Abstract:Quorum sensing (QS) is a communication system in bacteria that coordinates group behaviors. QS systems widely found in nature enhance the reproductive capacity of microbial communities by sensing the external environment. Due to its natural properties of autonomous perception, density-dependence coupled with modularity, and ease of engineering modification, QS has achieved rapid development and application, facilitated by synthetic biology technology. The elucidation of QS mechanisms has laid the foundation for the design of genetic circuits, which are then applied to verify and perform expected biological functions. However, how to ensure the effectiveness and functional stability of QS gene circuits is a major challenge in synthetic biology applications. Therefore, this review first summarized the natural and common QS regulatory mechanisms and the development of genetic circuits. Subsequently, an analysis and summary of the assembly optimization in intercellular communication were provided, followed by an overview of its application progress in communities. Finally, suggestions and development trends were proposed for the better application of QS genetic circuits in microbial engineering.

Abstract:Bacillus subtilis serves as a widely used elite microbial platform, playing a pivotal role in biomedicine and food industries. It is extensively employed in synthesizing a variety of enzymes, compounds, pharmaceuticals, and health products. The advancing genetic engineering and metabolic engineering approaches, together with comprehensive genomic sequences, genetic toolkits, and bioinformatics tools enable exploring the potential applications of B. subtilis. This exploration offers valuable guidance for related industries. Nonetheless, challenges remain in optimizing metabolic pathways to enhance desired yields, investigating the synthesis potential for other substances, and developing more efficient adapter biobricks. Additionally, ensuring the safety of B. subtilis in biomedicine and food is crucial to prevent adverse effects. This review encapsulates the use of B. subtilis in biosynthesis of medicine and functional foods, discusses the current application status of B. subtilis as a future green and safe microbial platform, and prospects the trends and technical development of its products. This review lays the groundwork for further probing into the application and economic value of B. subtilis, showcasing its immense potential for green and sustainable development.

Abstract:The signal transduction system helps microorganisms adapt to complex environmental changes. In Gram-negative bacteria, the two-component system (TCS) composed of the sensor kinase GacS and the response regulator GacA is a global regulatory system and plays an important role in regulating secondary metabolism and signal communication. The GacS/GacA two-component system regulates multiple life activities of bacteria, including the adaptation to soil environment, the pathogenicity in plants, and antibiotic resistance. GacS and GacA in Pseudomonas present highly homologous structures and discrepant regulatory mechanisms in different species and pathogenic variants. This paper summarizes the research progress of the GacS/GacA two-component system in Pseudomonas from signal transduction, regulatory network, and main regulatory functions. This review is expected to provide reference for the research on the mechanism of the GacS/GacA two-component system in regulating bacterial pathogenicity.

Abstract:As one of the key pathogenic bacteria of periodontitis, Porphyromonas gingivalis is closely associated with the occurrence and development of Alzheimer’s disease (AD). P. gingivalis promotes the development of AD by secreting various virulence factors, such as lipopolysaccharides (LPS), gingipains, and outer membrane vesicles (OMVs). These virulence factors are capable of inducing systemic inflammation, β-amyloid (Aβ) deposition, Tau protein phosphorylation, neurotoxicity, and damage to the blood-brain barrier (BBB), playing a role in the pathogenesis of AD. This review summarizes the association between P. gingivalis and AD, aiming to provide a new target for the prevention and treatment of AD.

Abstract:Drought is a serious abiotic stress dramatically reducing crop yields, which urgently necessitates the development and application of environmentally friendly biological methods capable of promoting plant growth. We retrieved 1 986 articles on drought-tolerant microorganisms from the CNKI and the Web of Science that were published during 2003−2023. By reviewing these articles, we summarized the research hotspots and progress in this field and discussed the biodiversity of drought-tolerant microorganisms and the mechanisms of these microorganisms in protecting plants from drought stress. This review aims to provide guidance for the isolation and screening of drought-tolerant microorganisms and the creation of effective microorganism-plant combinations in response to drought and offers new solutions for the challenges posed by global drought to agriculture and food production.

Abstract:Spinal cord injuries, as a destructive disorder of the central nervous system, not only impair the patients’ motor and sensory abilities but also lead to varying degrees of cognitive dysfunction, affecting the quality of life of the patients. In recent years, studies have found a close association between gut microbiota and central nervous system function, especially concerning the mechanism of cognitive dysfunction in the individuals with spinal cord injuries. This paper reviews the progress in the role of gut microbiota in cognitive dysfunction after spinal cord injuries via three pathways: the hypothalamic-pituitary-adrenal axis, neurotransmitters, and the immune system.

Abstract:The production of green and high-quality agricultural products has become a new trend, especially in the context of developing green agriculture. However, the excessive use of fertilizers and pesticides in orcharding has caused severe pollution of the farmland environment, resulting in low-quality fruits and posing a threat to human health. Microbial fertilizers are a new type of green fertilizers that contain beneficial microorganisms to enhance soil ecology, promote plant development, and increase productivity and can reduce the application of chemical fertilizers. Although the current research on microbial fertilizers is limited to a few microbial species and single crops, the studies have shown the potential of microbial fertilizers in improving soil, yield, and plant quality, while the mechanisms and effectiveness of these fertilizers need systematic investigation. Therefore, this article reviews the mechanisms of microbial fertilizers in improving soil ecology and enhancing plant resistance to disease and stress. Taking fruit trees as an example, we focus on the application of microbial fertilizers in improving the fruit yield and quality as well as the agricultural environment. In addition, we discuss the technical bottlenecks and put forward new research ideas and directions, aiming to provide theoretical references for improving the agricultural environment and promoting sustainable agricultural development.

Abstract:[Background] (R,S)-2-chloro-1-(6-fluoro-3,4-dihydro-2H-1-benzopyran-2-yl)-ethanol [NEB-8(R,S)] is an important chiral intermediate for the synthesis of nebivolol. It is synthesized by asymmetric reduction of aromatic heterocyclic ketones under the catalysis of ketoreductase. However, the low catalytic efficiency and poor enantioselectivity of natural ketoreductases and the unclear source of commercial ketoreductases result in low conversion rates. [Objective] To develop a new method for the asymmetric synthesis of NEB-8(R,S) with high enantioselectivity, good stability, and high catalytic efficiency. [Methods] We mined a ketoreductase gene mradh from Modestobacter roseus based on the existing protein sequences of ketoreductases, expressed this gene in Escherichia coli BL21(DE3), and determined the enantioselectivity of the protein. Furthermore, we characterized the enzymatic properties and optimized its reaction conditions under high concentrations of substrate. [Results] In this study, a novel ketoreductase MrADH was identified which belongs to the medium-chain alcohol dehydrogenase superfamily and exhibits both oxidative and reductive activities. The oxidation and reduction activities of MrADH were the highest at pH 9.5 and pH 7.0, respectively. MrADH had good reduction and oxidation activities for ketoesters, meta-substituted aromatic ketones, heterocyclic ketones, and secondary alcohols. In addition, it had a half-life of up to 207.0 h at 40 ℃, demonstrating good thermal stability. MrADH efficiently catalyzed the reduction of 600 mmol/L (S)-2-chloro- 1-(6-fluoro-3,4-dihydro-2H-1-benzopyran-2-yl)-ethanone to synthesize the product alcohol with the enantiomeric excess (e.e.) near 100% and a conversion rate of 99.7%. [Conclusion] The ketoreductase from M. roseus can efficiently synthesize high-optical purity intermediate of nebivolol hydrochloride, laying a foundation for the synthesis of nebivolol hydrochloride.

Abstract:[Background] Saccharomyces cerevisiae has the high-affinity myo-inositol transporter Itr1, and we have constructed a S. cerevisiae strain capable of transporting exogenous myo-inositol via Itr1 during the synthesis of glucaric acid. However, the Itr1 degradation induced by myo-inositol hinders the efficient transport of exogenous myo-inositol, limiting the potential for increasing the glucaric acid production. [Objective] To study the effects of mutating lysine residues at potential ubiquitination sites located at the N-terminus and C-terminus of Itr1 on the degradation of Itr1 and further investigate the effects of these mutations on extracellular myo-inositol uptake and glucaric acid biosynthesis in budding yeast cells. [Methods] Different genetic elements were fused by fusion PCR, and the obtained fragments were then integrated on the S. cerevisiae genome by homologous recombination to construct engineered stains containing Itr1 mutants and Itr1 and GFP (green fluorescent protein, GFP) fusion protein, respectively. The membrane localization of the fusion protein was visualized by fluorescence microscopy. The production of glucaric acid was quantified by HPLC, RNA sequencing and qRT-PCR were employed to analyze changes in the intracellular gene transcription levels. [Results] The C-terminal mutation weakened Itr1 degradation. The proportion of cells with complete Itr1 membrane localization in the N-terminal mutant strain increased in a short term of fermentation. The glucaric acid production and biomass of the N-terminal mutant strain during shake flask fermentation significantly increased compared with those of the control strain. Furthermore, the N-terminal mutant strain presented up-regulated expression of ino1 and inm1 and down-regulated expression of pis1, which increased the accumulation of intracellular myo-inositol and facilitated the flow of myo-inositol to glucaric acid synthesis. On this basis, the fermentation conditions were optimized, after which the glucaric acid titer reached 3.30 g/L, 95.3% higher than that of the control strain. [Conclusion] This study confirmed the weakening effect of the C-terminal mutation on the degradation of Itr1 and discovered that the N-terminal mutation increased glucaric acid production. The findings lay a theoretical foundation for further improving myo-inositol utilization and glucaric acid production.

Abstract:[Background] Orchids form a close symbiotic relationship with mycorrhizal fungi throughout their life cycle. The symbiotic fungi provide essential nutrients during seed germination and seedling establishment of orchids. [Objective] To reveal the diversity and dynamics of the endophytic (symbiotic) fungi of Dendrobium devonianum seedlings at different developmental stages. [Methods] The seedlings of D. devonianum were developed from in situ symbiotic seed germination, and the root samples were collected from the seedlings two, three, four, and six months after germination, respectively. Amplicon sequencing was employed to analyze the fungal community composition, abundance, and diversity. [Results] A total of 944 amplicon sequence variants (ASVs) were obtained from roots of seedling at all the four stages, belonging to 218 genera, 144 families, 71 orders, 24 classes of 5 phyla. The dominant fungal genera in D. devonianum seedlings of two to four months were Serendipita, Talaromyces, and Curvularia, respectively, while Talaromyces and Sebacina were dominant in the roots of six-month-old seedlings. The dominate symbiotic fungi underwent two shifts during seedling development. The first switch was from Tulasnella to Serendipita in the seedlings less than two months old and the second was from Serendipita to Sebacina in the seedlings of four to six months old. [Conclusion] The fungi in D. devonianum seedlings experience dynamic changes. The seedlings may actively choose the most compatible fungal partners or may be passively associated with the mycorrhizal fungi with high relative abundance in the environment. These new insights into the dynamics of symbiotic fungi during orchid seedling development offer a scientific basis to isolate fungal strains that might be employed to promote the growth and improve the survival of D. devonianum seedlings.

Abstract:[Background] Microbial degradation is an effective measure to promote the decomposition and transformation of lignocellulose. [Objective]To investigate the degradation efficiency of straw and evaluate its adaptability and stability to natural carbon sources. [Methods] To study the straw degradation efficiency of the microbial consortia M1, M2, M14, M36, and M44 screened out in the previous study and evaluate their adaptability and stability when being cultured with natural carbon sources. We used sterilized (S) corn stover and non-sterilized (NS) corn stover as the carbon sources for restrictive passage of M1, M2, M14, M36, and M44. [Results] Neither the degradation rate of corn stover nor the enzyme activity had significant difference across different passages, which indicated that the microbial consortia M1, M2, M14, M36, and M44 could maintain stable straw degradation efficiency. M1, M2, M14, M36, and M44 in the NS group exhibited the corn stover degradation rates of 30.99%, 33.41%, 33.97%, 31.76%, and 35.05%, respectively, which were higher than those in the S group. The richness and diversity of microbial consortia cultured with different carbon sources became similar as the passage continued. Specifically, the relative abundance of Firmicutes and Trichococcus in M1, M2, M14, M36, and M44 in the NS group was 31.5%, 48.97%, 41.95%, 2.64%, 67.41% and 27.95%, 41.71%, 33.63%, 15.75%, 63.22%, respectively, higher than that in the S group. [Conclusion] The microbial consortia demonstrated robust stability and adaptability when being cultured with non-sterilized corn stover, showcasing promising advantages and potential utility.

Abstract:[Background] In recent years, with the expansion of the animal farming scale, a large amount of breeding sewage rich in heavy metal ions is produced. The conventional nitrogen removal technologies have limitations in treating such sewage, demonstrating reduced nitrogen removal efficiency. [Objective] To isolate and screen heavy metal-tolerant heterotrophic nitrifying-aerobic denitrifying bacteria from sewage and sludge of a sewage treatment plant and study the nitrogen removal efficiency of the isolates. [Methods] We identified the strains by observing the morphological characteristics of colonies and cells and analyzing the 16S rRNA gene sequences. With NH₄⁺-N, NO₃⁻-N, and NO₂⁻-N as the only nitrogen sources, the nitrification and denitrification performance of the strains, as well as the removal capacity of ammonia nitrogen in the presence of heavy metals (Cu, Zn, Cd, Cr, and Pb), was investigated. [Results] Two strains of heterotrophic nitrifying-aerobic denitrifying bacteria were isolated from sewage and sludge, identified as Providencia sp., and named WS-A and WH-K. Both WS-A and WH-K could grow in the media with (NH₄)₂SO₄, NaNO₃, or NaNO₂ as the only nitrogen source, with the NH₄⁺-N removal rates of 84.93% and 84.48% within 48 h, the NO₃⁻-N removal rates of 82.5% and 86.7%, and the NO₂⁻-N removal rates of 93.60% and 93.84%, respectively. WS-A and WH-K showcased the ammonia nitrogen removal rate more than 80% in the presence of 100 mg/L Zn²⁺ and the ammonia nitrogen removal rate within the range of 56% to 77% in the presence of 1 000 mg/L Cu²⁺ or 80 mg/L Cr³⁺, Cd²⁺,and Pb²⁺. [Conclusion] We screened out two strains of heterotrophic nitrifying-aerobic denitrifying bacteria showing good nitrogen removal performance under the stress of five heavy metal ions and examined their heavy metal tolerance. The findings provide technical guidance for practical application.

Abstract:[Background] With rich metabolites and unique physiological properties, Dunaliella has wide applications in the pharmaceutical, food, aquaculture, chemical, and light industries. [Objective] To analyze the factors affecting the biomass of Dunaliella and the optimal culture conditions with a view to increasing the biomass of Dunaliella and identify the secondary metabolites of Dunaliella under the optimal culture conditions. [Methods] D. pseudosalina ZBY-1 was isolated by the culture method and identified by 18S rRNA gene sequencing. The growth conditions (nutrients and concentrations) were optimized by single factor and orthogonal experiments. The secondary metabolites of strain ZBY-1 cultured under the optimal conditions were then analyzed by LC-MS. [Results] The strain ZBY-1 showcased the best growth performance at 10% NaCl, pH 8.5, and 25 ℃. The optimal carbon, nitrogen, and phosphorus sources and their concentrations for this strain were NaHCO₃ 1.26 g/L, CO(NH₂)₂ 0.84 g/L, and NaH₂PO₄ 0.06 g/L, respectively. The cell density of strain ZBY-1 cultured under the optimal conditions reached (2.57±0.12)×10⁷ cells/mL, which increased by 1.25 times compared with that before optimization. LC-MS results showed that secondary metabolites were mainly terpenoids, alkaloids, phenylpropanoids, and amino acid-related compounds. The enriched metabolite pathways were the cofactor biosynthesis pathway, plant-derived metabolite biosynthesis pathway, and the ABC transport pathway. [Conclusion] Zabuye Salt Lake has a special geographical location, whereas the algal resources remain to be exploited. The isolated strain ZBY-1 can adapt to the high saline-alkali environments, which provide a basis for subsequent development and application of the metabolites of this strain.

Abstract:[Background] The quorum sensing signal molecule AI-2 is spontaneously cyclized from 4,5-dihydroxy-2,3-pentanedione (DPD), which is derived from S-adenosylhomocysteine (SAH) via catalysis by S-ribosylhomocysteinase (LuxS) and S-adenosylhomocysteine nucleosidase (Pfs, also known as MtnN). AI-2 regulates a variety of physiological processes including chemotaxis, bioluminescence, and biofilm formation of bacteria. However, the effect of AI-2 on the salt adaptability of Halobacillus halophilus has not been reported. [Objective] To synthesize AI-2 in vitro and reveal its effect on the salt adaptability of H. halophilus. [Methods] The relationship between luxS transcript level in H. halophilus and salt concentration was assessed by real-time quantitative PCR. Then, multiple sequence alignments of LuxS, MtnN-1, MtnN-2, and MtnN-3 were performed to identify the key amino acid sites, and the four proteins were heterologously expressed and purified for the synthesis of AI-2 in vitro. Finally, luxS was knocked out by homologous recombination, and the effect of luxS on the salt adaptability of H. halophilus was studied through salt stress assay, intracellular compatible solute content determination, and biofilm formation assay. [Results] The transcript level of luxS in H. halophilus increased with the elevation in salt concentration and was positively regulated by the Cl^– concentration. The growth curve and bioluminescence assay showed that as H. halophilus grew, the AI-2 activity in the supernatant of the culture medium reached the maximum at 15 h, and it enhanced with the increase in salt concentration. The in vitro enzymatic reaction assay showed that LuxS collaborated with MtnN-1 or MtnN-2 to catalyze the synthesis of AI-2. The luxS-deleted mutant of H. halophilus was successfully constructed by homologous recombination. Under a low salt concentration (0.5 mol/L NaCl), there were no significant differences in the growth curves between the wild type, luxS-deleted mutant, and complementary strain. However, under high salt (3.5 mol/L NaCl), the luxS-deleted mutant grew slow, while the complementary strain demonstrated a growth trend similar to that of the wild type. Furthermore, the deletion of luxS led to decreases in the survival rate, intracellular compatible solute content, and biofilm formation of H. halophilus under salt stress, whereas the complementary strain could recover to the levels close to those of the wild type. [Conclusion] H. halophilus can synthesize AI-2, and its luxS is positively regulated by the Cl^– concentration and plays an important role in regulating salt adaptability. The findings provide a basis for further research on the regulatory mechanism of salt adaptability in H. halophilus.

Abstract:[Background] Talaromyces marneffei is an important lethal pathogenic fungus. [Objective]To investigate the basic characteristics and expression patterns of the Septin gene family in T. marneffei. [Methods] In this study, bioinformatics methods were used to identify the members of the Septin gene family in T. marneffei and analyze gene structure, physicochemical properties, secondary and tertiary structure, and subcellular localization. Additionally, real-time fluorescence quantitative PCR was employed to analyze the expression of the Septin gene family in the mycelial phases and yeast phases, respectively. [Results] This paper identified 5 members of the Septin gene family, with amino acid lengths ranging from 346 to 575 aa. All members possess GTP-CDC binding domains and are hydrophilic proteins. Subcellular localization was mainly located in the cell nucleus and mitochondrial matrix. The secondary structure is mainly composed of α-helices and random coils, with a complex tertiary structure. The core Septin is highly conserved among different pathogenic fungi. The mRNA expression levels of TmSep2 and TmSep4 were significantly higher in the yeast phase compared to the mycelial phase, while the mRNA expression level of TmSep5 was significantly lower. The mRNA expression levels of TmSep1 and TmSep3 showed a slight increase in the yeast phase compared to the mycelial phase but without significant differences. [Conclusion] The expression of Septin genes varies in different phases of T. marneffei during the dimorphic transition, with some significant differences, which implies the potential roles of Septin in the dimorphic transition and pathogenesis of T. marneffei. This study provides a theoretical basis for further exploration of the functions and regulatory mechanisms of Septin in T. marneffei.

Abstract:[Background] Studies have shown that some microorganisms can promote the growth and improve the salt tolerance of crops. [Objective] To study the physiological and biochemical characteristics of a strain named F-06 isolated from a saline-alkali field in northern Ningxia, and evaluate the growth-promoting effect of the strain on maize seedlings under salt stress. [Methods] Strain F-06 was identified based on the morphological, physiological, and biochemical characteristics and the 16S rRNA gene sequence. Its growth-promoting effect on maize seedlings was evaluated by the sand culture under 100 mmol/L NaCl stress. [Results] Strain F-06 was a short rod-shaped Gram-negative bacterial strain capable of growing normally within the ranges of 2%–10% NaCl and pH 8.0–11.0. It can fix nitrogen, solubilize organophosphorus and potassium, and produce siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and indole-3-acetic acid (IAA) and was identified as Serratia plymuthica. Compared with the control group without NaCl, 100 mmol/L NaCl significantly inhibited the growth of maize seedlings. The plant height, stem diameter, fresh weight of stems and leaves, dry weight of stems and leaves, fresh root weight, and dry root weight of maize seedlings in the NaCl+F-06 group increased by 11.36%, 15.97%, 36.63%, 18.42%, 8.54%, and 10.0%, respectively, compared with those in the NaCl group (P<0.05). In addition, the leaves of maize seedlings in the NaCl+F-06 group showcased increased content of proline, decreased content of chlorophyll and malondialdehyde (P<0.05), superoxide dismutase (SOD) activity decrease of 5.3%, peroxidase (POD) activity decrease of 61.9%, and catalase (CAT) activity increase of 40.33% compared with the NaCl group (P<0.05). [Conclusion] Strain F-06 promoted the growth of maize seedlings exposed to 100 mmol/L NaCl.

Abstract:[Background] Tea gray blight is a major disease attacking tea plants. Chemical methods are mainly used to control this disease, and the chemical residues and pathogen resistance caused by chemical control need to be solved urgently. Exploring biocontrol microorganisms is an important measure to ensure the safety and increase the yield of tea production. [Objective] To screen the Bacillus strains with inhibitory effects on tea gray blight and clarify the inhibitory activity and field control effect of the strain screened out, providing support for the development of biocontrol methods for tea gray blight. [Methods] A plate confrontation experiment was conducted to screen out the strain with antagonistic effect on Pseudopestalotiopsis theae, the pathogen causing tea gray blight. The strain was identified based on morphological, physiological, and biochemical characteristics and sequence analysis of the 16S rRNA. Various plates were utilized to examine the production of enzymes lysing fungal cell walls by the strain. Plate confrontation tests were conducted to determine the inhibitory activities of different metabolites produced by the strain on Ps. theae. The inhibition rates against nine common species of plant pathogenic fungi were measured to assess the antifungal spectrum of the strain. Finally, field experiments were conducted to evaluate the effects of the strain on tea gray blight and yield of tea plants. [Results] A strain kc-16 with antagonistic effect on Ps. theae was screened out, with the inhibition rate of (79.62±0.82)%, and it was identified as Bacillus subtilis subsp. inaquosorum by morphological, physiological, and biochemical characteristics and 16S rRNA gene sequence analysis. Strain kc-16 demonstrated nitrogen-fixing, iron carriers producing and phosphorus-solubilizing abilities but lacked the potassium-solubilizing ability, and it could secrete protease, cellulase, β-1,3-glucanase, and chitinase. In addition, strain kc-16 inhibited nine species of pathogenic fungi, with inhibition rates ranging from 46.67% to 81.00%. The extracellular substances of strain kc-16 exhibited inhibitory effects on the pathogen of tea gray blight. Specifically, the cell-free filtrate, crude protein extract, volatile substances, and non-volatile substances of this strain showcased the inhibition rates of 69.00%, 58.00%, 47.50%, and 78.71%, respectively. In field experiments, B. subtilis subsp. inaquosorum showed tea gray blight-preventing and growth-promoting effects on tea plants. It reduced the incidence of tea gray blight while increasing the fresh weight of tea leaves (one bud and one leaf) by 25.0% compared with the blank control. [Conclusion] B. subtilis subsp. inaquosorum inhibits tea gray blight and promotes the growth of tea plants, demonstrating the application potential. The results of this study provide theoretical support for the future research and application of this strain in the control of plant diseases.

Abstract:[Background] The amount of phosphorus available for direct absorption and utilization by plants in the soil is limited, and the traditional methods of applying phosphorus fertilizer can lead to environmental pollution and problems such as damage to soil structure and function. [Objective] This study aimed to investigate the salt tolerance and phosphorus solubilization mechanism of Bacillus megaterium and Providencia rettgeri and their effects on soybean seed germination, to lay a solid foundation for inoculation and colonization of plant rhizosphere in saline-alkali soil. The problem of phosphorus deficiency in crops is expected to be solved through the phosphorus-solubilization effect of phosphorus-solubilizing bacteria in rhizosphere soil. [Methods] The inoculation with needlepoint, plate method, liquid culture method, and box germination experiment were conducted to analyze the salt-alkali tolerance, phosphorus-solubilization effect, and promotion effect on soybean germination of two phosphorus-solubilizing bacteria strains. [Results] Both B. megaterium and P. rettgeri could grow in environments with salt concentrations ranging from 0−10% and 0−6%, and pH values ranging from 7.0 to 12.0. The D/d values of B. megaterium and P. rettgeri on plates reached 2.17 and 2.05, respectively. The value of dissolved phosphorus in the liquid medium reached a peak on the 4th day, which were 355.53 and 272.17 mg/L, respectively, and the pH value of the culture medium decreased from 7.5 to 4.61 and 4.81, respectively. The phosphorus solubilization effect of B. megaterium and P. rettgeri showed a trend of “slightly increasing at first and then continuously decreasing” with the increase of NaCl concentration, and the pH value showed a trend of “slightly decreasing at first and then continuously increasing”. The best phosphorus solubilization effects were observed at NaCl concentrations of 0.4 and 0.2 mol/L, respectively, with the peak solubilization value of 364.35 and 285.58 mg/L, and the pH value of the culture medium decreased to the minimum value of 4.28 and 4.73, respectively. B. megaterium and P. rettgeri both increased the germination rate of seeds and elongation of the embryonic axis and radicle. Compared with the control group, in normal environments, the average germination rate, and the embryonic axis and radicle elongation rate of soybeans after soaking in the two bacterial solutions were 2.70%, 10.10% and 9.00%; in NaCl-treated environments, the corresponding value were 5.40%, 19.40% and 20.30%. [Conclusion] Both strains have strong salt tolerance and phosphorus solubilization effect and can promote seed germination, providing a theoretical basis for the inoculation and application of phosphorus-solubilizing bacteria.

Abstract:[Background] The pathogen responsible for quinoa Choanephora rot is Choanephora cucurbitarum. However, the metabolic changes of quinoa in response to the infection remain unclear. [Objective] We studied the changes of metabolites and key metabolic pathways in quinoa after infection with C. cucurbitarum, aiming to understand the physiological and biochemical mechanisms of the disease. [Methods] We employed non-targeted metabolomics and multivariate statistical analysis to investigate the changes in metabolites and metabolic pathways in quinoa stems after infection with C. cucurbitarum. [Results] Compared with the control, infection with C. cucurbitarum in quinoa resulted in 512 differential metabolites (P<0.01), including 283 upregulated metabolites and 229 downregulated metabolites. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed 19 main differential metabolites in the quinoa stems in response to infection (P<0.05). These differential metabolites were enriched in four metabolic pathways: arachidonic acid metabolism, linoleic acid metabolism, alpha-linolenic acid metabolism, and flavone and flavonol biosynthesis. [Conclusion] C. cucurbitarum infection leads to changes in arachidonic acid metabolism, linoleic acid metabolism, α-linolenic acid metabolism, and flavone and flavonol biosynthesis in quinoa. The accumulation of jasmonic acid from α-linolenic acid metabolism and the blocked biosynthesis of flavone and flavonol may be involved in the response of quinoa to C. cucurbitarum infection.

Abstract:[Background] Brown rot is one of the most destructive diseases in peaches worldwide, causing serious economic loss of the peach industry. [Objective] To identify the causative agent of peach brown rot in Taigu District of Shanxi Province and screen efficient antagonistic yeast against the pathogen causing peach brown rot. [Methods] The fungus causing brown rot was isolated from the symptomatic fruits of the peach variety ‘Cuiyu’ and identified by morphological observation, pathogenicity test, and molecular methods. The antagonistic yeast strains were screened by in vitro and in vivo assays and identified based on morphological, physiological, biochemical characteristics and molecular evidence. Moreover, the activities of defense-related enzymes and other indicators were determined to evaluate the effects of the antagonistic yeast treatment on peach resistance to brown rot. [Results] Monilinia fructicola was identified as the main fungus causing the brown rot of peach fruits in Taigu District of Shanxi Province. The optimal antagonistic yeast strain HYA-4.1 was identified as Wickerhamomyces anomalus, which showed an inhibition rate of 78.31% on the mycelia of M. fructicola and increased the activities of antioxidant-related enzymes in peach fruits. The results suggested that the strain inhibited peach brown rot. [Conclusion] We identified the causative agent of peach brown rot and screened out an antagonistic yeast strain with significant inhibitory effect, which provided a reference for the screening and application of biocontrol strains.

Abstract:[Background] Soil salinization is a global problem, and there are a large number of undeveloped functional microorganisms in the rhizosphere of salt tolerant plants, such as plant growth-promoting rhizobacteria (PGPR). These microorganisms can help plants resist salt alkali stress and promote plant growth through their own growth promoting functions. [Objective] This study screened plant growth-promoting rhizobacteria (PGPR) with salt-alkali tolerance and evaluated their growth-promoting effects, aiming to provide candidate strains for the development of microbial fertilizers for saline-alkaline land. [Methods] A bacterial strain Bachu49 with salt-alkali tolerance was isolated from the rhizosphere soil of wild Tamarix chinensis in Kashgar Prefecture of Xinjiang. This strain Bachu49was identified based on morphological, physiological, and biochemical characteristics and 16S rRNA gene sequence. Multiple media for functional identification were used to examine the growth-promoting effects [solubilizing potassium, fixing nitrogen, solubilizing phosphorus, synthesizing indole-3-acetic acid (IAA), secreting 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and producing siderophores] of Bachu49. The Petri dish with two compartments was used to examine the production of volatile acid substances by Bachu49. Finally, the effects of Bachu49 on the growth of Arabidopsis and maize seedlings were analyzed by plate and pot experiments, respectively. [Results] A strain Bachu49 with salt-alkali tolerance was isolated from the soil samples. This strain was identified as Alkalibacterium sp. and named Alkalibacterium sp. Bachu49. Strain Bachu49 had the effects of fixing nitrogen, solubilizing organic phosphorus, and synthesizing IAA. It survived within the salt concentration of 0−160 g/L and pH 7.0−11.0 and showed the ability of reducing alkali. At pH 8.0, 9.0, and 10.0, the alkali reduction rates of Bachu49 were 9.75%, 15.56%, and 20.60%, respectively. Strain Bachu49 promoted the growth of Arabidopsis and maize seedlings under salt-alkali stress. Specifically, at pH 8.0 and 2 mmol/L NaHCO₃, inoculation with strain Bachu49 increased the root length, number of lateral roots, fresh weight, and number of leaves of Arabidopsis by 239.86%, 1 952.83%, 389.71%, and 91.23%, respectively. Inoculation of this strain increased the underground fresh weight of maize seedlings by 10.14% in the presence of 15 g/kg salt-alkali, and it increased the aboveground fresh weight, stem diameter, and plant height of maize seedlings by 42.04%, 23.14%, and 40.91%, respectively, under 30 g/kg salt-alkali stress. [Conclusion] Alkalibacterium sp. Bachu49 has excellent salt-alkali tolerance and plant-growth promoting effects under salt-alkali stress. This study provides a candidate strain and a theoretical basis for the future development of specialized microbial fertilizers for saline-alkali soil.

Abstract:[Background] Bovine infectious rhinotracheitis virus (IBRV) represents a common pathogenic threat to cattle, causing substantial economic losses in the livestock industry. Therefore, it is urgent to establish a rapid detection method for IBRV. [Objective] To establish a visual rapid detection method for IBRV by leveraging recombinase polymerase amplification (RPA) in conjunction with microfluidic chip. [Methods] The ul52gene of IBRV was selected as the target fragment for molecular detection. Pseudorabies virus, herpesvirus of turkey, and duck plague herpesvirus were selected as the controls. The DNA extract dilutions of IBRV were used to evaluate the sensitivity of the established method. Thirty-four serum and nasal swab specimens from the cattle exhibiting symptoms of acute IBRV infection were used to evaluate the applicability of the established method. [Results] The size of ul52 gene amplicon was 403 bp. Sequencing results confirmed the amplicon as the ul52 gene (NC_063268.1) of IBRV, with the homology of 100%, and no amplification was observed in the control groups. The limit of detection of the established method was 6.9×10³ copies/µL. Furthermore, the established method detected IBRV in cattle with the identification number of SD0213, SD0518, and SD0701, which were consistent with the strain isolation results from both serum and nasal swab specimens. The entire process, from sample preparation to result acquisition, required 110 min. [Conclusion] We successfully developed a visual rapid molecular detection method for IBRV by combining RPA, magnetic probe capture, and microfluidic chip. The established method demonstrates good specificity and sensitivity.

Abstract:[Background] Streptococcus pluranimalium was initially reported by Devriese et al. in 1999 as a potential zoonotic pathogen with a broad range of hosts. Although this pathogen has been isolated and identified from infected tissues of several species, including cattle, sheep, pigs, and broilers, there are few studies reporting its pathogenicity, antibiotic resistance, and genomics, which remain to be studied. [Objective] This study aims to identify a S. pluranimalium strain isolated from bovine respiratory tract and analyze its pathogenicity and antibiotic resistance. The basic characteristics of the genome and some virulence factors and antibiotic resistance genes were identified by genome sequencing. [Methods] Nasal swabs were collected from diseased cattle for identification of the pathogenic bacteria by 16S rRNA sequencing. Furthermore, the pathogenicity of the isolate in rabbits and the drug susceptibility of the strain were studied. Illumina sequencing and assembly were carried out to obtain an overview of the genome of the strain. Swiss-Prot, NR, GO, COG, KEGG, CAZy, TCDB, and Pfam were used for gene annotation and function analysis. PHI, VFDB and CARD were employed to annotate the virulence factors and drug resistance genes of the strain. [Results] S. pluranimalium Bov5 was successfully isolated, which induced pulmonary septal thickening and inflammatory cell infiltration in the rabbit lung tissue. The strain was resistant to lincomycin and clindamycin and showcased intermediate resistance to streptomycin. The genome size of the strain was determined to be 2 038 579 bp (2.04 Mb). A total of 1 981 coding genes were annotated, including 100 virulence factors, 28 genes conferring enhanced pathogenicity due to mutations, and 83 antibiotic resistance genes. [Conclusion] We isolated a bovine-derived S. pluranimalium strain with strong pathogenicity, constructed the genome framework of the strain, and mined the virulence and antibiotic resistance genes. The findings laid a foundation for further studying the pathogenic genes and antibiotic resistance genes of S. pluranimalium.

Abstract:[Background] Bacterial soft rot poses a significant threat to plant roots, resulting in substantial agricultural losses. Our team identified Pseudomonas glycinae as the causative agent of bacterial soft rot in ginseng in 2023. [Objective] To delve into the genomic characteristics of P. glycinae XJFL-1, conduct a comparative genomics analysis for XJFL-1 with intra- and intergenus strains, and predict putative virulence factors and effectors of type II and III secretion systems (T2SS and T3SS, respectively). [Methods] We performed genome annotation, comparative genomics analysis, and gene family analysis to predict the genomic characteristics, genetic characteristics, and virulence genes. [Results] Genome annotation revealed the presence of genes encoding the enzymes involved in carbohydrate, amino acid, and protein metabolism, as well as key genes associated with flagellar movement, membrane biogenesis, and quorum sensing. Strain XJFL-1 was identified as P. glycinae based on ANI, dDDH, and collinearity analyses, and a high degree of intraspecific gene conservation was found for P. glycinae. Strain XJFL-1 encoded 37 plant cell wall-degrading enzymes (PCWDEs) including glycoside hydrolases (GHs), carbohydrate esterases (CEs), and polysaccharide lyases (PLs). In addition, the strain carried the genes encoding effectors of T2SS (e.g. lapA, lapB, lapC, phoA2, plcA, and cbpD) and T3SS (e.g. ipaH9.8, ipaH7.8, ipaH4.5, ipaH3, ipaH1.4, slrP, sspH2, sspH1, and NGR_a03640). However, pectinase genes were conspicuously absent. The results of the pectinase activity assay indicated that strain XJFL-1 was unable to secrete pectinase. [Conclusion] The results of comparative genomics and gene family analyses clarified the genetic relationship of strain XJFL-1 with representative strains of Pseudomonas and the intraspecific genetic characterization of P. glycinae. Additionally, the strain carried abundant genes encoding PCWDEs and effectors of T2SS and T3SS associated with pathogenicity.

Abstract:[Background] Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most serious bacterial disease in rice production. Fatty acid synthesis is one of the most important basic metabolisms in bacteria, essential for cell growth, and the synthesis of membrane phospholipid and bioactive substances. However, little is known about the functions of fatty acid synthesis-related genes in Xoo. [Objective] This study aims to investigate whether the gene PXO_01118 (XoofabZ) in the genome of Xoo strain PXO99A encodes 3-hydroxyacyl-ACP dehydratase and participates in de novo fatty acids synthesis, providing new insights into the prevention and control of bacterial leaf blight in rice. [Methods] The protein activity of XooFabZ was analyzed through allogeneic genetic complementation and in vitro enzyme activity detection. Further, genetic analysis of XoofabZ was conducted using homologous recombination principles. The pathogenicity of the replacement mutant strains to the host rice (Oryza sativa L. ssp. Japonica cultivar Nipponbare) was detected by leaf clipping. [Results] Combining allogeneic genetic complementation and in vitro enzyme activity detection to demonstrate that XooFabZ exhibits 3-hydroxyacyl-ACP dehydratase activity in the initiation and dehydration reactions of fatty acid synthesis. It was not possible to directly obtain XoofabZ gene knockout mutants, indicating that XoofabZ is an essential gene in Xoo. The pathogenicity of Escherichia coli EcfabZ gene replacement mutant strains on the host rice was significantly reduced. [Conclusion] XoofabZ is an essential gene in Xoo, encoding 3-hydroxyacyl-ACP dehydratase, participating in de novo fatty acids synthesis reactions, and the formation of pathogenicity in Xoo.

Abstract:[Background] Trichophyton mentagrophytes is a common superficial skin pathogen, and dermatophytosis caused by this pathogen has a high incidence, posing a threat to human health. [Objective] To investigate the inhibitory activity and mechanism of oleuropein against T. mentagrophytes. [Methods] We determined the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). RNA-Seq was performed for T. mentagrophytes treated with oleuropein and the obtained sequences were subjected to quality evaluation and information annotation. DESeq2 was used to identify the differentially expressed genes (DEGs), which were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. RT-qPCR was conducted to validate the results. [Results] The MIC and MBC of oleuropein against T. mentagrophytes were 400 μg/mL and 800 μg/mL, respectively. A total of 534 DEGs were identified between the treatment group and the control group, including 401 genes with upregulated expression and 133 genes with downregulated expression. The sequence has been submitted to Sequence read archive (SRA) of the NCBI, with the accession number PRJNA1091040. These DEGs were mainly enriched in pathways related to oxidative phosphorylation, amino acid metabolism, and glyoxylate and dicarboxylate metabolism, with significant expression (P<0.05). The RT-qPCR results were consistent with the results from transcriptomics, demonstrating the reliability of RNA-Seq findings. [Conclusion] We investigated the mechanism underlying the inhibitory effect of oleuropein on T. mentagrophytes, providing a theoretical basis for deciphering the antifungal mechanism of oleuropein.

Abstract:[Background] Spinal cord injury, a severe trauma of the central nervous system, causes not only motor, sensory, and autonomic nerve dysfunction but also gastrointestinal dysfunction, being not conducive to subsequent functional recovery. Studies have shown that curcumin has a therapeutic effect on spinal cord injury, while little is known about whether curcumin can regulate intestinal microbiota after spinal cord injury or not and the treatment-related pathways. [Objective] To observe the effects of curcumin on the behaviors, the spinal cord histomorphology, the diversity and metabolites of cecal microbiota, and the spinal cord transcriptomics in the rats with spinal cord injury. [Methods] A total of 50 female SD rats of 6−8 weeks and 220−240 g were randomized into a sham operation group, a model (spinal cord injury) group, and low-, medium-, and high-dose (50, 100, and 200 mg/kg, respectively) curcumin+spinal cord injury groups. Curcumin 50 mg/kg, 100 mg/kg, and 200 mg/kg was intraperitoneally injected 30 min after the establishment of the rat model of spinal cord injury, once a day for a week. The Basso, Beattie & Bresnahan (BBB) locomotor rating scale was used for scoring of the motor function. Hematoxylin-eosin staining was used to observe the histomorphological changes in the spinal cord of rats. High-throughput sequencing of the V3+V4 variable region of 16S rRNA gene was carried out to analyze the α diversity, β diversity, and relative abundance of microflora, and the levels of short-chain fatty acids were measured, on the basis of which the changes of intestinal microbiota before and after treatment were evaluated. [Results] The medium dose (100 mg/kg) of curcumin significantly improved the limb motor function after spinal cord injury, demonstrating protective and repair effects on the damaged spinal cord. Curcumin administration in the rat model of spinal cord injury improved the diversity of microbiota and elevated the levels of short-chain fatty acids. The spinal cord injury altered the signaling pathways of intestinal microbiota, which was restored after the administration of curcumin. [Conclusion] Curcumin can affect intestinal microbial diversity and increase the levels of short-chain fatty acids in the rat model of spinal cord injury, and had a therapeutic effect on rats with spinal cord injury.

Abstract:[Background] Human adenovirus species B (HAdV-B) can cause respiratory tract infections and severe pneumonia with high mortality rates. Currently, there is a lack of rapid and accurate detection methods for HAdV-B. [Objective] To develop a highly specific, sensitive, and user-friendly detection method for HAdV-B. [Methods] Conserved sequences of HAdV-B were screened in the human adenovirus E4 gene region, and specific recombinase-aided amplification (RAA) primers and CRISPR RNA (crRNA) were selected. We then established a rapid nucleic acid detection method targeting HAdV-B by combining RAA, CRISPR-Cas13a system, and easy-readout and sensitive enhanced (ERASE) nucleic acid test strip. [Results] The established method could detect HAdV-B DNA as low as 10⁰ copy/μL within 35 min, with the sensitivity comparable to real-time PCR. No cross-reactivity with other respiratory pathogens was observed. The testing results with simulated samples showed that the method can detect the weak positive samples with a Ct value of 36.19. [Conclusion] The test strip assay established in this study for HAdV-B can detect the target nucleic acids in a simple, rapid, and accurate manner without the need for specialized nucleic acid detection equipment, which provides a new method for detecting HAdV-B.

Abstract:[Background] The balance between skin microbiome and animals is crucial for the health of the hosts. Skin microbiome affects the metabolic and immune processes of the host, endowing the host with specific physiological functions. Changes in the structure and function of the skin can affect the composition of the skin microbiome. [Objective] To explore the research progress, frontiers, and prospects in animal skin microbiome and shed light on the future research by visual analysis of articles in the field published during 2009–2023. [Methods] We employed CiteSpace to visually analyze the articles about animal skin microbiome published in the Web of Science (WOS) core collection from three aspects: research progress, main research strength, and research hotspots and frontiers. [Results] Since 2012, the annual number of publications in animal skin microbiome has risen with fluctuations, indicating that research in this field has been deepening and advancing. The research in this field has expanded from the basic discipline microbiology to interdisciplinary fields. Globally, the United States had the most prominent research strength in this field, forming a collaborative network centered on universities. China ranked third in the world in terms of publications, demonstrating unique status and significant contributions. The available studies in this field mainly focused on Bartrachochytrium dendrobatidis, chytridiomycosis, skin bacteria, skin fungi, etc., and often took gut microbiota into account. [Conclusion] The research on animal skin microbiome is still experiencing rapid development and has giant research potential. Classic topics such as microbial diversity, skin diseases, host health, and immune defense will still be key research directions in the future.

Abstract:[Background] Cellulose-degrading microbes in the insect gut have gradually garnered attention from scholars. Despite the increasing research papers, systematic reviews and visual analyses of these publications remain scarce. [Objective] To explore the research status and development direction and provide a basis for the subsequent research on cellulose-degrading microbes in the insect gut. [Methods] We conducted a bibliometric analysis of 193 papers about the cellulose-degrading microbes in the insect gut that were retrieved from the Web of Science Core Collection with the time interval of 1995 to 2023. The analysis encompassed various aspects, including publication counts, keywords, host insects, research methods, and microbial species. [Results] The annual publications of cellulose-degrading microbes in the insect gut generally showed an increasing trend. Frontiers in Microbiology had the largest publication count, and Microbial Ecology maintained the highest total cites and the highest average cited frequency per paper. China ranked second in the world in terms of publication count, whereas its average cited frequency per paper fell below that of six countries (regions), including Japan, the UK, and Germany. A total of 49 host insect species were counted, of which agricultural and forestry pests accounted for 77.97%, followed by property pests such as termites (11.86%), and Coleoptera had received increasing attention for many years. A total of 135 cellulose-degrading microbial species in the insect gut were involved, belonging to 63 bacterial genera (such as Bacillus, Pseudomonas, and Klebsiella) and 14 fungal genera (such as Cladosporium, Gliocephalotrichum, and Penicillium). Carboxymethyl cellulose was the most commonly used test cellulose, and the Congo red hydrolysis circle method was the most common method for verifying the function of cellulose degradation. The conventional isolation and culture method played a key role in this field, and 16S rRNA gene sequencing was increasingly introduced for the research on microbial diversity and molecular mechanism in recent years. [Conclusion] We conduct a bibliometric analysis of the publications about the cellulose-degrading microbes in the insect gut, which helps to deepen the understanding and provide a basis for subsequent research in this field.

Abstract:[Background] Extracellular polymeric substances (EPS), polymers secreted by microorganisms, have been applied in environmental management, material science, and biomedicine. [Objective] To discuss the research status, hotspots, and trends of EPS. [Methods] We retrieved the publications related to EPS in the last 10 years from the Web of Science Core Collection and employed VOSviewer to perform the statistical analysis. [Results] The number of publications about EPS was on the rise. China had the largest number of publications, the quality of which, however, remained to be improved. The research on EPS mainly involved environmental governance, biomanufacturing, and biomineralization. The degradation of microplastics is one of the hotspots. [Conclusion] This study provides a basis for understanding the research status and trends of EPS.

Abstract:As the first class of Medical Microbiology, the “Introduction” plays a crucial role in guiding the course. Our team carried out the “student-centered” teaching design based on the results of the pre-class questionnaires and adopted the blended teaching mode of three stages-two combinations (before class, during class, and after class; online-offline). The key knowledge points of this class were linked through “3W (Who, What, Why)+1H (How)”, and the knowledge system of Medical Microbiology that was led by the “Introduction” was constructed. A multiple evaluation system combining process evaluation and terminal evaluation was established. The results showed that the improved teaching design helped students gain a deeper understanding of the importance of this course and aroused their interest in learning. Moreover, it helped them understand the course features, master the overall knowledge framework, set up learning goals, and develop effective learning schemes, thereby improving the teaching quality. Additionally, we integrated ideological and political education into the teaching process to foster students’ patriotic sentiments, scientific literacy, and professional accomplishment, thus cultivating medical talents with both virtue and ability.

Abstract:Medical Microbiology is a core compulsory course for medical students. Under the background of developing New Medicine, which emphasizes disciplinary crossing, system integration, and advanced technology, we have taken measures to reform and innovate the teaching of Medical Microbiology in view of the weakness in application ability, overall view and critical thinking, and prevention and responsibility senses. Specifically, we designed the curriculum objectives based on explicit and implicit subjects, reorganized the teaching contents aimed at cultivating systematic thinking and critical thinking, and built a teaching model characterized by four combinations (lecturing and discussion, professional knowledge and practical cases, basic knowledge and frontiers, and online blended with offline) and a developmental multiple evaluation system. The innovation results show that students’ academic performance, knowledge application ability, systematic thinking, critical thinking, professional responsibility sense, and innovation drive have been significantly improved. This study provides a new direction for the teaching reform of basic curriculums from the view of New Medicine.