit pathogen adhesion through competitive colonization, regulate immune responses, and repair the intestinal barrier function through metabolic products, thereby improving intestinal motility and osmotic balance. This review discusses the specific effects and potential pathways of probiotics on constipation, diarrhea, abdominal pain and distension, and mental symptoms in IBS patients. However, the clinical application of probiotics still faces challenges, including strain heterogeneity, host individual differences, and the lack of standardized treatment plans. In the future, it is necessary to combine multi-omics technologies to screen biomarkers, develop individualized intervention strategies, and optimize efficacy through dynamic monitoring, which are expected to provide more precise microbial-targeted therapy for the treatment of IBS.

The gut microbiota maintains a close dialogue with the host’s immune system, being capable of influencing immune responses through various pathways. It has been extensively documented that synchronous regulation of the gut microbiota and the host immune response exerts immunoenhancing, anti-inflammatory, and gut homeostasis-maintaining effects. By systematically reviewing the relevant literature published in the past three years, this article first elaborates on the interactions between the gut microbiota and the host’s immunity via multiple routes. It further summarizes recent studies on natural products that exert immunomodulatory functions (encompassing both immunoenhancing and anti-inflammatory actions) through gut microbiota pathways. Regarding immune dysregulation diseases, this review further elucidates how natural products achieve precise regulation of the host immune function by optimizing the gut microbiota structure, regulating microbiota-immune signaling pathways (e.g., NF-κB, TLR, and MAPK), maintaining intestinal barrier homeostasis, and intervening in microbiota-derived metabolites (such as short-chain fatty acids and tryptophan-indole derivatives). Additionally, this article discusses the process by which the gut microbiota enhances the immunomodulatory effects of natural products through metabolic conversion and biotransformation of natural products into highly active secondary metabolites. The immunoregulatory effects of natural products through the gut microbiota may become a potential therapeutic strategy for immune-related disorders.

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.

Siderophores are low-molecular-weight, high-affinity iron-chelating molecules produced by bacteria in response to iron deficiency. Pseudomonas secrete siderophores to efficiently chelate insoluble Fe³⁺ in the environment, which is a crucial mechanism for their adaptation to iron-limited conditions. This article systematically reviews the types, structural characteristics, biosynthetic pathways (the non-ribosomal peptide synthetase,NRPS), and regulatory mechanisms of siderophores in Pseudomonas. Several regulatory factors at multiple levels were vitally elucidated, including Fur protein, σ factors, quorum sensing, and two-component system. Moreover, siderophores not only promote iron absorption in plants and bioremediation to remove pollutants but also are virulence factors in pathogen infection and factors in microbial spoilage. The siderophore-iron complex can be specifically recognized and actively taken up by bacteria, which is known as the “Trojan horse” mechanism, enabling covalently conjugated antibiotics to enter the cell and thus significantly boosting antibiotic efficacy. Future research should delve into the molecular regulatory networks and microbial interaction mechanisms to promote the application and development of siderophores in agriculture, medicine, and environmental protection.

The global prevalence of obesity and its associated metabolic disorders keeps rising, presenting a major challenge to public health. The gut microbiota plays a pivotal role in obesity onset and development, and its dysbiosis and dysfunction are closely associated with obesity and its complications. This review synthesizes the pathological mechanisms underlying the heredity, neuroendocrine, chronic inflammation, and the gut microbiota-metabolism axis of obesity. Then, we explore the positive and negative regulatory effects of opportunistic pathogens (e.g., Desulfovibrio spp., Megamonas spp.) and putative beneficial bacteria (e.g., Lactobacillus spp., Akkermansia muciniphila) on obesity. Furthermore, we summarize the mechanisms by which these signature gut microbes drive the development of obesity-related conditions, including type 2 diabetes mellitus, metabolic dysfunction-associated steatotic liver disease, cardiovascular diseases, and hypertension. We firstly propose a gut microbiota trajectory hypothesis to delineate the interrelationships between these representative gut microbial signatures and the onset and progression of obesity and its complications. Finally, the review discusses future research directions and the potential for developing early diagnostic technologies based on these microbial signatures. Collectively, this work aims to provide novel strategies for the early diagnosis and precision intervention of obesity and related metabolic disorders, thereby advancing the development of personalized therapeutics.

The mandarin fish (Siniperca chuatsi) is one of the most economically important cultured fish species in Asian countries. With the expansion of artificial farming, infectious diseases have become a major threat to the mandarin fish farming industry, posing a challenge to its sustainable development. Siniperca chuatsi rhabdovirus (SCRV) is a major pathogen infecting this fish species. In recent years, substantial progress has been made in the research on SCRV, yet no comprehensive review is currently available. This paper summarizes and discusses the research advances in SCRV, including viral characteristics, virus rescue, host-virus interactions, and prevention strategies, while also analyzing the current challenges in this field.

Numb-associated kinases (NAKs) are a family of evolutionarily conserved serine/threonine kinases, encompassing adaptor-associated kinase 1 (AAK1), cyclin G-associated kinase (GAK), bone morphogenetic protein 2-inducible kinase (BMP2K), and serine/threonine kinase 16 (STK16). NAKs are widely involved in various physiological processes, such as endocytosis, intracellular transport, cell differentiation, autophagy, and signal transduction. In recent years, studies have shown that NAKs play a key role in different life cycle stages including virus entry, assembly, release, and immune escape of various viruses. Furthermore, small-molecule inhibitors targeting NAKs have been applied in clinical research and treatment of related physiological or viral infectious diseases. This article systematically reviews the primary physiological functions of NAKs and their roles in viral infection, aiming to provide a theoretical foundation for elucidating the pathogenic mechanisms of viruses and developing novel therapeutic drugs targeting NAKs.

[Objective] To investigate the biocontrol potential of Penicillium sinense GS218, a new endophytic fungus, and to analyze the antifungal mechanism, so as to provide elite strain resources and lay a theoretical foundation for the biocontrol of Colletotrichum gloeosporioides in pepper. [Methods] Plate assays were employed to determine the hydrolase activity and siderophore production capacity of GS218. The inhibitory effects of GS218 on different phytopathogenic fungi were evaluated by the plate confrontation method. Whole genome sequencing was performed to obtain insights into the genetic information and physiological functions of the strain. The metabolome of strain GS218 co-cultured with C. gloeosporioides was analyzed to explore the potential active substances for the inhibitory effects. The medicated plate method was employed to validate the inhibitory activities of differential metabolites. [Results] Strain GS218 had hydrolase activity, produced siderophores, and exhibited strong inhibitory effects on five pathogenic fungi (with the inhibition rate of 72.76% on C. gloeosporioides in pepper). The sterile fermentation filtrate of strain GS218 demonstrated a good control effect on pepper anthracnose. The genome size of strain GS218 was 27.77 Mb, which has abundant metabolic pathways, and its genome contained 30 synthetic gene clusters for secondary metabolites. The metabolomics analysis showed that strain GS218 contained rich antimicrobial substances in organic acids and derivatives, phenylpropanoids and polyketides, and lipids and lipid-like molecules (including terpenoids). Compounds such as 7-ethoxycoumarin and pyruvic acid showed inhibitory effects against C. gloeosporioides in pepper. [Conclusion] The new strain, P. sinense GS218, has significant inhibitory effects on C. gloeosporioides and promising application prospects in the green development of agriculture. Whole genome sequencing and metabolomics analysis provide a theoretical basis for deciphering the biocontrol mechanism of strain GS218.

[Objective] This study examined the characteristics of the microbial communities and their associations with chemical components in aged tobacco leaves from different production areas in Yunnan Province, aiming to provide a theoretical foundation for the targeted exploitation of tobacco microbial resources and quality improvement of tobacco. [Methods] A systematic approach integrating metagenomic sequencing, GC/LC-MS, and Spearman’s correlation analysis was employed to investigate the microbial communities, chemical components, and their correlations of aged tobacco leaf samples collected from Dali, Wenshan, Honghe, Luoping, Pu’er, Zhaotong, and Lincang. [Results] The dominant bacterial phylum was Pseudomonadota in aged tobacco leaf samples. The dominant bacterial genera varied among different production areas. Specifically, Salinivibrio was identified as the core genus in the samples from Wenshan, while Methylobacterium and Sphingomonas exhibited significant enrichment in the samples from Luoping. For fungal communities, Ascomycota and Mucoromycota were the predominant phyla, and dominant fungal genera showed negligible variations. Alpha diversity analysis revealed the highest microbial richness and diversity in the samples from Lincang and the lowest in the samples from Wenshan. KEGG analysis revealed that metabolic pathways exhibited high relative abundance across samples from all regions, whereas environmental information processing pathways were more abundant in the samples from Wenshan. CAZy analysis showed that genes annotated as glycoside hydrolases (GHs) and glycosyl transferases (GTs) were the most prevalent, with both generally exhibiting lower abundance in the samples from Wenshan. Chemical profiling revealed that reducing sugar, total sugar and other conventional components were more concentrated in the samples from Dali, whereas total sugar-to-nicotine ratio and potassium-to-chloride ratio were elevated in the samples from Pu’er. Additionally, neutral aroma compounds, including benzyl alcohol, had significantly higher levels in the samples from Wenshan, while polyphenols such as anthocyanins exhibited markedly higher concentrations in the samples from Luoping. Correlation analysis further disclosed that Microbacterium had a significantly positive correlation with total nitrogen, while Aureobasidium showed a significantly negative correlation with total nitrogen. Leucosporidium exhibited significantly positive correlations with potassium ions and potassium-to-chloride ratio. Salinivibrio had significantly positive correlations with multiple neutral aroma components. In contrast, Methylobacterium and Friedmanniomyces showed significantly negative correlations with the majority of neutral aroma components. Additionally, Methylobacterium, Sphingomonas, Friedmanniomyces, and Metschnikowia had significantly positive correlations with multiple polyphenols. [Conclusion] Microbial communities and chemical components of aged tobacco leaves exhibited marked differences across different production areas in Yunnan. Notably, dominant genera are strongly correlated with aroma compounds, which lays a theoretical basis for targeted screening of functional microbes and the development of biotechnologies to improve tobacco quality.

[Objective] To explore the structural differences and associated environmental factors of bacterial communities in the water and sediment of river ecosystems during winter. [Methods] Fourteen sampling sites were established for Diannong River in winter. We employed high-throughput 16S rRNA gene sequencing to systematically analyze the bacterial community composition and diversity, constructed co-occurrence networks, and evaluated the roles of random processes in community assembly. Furthermore, we performed correlation analysis with environmental factors. [Results] The bacterial communities in the sediment had higher alpha diversity indexes than those in the water (P<0.001) and more stable community structures. The beta diversity decomposition showed that the community differences between water and sediment were mainly related to species turnover. Random processes dominated community assembly in both habitats. The co-occurrence network of bacteria in the sediment was more complex with stronger cooperation. Key species were primarily involved in carbon and sulfur cycles, and rare taxa played an important role in network stability. The bacterial communities in water were mainly influenced by environmental factors such as dissolved oxygen, chlorophyll a, and water temperature, while those in the sediment were influenced by pH, organic matter, and nitrogen factors. [Conclusion] This study systematically reveals the differences in the structure, co-occurrence network, and related environmental factors of bacterial communities in the water and sediment of Diannong River during winter, providing scientific evidence for a deeper understanding of the ecological adaptability of river bacterial communities in the freezing period and the different patterns of bacterial communities between water and sediment.

[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] 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.

[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.

Monascus, as a genus of edible fungi used in fermentation, are widely used in various industries such as wine making, food colorants, and pharmaceuticals due to their abundant secondary metabolites. McrA, a global regulator discovered in Aspergillus nidulans, has the function of regulating the growth and secondary metabolism of filamentous fungi. We had identified and cloned mcrA in Monascus purpureus in the previous study. [Objective] On the basis of transcriptome analysis, we mined the differentially expressed genes (DEGs) of ΔmcrA and trpC:mcrA strains to explore the function of mcrA. [Methods] The knockout strain ΔmcrA and overexpression strain trpC:mcrA of M. purpureus were constructed by homologous recombination. The colonies and microscopic morphology on different media were observed. The yields of Monascus pigments and citrinin were determined. The metabolic pathways involving DEGs were analyzed by transcriptome sequencing. [Results] The yields of Monascus pigments and citrinin of ΔmcrA decreased. Transcriptome sequencing results showed that the ΔmcrA strain up-regulated 111 genes and down-regulated 47 genes. The metabolic pathways involving the DEGs of ΔmcrA were mainly glycolysis, pyruvate metabolism, fatty acid synthesis, tyrosine metabolism and so on. The trpC:mcrA strain up-regulated 1 199 genes and down-regulated 867 genes. The main metabolic pathways involving the DEGs of trpC:mcrA were tryptophan metabolism, sucrose and starch metabolism, arginine and proline metabolism, fatty acid degradation, etc. [Conclusion] McrA is a global transcriptional regulator, and the knockout and overexpression of its gene will affect carbohydrate, lipid, and amino acid-related metabolic pathways, thus affecting the production of secondary metabolites.

[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.

[Objective] Kiwifruit bacterial canker (KBC), caused by Pseudomonassyringae pv. actinidiae (Psa), has become the primary bottleneck restricting the sustainable development of the kiwifruit industry in China, highlighting an urgent need for eco-friendly and residue-free biocontrol strategies. [Methods] The kiwifruit variety ‘Hongyang’ was used to systematically evaluate the biocontrol efficacy of Bacillus pumilus H-46 through leaf disc and shoot inoculation assays. The active components were fractionated into three groups (small-molecule metabolites, proteins, and polysaccharides) via sequential extraction, with the major bioactive fraction identified through antimicrobial activity and disease control assessments. An integrated approach combining histochemical staining, antioxidant enzyme activity assays, and RT-qPCR of defense-related genes was employed to elucidate the mechanism of induced systemic resistance (ISR). Furthermore, pathogen migration and colonization assays were conducted to evaluate the inhibitory effects of the active components against Psa. [Results] B. pumilus H-46 showed excellent control effect against KBC, with the disease control efficacy of 86.54% in leaf disc assays. Its main active components (small-molecule metabolites, fraction A) achieved the control efficacy of 88.16% against KBC through non-antimicrobial mechanisms. The mechanisms included triggering early H₂O₂ accumulation and callose deposition, significantly increasing superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities, and activating the expression of key genes (AcMYC2, AcAOC, AcERF2, and AcEIN3) in jasmonicacid (JA) and ethylene (ET) signaling pathways to activate ISR. Consequently, the disease resistance of kiwifruit was enhanced, resulting in a reduction of 37.8% in Psa migration distance in leaf veins and a decrease of 96.6% in colonization ability. [Conclusion] Our findings demonstrate that the small-molecule metabolites (fraction A) of B. pumilus H-46 activates JA/ET-mediated ISR via non-antimicrobial mechanisms, offering a sustainable solution for the control against KBC and establishing a prototype for next-generation plant immunity activators in crop protection.

[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.

[Objective] We explored the nuclear translocation dynamics and pathways of the structural protein VP1 of Junonia coenia densovirus (JcDV) in the epidermal cell line HaEpi derived from the larvae of Helicoverpa armigera, aiming to provide theoretical support for clarifying the assembly and proliferation processes of JcDV. [Methods] The wild-type and mutant plasmids of VP1 protein fused with green fluorescent protein (GFP) were constructed and transfected into HaEpi cells. Subsequently, the subcellular localization dynamics of the VP1 protein were analyzed, and the nuclear localization signal (NLS) and key amino acid residues of the protein were identified. The importin genes expressed by HaEpi cells were cloned. Subsequently, the plasmids of importins fused with DsRed2 were constructed to analyze their subcellular localization. The co-localization and co-immunoprecipitation (Co-IP) assays were employed to analyze the interactions between VP1 protein and importins. [Results] The VP1 protein was located in the cytoplasm at 6 h post transfection, and then gradually translocated to the nucleus until 48 h. The NLS of VP1 protein was located at 325-EGTKRKADTPVEEGPSKKGAH-345, among which K328, R329, K341 were the key amino acid residues affecting the nuclear localization. The importins Haimpα1, Haimpα4, and Haimpα7 were located in the nucleus, while Haimpβ1 was mainly located around the nuclear membrane. The co-localization and Co-IP results indicated that the VP1 protein interacted with Haimpα1, Haimpα4, and Haimpβ1 but not with Haimpα7. [Conclusion] The structural protein VP1 of JcDV can be translocated into the nucleus through the dual pathways of importin α/β and importin β.

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] Aluminum (Al) toxicity in acidic soils severely inhibits plant growth by inducing oxidative stress. Ectomycorrhizal fungus (ECMF) can enhance host plant Al tolerance, but the underlying physiological mechanisms, particularly in fine roots, are not fully understood. This study investigates how ECMF colonization mitigates Al toxicity by modulating the antioxidant physiology of plants, with an aim in applying ECMF for the ecological restoration of Al-contaminated acidic soils. [Methods] Pinus massoniana seedlings were inoculated with Lactarius deliciosus 2 or Pisolithustinctorius 715, with non-ectomycorrhizal seedlings as the control. After a 6-month exposure to 0.0 mmol/L or 1.0 mmol/L Al³⁺, we assessed seedling biomass, fine root morphology, plasma membrane permeability, reactive oxygen species (ROS) levels, antioxidant enzyme activities, and osmoregulatory substance content. [Results] Under Al stress, inoculation with either L. deliciosus 2 or P. tinctorius 715 significantly promoted seedling growth and fine root development. The inoculated seedlings exhibited 1.26-1.33 folds greater biomass and 2.25-3.99 folds increases in the total root length, root surface area, root volume, and root tip number compared to the non-inoculated control. The ECMF inoculation also significantly reduced the accumulation of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), proline, and soluble proteins in fine roots. Furthermore, inoculation with L. deliciosus 2 resulted in significantly higher root surface area and root volume, along with greater peroxidase (POD) and catalase (CAT) activities and a more pronounced reduction in proline content in fine roots, compared to inoculation with P. tinctorius 715. [Conclusion] Our findings demonstrate that ECMF inoculation alleviates Al stress in P. massoniana seedlings by promoting fine root development, bolstering the antioxidant system (notably through increased POD and CAT activities), reducing H₂O₂ accumulation, preserving plasma membrane integrity, and decreasing the synthesis of osmoregulatory substances. The superior performance of L. deliciosus 2 highlights its potential for its application in the ecological restoration of Al-contaminated acidic soils.

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 investigate the interactions between coral-associated Symbiodiniaceae and bacteria in mediating heat stress adaptation of corals. [Methods] Using Pocillopora damicornis harbouring distinct Symbiodiniaceae clades, we performed a laboratory-controlled heat stress simulation experiment to examine the dynamics of symbiotic bacterial community shifts via 16S rRNA gene amplicon sequencing. [Results] Bacterial alpha diversity exhibited a transient increase during the initial stress, followed by a significant decrease under prolonged stress, in P. damicornis harbouring clade C (Cladocopium spp.) or clade D (Durusdinium spp.) algal symbionts (i.e., PdC versus PdD holobionts). Compared with PdD, PdC demonstrated enhanced bacterial community shifts, alongside progressively diminished network stability and complexity with prolonged heat stress. Analysis of bacterial abundance at the class level revealed divergent trajectories of the two holobionts, with the abundance of Alphaproteobacteria increasing in both PdC and PdD, whereas that of Cyanobacteriota increasing in PdC but decreasing in PdD over the course of the experiment. During the later stage of heat stress, Cladocopium spp. in PdC showed increased sensitivity, coinciding with the enrichment of potentially opportunistic pathogens, whereas Durusdinium spp. in PdD were thermotolerant, coinciding with elevated abundance of bacteria possibly involved in photosynthesis, quorum sensing, calcification, and ABC transport. [Conclusion] These findings suggest that different clades of Symbiodiniaceae might interact with bacteria to differentially regulate the P. damicornis response to heat stress. Thermal sensitive Cladocopium spp., combined with the proliferation of potential opportunistic pathogens, may exacerbate the risk of thermal bleaching in PdC, whereas resilience could be strengthened in PdD via thermotolerant Durusdinium spp. coordinating with beneficial bacteria with supportive metabolic potential (e.g., photosynthesis, calcification, and quorum sensing). This algal-bacterial interaction mode provides critical insights into the microbially-mediated thermal bleaching mechanisms and an important reference for the practice of reef restoration in the context of global climate change.

[Objective] Birds, with unique life history characteristics, are ideal models for studying gut microorganisms. The niche overlap between wild birds and poultry increased the risk of interactive transmission of pathogens. This study focused on the community characteristics of gut fungi and pathogens in wild birds (crested myna, tundra swan, and common coot) and sympatric poultry (domestic duck and domestic chicken) in Chaohu Lake. [Methods] High-throughput sequencing (Illumina MiSeq) was employed to analyze the fungal communities in guts of wild birds and sympatric poultry in Chaohu Lake of China, and the characteristics of gut pathogens of each species were particularly studied. [Results] The gut fungal diversity of domestic duck and common coot was significantly higher than that of domestic chicken, crested myna, and tundra swan. There were significant differences in gut fungal community composition among different species. Due to grain-based diets, the guts of poultry were significantly enriched with the fungal taxa related to grain degradation, such as Ascomycota, Mortierellomycota, and Kazachstania. Tundra swan is herbivorous waterfowl. The genus Cladosporium, efficient plant-degrading fungi, dominated in the gut of tundra swan. The gut of tundra swan maintained higher relative abundance of plant saprotroph. The fungal community assembly in guts of wild birds was dominated by deterministic processes, which indicated that wild birds had a stronger gut filtering capacity. In addition, wild birds had lower diversity and relative abundance of pathogens. [Conclusion] The characteristics of gut fungal communities in wild birds and domestic poultry showed significant host specificity. Due to grain-based diets, the guts of poultry were significantly enriched with fungal groups related to grain degradation. The guts of wild birds had a stronger filtering capacity, which reduced the diversity and relative abundance of pathogens.

Citrus reticulata cv. Gonggan in Deqing is a national geographical indication product of China, and its quality formation is intricately linked to microbial ecology. In-depth exploration of the microbial resources associated with Gonggan is of great significance for enhancing the quality and increasing the yield of this fruit. [Objective] To isolate and culture bacteria from the rhizosphere soil and phyllosphere surface of Gonggan in Deqing and systematically evaluate their plant growth-promoting functions, thus providing applicable bacterial resources for the eco-friendly cultivation of Gonggan in Deqing. [Methods] Samples of rhizosphere soil and leaves of Gonggan in Deqing were collected. Bacteria within the samples were isolated via the dilution plating method. Bacterial strains were identified based on the homology of their 16S rRNA gene sequences. The functional media for phosphate solubilization, potassium release, nitrogen fixation, and siderophore production were used to evaluate the plant growth-promoting ability of bacterial strains, and the strains with strong plant growth-promoting functions were screened out. Ultimately, pot experiments were conducted to validate the plant growth-promoting functions of the selected strains. [Results] A total of 240 bacterial isolates were obtained, including 96 strains from the rhizosphere soil and 144 strains from the phyllosphere. These strains belonged to 51 genera, 29 families of 4 phyla, where Pseudomonadota was the dominant phylum and Bacillaceae was the dominant family. Functional characterization revealed that 230 (95.83%) strains exhibited at least one plant growth-promoting function, while 123 strains (51.25%) possessed three or more such functions. Given the extended growth cycle of Gonggan in Deqing, we utilized tomato as a model plant to evaluate the plant growth-promoting functions of eight bacterial strains possessing at least two functions through pot experiments. The results demonstrated that the tested strains significantly increased both plant height and fresh weight of tomato plants. [Conclusion] The rhizosphere soil and phyllosphere of Gonggan in Deqing harbor abundant functional microbial resources. This study successfully screened multiple strains of plant growth-promoting bacteria, and pot experiments demonstrated their significant ability to promote tomato growth. These findings provide a solid theoretical foundation for exploiting microbial resources of Gonggan in Deqing and advancing eco-friendly cultivation practices.

[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.