[Objective] To investigate the removal efficiency and mechanism by a strain ofRhodotorula. [Methods] The strain was identified based on the morphological characteristics and the phylogenetic tree based on 26S rRNA gene sequences. Then, the removal effect of the strain on Mn(Ⅱ) was studied at different initial pH and Mn(Ⅱ) concentrations. Finally, the products were characterized by scanning electron microscopy, X-ray diffraction analysis, and X-ray photoelectron spectroscopy. [Results] The isolate was identified asRhodotorula taiwanensis, which could grow well at pH 2.0 and 2 000 mg/L Mn(Ⅱ). The removal rate of Mn(Ⅱ) by the strain reached 98.52% at the initial pH 6.0 and Mn(Ⅱ) concentration of 300 mg/L after 144 h, while higher concentrations (≥500 mg/L) of Mn(Ⅱ) caused toxicity to the cells and weakened the removal effect. The strain could oxidize Mn(Ⅱ) to manganese oxides (mainly amorphous MnO₂, Mn₂O₃, and MnO), which produced layered minerals accumulated on the cell surface. In addition, the process of removing Mn(Ⅱ) by the strain increased the pH of the medium (initial pH 7.0, Mn(Ⅱ) concentration of 100 mg/L) up to 8.4 after 144 h. [Conclusion] R.taiwanensis MF4 isolated in this study can tolerate low pH and high concentrations of Mn(Ⅱ), remove Mn(Ⅱ), and increase medium pH. The findings have a reference value for the end process design in the remediation and treatment of acid mine drainage.

Polycyclic aromatic hydrocarbons (PAHs) are a kind of teratogenic, carcinogenic, and mutagenic organic pollutants. In recent years, the pollution of PAHs in mangrove ecosystems has attracted widespread attention, for which microbial degradation has been recognized as an effective, economical, and multifunctional treatment approach. Researchers have identified a large number of bacteria that utilize PAHs as carbon and energy sources, whereas these bacteria generally suffer from low degradation efficiency, narrow degradation spectra, and poor adaptability to high-salinity environments. In addition, the degradation mechanisms of PAH-degrading bacteria from mangroves remain to be fully explored. [Objective] The present study screened efficient and broad-spectrum PAH-degrading strains in mangrove sediments and explored their degradation efficiency and mechanism, with a view to providing a solid scientific foundation for the innovative research and development of microbial remediation technologies in mangrove ecosystems in the future. [Methods] A new PAH-degrading strain P-9^T was isolated from mangrove sediments collected from Futian, Shenzhen and identified based on the phenotypic and biochemical characteristics and phylogenetic relationship. The genomic DNA of this strain was extracted and sequenced, and the potential of P-9^T in degrading PAHs was investigated by genomic analysis. The degradation ability of P-9^T was measured at different temperatures (25–40 ℃), pH (5.0–9.0), and substrate conditions. Finally, according to the intermediate metabolites detected by high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS), we preliminarily revealed the mechanism of P-9^T in degrading PAHs. [Results] Strain P-9^T was proposed to represent a potential novel species belonging toAquabacter ofXanthobacteraceae and named asAquabacter sediminis P-9^T, which was also the first PAH-degrader identified within this genus. A complete benzoate degradation pathway and key genes encoding dehydrogenase, salicylate hydroxylase, and cytochrome P450 involved in PAHs degradation were found identified in the genome of P-9^T. Strain P-9^T could use naphthalene, phenanthrene, or pyrene as the sole carbon and energy source and grow at 25–40 ℃ and pH 5.0–8.0. In a mineral salt medium (MSM) with phenanthrene (50 mg/L) as the substrate, the degradation efficiency reached 100% after five days. Several metabolites, such as 1-hydroxy-2-naphthoic acid, 1,2-naphthalenediol, catechol, and 1-hydroxy-2-naphthaldehyde were detected, which indicated that strain P-9^T might degrade PAHs via the salicylate pathway. [Conclusion] A.sediminis P-9^T, the first strain ofAquabacter identified to be capable of degrading PAHs could efficiently degrade naphthalene, phenanthrene, and pyrene via the salicylate pathway, with the optimum degradation performance at 37 ℃ and pH 7.0.

[Objective] Bio-inspired artificial mineral shells are used to protect living bacterial cells. [Methods] Bacterial cells were encapsulated in firm and intact mineral shells, where the limited physical space and substance exchange induced the dormancy of living bacteria to decrease the viability loss during long-term preservation and even in extreme environments. Moreover, acids can erode the shells to reactivate the bacteria. [Results] Compared with the un-mineralization treatment (EcN), the mineralization treatment (EcN@CaCO₃) increased the bacterial viability by a maximum of 262 folds in a 32-day storage experiment and the survival rate by 837, 171, 59.1, and 729.7 folds at pH 2.5, pH 12.0, 80 ℃, and in the presence of an antibiotic, respectively. [Conclusion] We employed biomimetic mineralization to improve the stability of bacterial cells in storage, which can provide a research basis for the application of microorganisms in environmental engineering, food production, and biomedical engineering.

Transfer-message RNA (tmRNA) is a ubiquitous and stable non-coding small RNA in bacteria, with characteristic regions similar with both tRNA and mRNA. tmRNA is known to mediate the ribosome rescue mechanism called trans-translation and has effects on the pathogenicity and stress responses of pathogenic bacteria. [Objective] To study the function of tmRNA in Aeromonas veronii causing threats to aquaculture and human public safety, so as to reveal the molecular mechanism for the pathogenicity of A. veronii. [Methods] IntaRNA 2.0 was used to predict the downstream targets binding to tmRNA. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted to predict the biological processes and signaling pathways involving the predicted targets. Real-time qPCR was employed to compare the expression levels of the candidate target genes among the wild type, tmRNA knockout strain, and smpB knockout strain of A. veronii, thus identifying the potential targets regulated by tmRNA in the form of sRNA. [Results] One hundred potential specific downstream targets might bind to tmRNA at the 3′-end tRNA-like domain (tRNA-like domain, TLD), H2 domain, and PK3 and PK4 regions, thus participating in the general metabolic pathways of the pathogen. The results of qPCR indicated that the expression of WP_201994931.1 was regulated by tmRNA in an SmpB-independent manner, while the expression of WP_201954220.1, WP_005335875.1, WP_265062582.1, WP_265061484.1, and WP_265061494.1 was regulated by SmpB. [Conclusion] We preliminarily identified that WP_201994931.1 might constitute a downstream target regulated by tmRNA as an sRNA. This study provides basic information for expanding the functions of tmRNA in the form of sRNA and facilitates the further studies regarding the molecular mechanisms of the pathogenicity and environmental adaptation of A. veronii.

CRISPR-Cas is a defense system ubiquitous in bacteria and archaea. It has been successfully applied in genome editing in a variety of organisms. At present, CRISPR-Cas9 and CRISPR-Cas12a are the most widely used genome editing tools. However, the large protein sizes of Cas9 and Cas12a (more than 1 000 amino acids (aa)) hinder their delivery. TnpB and IscB (about 400 aa) encoded by the transposon family are considered ancestors of Cas12 and Cas9, respectively, whereas their functions are revealed just recently. They are named as obligate mobile element-guided activity (OMEGA), with the associated RNA named ωRNA. Since then, the OMEGA system has become one of the research hotspots in genome editing. OMEGA systems are diverse, with wide distribution in all the three domains of life. The in-depth research on the OMEGA system will aid in the development of new genome editing tools that are streamlined, efficient, and safe. Here, we reviewed the discovery history, structural characteristics, mechanisms of cleavage, and genome editing applications of OMEGA systems, aiming to lay a foundation for the development and optimization of genome editing tools.

ThiD encoded by thiD in Thermoanaerobacter tengcongensis is a key enzyme in the biosynthesis of thiamine. The structure and functions of thiD have been elucidated in fungi, yeasts, and plants, while the role of thiD in thermophiles remains unclear.[Objective] This study aims to explore the thermal adaptation mechanism of T. tengcongensis and reveal the role of thiD in the thermal adaptation of T. tengcongensis at different temperatures. [Methods] The thiD-deleted mutant (ΔthiD) of T. tengcongensis was constructed by homologous recombination. The growth trends of the wild type (WT) and ΔthiD at 50 ℃, 60 ℃, 75 ℃, and 80 ℃ were observed and compared. The differentially expressed genes (DEGs) between ΔthiD and WT cultured at 75 ℃ were determined by RNA-seq. The transcript levels of 13 genes and 3 sRNAs in WT and ΔthiD at 50 ℃, 60 ℃, 75 ℃, and 80 ℃ were compared and analyzed by real-time PCR. [Results] ΔthiD was successfully constructed, with the growth rate not significantly different from WT at 50 ℃. However, ΔthiD show cased slower growth than WT at 60 ℃ and 75 ℃ and did not grow at 80 ℃. The transcriptome results revealed 503 DEGs in ΔthiD compared with WT, including 278 DEGs with up regulated expression and 213 DEGs with down regulated expression. The Kyoto encyclopedia of genes and genomes (KEGG) analysis indicated the following pathways associated with thermophilic adaptation, involving thiamine metabolism, pyrimidine metabolism and purine metabolism, peptidoglycan biosynthesis, fatty acid metabolism, amino acid metabolism, two-component system, DNA replication, homologous recombination, mismatch repair, and phosphotransferase system. The transcript levels of 13 genes and 3 sRNAs related to thermal adaptation in WT and ΔthiD changed at specific temperatures. [Conclusion] thiD plays an important role in the thermal adaptation of T. tengcongensis. This study provides experimental data and a theoretical basis for revealing the role of thiD in the thermal adaptation of thermophiles at different temperatures.

[Objective] Over 7 million people die from bacterial infections every year due to the inappropriate or untimely use of antibiotics. Antimicrobial susceptibility test (AST) is a routine method guiding antibiotic therapy in clinical practice, while the existing methods have limitations as they require at least 16–20 h to get the results. We aimed to develop a novel rapid AST method based on bacterial morphology analysis, which can improve the diagnosis efficiency and provide timely treatment for the patients with bacterial infections, especially for urgent cases. [Methods] We developed an in-situ time-lapsed imaging (ISM-TLI) technique for microcolonies by combining bacterial incubation, in vitro antibiotic treatment, microscopic imaging, and image processing algorithm. The combination of the imaging device with the algorithm enabled the tracing of the morphological changes of colonies treated with different concentrations of antibiotics in-situ and the rapid obtainment of AST results. [Results] This technique worked effectively for both Gram-positive and Gram-negative bacteria and could determine the minimum inhibitory concentration (MIC) within 2 h, with the results in agreement with those obtained with the clinical gold standard method. [Conclusion] Our rapid AST technique significantly reduced the turn-around-time for obtaining the AST profile and had great potential for AST of a wide range of other strains.

[Objective] Soft rot is one of the major diseases affecting the yield and quality of konjac. This study screened a strain with antagonistic effect on Pectinobacterium aroidearum from the rhizosphere soil of konjac, aiming to provide germplasm resources for the biocontrol of soft rot in konjac. [Methods] An antagonistic strain was screened by the plate confrontation method, and its antagonistic effects on pathogenic fungi were measured. The control effect of GZA12 on soft rot in konjac was examined by the inoculation in konjac corm tissue, pot experiment, and root irrigation. The growth-promoting effect of this strain was tested indoors and preliminarily verified by tomato pot experiments. [Results] A strain GZA12 with antagonistic effect was screened out and identified as Bacillus velezensis. This strain showed the inhibition zone diameter of 21.33 mm against P. aroidearum and the inhibition rates of 58.16%, 47.30%, and 54.53% against Botryosphaeria dothidea, Fusarium oxysporum, and F. solani, respectively. Inoculation of GZA12 in konjac corm tissue decreased the disease index by 26.67%, 33.33%, and 40.00%, respectively, compared with the inoculation of B. dothidea alone. In the pot experiment, the treatment with GZA12 suspension decreased the disease index by 22.85% compared with the control group and reached the control effect of 53.31%. The results from the root irrigation experiment showed that compared with water irrigation, irrigation with GZA12 fermentation broth reduced the disease index by 4.89% and reached the control effect of 21.57%. Strain GZA12 had the ability to fix nitrogen, solubilize phosphorus, and produce siderophores and indole-3-acetic acid (IAA). Inoculation with GZA12 suspension promoted the growth of tomato seedlings in a concentration-dependent manner. [Conclusion] Strain GZA12 can inhibit the pathogen causing soft rot and promote the growth of konjac, demonstrating the potential for further development and utilization.

L-threonine is one of the eight essential amino acids that cannot be synthesized by the human body and must be taken from food. It is an important component of protein synthesis and is widely used in food, feed, medicine and other fields. At present, Escherichia coli can achieve a high threonine yield in fermentation, being the main bacterium used for industrial production of threonine. With the development of metabolic engineering, the modification of strains is no longer limited to mutagenesis, and the directed modification of strains greatly improves the production of L-threonine, facilitating the development of the L-threonine industry. This paper introduces the physicochemical properties and synthesis pathway of L-threonine and reviews the achievements in improving L-threonine production by metabolic engineering, aiming to enrich the knowledge about the modification of Escherichia coli for efficient synthesis of threonine.

Bacterium-mediated cancer immunotherapy (BCI) presents numerous advantages in cancer treatment, while the immune response mechanism of dexamethasone (DEX) combined with BCI for tumor treatment remains unclear. [Objective] To investigate the therapeutic efficacy and mechanism of dexamethasone in combination with attenuated Salmonella typhimurium St.ΔppGpp-mediated BCI. [Methods] The inhibitory effects of St.ΔppGpp+DEX on cancer were evaluated in a murine model of colorectal cancer. In vivo imaging was utilized to determine the tumor targeting and colonization duration of St.ΔppGpp. Organ toxicity resulted from St.ΔppGpp+DEX treatment was assessed by hematoxylin and eosin (H&E) staining. Macrophage polarization, neutrophil recruitment, and T-cell responses were analyzed by flow cytometry and immunofluorescence assay of sections. The changes in inflammatory cytokines in the tumor microenvironment were examined via qRT-PCR. A mouse model transplanted with human colorectal cancer was employed to confirm the effect of T cell depletion on the therapeutic efficacy of St.ΔppGpp+DEX. [Results] The combined treatment St.ΔppGpp+DEX significantly decreased tumor size and enhanced the survival rate of mice. DEX extended the colonization of St.ΔppGpp in tumor cells. Furthermore, St.ΔppGpp+DEX did not induce damage to vital immune organs, and it facilitated the polarization of macrophages from M2 to M1 phenotype while suppressing neutrophil recruitment. T cell depletion did not influence the efficacy of St.ΔppGpp+DEX. [Conclusion] DEX can enhance the anti-tumor effects of St.ΔppGpp by inhibiting neutrophil recruitment and increasing the proportion of M1 macrophages in the tumor microenvironment.