[Objective] To improve the fermentation performance by optimizing the fermentation medium and conditions of Bacillus subtilis subsp. spizizenii YC25, thereby providing a theoretical basis for the subsequent industrial development and application of the strain. [Methods] With the spore yield as the indicator, the optimal fermentation conditions were screened by single factor tests. On this basis, the response surface methodology was employed to optimize the fermentation medium. Pot experiments were conducted to evaluate the control effects of the optimized fermentation broth on tobacco black shank and tobacco Fusarium root rot. [Results] The optimum fermentation conditions were as follows: 30 ℃, 180 r/min, an inoculation amount of 2%, a liquid-loading volume of 20%, and fermentation time 36 h. The optimum fermentation medium was as follows: corn starch 15.53 g/L, soybean meal 8.70 g/L, KH₂PO₄ 0.50 g/L, MgSO₄ 0.92 g/L, and CaCO₃ 0.50 g/L. Under these conditions, the spore yield reached 1.423 3×10¹⁰ CFU/mL. The results of pot experiments showed that the control effects of the fermentation broth diluted by 20 times on tobacco black shank and tobacco Fusarium root rot were 77.88% and 62.09%, respectively. [Conclusion] The optimized medium could significantly increase the spore yield of strain YC25, and the disease indexes of tobacco black shank and tobacco Fusarium root rot were significantly reduced after the application of YC25 fermentation broth. This study provides a theoretical basis for the development and application of the biocontrol strain YC25 and the prevention and control of field diseases in the future.

[Objective] To explore the antifungal activity and inhibitory mechanism and identify the main antagonistic substances of the crude extract of Pseudomonas protegens FD6 in fermentation. [Methods] The plate confrontation test was employed to screen the optimal medium, extractant, and solvent and determine the antifungal activity stability of the crude extract. The main antifungal substances in the crude extract were identified by MALDI-TOF/TOF mass spectrometry, and the antifungal spectrum of the crude extract was explored. The inhibition mechanism of the crude extract against Botrytis cinerea was investigated by mycelial morphology observation, spore germination test, PI staining, and conductivity determination. [Results] The crude extract of FD6 in the potato juice medium without any carbon source displayed the strongest antifungal activity. The methanol-solved crude extract obtained with ethyl acetate as the extractant had the strongest inhibitory activity. The main antifungal substance of the crude extract was identified as a cyclic lipopeptide, orfamide A, based on mass spectrometry data. In addition, the crude extract displayed broad-spectrum inhibitory activities against Phomopsis amygdali, Fusarium graminearum, Colletotrichum gloeosporioides, and Monilinia fructicola. The antifungal activity of the crude extract was stable after treatment at 121 ℃ for 20 min, within the range of pH 4.0-10.0, and with protease K and trypsin. The mycelial morphology of B. cinerea became abnormal after treatment with the crude extract. The treatment with 2.0 mg/mL crude extract completely inhibited the conidial germination of B. cinerea, caused a 50% damage of the cell membrane, increased the conductivity, and led to leakage of intracellular nucleic acids and proteins. [Conclusion] The metabolites produced by P. protegens FD6 have broad-spectrum and stable antifungal activities, serving as lead compounds for exploration of new green fungicides.

[Objective] To study the response relationship of the biological properties of bacterial communities to long-term climate change. [Methods] The loess (YL, PL, and RL) and paleosol (YS, PS, and RS) sequences, which have persisted for approximately 500 000 years at Shimao (Y), Potou (P), and Renjiapo (R), were sampled. The structures and functions of the soil bacterial communities were predicted by bioinformatics approaches, including high-throughput sequencing and FAPROTAX. [Results] The physical and chemical characteristics associated with the loess-paleosol alternation in the three regions reflected the shifts in climatic conditions, including dry, cold, warm, and wet phases during soil development. Over this period, the climate at Renjiapo was characterized by the highest temperatures and precipitation levels, with strong influences from summer winds. Shimao experienced the driest conditions and the lowest temperatures. Potou exhibited the intermediate climatic conditions between Renjiapo and Shimao. The abundance and diversity indices of the bacterial communities in Shimao were higher than those in Potou and Renjiapo. Across all the three regions, the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Acidobacteria although their relative abundance varied significantly. The bacterial communities in the loess and paleosol layers of Shimao showed greater compositional similarity, forming a network structure driven by synergistic interactions. The ecological functions of the bacterial communities in the loess-paleosol sequences were primarily associated with carbon, nitrogen, and sulfur cycling. Carbon and nitrogen cycling was weakly expressed in Shimao, while nitrogen cycling was more prominent in Potou. Renjiapo exhibited the most pronounced carbon cycling. [Conclusion] Soil bacterial communities in warm and humid climates tend to exhibit more complex network structures and greater functional diversity. In contrast, bacterial communities in dry and cold climates are characterized by similar composition and synergistic patterns, which enable these communities to adapt to harsh conditions by increasing their abundance and diversity, compensating for nutrient limitations associated with reduced carbon and nitrogen cycling.

[Objective] To study the cytopathic effects (CPE) and replication characteristics of HCoV-OC43 VR1558 strain in cell lines derived from different species. [Methods] Thirteen cell lines from humans (MRC-5, HRT-18, Huh7, Huh7.5, RD, and HeLa), non-human primates (LLC-MK2 and Vero), and rodents (17Cl-1, Mv.1Lu, BHK-21, BHK-21-APN, and Neuro 2a) were selected and infected with HCoV-OC43 VR1558 strain. CPE were observed for several consecutive days. Virus-infected cells and supernatants were collected daily. RT-qPCR was conducted to monitor the changes in viral RNA copy number. The load of viruses with infectious ability was determined based on the tissue culture infectious dose 50% (TCID₅₀), and the kinetic curves of viral replication in different cell lines were established. [Results] Following infection with HCoV-OC43 VR1558 strain, CPE were observed in all the 13 cell lines. CPE primarily manifested as cell aggregation, shrinkage, rounding, and detachment. CPE appeared early in MRC-5, Mv.1Lu, HeLa, and 17Cl-1 cells, being noticeable within 72 h post-infection (hpi). The virus induced CPE in other cell lines after 120 hpi, and CPE were the mildest in HRT-18 and Huh7.5 cells. RT-qPCR results indicated that the viral RNA copy number increased most significantly within 24 hpi, although the time to reach the peak and the peak copy number varied among cell lines. Specifically, the RNA copy number in Huh7.5 cells reached the peak (10⁷ copies/mL) at 24 hpi, and that in 17Cl-1, BHK-21-APN, Mv.1Lu, and BHK-21 cells reached the peaks (10⁷ to 10⁹ copies/mL) at 48 hpi. In MRC-5, LLC-MK2, Neuro 2a, and Vero cells, the replication peaks (10⁶ to 10⁹ copies/mL) occurred at 72 hpi. In HRT-18, HeLa, Huh7, and RD cells, the viral RNA copy number peaked after 96 hpi, reaching 10⁸ to 10⁹ copies/mL. TCID₅₀ assay results demonstrated rapid viral proliferation within 24 hpi, while the time to reach the peak titer and the peak titers varied. The peak titer (2.68× 10⁷ TCID₅₀/mL) in BHK-21-APN cells was observed at 48 hpi. In BHK-21 and Neuro 2a cells, the peak titers (10⁶ to 10⁷ TCID₅₀/mL) were observed at 72 hpi. In MRC-5, 17Cl-1, HeLa, Huh7, Huh7.5, Mv.1Lu, LLC-MK2, and RD cells, the peak titers (10⁶ to 10⁸ TCID₅₀/mL) were observed at 96 hpi. In Vero cells, the virus strain reached the peak titer (10⁵ TCID₅₀/mL) at 120 hpi, while the strain reached the peak titer of 10⁸ TCID₅₀/mL in HRT-18 cells at 144 hpi. [Conclusion] HCoV-OC43 VR1558 strain exhibits a wide spectrum of cell tropism, demonstrating rapid replication and proliferation within 24 hpi across 13 cell lines derived from various species. However, the time to reach the replication peak varied among different cell lines. The highest viral titer achieved was 10⁸ TCID₅₀/mL, observed in MRC-5 and HRT-18 cells. This study provides experimental reference for further investigation of the replication characteristics, infection mechanism, and pathogenicity of HCoV-OC43, as well as for the screening and evaluation of antiviral drugs.

[Objective] To investigate the antibiotic resistance and virulence of pet-derived Klebsiella pneumoniae in some areas of Guangdong Province. [Methods] Fecal swabs were collected from dogs and cats for strain isolation, and 16S rRNA and khe genes were amplified by PCR to identify the strains. The sensitivity of K. pneumoniae isolates to 17 antibiotics was determined by the agar diffusion method. PCR was employed to detect resistance genes to β-lactams (bla_SHV, bla_CTX, and bla_TEM), carbapenems (bla_KPC and bla_NDM), aminoglycosides (rmtB), quinolones (qnrS and oqxAB), sulfonamides (Sul1 and Sul2), amphenicols (floR), tetracyclines (tet(A)), and fosfomycin (fosA3) and some virulence genes (rmpA, maga, fimH, mrkD, uge, WabG, kfu, Aerobactin, and ureA). [Results] A total of 126 strains of K. pneumoniae were isolated from 428 fecal samples, with an isolation rate of 29.4%. The 126 isolates had high resistance rates to amoxicillin (75.40%), ampicillin (73.81%), and cotrimoxazole (61.90%). They were moderately sensitive to ceftazidime, amikacin, apramycin, and enrofloxacin, and they were sensitive to tigecycline, colistin, and meropenem. The detection rate of the resistance gene oqxAB was the highest, which was 86.51%, followed by those of the β-lactam resistance gene bla_SHV (73.81%) and the tetracycline resistance gene tet(A) (52.68%). Other resistance genes were detected to varying degrees (0.79%-46.03%) and the carbapenem resistance gene bla_KPC, colistin resistance gene mcr-1, and aminoglycoside resistance gene rmtB were not detected. Among the virulence genes, the urease gene urea, lipopolysaccharide-related gene uge, and fimbria-related gene fimH showed the detection rates of 100.00%, 95.54%, and 91.07%, respectively. Other virulence genes were detected to varying degrees (2.70%-8.90%), while the capsule-related gene magA and the fimbria-related gene mrkD were not detected. [Conclusion] In some areas of Guangdong Province, the antibiotic resistance of pet-derived K. pneumoniae is serious, but its pathogenicity is relatively weak. Monitoring of its drug resistance and pathogenicity should be strengthened. In addition, antibiotics should be strictly managed and rationally used in the clinical practice, so as to avoid the generation and dissemination of multidrug resistant strains of K. pneumoniae.

[Objective] Stenotrophomonas can promote the growth of plants and aquatic algae. However, limited studies have focused on the bacteriophages infecting Stenotrophomonas. In this study, we isolated bacteriophages infecting Stenotrophomonas from water and studied their biological and genomic characteristics, aiming to improve our understanding of the ecological functions of Stenotrophomonas and its bacteriophages. [Methods] The double-layer plate method was employed to isolate bacteriophages infecting S. indicatrix EB12 from lake water. The biological characteristics, whole genome sequence characteristics, gene functions, phylogenetic relationship, and protein structures of the isolates were analyzed. [Results] Transmission electron microscopy showed that two isolates Ste-X and Ste-D were short-tailed bacteriophages. The incubation period of both strains was 20 min. Ste-X and Ste-D showed the optimal multiplicities of infection being 1 000 and 10, burst sizes of 28.8 PFU/cell and 131.1 PFU/cell, temperature tolerance ranges of 20-60 °C and 20-70 °C, and pH tolerance ranges of pH 4.0-13.0 and pH 3.0-12.0, respectively. Ste-X and Ste-D were deactivated by UV irradiation for 60 min and 120 min, respectively. Their host ranges were narrow. The genomes of both strains showed the lengths of 39 429 bp, with the G+C content of 57.80% and 57.85%, respectively, and both of them contained 65 open reading frames (ORFs). The genomes of the two strains contained only three different bases. However, their homology with other bacteriophages was low, which suggested that the two strains were novel short-tailed bacteriophages. The structures of the proteins encoded by ORF34 and ORF52 were predicted. Result showed thant the proteins encoded by ORF34 were acidic, stable, and hydrophilic, containing two conserved domains, ChtBD3 and PHA00661, with the three-dimensional structures dominated by random coils. The proteins encoded by ORF52 were alkaline, unstable, hydrophilic, with no conserved domain and the three-dimensional structures dominated by α-helixes. [Conclusion] Two novel strains of short-tailed bacteriophages with high genome similarity but distinct biological characteristics were isolated from water.

[Objective] Listeria monocytogenes (Lm) is a Gram-positive foodborne pathogen causing human and animal listeriosis with high case fatality rates (20%-30%). Lm can grow at low temperatures, which brings great risks to food safety and human health. Exploring the mechanism of Lm growth at low temperatures will provide a theoretical basis for the formulation of measures to control Lm growth at low temperatures and the development of low-temperature growth inhibitors. Studies have shown that LisK/R, a two-component signal transduction system (TCS) in Lm, plays a role in regulating the growth of Lm at low temperatures, while the specific mechanism remains unclear. This study aims to reveal the mechanism of LisK/R in regulating the growth of Lm at low temperatures. [Methods] With the Lm strain LM201 isolated from foodstuff as the parental strain, we constructed three strains: ΔlisR (RR-deleted mutant of LisK/R), ΔlisRc (complementary strain of ΔlisR), and ΔlisKc (complementary strain of ΔlisK, which was constructed before this study in our laboratory). The growth curves of these strains were determined at 4 ℃. RNA-Seq was performed for ΔlisK and the parental strain growing at 4 ℃, and the obtained data were analyzed. We assayed the swarming area diameter on soft agar plate, flagellar biosynthesis by transmission electron microscopy, and transcriptional levels of flagellar genes by RT-qPCR for all the strains at 4 ℃. [Results] The growth of deletion mutants was slower than that of the parental strain (P<0.05), and the growth of complementary strains was consistent with that of the parental strain at 4 ℃. The RNA-Seq data showed that compared with that in the parental strain, the expression of flagellar genes in ΔlisK was up-regulated (P<0.05). At 4 ℃, the swarming area diameters of deletion mutants on soft agar plates were bigger than those of the parental strain and complementary strains (P<0.05); the deletion mutants had more flagella, while the parental and complementary strains had fewer flagella; the expression of flagellar genes in the deletion mutants was higher than that in the parental and complementary strains (P<0.05). [Conclusion] At 4 ℃, the LisK/R mutants with slow growth had more flagella, while the parental strain with rapid growth had fewer flagella. The results indicate that LisK/R inhibits the expression of flagellar genes in Lm to reduce flagellar production, and the energy is used to promote Lm growth at low temperatures. The specific molecular regulatory mechanism of LisK/R needs further study. This study provides new information for elucidating the mechanism of Lm growth at low temperatures.

[Objective] To delineate the fungal diversity characteristics and disparities in the rhizosphere soil of naked barley from fields exhibiting different root rot incidences, thereby informing targeted and effective disease management strategies. [Methods] Rhizosphere soil samples of naked barley were collected from the healthy field and the fields with root rot incidences of 5%, 10%, 15%, and 20%, respectively. The 18S rRNA gene of fungi from the samples was amplified, and high-throughput sequencing was conducted on the Illumina-MiSeq platform. Following quality control, classification, and annotation, the data were analyzed for fungal diversity from various perspectives and taxonomic levels. [Results] The healthy sample and the sample with the root rot incidence of 5% had the highest fungal diversity, while the sample with the incidence of 10% exhibited the lowest diversity. Additionally, co-occurrence network analysis revealed more complex species interactions in the healthy sample and the sample with the incidence of 5%. The root rot incidence had a negative correlation with the relative abundance of Ascomycota but a positive correlation with the relative abundance of Basidiomycota and Glomeromycota. Dominant fungal classes were Agaricomycetes, Chytridiomycetes, and Sordariomycetes. Significant variations in the distribution of fungal groups with high average relative abundance were noted across samples. Specially, the healthy sample had the highest relative abundance of Eurotiales and the lowest relative abundance of Glomerales, which were converse in diseased samples. Arthrodermataceae was significantly enriched in the healthy sample, while Sordariaceae, Myxotrichaceae, and Olpidiaceae were preferentially associated with the samples exhibiting incidences of 10%, 15%, and 20%, respectively. At the genus and species levels, the composition of dominant fungal communities in the healthy sample and the sample with the incidence of 5% was similar, and it was similar in the samples with incidences of 10%, 15%, and 20%. FUNGuild predicted a decrease in the relative abundance of plant pathogens and an increase in the relative abundance of saprotrophs with the increase in disease incidence. [Conclusion] The progression of naked barley root rot is intricately linked to the disruption of the equilibrium within the rhizosphere fungal community. In the context of precision management of naked barley root rot, it is imperative to regulate and sustain the balance of the abundance of dominant fungal taxa in the rhizosphere.

The aggravating soil-borne diseases threaten the production of a variety of crops and undermine the sustainable development of agriculture. Streptomyces-based bio-agents have been widely explored as an environmentally safe and economically durable biocontrol resource. However, the biocontrol efficacy and influencing factors require further optimization. [Objective] Here we conducted a meta-analysis to evaluate the efficacy of Streptomyces-based bio-agents in controlling the two common soil-borne diseases and identify the key influencing factors. [Methods] The relevant articles were retrieved from Web of Science and CNKI with the keywords “Streptomyces” and “Fusarium wilt”, “Streptomyces” and “bacterial wilt”, “Streptomyces” and “Fusarium oxysporum”, and “Streptomyces” and “Ralstonia solanacearum (or Pseudomonas solanacearum)”. The articles containing comparable treatment groups (with Streptomyces application) and control groups (without Streptomyces application), disease incidence, sample sizes, and mean values were systematically selected. Finally, 76 articles (113 groups) on Streptomyces-based bio-agents for Fusarium wilt control and 19 articles (28 groups) on those for bacterial wilt control were obtained. [Results] After the application of Streptomyces-based bio-agents, the disease incidence of Fusarium wilt decreased from 75.58% to 24.49% (average control efficacy of 67.60%), and that of bacterial wilt decreased from 73.75% to 19.83% (average control efficacy of 73.11%). The soil density of Streptomyces, the final concentration ratio of Streptomyces to pathogen in soil, and climate types were vital for the biocontrol performance of Streptomyces-based bio-agents. Moreover, Streptomyces at the final concentration of 10⁷ CFU/g demonstrated the best biocontrol performance on both diseases. The biocontrol effect of Streptomyces on Fusarium wilt was better when the final concentration ratio of Streptomyces to pathogen was 1:1, whereas the biocontrol effect on bacterial wilt disease was better when the ratio was 10:1 or 100:1. Notably, Streptomyces demonstrated enhanced biocontrol effects on the both diseases in tropical monsoon climate regions. [Conclusion] The application dose of Streptomyces-based bio-agents in soil-borne disease management should be adjusted according to the species and concentration of the pathogen. In addition, it may be better to apply Streptomyces-based bio-agents in tropical monsoon climate regions.

Saccharomyces cerevisiae is a classic model organism for studying the biochemical mechanisms of eukaryotic cells. Eukaryotes have three main types of RNA polymerases: RNA polymerase I (RNAPI), RNA polymerase II (RNAPII), and RNA polymerase III (RNAPIII). Among them, RNAPIII has the most complex structure, consisting of 17 subunits, and it is primarily responsible for the synthesis of transfer RNA (tRNA). Compared with RNAPII consisting of 12 subunits, RNAPIII contains a unique heterotrimer Rpc82/31/34 and a heterodimer Rpc53/37 which is homologous to the counterpart of RNAPI. This paper reviews the structures and functions of the specific heterotrimer and heterodimer in RNAPIII, aiming to lay a theoretical foundation for further studies on the modification mechanisms and assembly processes of specific subunits of RNAPIII in S. cerevisiae.