Viruses are the most abundant biological entities on Earth and widely exist in various ecosystems. They play a role in regulating microbial community composition, influencing microbial evolution, participating in element biogeochemical cycles, and even causing plant and animal diseases. Soil is an important reservoir of viruses. Due to the limitations of soil heterogeneity, adsorption of soil colloids, and lack of research and analysis methods, the research on soil viruses lags far behind that on viruses in marine or other aquatic ecosystems. In recent years, the rapid development of molecular biology and the gradual improvement of ecological theory have promoted the research on soil viruses, researchers gradually paid attention to the function of viruses in soil ecosystem. In this paper, we summarized the research status and progress of soil viruses in terms of the types, research methods, and ecological functions. On this basis, the future development trends and key research directions of soil viruses were prospected in this paper. This review can deepen people’s understanding of soil viruses and provide scientific reference for the research on soil viruses.

Antimicrobial susceptibility testing (AST) is of great significance for the detection of antibiotic residues, as well as the prevention and treatment of bacterial diseases. Conventional methods of AST are time-consuming and labor-intensive due to the processes of bacterial culture and colony counting. ATP bioluminescence has been widely employed to assess bacterial contamination in food and healthcare and appears to be a rapid and sensitive alternative to conventional methods of AST. This review illustrates the influencing factors of ATP bioluminescence-based AST in detail. It mainly focuses on how these factors influence the detection performance of the method, giving insights into AST in clinical, environmental, and food analyses.

[Objective] The enzymatic depolymerization of polyethylene terephthalate (PET) involves the hydrolysis of PET catalyzed by PET hydrolases, leading to the production of terephthalic acid and ethylene glycol. In this study, we identified a new PET hydrolase through gene mining, with the goal of providing enzymes for efficient depolymerization of waste PET. [Methods] A previously uncharacterized functional enzyme, named as AePETase, was identified through gene mining. This enzyme demonstrated the ability to hydrolyze amorphous PET films. Subsequently, heterologous expression, purification, and enzymatic characterization were performed for AePETase. [Results] AePETase showed a T_m value of (53.0±0.7) ℃, and an optimal reaction temperature of 45 ℃. The optimal buffer was Na₂HPO₄-NaH₂PO₄ (100 mmol/L, pH 8.0), and the optimal enzyme concentration was 1 µmol/L. After 72 h, the hydrolysis of amorphous PET films by AePETase resulted in 13.4-fold more products than that by the reported IsPETase. [Conclusion] AePETase demonstrates significant hydrolytic activity on PET and represents a promising new enzyme for hydrolyzing PET.

[Objective] Using Sphingomonas paucimobilis as the starting strain, a high-yield gellan gum-producing engineered strain was constructed through metabolic engineering, and fermentation process optimization was performed, providing both theoretical support and technical foundations for the efficient biosynthesis of gellan gum with this bacterium. [Methods] A CRISPR-Cas9-based gene editing system was developed for S. paucimobilis, and subsequently employed to genomically integrate two key gellan gum biosynthesis genes: the regulatory protein gene (gelA) and the β-1,4-glucuronosyltransferase gene (gelK), both under the control of constitutive promoters. Building upon this foundation, fermentation parameters including carbon source, nitrogen source, pH, and dissolved oxygen were systematically optimized through single-factor experiments. [Results] The engineered strain FMME-GG08 achieved a gellan gum yield of 10.8 g/L in shake-flask cultivation, representing a 130.2% enhancement over the parental strain. Following fermentation process optimization, the production level reached 20.1 g/L in 15 L scale bioreactors, with a sucrose conversion efficiency of 0.50 g/g. [Conclusion] This study not only successfully constructed a high-yield gellan gum-producing strain and established an efficient fermentation process, providing a reliable technical solution for industrial production, but also developed a genetic editing strategy that serves as an important reference for metabolic engineering of non-model microorganisms to produce other high-value exopolysaccharides.

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.

This article explores the dynamic regulation of fluid shear stress on the biofilm formation of Streptococcus mutans, aiming to elucidate the pathogenic mechanism of this bacterium and provide references for the prevention of dental caries. S. mutans is a major cariogenic bacterium in the oral cavity, and it destroys the tooth tissue by forming biofilms and producing acids by metabolism. Studies have shown that fluid shear stress can regulate the physical structure, secretion of extracellular polymeric substances, adhesion, and quorum sensing of biofilms, thereby affecting the pathogenicity. This study provides a theoretical basis for deeply understanding the ecological adaptability of pathogens in fluid environments and the development of new intervention measures in clinical practice.

[Objective] To develop a new and rapid fluorescent recombinase-aided amplification (RAA) method for the detection of Enterocytozoon hepatopenaei (EHP), one of the major pathogens restricting the development of the prawn farming industry. [Methods] Multiple pairs of RAA primers were designed based on the highly conserved 18S rRNA gene of EHP, and the primers with the highest amplification efficiency were screened by basic RAA and fluorescent RAA. The reaction system and conditions of fluorescent RAA were then optimized. The optimization results showed that the developed method achieved detection at 37 ℃ within 20 min. Finally, the sensitivity, specificity, precision, stability, and actual sample application of the developed fluorescent RAA method were evaluated. [Results] The fluorescent RAA method had high specificity and was only sensitive to EHP, and it had no response to other pathogens causing mixed infection or secondary infection. Moreover, it had high sensitivity and high precision, with the limit of detection being 5 copies/μL and the coefficient of variation less than 5% for repeat test results. The lyophilized premix of primers and probe demonstrated good stability. It can be stably transported, used, and stored for 10 d at room temperature (25 °C) and 5 d at the high temperature (37 °C) in summer, with the shelf life longer than one year at -20 ℃. Additionally, the detection results of ninety clinical samples of prawn by the developed method were consistent with those obtained by the fluorescence quantitative PCR method recommended by fishery industry standard Code of Diagnosis for Enterocytozoon hepatopenaei Disease (SC/T 7232—2020), with the result coincidence rate of 97.78% (88/90). In addition, the fluorescent RAA method showed the sensitivity of 100.00% (30/30) and the specificity of 96.67% (58/60). [Conclusion] The established fluorescent RAA method has the characteristics of rapid detection, simple operation, high sensitivity, high specificity, high precision, and good stability, providing a technical reference for the field rapid detection of EHP. It has a wide market application prospect in the accurate and rapid detection of aquatic diseases.

Transcription factors are essential for the survival of bacteria, and revealing their functions is conducive to the development of antimicrobials, industrial applications, and environmental protection. At present, there are many methods and strategies for the research on transcription factors, which have been developed rapidly in the fields of bioinformatics and molecular biology. This paper summarizes the methods for identifying unknown transcription factors, unveiling the regulatory functions of transcription factors, constructing regulatory networks of transcription factors, and validating the regulatory genes of transcription factors. This review aims to provide new strategies and new ideas for the analysis and verification of the regulatory functions of bacterial transcription factors.

The vpa1443-vpa1445 gene cluster (mfpABC) encoding the membrane fusion protein (MFP) is hypothesized to be involved in the biofilm formation of Vibrio parahaemolyticus (Vp). The gene mfpA (vpa1445) encodes a Ca²⁺-binding extracellular protein containing a repeats-in-toxin (RTX) domain, while its function is still under exploration. [Objective] To study the influences of mfpA mutation on the biofilm formation and motility of Vp. [Methods] The single mutants of three genes in the mfpABC gene cluster were constructed, and the Vp motility was compared between the three mutants and the wild type. Furthermore, the influences of mfpA mutation on bacterial motility and biofilm formation were analyzed in detail, and the expression of related genes was analyzed by RT-qPCR. Moreover, the cytotoxicity of ΔmfpA to HeLa cells was investigated. [Results] The mutation of mfpA significantly reduced the swimming and swarming motility of Vp. Crystal violet staining and scanning electron microscopy results showed that the mutation of mfpA enhanced the biofilm formation and increased the content of extracellular polysaccharides and proteins. RT-qPCR confirmed that the expression levels of flagellar genes were downregulated, while those of extracellular polysaccharide synthesis-related genes were upregulated in ΔmfpA. The cytotoxicity of ΔmfpA significantly decreased compared with that of wild type. [Conclusion] The mutation of mfpA can affect the expression of genes associated with flagella and extracellular polysaccharides to reduce the motility, enhance the biofilm formation, and attenuate the cytotoxicity of Vp.

Hydroxylamine, as an important intermediate product in the nitrogen cycle, connects ammonia oxidation and nitrite oxidation, influencing the velocities and directions of processes like ammonia oxidation, nitrite oxidation, and denitrification. Because of the close associations with the generation of N₂O through enzymatic reactions and self-decomposition or reactions with other substances, hydroxylamine has become a focus and hotspot of research. This paper summarized the generation and transformation of hydroxylamine in autotrophic and heterotrophic ammonia oxidation, the key role of hydroxylamine in the nitrogen cycle, and the promoting effect of hydroxylamine on N₂O emissions. It analyzed the processes of autotrophic and heterotrophic ammonia oxidation and their enzymatic differences, aiming to provide a theoretical reference for in-depth research on the role of hydroxylamine in the microbial nitrogen cycle and for the research and development of measures to reduce N₂O emissions and protect the atmospheric environment.