Abstract:Lactic acid bacteria (LAB) have extensive applications in food and medicine fields. They are used as starters and functional probiotics in food fermentation. The activity and performance of LAB are influenced by various environmental stresses involving osmotic pressure, temperature, oxygen, acidity, and bile salts. Edible LAB can provide numerous health benefits. However, their viable counts decrease during production, storage, and digestion. This paper systematically discusses the different stressful environments faced by LAB during production, storage, and digestion, as well as their stress responses. Furthermore, this paper summarizes existing high activity protection strategies and mechanisms from two aspects: isolating from stressful environments and enhancing strain resistance. This review aims to provide theoretical support for LAB strain engineering and product development.

Abstract:Human papillomavirus (HPV) infection is a major global health challenge closely related to diseases such as cervical cancer. At present, there is no effective treatment for HPV, and thus it is essential to develop new antiviral biological agents to reduce the harm of HPV infection. Recent studies have revealed a complex relationship between HPV infection and the human microbiome, suggesting that HPV infection can disrupt the balance of the microbiome and cause immune dysfunction in the body. In recent years, studies have found that oral or topical use of specific probiotic strains can reduce HPV titers in patients and prevent viral infection-related cancers, demonstrating probiotics as a new class of anti-HPV preparations with a development value. From the molecular biological characteristics of HPV, this article systematically summarizes the pathogenic mechanism of HPV infection and explains the antiviral mechanisms of probiotics from four perspectives: inhibiting virus replication, regulating immune responses, enhancing the mucosal barrier function, and reshaping the human microbiome. This review aims to provide theoretical references for the efficient breeding and mechanism analysis of anti-HPV probiotics.

Abstract:chitooligosaccharide (COS) are degradation products of chitin or chitosan, demonstrating good biocompatibility, degradability, non-toxicity, and multiple bioactivities. COS have been widely used in food, cosmetics, composite materials, wastewater treatment, and biomedical industries. Currently, researchers mainly use physical, chemical, and biological enzyme methods to prepare COS. Physical and chemical methods have large limitations, and it is difficult to synthesize the target products with specific requirements in an efficient and green way. Bio-enzymatic preparation of COS shows a mild, controllable, and environmental friendly reaction process, overcoming the drawbacks of physical and chemical methods. The purity of COS can be improved by separation and purification techniques such as membrane separation, gel filtration chromatography, CM-SephadexC-25 ion-exchange column chromatography, and immobilized metal affinity chromatography. This review summarized the research progress in COS preparation using bio-enzymatic technology, aiming to lay theoretical foundation for high-quality industrial COS preparation. It also gave an overview of the structure, properties, and application of COS, contributing for the research on COS preparation and isolation.

Abstract:Succinic acid is an important four-carbon dicarboxylic acid widely used in the food, pharmaceutical, and chemical industries. Compared with petrochemical-based chemical synthesis methods, microbial fermentation offers an economical and environmentally friendly alternative for succinic acid production, presenting significant potential for industrial applications. Due to the robust environmental tolerance, yeast cell factories for succinic acid production have gradually become a research focus. This review centers on succinic acid production in yeast, providing an overview of metabolic engineering and regulatory strategies for constructing yeast cell factories. The research hotspots in this field include the development of succinic acid biosynthetic pathways, optimization of cofactor supply, and modification of transmembrane transport systems. Additionally, recent advances in cost-effective succinic acid biosynthesis and approaches to enhance yeast strain robustness are discussed. Finally, the review provides the prospects of yeast in succinic acid biosynthesis.

Abstract:Due to the unique spatial and functional relationship with the host, plant endophytes are known as the second genome of plants and have become a research hotspot of plant sciences and microbiology. According to the origins, plant endophytes can be classified into horizontally transmitted endophytes (HTE) and vertically transmitted endophytes (VTE). Among them, VTEs have the potential to be further transmitted into later-generation plants through propagules (both sexual and asexual propagules) to produce host effects. The behaviors and functions of VTE along host generations are likely to be an acquired “heritable” trait of the host that can be applied in agricultural practices for plant trait improvement. Therefore, in-depth understanding and research on plant VTEs are of great theoretical and practical importance. We reviewed the research advances in the diversity, transmission, and physiological and ecological functions of plant VTEs and provide perspectives for future research and application of VTE resources.

Abstract:Interactions between microbial symbionts and insects are essential for the growth, development, and reproduction of insects. This review focuses on how microbial symbionts regulate lipid metabolism in insects via signaling pathways. Microbial symbionts affect lipid metabolism in insects through a variety of mechanisms. Microbial symbionts provide lipids or lipid precursors such as steroids to their insect hosts. Microbial symbionts can also modulate host insulin signaling pathway by producing short-chain fatty acids or activating immune signaling pathways, thereby changing the lipid content of insects. In addition, microbial symbionts can activate target of rapamycin and adipokinetic hormone signaling pathways to regulate lipid metabolism in insects. Further research in the similarities and differences of these signaling pathways in different insect species is of great significance for comprehension of insect ecological adaptability and reproductive strategies, and development of new pest management strategies.

Abstract:Plants require a large amount of phosphorus for metabolic processes. However, the available phosphorus in the soil is typically less than 0.1% of total phosphorus, which is difficult to meet the growth and development of plants. The symbiosis system of ectomycorrhizal fungi and mycorrhizal helper bacteria can significantly improve the availability of soil phosphorus and promote the efficient uptake of phosphorus by plants. In this review, we discussed the solubilization and mineralization of chelated inorganic phosphorus, soluble organic phosphorus, and chelated organic phosphorus by ectomycorrhizal fungi and mycorrhizal helper bacteria. Ectomycorrhizal fungi mainly promote the solubilization of chelated inorganic phosphorus by regulating the organic acid and proton metabolism of mycorrhizal helper bacteria. They accelerate the mineralization of soluble organic phosphorus by enhancing the activities of related phosphatases in themselves and in mycorrhizal helper bacteria. Ectomycorrhizal fungi may first stimulate the mycorrhizal helper bacteria to secrete organic acids for solubilizing chelated organic phosphorus into soluble phosphorus before mineralization. Moreover, we explored the molecular mechanisms of metabolite signal exchange and secretion in the symbiosis system and outlined the prospects for studying the interactions between ectomycorrhizal fungi and mycorrhizal helper bacteria in promoting plant phosphorus uptake.

Abstract:Senescence, a complex process involving multiple physiological and biochemical processes accompanied by degradation of cellular and organ functions and physiological damage, is influenced by both environmental and genetic factors. Filamentous fungi have been widely used in the study of senescence mechanism because of the easy genetic manipulation, short life cycle, and easy qualification of senescence characteristics. In this paper, we reviewed the senescence characteristics of filamentous fungi and summarized the factors influencing aging, such as environmental factors, mitochondrial stability, oxidative stress, and metabolic level. This review is expected to give new insights into the industrial application of filamentous fungi and the research on human senescence.

Abstract:Cryptococcus, a genus of invasive fungi with global distribution, have caused serious public health problems. Notably, Cryptococcus neoformans (Cryptococcus neoformans, C. neoformans) represents the main pathogenic species of Cryptococcus. The infection of C. neoformans can cause pulmonary cryptococcosis and cryptococcal meningitis with high mortality rates. The commonly used antifungal drugs are polyenes, flucytosine, echinocandins, and azoles, which have limited efficacy and may induce resistance when being used alone in clinical practice. Therefore, researchers have studied combined therapy. They have discovered that the combinations of some traditional Chinese medicines and natural plant extracts and derivatives with the commonly used antifungal drugs demonstrate synergistic effects in the treatment of cryptococcosis. This paper reviews the research progress in the combined application of antifungal drugs and traditional Chinese medicines.

Abstract:Kinases are the major category of proteins that regulate intracellular signal transduction by phosphorylating target proteins. They catalyze the transfer of phosphate groups of high-energy donor molecules to specific substrates, serving as the key regulators of cell functions. Host kinases constitute a large protein family with diverse functions, guiding the activation, subcellular localization, and conformational changes of target proteins. In recent years, more and more studies have shown that host kinases play a regulatory role in the processes of picornavirus infections. Picornaviruses can cause a variety of diseases in human and animals. They lead to serious public health problems and huge economic burden in a global scope. A comprehensive understanding of the infection processes of picornaviruses is helpful for the prevention and treatment of these diseases. This paper reviews the research progress in the regulation of picornavirus infections by host kinases, aiming to comprehensively elucidate the mechanisms for interactions between host kinases and picornaviruses. At the same time, we discuss the potential of host kinases as effective treatments and drug targets against picornaviruses infection, aiming to provide implications for the development of new anti-picornavirus agents and vaccines in the future.

Abstract:Phaseolus vulgaris L. is one of the key edible legumes in the world. Rhizosphere microorganisms have mutually beneficial interactions with plants, being important factors promoting crop growth and health. However, studies are limited regarding how to utilize the microbiomes of legumes to promote crop growth.Objective To investigate the structural and functional differences of microbial communities in the rhizosphere and root nodules between two varieties (‘Ziguan’ and ‘Juguan’) of P. vulgaris, screen rhizobial strains, and evaluate their nitrogen-fixing and growth-promoting properties.Methods We employed 16S rRNA gene sequencing to analyze the bacterial community structures in the rhizosphere and root nodules of the two varieties. The rhizobial strains were screened by the plate streaking method. Pot experiments with nitrogen-free vermiculite were carried out to evaluate the nitrogen-fixing performance of the 11 rhizobial strains screened out.Results The bacterial diversity in the rhizosphere soil of ‘Juguan’ was significantly lower than that of ‘Ziguan’, and the bacterial diversity in the rhizosphere soil samples of both varieties was significantly higher than that in the root nodule samples. In addition, the rhizosphere of P. vulgaris harbored beneficial bacterial genera such as Rhizobium, Sphingomonas, Burkholderia, among which Rhizobium was dominant in the root nodules of both varieties. Gephi network analysis showed that bacterial communities in the rhizosphere and root nodules had positive correlations, with the relative abundance of 75.52% and 86.67%, respectively. PICRUSt2 function prediction indicated that the bacteria in the rhizosphere mainly had the functions related to carbohydrate, amino acid, and lipid metabolism, with abundant genes involved in nitrogen metabolism. Pot experiments showed that Rhizobium lusitanum NZ5 and R. etli GLJ10 increased the underground dry weight of ‘Ziguan’ by 43.21% and 48.15%, respectively. R. lusitanum NZ5, R. etli GLZ1, and R. changzhiense GLJ12 increased the underground dry weight of ‘Juguan’ by 77.37%, 68.42%, and 67.37%, respectively.Conclusion P. vulgaris possesses ability to selectively enrich a variety of microorganisms in the soil, establishing a closely coordinated and highly functional microbial community in the rhizosphere. Moreover, different rhizobial strains exerted varied growth-promoting effects on P. vulgaris.

Abstract:Objective To understand the microbial community structure and its relationship with soil quality in the rhizosphere of the dominant plant Xanthium sibiricum in the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir.Methods We collected the rhizosphere soil samples of X. sibiricum exposed to different flooding stress conditions in a typical WLFZ in Yunyang County, the heart of the Three Gorges Reservoir area. High-throughput sequencing was carried out to analyze the microbial diversity and community structure, and the redundancy analysis was then conducted.Results Proteobacteria was the dominant bacterial phylum in the rhizosphere bacteria of X. sibiricum under strong flooding stress (XaRLL) and weak flooding stress (XaRHL), while Ascomycota and Basidiomycota were the dominant fungal phyla in the two types of soil, respectively. Regardless of bacteria or fungi, the linear discriminant analysis effect size (LEfSe) showed that XaRLL always had more key biomarkers than XaRHL. Functional prediction revealed that PWY-3781 associated with aerobic respiration was a dominant metabolic pathway enriched by microorganisms from both XaRLL and XaRHL. Overall, the bacteria and fungi in the rhizosphere of X. sibiricum had strong responses to changes in soil physicochemical properties and enzyme activity.Conclusion The results provide a theoretical basis for understanding the relationship between plants and their rhizosphere microorganisms in the WLFZ, as well as their adaptability to strong flooding stress.

Abstract:Objective To isolate and identify actinomycetes from two mangrove soil samples in Quanzhou Bay as well as secondary metabolites from the target strain Streptomyces sp. W444 with antifungal activity.Methods The rhizosphere soil samples of two different mangrove plants were collected from Luoyang River in Quanzhou Bay. Actinomycetes were isolated from the soil samples by the dilution plating method. The isolates were classified by the phylogenetic tree constructed based on 16S rRNA gene sequences. The antifungal activities of the isolates were examined by the agar diffusion method. The target strain Streptomyces sp. W444 was subjected to fermentation scale-up for the isolation of secondary metabolites. Furthermore, the biosynthetic gene clusters were analyzed to deduce the biosynthetic pathway of staurosporine.Results A total of 56 strains of actinomycetes were isolated from mangrove soil samples and categorized into 8 genera belonging to 6 families of 6 orders. Among them, Streptomyces and Micromonospora were dominant, with the relative abundance of 41.0% and 33.9%, respectively. Strain Streptomyces sp. W444 exhibited excellent antifungal activity, and three indoles (staurosporine, K252c, and streptochlorin) were isolated and identified from this strain. The biosynthetic gene cluster of staurosporine was localized in the genome of Streptomyces sp. W444 by bioinformatics analysis. The biosynthetic pathway of staurosporine was then proposed.Conclusion Actinomycetes in the rhizosphere soil of mangrove plants in Quanzhou Bay had high diversity and contained potential natural product resources. Staurosporine, K252c, and streptochlorin were isolated from strain W444. These findings lay a solid foundation for studying the diversity and secondary metabolites of cultivable actinomycetes in mangrove forests in Quanzhou Bay.

Abstract:Objective To isolate the strain for solubilizing both inorganic and organic phosphorus (P) from the rhizosphere of Moso bamboo (Phyllostachys edulis) and mine the related genes, laying a foundation for activating the soil P pool and improving P bioavailability by P-solubilizing microorganisms (PSM).Methods High-throughput screening was employed to isolate PSM strains from the rhizosphere of Moso bamboo, an important economic plant in subtropical regions. The P-solubilizing activities of the strain under various carbon sources and soil P levels were investigated by microplate culture and soil inoculation experiments, respectively. The genes involved in P solubilizing of the strain were mined by whole-genome sequencing.Results The strain zafu-3 (Achromobacter xylosoxidans) capable of solubilizing P via multiple pathways was isolated from the rhizosphere of Moso bamboo. The strain solubilized Ca₃(PO₄)₂, FePO₄, AlPO₄, lecithin, and calcium phytate by using four carbon sources such as glucose and citric acid, with the highest P-solubilizing activity of 32.75 mg/(L·d). Compared with the control group, the zafu-3 inoculation group showed increases of 4.21%-33.88% and 13.54%-112.06% in activities of acid phosphatase and alkaline phosphatase, respectively. In the high P-level soil, inoculation of the strain decreased the soil pH by 0.04 and increased the available P content by 16.32%. The whole genome of strain zafu-3 contained 35 genes encoding phosphohydrolases and 53 genes involved in organic acid metabolisms. Furthermore, strain zafu-3 carried the genes associated with the production of indole-3-acetic acid and siderophores, and the degradation of lignin.Conclusion Strain zafu-3 directly solubilized inorganic and organic P by secreting diverse organic acids and phosphatases, and indirectly activated soil P pools by promoting plant growth. These findings provide an important microbial resource and theoretical foundation for the development of multifunctional biofertilizers.

Abstract:Objective To explore the role of VraSR in regulating the biological functions of Staphylococcus epidermidis via the CidA-LrgAB system.Methods The recombinant plasmid pKOR1-ΔlrgAB was constructed and then electroporated into SE1457 ?vraSR to delete lrgAB from the genome of ?vraSR by homologous recombination. The suspected mutant ?vraSR-lrgAB was verified by PCR, RT-PCR, and sequencing. The growth, drug susceptibility, autolysis, and biofilm formation of ?vraSR-lrgAB were determined.Results The S. epidermidis mutant ?vraSR-lrgAB was successfully constructed. Compared with SE1457, ?vraSR, and ?lrgAB, ?vraSR-lrgAB exhibited retarded growth, especially at 25 ℃ and 40 ℃ (P<0.001), increased drug susceptibility (P<0.01), enhanced autolysis (P<0.001), and reduced biofilm formation (P<0.01).Conclusion VraSR may regulate the growth, drug susceptibility, autolysis, and biofilm formation of S. epidermidis partly via the LrgAB system.

Abstract:Salmonella as common zoonotic pathogens can cause a variety of foodborne diseases. Salmonella Typhimurium (STM) is one of the key serotypes, and the research, prevention, and control of STM are of great significance to public health.Objective To investigate the effects of greA and greB on the biological characteristics and pathogenicity of STM.Methods Red homologous recombination was employed to construct the greA- and greB-deleted STM strains well as the complemented strains. The strains were then characterized in terms of growth characteristics, biofilm formation, and adhesion and invasion in Caco-2 cells. Mouse models were used to evaluate the effects of greA and greB deletion on STM pathogenicity.Results The mutant strains STM LT2ΔgreA and STM LT2ΔgreB were successfully constructed. Compared with the wild-type strain, the deletion of greA and greB did not affect the cell growth rate, while inhibiting the biofilm formation, adhesion, and invasion of STM. In addition, the deletion of greA and greB decreased the colonization of STM in the liver and spleen of mice, increasing the LD₅₀ of STM by 39.81 times and 2.5 times, respectively.Conclusion The deletion of greA and greB could reduce the pathogenicity of STM. This finding provides a theoretical basis for further revealing the pathogenicity of Salmonella.

Abstract:Galacto-oligosaccharides (GOS) as prebiotics can regulate gut microbiota to improve brain development, whereas antibiotics can affect the nervous system by interfering with gut microbiota. The mechanisms of antibiotics and GOS in regulating brain neurotransmitters and animal behaviors remain unknown.Objective To investigate the effects of antibiotics and GOS on the behaviors and neurotransmitters in weaned Sprague-Dawley (SD) rats.Methods Forty 3-week-old male SD rats were selected and assigned into four groups: control (CON, sterilized water), antibiotics (ABX), GOS (5 g/L), and antibiotics+GOS (AG). The antibiotics used in the experiment were composed of ampicillin, vancomycin, ciprofloxacin hydrochloride, imipenem, and metronidazole. The experiment lasted for 16 days.Results The body weight of rats in the ABX group was lower than that in the GOS group (P<0.05), and the liver index in the ABX, GOS, and AG groups was lower than that in the CON group (P<0.05). Compared with the CON group, the ABX group showcased decreased phototaxis index (percentage of time in bright during bright-dark box test) and reduced times of self-grooming (P<0.05), and the GOS group had reduced times of self-grooming (P<0.05). The AG group had longer resting time in the open field than the other three groups (P<0.05) and shorter distance, shorter time, and slower movement than ABX and GOS groups (P<0.05). Compared with the CON group, the ABX group showcased elevated level of norepinephrine and lowered level of levodopa in the hippocampus (P<0.05). Compared with the CON group, the GOS and AG groups demonstrated elevated levels of norepinephrine and declined levels of levodopa and epinephrine (P<0.05). Compared with the CON group, the ABX and AG groups presented decreased microbial diversity (P<0.05), where Escherichia_Shigella became dominant. The Chao1 index in the GOS group was lower than that in the CON group (P<0.05). The dominant bacteria in the GOS group were Firmicutes and Bacteroidota. Compared with that in the ABX group, the relative abundance of Lactobacillus increased in the AG group (P<0.05).Conclusion ABX decreased anxiety-like behaviors compared with CON, while reducing levodopa and increasing norepinephrine in the hippocampus and enriching potentially pathogenic bacteria. GOS improved growth without influencing the behaviors of rats, and meanwhile it increased the relative abundance of Lactobacillus and decreased levodopamine and norepinephrine in the hippocampus. The combined use of ABX and GOS decreased the locomotor activity and increased the anxiety-like behaviors of rats.

Abstract:The antibiotic resistance and virulence of Acinetobacter baumannii are increasingly serious. Studies have shown that the CRISPR-Cas system in A. baumannii attenuates the antibiotic resistance and virulence, while the effects of CRISPR-Cas system components on A. baumannii remain unclear.Objective Investigation of the role of components of the CRISPR-Cas system in the modulation of bacterial drug resistance and virulence in A. baumannii.Methods The impact of cas1 overexpression on bacterial growth, serum resistance, bacterial drug resistance, biofilm formation ability, and survival rate of mice in a mouse model of bacterial infection was investigated by constructing cas1 overexpression strains and corresponding with them to detect the aforementioned changes.Results The resistance of the bacterial strain AB26::cas1 to 22 commonly used antibiotics was determined using the paper diffusion method. Of these antibiotics, six were found to have an effect on the strain, causing it to change from resistant to sensitive. The capacity of the bacterial strain AB26::cas1 to form biofilms was evaluated through the use of crystal violet staining, which revealed a reduction in biofilm formation ability when compared to the AB26 strain. The intraperitoneal injection of the infected mice model demonstrated that no mortality occurred in the AB26::cas1 strain in vivo infected group in comparison to the AB26 strain in vivo infected group. The fluorescence quantitative PCR assay demonstrated a reduction in mRNA expression of the majority of resistance and toxicity genes. The survival assay, which involved incubating normal human serum with inactivated serum, revealed no statistically significant difference in serum resistance between the wild strains and the overexpression strains.Conclusion The cas1 gene, derived from strain AB43, was observed to exert an inhibitory effect on the drug resistance and biofilm-forming ability of A. baumannii, as well as the pathogenicity of the bacteria in mice.

Abstract:Objective To investigate the in vitro inhibitory activity of Gan Dan oral liquid (GD) against Vibrio parahaemolyticus and decipher the inhibition mechanism at the transcriptome level.Methods The in vitro inhibitory activity of GD against V. parahaemolyticus was evaluated based on the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and growth curve. Scanning electron microscopy and transmission electron microscopy were employed to analyze the effect of GD on the cellular structure of V. parahaemolyticus. Transcriptome sequencing coupled with bioinformatics methods were employed to investigate the effect of GD at 1/4MIC on the transcriptome of V. parahaemolyticus, and the obtained results were examined by real-time quantitative reverse transcription PCR (RT-qPCR).Results GD exhibited high in vitro inhibitory activity against V. parahaemolyticus, with the MIC and MBC of 7.6 mg/mL and 15.2 mg/mL, respectively. The GD treatment at a concentration of 1/4MIC disrupted the cell wall integrity and increased cell membrane permeability of the pathogen, and leading to the leakage of intracellular macromolecules. The results of transcriptome sequencing showed that GD treatment significantly altered the transcriptome profile of V. parahaemolyticus, resulting in significant upregulation of 1 074 genes and significant downregulation of 1 179 genes. The downregulated genes were mainly enriched in pathways related to the synthesis of inosinate and ribonucleoside, whereas the upregulated genes were primarily categorized into pathways associated with transcription factor activity and cell wall synthesis.Conclusion GD may inhibit V. parahaemolyticus by disrupting cell structure and inhibiting cellular energy metabolism and biosynthesis.

Abstract:Objective In view of the difficulty in the culture of chemoautotrophic bacteria, this study analyzed the reasons for the difficulty based on the theory of electron distribution and explored the feasibility of using the electron distribution strategy for increasing the biomass of chemoautotrophic bacteria based on pure culture.Methods From the perspective of maintaining intracellular pH balance and optimal energy metabolism, we calculated the optimal distribution ratios of electrons produced by the sulfur-oxidizing bacterial strain Halothiobacillus sp. DCM-3, nitrite-oxidizing bacterial strain Nitrobacter sp. N1, and ammonia-oxidizing bacterial strain Nitrosomonas sp. SCUT-1 to O₂ and CO₂ by oxidizing corresponding substrates. Furthermore, different molar ratios of O₂ to HCO₃^- (CO₂) were set respectively to form different electron distribution ratios for pure culture verification of the strains. Substrate and product concentrations were measured by ion chromatography and ultraviolet spectrophotometry, and cell density was measured by the dilution coating method.Results The optimal electron distribution ratios of strains DCM-3, N1, and SCUT-1 were 0.733:0.267, 0.867:0.133, and 0.6:0.4, respectively. Based on the optimal electron distribution ratios, strains DCM-3, N1, and SCUT-1 could synthesize 3.967 ATP/S₂O₃^2-, 0.433 ATP/NO₂^-, and 1.35 ATP/NH₃, respectively. According to the calculation results, the main reasons for the difficulty in culture were the small amount of ATP synthesized with the energy provided by per unit substrate and the need to control a low oxygen concentration and supplement an appropriate amount of inorganic carbon. The results of pure culture verification showed that the biomass of DCM-3 under the optimal ratio was 6.5×10⁷ CFU/mL, which was 2.2 times that of the control group. The biomass of N1 under the optimal ratio was 7×10⁶ CFU/mL, which was not significantly different from that of the control group. However, the HCO₃^- concentration (0.4 mmol/L) of the optimal ratio of strain N1 was significantly lower than that (2.5 mmol/L) of the control group, which meant that the strain showed a growth characteristic of tending to higher oxygen concentration but lower CO₂ demand, which was consistent with the calculated optimal ratio. The biomass accumulation per unit NH₄⁺ concentration of SCUT-1 strain in the group with controlled O₂ and CO₂ was more than 1.3×10⁶ CFU/(mL·(mmol/L)), which was 25%-40% higher than that obtained under sufficient O₂ and CO₂.Conclusion The culture strategy of chemoautotrophic bacteria based on electron distribution restricts the culture conditions of electron distribution by limiting the molar amounts and forming a certain ratio of O₂ and CO₂, which helps to improve the biomass accumulation under the same substrate condition and provides certain strategic reference for the culture of chemoautotrophic bacteria.

Abstract:Objective To develop a rapid detector for biochemical oxygen demand (BOD) in the wastewater from ships entering ports in response to the stringent mandates of the International Maritime Organization (IMO). The objective is to facilitate swift detection of domestic wastewater produced by the multitude of vessels arriving at the port.Methods When testing the BOD standard solution, Clostridium butyricum and Bacillus subtilis were used to manufacture the biosensitive elements inducing electron transfer during the consumption of dissolved oxygen (DO), which led to a change in electrical conductivity (COND). By treating dissolved oxygen as a pivotal indicator and an intermediary in the monitoring process, this study explored the correlation between changes in electrical conductivity and sample concentration. Through the development of a quadratic polynomial fitting model that correlates electrical conductivity with dissolved oxygen levels, and by establishing a connection between dissolved oxygen and sample concentration, this research delves into the correlation between variations in electrical conductivity and the concentration of the sample.Results The changes in electrical conductivity exhibited by different solutions enabled the detector to rapidly distinguish between the wastewater with a BOD concentration higher than 25 mg/L (the slope of the COND variation value is less than -0.01) and that below 25 mg/L (the slope of the COND variation value is greater than -0.01). By establishing a highly correlated fitting curve between dissolved oxygen and electrical conductivity (coefficient of determination R²=0.977 83), this study achieved precise reading of samples within the ultra-low concentration range (BOD<25 mg/L). The accuracy rate of the measurements exceeded 85% in the in-suit tests conducted in Qinhuangdao, Hebei, China.Conclusion The measurement data read by the rapid detector for BOD is highly consistent with the results obtained by the dilution inoculation method. Moreover, the detector is capable of performing rapid quantitative analysis of BOD in domestic wastewater from ships entering ports within 30 min, demonstrating high detection efficiency.

Abstract:Objective To investigate the plant microbiome changes in response to wheat head blight and the correlation between the abundance of differential microorganisms and the pathogen Fusarium graminearum, and elucidate the intricate interplay between plant microbiome and disease occurrence.Methods We collected samples from both healthy and diseased plants in the field, combined with high-throughput sequencing to analyze the characteristics of plant microbiome changes, and the abundance of pathogen was determined by RT-qPCR to reveal the response of plant microbial community changes to wheat head blight.Results The alpha diversity of bacteria in wheat spikes and fungi in the rhizosphere significant increased under the disease stress, with enrichment of potentially beneficial bacteria in spikes of diseased wheat plants. Healthy plants displayed higher stability of microbial community and network than diseased plants. Plant microbial diversity can predict alterations in pathogen abundance. Notably, the microbial diversity and community stability explained the most (76.95%) variations in pathogen abundance. High fungal diversity and community stability were associated with reduced pathogen colonization.Conclusion Significant discrepancies of the plant microbiome were identified between healthy and diseased plants. The stable microbial community and network interactions in the spikes of healthy plants facilitate the resistance against F. graminearum infection. Additionally, the “call for help” phenomenon was observed as wheat plants recruited beneficial microflora in spikes, expanding the applicability of the “call for help” strategy. By examining the connection between plant microbiome and disease occurrence, this study presents crucial data and a theoretical framework for the targeted manipulation of plant microbiome to enhance disease prevention and control.

Abstract:Crop diseases caused by phytopathogens result in great harm to global agriculture. Biocontrol has garnered increasing attention in plant disease prevention and control because of its effectiveness and environmental friendliness.Objective To identify, analyze the genome, and evaluate the disease-resistant and plant growth-promoting effects of the strains with antagonistic activities that were screened from the culture collection.Methods Antagonistic strains were screened by plate confrontation method. and identified by morphological observation, phylogenetic analysis based on the 16S rRNA gene and genome, comparative analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, and physiological and biochemical tests. The whole genome sequence of the target strain was analyzed for the mining of functional genes. The plant growth-promoting effect of the target strain was characterized in terms of the phosphorus-solubilizing, siderophore-producing, and proteinase- and cellulose-producing properties. The inhibition of volatile gas produced by the target strain on phytopathogenic fungi was examined in petri dishes with a septum. The effects of the target strain on tomato growth and diseases were studied by pot experiments.Results Strain MB1019 with obvious inhibitory effects on Ralstonia solanacearum and three phytopathogenic fungal strains was screened out and identified as Bacillus velezensis. The physiological and biochemical tests showed that strain MB1019 tolerated the temperature of 15-50 ℃, 10.0% NaCl, and pH 5.0-9.0. The genome of strain MB1019 was 3.8 Mb in length, with the G+C content of 46.4%. The prediction on antiSMASH suggested that the MB1019 genome had 17 synthetic gene clusters for secondary metabolites. The prediction on dbCAN2 suggested that MB1019 carried 108 genes belonging to 52 types of the CAZy family, among which glycoside hydrolases (GHs) were the richest and most abundant. The volatile gas produced by MB1019 significantly inhibited the growth of phytopathogenic fungi. The results of pot experiments showed that MB1019 promoted the growth and inhibited the diseases of tomato seedlings.Conclusion B. velezensis MB1019 capable of antagonizing R. solanacearum and phytopathogenic fungi has tolerance to high temperatures and saline-alkali and demonstrates plant growth-promoting effects. Its genome contains a large number of functional genes, and the volatile gas produced by this strain can inhibit the growth of pathogenic fungi. The fermentation broth of MB1019 has the effects of promoting the growth and preventing the diseases of tomato seedlings. In summary, B. velezensis MB1019 can be used as an elite strain in the research and development of microbial fertilizers and pesticides, demonstrating promising development and application prospects.

Abstract:Oudemansiella raphanipes is a rare edible and medicinal mushroom, while it is highly susceptible to cobweb disease caused by Cladobotryum varium.Objective To obtain bacteria capable of controlling cobweb disease and promoting the mycelial growth of O. raphanipes from casing soil.Methods Bacteria were isolated from the casing soil of O. raphanipes, and their antagonistic activity against the mycelial growth of both O. raphanipes and C. varium was evaluated. The strains with disease-preventing and growth-promoting properties were screened out, and their functioning mechanisms were studied based on genome data.Results A total of 90 bacterial strains were isolated from the casing soil, of which 38 strains showed significant inhibitory activity against the mycelial growth of C. varium and no inhibitory activity against that of O. raphanipes. The supernatants of two strains significantly inhibited the mycelial growth of C. varium and promoted that of O. raphanipes. Based on the genome data, the above two strains were identified as Peribacillus simplex and Ochrobactrum rhizosphaerae, respectively, and they carried multiple functional genes and biosynthetic gene clusters of secondary metabolites.Conclusion Two bacterial strains capable of controlling the disease and promoting the growth of edible fungi were obtained, providing valuable microbial resources for the future biocontrol of cobweb disease.

Abstract:Objective To investigate the regulatory effect of transforming growth factor-beta 1 (TGF-β1)/Smad3 on orosomucoid (ORM) expression during infection with influenza A/WSN/33 virus (hereinafter referred to as WSN).Methods A549 cells were either infected with WSN or treated with TGF-β1, followed by treatment with Smad3 inhibitors. The mRNA levels of ORMs were assessed by RT-PCR. Subsequently, cell lines with signal transducer and activator of transcription 3 (STAT3) overexpression and knockdown were established, and RT-PCR and Western blotting were employed to evaluate the impact of STAT3 on ORM expression induced by the influenza virus. Furthermore, A549 cells underwent treatment with TGF-β1, after which the phosphorylation status of STAT3 was analyzed via Western blotting. Finally, the phosphorylation level of STAT3 was detected after inhibiting the activity of Smad3 or knocking down the expression of Smad3 in A549 cells infected with WSN or treated with TGF-β1.Results TGF-β1 regulated the expression of ORM1 and ORM2 through the activation of Smad3, a key mediator in the TGF-β signaling pathway. Concurrently, STAT3 was implicated in modulating ORM1 and ORM2 expression during WSN infection. Additionally, TGF-β1 was shown to induce STAT3 phosphorylation. Notably, inhibiting Smad3 activation or knocking down Smad3 expression suppressed STAT3 phosphorylation.Conclusion The regulation of ORM1 and ORM2 expression by WSN relied on STAT3 phosphorylation mediated by TGF-β1/Smad3.

Abstract:Objective Rummeliibacillus, a genus encompassing three known species, R. stabekisii, R. pycnus, and R. suwonensis, has a wide range of potential applications in biodegradation, probiotics, animal feed, and production of arginine, caproic acid, and other compounds. This study aims to explore the genetic diversity of this genus at the genomic level.Methods A comparative pangenome analysis of 12 strains isolated from different sources was conducted. In addition, the phylogenetic analysis, functional annotation, genomic metabolic pathway analysis, and prediction of mobile genetic elements were carried out.Results A total of 8 024 gene clusters were identified. The core genome, accessory genome, and strain-specific genes comprised 1 550, 3 941, and 2 533 gene clusters, respectively. In the core genome, the arginine cycle of six strains was complete. Seven strains had the ability to completely biosynthesize acetoin. However, only R. pycnus and R. suwonensis 3B-1 were able to completely biosynthesize caproic acid. The phylogenetic tree, DNA-DNA hybridization, and average nucleotide identity showed that Rummeliibacillus sp. G93 and Rummeliibacillus sp. TYF-LIM-RU47 were strains of R. stabekisii. Rummeliibacillus sp. POC4 and Rummeliibacillus sp. TYF005 may belong to a new species of this genus. In addition, genomic islands were identified in all the 12 strains, with the number ranging from four (R. stabekisii DSM 25578 and R. stabekisii NBRC 104870) to 14 (Rummeliibacillus sp. SL167 and Rummeliibacillus sp. TYF005), and prophage sequences were found in five of the 12 strains.Conclusion This study provides a genomic framework for Rummeliibacillus that could assist the further exploration of this genus.

Abstract:Acheta domesticus densovirus (AdDV) was first isolated from infected crickets in Switzerland, 1977 and caused several outbreaks in Europe and the United States. Cricket iridovirus (CrIV), first identified in the Netherlands in 1996, caused a high mortality rate, reduced the fertility, and shortened the life span of infected crickets. The house cricket (Acheta domesticus), was originated from south west Asia and introduced into China as food for reptile pets in recent decades. AdDV and CrIV are common pathogenic viruses that infect house crickets. Unveiling the virus epidemics of house crickets becomes increasingly important with the development of the house cricket industry.Objective To understand the epidemic status of AdDV and CrIV in China, so as to lay a theoretical basis for controlling AdDV and CrIV infections in the house cricket industry and developing effective prevention and control measures.Methods Virus-specific PCR was performed to detect pathogens of the crickets reared in farms spanning different regions of China. The pathogens of the infected crickets were further proved by Sanger sequencing. Transmission electron microscopy was employed to observe the virions in different tissue samples (e.g., gut and fat body) of the infected crickets.Results AdDV virions were icosahedral-shaped particles, nearly spherical, without envelope, with a diameter around 20 nm. It formed dense chromatin regions in the nucleus of the host cell, showing typical features of densovirus. CrIV virions were nonenveloped icosahedral-shaped particles with a diameter of 120-140 nm. A large number of CrIV virions formed a lattice-like arrangement in the cytoplasm, which is a typical feature of iridovirus. The virus-specific PCR detected AdDV in crickets collected from all the on-line shops distributed in different regions of China. CrIV was also detected in crickets collected from most (91%) of the on-line shops. The majority (91%) of detected crickets were infected with both AdDV and CrIV.Conclusion For the first time AdDV and CrIV were found to have been widely spread in China.

Abstract:Objective Microorganisms are key executors of the migration and transformation of geochemical elements in intertidal zones. Fungi play an important role in the cycling of carbon, nitrogen, and phosphorus and the degradation of organic pollutants.Methods In this study, soil samples were collected from the rhizosphere and non-rhizosphere of Phragmites australis, Tamarix chinensis, and Suaeda salsa (intertidal zone and saline inland), which were the typical intertidal plants in the Yellow River Delta. The fungal community structures in different soil samples were investigated by high-throughput sequencing.Results In the rhizosphere, the soil sample of S. salsa in saline inland showed higher fungal abundance, richness, and evenness than other soil samples, with a distinct fungal community structure. In the non-rhizosphere, the fungal abundance, richness, and evenness were the highest in the soil samples of P. australis, S. salsa in saline inland, and T. chinensis, respectively, and the fungal community structure of P. australis was similar with that of S. salsa in saline inland. Ascomycota and Basidiomycota were the dominant fungal phyla in both the rhizosphere and non-rhizosphere. However, the functional fungi were different among plants. Saprophytic fungi such as Alternaria and Aspergillus were the dominant functional fungi in the rhizosphere and non-rhizosphere of P. australis, T. chinensis, and S. salsa in saline inland, with the relative abundance of 13.60%, 6.33%, and 20.16% in the rhizosphere and 11.98%, 24.25%, and 8.52% in the non-rhizosphere, respectively. Saprophytic fungi were essential for the production of humus by decomposition of organic matter and the improvement of soil aeration and physicochemical properties. Aureobasidium (1.51%) were identified in the non-rhizosphere of T. chinensis, and they were haloduric fungi and could work synergistically with plants to prevent soil salinization. The dominant functional fungi in the rhizosphere of S. salsa in intertidal zone were mainly Talaromyces (15.90%) and Stachybotrys (0.53%), which were involved in sugar degradation. They were able to break down cellulose into glucose, produce humus, and form a stable soil aggregate structure to improve soil aeration. Trichoderma (0.13%) were identified in the rhizosphere of S. salsa in saline inland, and they could promote soil nitrogen and phosphorus conversion and prevent the soil pollution caused by excessive inorganic phosphorus. The relative abundance of functional fungi was less than 0.10% in the non-rhizosphere. In addition, Phanerochaete (0.15%) capable of degrading persistent organic pollutants and Penicillium (1.16%) capable of degrading quinones were identified in the non-rhizosphere, providing microbial resources for the remediation of organic pollution in soil. However, they were not identified in the plant rhizosphere. The fungal diversity and evenness in the rhizosphere were positively correlated with soil factors such as electrical conductance (EC), calcium concentration, and salinity. In the non-rhizosphere, the fungal richness and diversity were positively correlated with total nitrogen, while the fungal evenness was positively correlated with pH, salinity, and ammonia nitrogen.Conclusion This study established a framework for understanding the structures and functions of fungal communities in the intertidal zone of the Yellow River Delta. Additionally, it provides a theoretical foundation for the future application of different functional fungi in soil structure improvement, biodiversity maintenance, organic pollution treatment, ecological protection, and saline-alkali land restoration.

Abstract:Objective To analyze the application trends and distribution of artificial intelligence in synthetic biology from the patent perspective, providing practical insights and theoretical support for technological innovation, research and development (R&D) direction, and industrial layout of this field.Methods The paper presents a comprehensive overview of the research contents and methodologies of synthetic biology, and delves into the evolving landscape of artificial intelligence in synthetic biology by extensive patent network mining and literature analysis.Results Through thorough examination of pertinent patent data, this study unveils the application patterns and disclosure trends of artificial intelligence in synthetic biology alongside the major countries involved and key applicants. Furthermore, it analyzes the advancements in biosynthetic gene clusters, protein structure analysis, and transcription factor binding sites from the patent perspective. Additionally, this paper expounds the challenges confronting the integration of artificial intelligence into synthetic biology while offering recommendations to address them.Conclusion The findings presented herein offer valuable insights into understanding the technical developmental context surrounding artificial intelligence in synthetic biology while serving as a reference for relevant enterprises and research institutions when making R&D decisions. Moreover, this paper underscores the pivotal role played by artificial intelligence in advancing development of synthetic biology while emphasizing its significance. Simultaneously, it provides suggestions to further bolster research efforts on integrating artificial intelligence into synthetic biology with an aim to generate innovative ideas and technical support for constructing national science and technology information systems in global science and technology competition scenarios—particularly concerning advances in synthetic biology.

Abstract:The fermentation, morphological observation, and metabolite purification of mycelial pellets and the application of mycelial pellets in sewage treatment and energy recovery have gained widespread attention from researchers in the fields of environment and biology. To get a full picture of the research hotspots and trends of mycelial pellets. We screened 1 337 scientific articles related to the application of mycelial pellets that were published in the past 20 years from the Web of Science. The clustering and temporal trends of keywords and the co-occurrence of countries, authors or institutions were visually analyzed. The annual number of published articles was on the rise, involving a total of 97 topics, and interdisciplinary articles were abundant and tended to have higher cited frequency. China’s achievements in this field kept a leading position and China maintained close cooperation with other countries. The hot keywords remained stable (growth, morphology, fermentation, removal, degradation, mycelial pellets, biological control, fungi, culture, optimization, biodegradation, and biosorption), and the uptrending and emerging keywords changed in recent years. The application of mycelial pellets in water treatment had been increasingly studied, with the related keywords (waste water, performance) becoming increasingly frequent. Emerging keywords related to wastewater treatment with mycelial pellets as carriers (biomass, bacteria), synthesis by mycelial pellets (biosynthesis), and water treatment with both mycelial pellets and algae (Chlorella vulgaris, microalgae) remained hot. This result indicates that research on the application of mycelial pellets in water treatment has gradually evolved into more systematic research directions, which will become future research hotspots and opportunities.