Soil-borne diseases are currently the most significant type of plant disease restricting crop production and threatening food safety. The rhizosphere microbiome, often regarded as the “second genome of plants”, has shown considerable potential in controlling soil-borne crop diseases. The use of rhizosphere microbes to control soil-borne diseases offers many advantages, such as being environmentally friendly, efficient, and broadly applicable, which makes it a hot topic in rhizosphere microbe research. In this review, we first introduced rhizosphere microbes and their potential for controlling soil-borne crop diseases. Subsequently, by integrating the latest research advances, we systematically summarized seven mechanisms of microbial control against soil-borne diseases and categorized them into three pathways: (1) direct interactions between microbes and pathogens; (2) direct and indirect interactions between microbes and plants; (3) indirect interactions among microbes. Furthermore, we reviewed the current applications of the rhizosphere microbes in controlling soil-borne crop diseases. Finally, we analyzed the key research challenges in using rhizosphere microbes for soil-borne disease control and discussed potential solutions, aiming to provide references for advancing the green control of soil-borne diseases.

Interferon gamma-inducible protein 16 (IFI16), a pivotal member of the pyrin and hematopoietic expression, interferon-inducible nature, and nuclear localization (HIN) domain-containing protein (PYHIN) family, possesses a unique molecular structure that enables it to recognize diverse nucleic acid molecules within cells. As a key immunoregulatory factor, IFI16 participates in the transduction of innate immune signaling through multiple pathways and plays a significant role in host antiviral defense. This review systematically summarized the molecular characteristics of IFI16 and its regulatory mechanisms in innate immunity and viral infection, aiming to provide a theoretical basis for the development of therapeutic targets and antiviral drugs.

[Objective] To investigate the biostimulatory effects of Bacillus velezensis XZT106 on the tuber crop sweet potato (Ipomoea batatas) and elucidate the potential mechanisms underlying its yield increase. [Methods] Sweet potato plants were treated by foliar spraying with B. velezensis fermentation broth, with the plants treated with inactivated B. velezensis fermentation broth as the control. We analyzed the chloroplast content, chloroplast ultrastructure, and antioxidant enzyme activity as well as the structure and metabolite composition of endophyte communities in different ecological niches of sweet potato plants to delve into the mechanisms by which B. velezensis fermentation broth increases the sweet potato yield. [Results] Foliar application of B. velezensis increased the sweet potato yield, enhanced the antioxidant enzyme activity in the roots, induced changes of chloroplast ultrastructure, and led to a more compact matrix structure with enlarged intracellular starch granules. In addition, foliar application of B. velezensis caused significant changes of endophyte community structures in various parts of sweet potato plants, significantly reducing the relative abundance of Fusarium and increasing the relative abundance of Pantoea. Moreover, the foliar application significantly altered the metabolome profiles of leaves and soil. Riboflavin metabolism, zeatin biosynthesis, and isoflavone biosynthesis, which regulate growth and enhance stress resistance, were significantly upregulated in leaves. The axon regeneration pathway promoting lateral root development and the glycerophospholipid metabolism pathway promoting cell proliferation were significantly upregulated in soil. [Conclusion] B. velezensis fermentation broth exerts a plant growth-promoting effect by enhancing antioxidant capacity, improving leaf cell ultrastructure, reshaping the endophyte community structure, and activating key growth-promoting and stress response metabolic pathways in sweet potato plants. These findings provide a new theoretical foundation for the application of B. velezensis-based microbial inoculants in enhancing the sweet potato yield.

As a widely conserved interspecies quorum sensing signaling molecule, autoinducer-2 (AI-2) is involved in regulating various crucial physiological processes such as bioluminescence, chemotaxis, and biofilm formation. However, the effects of AI-2 on Halomonas elongata and its underlying mechanisms remain unreported. [Objective] To reveal the receptor that regulates the chemotaxis and biofilm formation of H. elongata in response to AI-2. [Methods] The quantitative capillary assay was employed to examine the chemotactic response of H. elongata to AI-2. We conducted protein domain identification, sequence alignment, and molecular docking of methyl-accepting chemotaxis proteins to identify the key amino acid sites in Tar1, the potential AI-2 receptor. The ligand-binding domain (LBD) of Tar1 and single-point mutants were expressed and purified, and the binding between Tar1-LBD and AI-2 was measured by the Vibrio harveyi MM32 bioluminescence assay. tar1 was deleted by homologous recombination, and the effects of AI-2 on the chemotaxis and biofilm formation of H. elongata were evaluated by quantitative capillary and biofilm formation assays. [Results] The quantitative capillary assay revealed that H. elongata exhibited chemotaxis to AI-2. Four methyl-accepting chemotaxis proteins were identified in H. elongata. Protein domain identification, sequence alignment, molecular docking, and V. harveyi MM32 bioluminescence assay demonstrated that Tar1-LBD bound to AI-2. The tar1-deleted mutant of H. elongata was successfully constructed by homologous recombination. The deletion of tar1 impaired the chemotaxis of H. elongata to AI-2, whereas the complementation of this gene restored the chemotaxis to level comparable to that in the wild-type. Furthermore, biofilm formation assay revealed that AI-2 enhanced the biofilm formation in H. elongatavia Tar1. [Conclusion] H. elongata exhibits chemotaxis to AI-2, and this signal molecule binds to the LBD of Tar1, thereby modulating chemotaxis and biofilm formation.

Probiotic products have attracted increasing attention for their potential to modulate the microbiota. However, most commercial products are designed for oral administration, and their probiotic properties relevant to topical use in the reproductive tract remain insufficiently evaluated. [Objective] To assess the probiotic properties of lactic acid bacteria (LAB) derived from probiotic products, with a particular focus on their potential for topical application, thus providing scientific evidence for their use in vaginal health. [Methods] Seven common oral probiotic products (P1-P7) containing at least two different LAB species were selected from major e-commerce platforms via keyword screening, along with one clinical probiotic product (P8). LAB strains were isolated and identified from these products. We evaluated the acid tolerance, as well as the growth characteristics under different pH conditions, of the isolates by culturing them in the media of varying pH values. The antimicrobial activities of the isolates were determined via co-culture assays with pathogenic microorganisms, while hemolysis assays and genomic comparison were conducted to assess safety. [Results] The isolation rates of LAB strains from P1 to P8 were 50.0% (2/4), 0 (0/4), 66.7% (2/3), 12.5% (1/8), 33.3% (2/6), 40.0% (2/5), 0 (0/7), and 100.0% (1/1), respectively. Most strains grew well at pH 6.0-7.0, and some maintained growth at pH 4.0. Strains P4 and P8 exhibited superior acid tolerance to the others. The inhibitory effects of different strains against common vaginal pathogens varied significantly. Strains P1-2, P5-1, P6-1 and P6-2 demonstrated moderate to strong broad-spectrum inhibitory activity against all tested pathogens. Other isolated strains except P8 exhibited inhibitory activity against Gardnerellavaginalis, while strain P8 showed weak inhibitory activities against the tested pathogens. Strains P4, P5-2, P6-1, and P6-2 achieved inhibition rates exceeding 99.73% against Candidaalbicans across all three tested inoculum concentrations, and strain P5-1 reached an inhibition rate of over 94.64%. None of the strains exhibited β-hemolytic activity, and no antibiotic resistance or virulence genes were detected. [Conclusion] Several LAB isolates from commercial probiotic products exhibited notable inhibitory activities against pathogenic microorganisms and demonstrated good safety profiles. Topical administration may therefore offer greater practical value in promoting female reproductive tract health.

[Objective] As soil acidification in southwestern China becomes increasingly severe, the labile phosphorus pool is transformed into a non-labile phosphorus pool, which reduces the availability of soil phosphorus, affecting crop yield and wasting phosphate fertilizer resources. In this study, we prepared a biochar-immobilized phosphorus-solubilizing bacterial agent with biochar as the carrier and a strain capable solubilizing both organic phosphorus and inorganic phosphorus as the immobilized strain and then optimized the preparation conditions. Furthermore, this bacterial agent was evaluated in terms of the stability and the solubilizing effects on insoluble phosphorus. [Methods] Selective media were used for the isolation of phosphorus-solubilizing bacteria from plant rhizosphere soil. The molybdenum-antimony colorimetric method was employed to quantify the ability of bacteria to solubilize phosphorus. The bacterial strain was identified through physiological and biochemical tests and molecular biological analysis. The immobilized bacterial agent was prepared by the adsorption method, and the preparation conditions were optimized by single factor experiments. The prepared agent was characterized by Fourier transform infrared spectrometry and scanning electron microscopy. Furthermore, the metabolic spectrum of organic acids and phosphatase activity were qualitatively and quantitatively tested by HPLC and the fluorescence method, respectively. [Results] The strain Klebsiella sp. was isolated for immobilization, and its abilities to solubilize lecithin and tricalcium phosphate were 236.5 mg/L and 200.3 mg/L, respectively. Genome analysis showed that the strain N107 carried 27 genes related to organic and inorganic phosphorus solubilization. The optimized preparation conditions were biochar addition of 30.0 mg/mL, N107 inoculation amount of 6.0%, immobilization temperature of 30.0 ℃, and immobilization time of 12.0 h. The bacterial agent prepared under the optimal conditions increased the phosphorus-solubilizing capacity for lecithin and tricalcium phosphate by 24.0% and 22.5%, respectively, compared with the free bacterial strain. The biochar-immobilized phosphorus-solubilizing bacterial agent contained more oxygen-containing functional groups, compared with the original biochar, its total specific surface area and external surface area increased by 61.9% and 165.1%, respectively. The mechanism of phosphorus solubilization by the immobilized bacterial agent was preliminarily analyzed. The results showed that the levels of tartaric acid, citric acid, and total acids changed significantly and the activities of acid and alkaline phosphatases in the culture medium were effectively improved, although the types of organic acids secreted by the agent had no obvious changes. The structural equation model showed that pH value was closely related to phosphatase activity and organic acid content, and the immobilized bacterial agent can promote the activation of insoluble phosphorus by increasing phosphatase activity and organic acid content. [Conclusion] The immobilized phosphorus-solubilizing bacterial agent prepared in this study provides a good bioremediation material for the activation of insoluble phosphorus. This study provides an innovative perspective for developing green remediation strategies based on microbiomes.

[Objective] To investigate the metabolite differences among different varieties and grades of flue-cured tobacco, as well as the impacts of nicotine-degrading bacteria on the quality of different grades of tobacco leaves. [Methods] This study employed untargeted metabolomics to identify and analyze metabolites in fermented tobacco leaves of ‘Yunyan 87’ and ‘Yunyan 97’, specifically B2F and C2F grades, while also examining the influences of nicotine-degrading bacteria on the quality of different grades of flue-cured tobacco leaves. [Results] There were significant metabolite differences between tobacco leaves of different varieties and grades. A total of 131 differential metabolites were identified between the samples of ‘Yunyan 87’ and ‘Yunyan 97’, while 138 differential metabolites were identified between B2F and C2F grades. These differential metabolites mainly included amino acids, flavonoids, alkaloids, and their derivatives. Analysis of KEGG metabolic pathways and enrichment levels for differential metabolites across different varieties and grades all indicated that flavonoid biosynthesis pathways were the most prominent. Furthermore, this study successfully isolated two bacterial strains, Pseudomonas sp. TR9 and Pseudomonas sp. TR14, from tobacco-cultivated soil, both capable of utilizing nicotine as the sole carbon and nitrogen source. Inoculation of the strain combination into different grades of tobacco leaves significantly reduced the content of nicotine, protein, and starch in lower-grade tobacco leaves. [Conclusion] This study reveals the mechanism by which varieties and grades affect the quality of tobacco leaves through the flavonoid biosynthesis pathways, and verifies the improvement effects of nicotine-degrading bacteria on low-grade tobacco leaves, providing theoretical support for the improvement of flue-cured tobacco quality and the optimization of fermentation processes.

Hyperuricemia is a pathological phenomenon in which the metabolism of uric acid in the human body is disrupted and blood uric acid levels remain above normal. In recent years, gut microbiota has become a research hotspot for various metabolic diseases, serving as a potential new target for the prevention and treatment of hyperuricemia. This article reviews the metabolic pathways and physiological effects of uric acid in the human body and elucidates the regulatory mechanisms of gut microbiota on hyperuricemia. Such mechanisms include inhibiting uric acid synthesis by the breakdown and internalization of purines, degrading uric acid and promoting uric acid excretion, repairing intestinal barriers, influencing intestinal metabolites, and regulating intestinal immunity. In addition, this article summarizes the potential applications of optimizing dietary structure, taking probiotics and prebiotics, and fecal microbiota transplantation in the treatment of hyperuricemia, providing new ideas and references for the prevention and treatment of hyperuricemia.

[Objective] To develop a low-cost and highly sensitive endotoxin detection reagent and detection method with recombinant horseshoe crab factor C enzymogen (rFC). [Methods] The Bac-to-Bac baculovirus expression system was used to express rFC in Sf9 cells and the activity of rFC was measured by the end-point fluorescence assay with endotoxin. The conditions of protein expression were optimized, and ion exchange was used for crude enzyme separation. An endotoxin detection method with rFC based on end-point fluorescence assay was established after the reaction conditions were optimized. Furthermore, the established method was compared with the conventional limulus amebocyte lysate (LAL). [Results] The expression level of rFC was 110.42 mg/L, increasing by 4.75 times. The linear range of endotoxin detection was 0.005-1.000 EU/mL in 1 h, with a good linearity and the limit of detection being 0.005 EU/mL. The applicability rate of this method for actual samples was 92.45%. The consistency of the detection results was 83.67%, and 89.80% of the samples had consistent detection limits with LAL. [Conclusion] This study achieves the efficient expression of rFC and establishes an endotoxin detection method with higher sensitivity than LAL, which has great potential for application.

To systematically analyze the current status and research trends and identify the key research hotspots in the field of gut microbiota and metabolic syndrome (MetS) from 2005 to 2024, thus providing references for future research and intervention strategies. Relevant literature on gut microbiota and MetS was retrieved and screened from the Web of Science Core Collection. Bibliometric tools such as VOSviewer, CiteSpace, and the R package bibliometrix were used to analyze the publication trends, countries and institutions, research themes, and emerging hotspots. A total of 4 210 relevant publications were included. The annual number of publications showed an increasing trend, which was particular rapid after 2010. China and the United States led in publication output, and major research findings were published in journals such as Nutrients, Gut, and Nature. Research hotspots primarily covered the fields of nutrition and diet, biochemistry and molecular biology, and microbiology. Keyword evolution analysis revealed a shift from early descriptive studies on gut microbiota composition to mechanism investigations focusing on dysbiosis-related pathways such as energy metabolism, inflammatory responses, and gut-organ axes. Co-occurrence analysis further indicated that key microbial metabolites (e.g., short-chain fatty acids and bile acids) and microbiota-targeted interventions (e.g., probiotics and fecal microbiota transplantation) had become focal points in recent studies. This bibliometric study comprehensively summarizes the research landscape of gut microbiota and MetS and highlights emerging trends and directions. Given the limitations of conventional therapies in terms of targeting specificity, patient adherence, and long-term safety, microbiota-based interventions offer a promising breakthrough for the prevention and treatment of MetS, providing valuable theoretical support for future precision medicine.