Nitrification inhibitors can affect the biological transformation process of ammonium nitrogen to nitrate nitrogen in soil by inhibiting the activity of ammonia-oxidizing bacteria (AOB). Objective To investigate the effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on the community structure and assembly mechanisms of AOB in coastal saline-alkaline paddy soil. Methods To study the effects of the typical nitrification inhibitor DMPP addition on the diversity, community structure, and community assembly process of AOB in soil under two salinity levels. Pot experiments and high-throughput sequencing were employed to determine the diversity, community structure, and community assembly process of AOB. Results The addition of DMPP increased the alpha diversity of AOB in soil, which reached a significant level in the high-salinity soil. The addition of DMPP significantly changed the community composition of AOB, reducing the relative abundance of taxa with high relative abundance and enriching the taxa with low relative abundance. The decrease in relative abundance of taxa with high relative abundance was the main reason for the inhibition of DMPP on nitrification. Principal coordinates analysis revealed that the community structure of AOB changed significantly after the addition of DMPP, which was more obvious in high-salinity soil. The null model analysis results showed that stochastic processes played a dominant role in the community assembly process of AOB, and the contribution of stochastic processes increased after the addition of DMPP. Canonical correspondence analysis and Mantel’s test indicated that soil pH, electrical conductivity, organic matter, total nitrogen, and alkaline-hydrolyzable nitrogen were the main physicochemical factors influencing changes in AOB community structure. Conclusion DMPP exerted significant impacts on AOB communities in coastal saline-alkaline paddy soils across varying salinity levels, with its inhibitory effects varying substantially with soil salinity.

Objective To compare the stress tolerance of recombinant Mycobacterium smegmatis strains Ms-PPE61 and Ms-Vec under different external stress conditions, investigate the activation/inhibition levels of the mitogen-activated protein kinase (MAPK)/nuclear factor (NF)-κB signaling pathway following their infection of macrophages, and explore differences in inflammatory cytokine expression after infection of RAW264.7 cells. Methods Ms-Vec and Ms-PPE61 were constructed and cultured to the logarithmic growth phase before being subjected to acidic, SDS, and H₂O₂ conditions. Colony-forming units (CFUs) were measured at different time points. Proteins were extracted from cells collected 1-48 h post-infection (hpi), and the expression levels of signaling pathway marker molecules were determined by Western blotting. The interleukin (IL)-6, tumor necrosis factor (TNF)-α, and IL-1β concentrations in the supernatants of RAW264.7 cells infected with Ms-Vec and Ms-PPE61 were measured by ELISA at 24 hpi and 48 hpi. GraphPad Prism 7.0 was used for analysis of variance of the data, and P<0.05 was considered significant. Results PCR revealed the presence of a target band in Ms-PPE61 but not in Ms-Vec. Coomassie brilliant blue staining confirmed consistent protein loading. Western blotting showed that Ms-PPE61 expressed a ~42 kDa Flag fusion protein, while Ms-Vec did not. Ultra-high-speed centrifugation was performed to separate the components of M. smegmatis. Western blotting revealed that the cytoplasmic marker protein GroES was expressed in the cytoplasmic fractions of both Ms-Vec and Ms-PPE61, while the Flag-tagged target protein was exclusively present in the cell wall of Ms-PPE61. After treatment under acidic conditions (pH 3.0) for 3 h, the survival rate of Ms-PPE61 was higher than that of Ms-Vec (P<0.000 1), while the survival rate showed no significant difference after treatment for 6 h and 9 h (P>0.05). After treatment with 0.2% SDS for 3, 6, and 9 h, the survival rate of Ms-PPE61 was higher than that of Ms-Vec (P<0.000 1). Similarly, after H₂O₂ treatment for 3 h and 6 h, the survival rate of Ms-PPE61 was higher than that of Ms-Vec (P<0.000 1). Western blotting showed that the Ms-PPE61 group had significantly lower p-p38 and p-ERK levels at 48 hpi and higher IκB-α levels at all time points than the Ms-Vec group. ELISA results indicated no differences in TNF-α secretion between the Ms-PPE61 and Ms-Vec groups at 24 hpi and 48 hpi (P>0.05), while the Ms-PPE61 group had lower IL-6 levels at 24 hpi and 48 hpi (P<0.000 1) and lower IL-1β level at 48 hpi (P<0.01) than the Ms-Vec group. Conclusion PPE61 can enhance the tolerance of recombinant Mycobacterium smegmatis to acidic, SDS and H₂O₂ stress, inhibit the MAPK and NF-κB signaling pathways by down-regulating the expression of p-p38 and p-ERK and up-regulating the expression of IκB-α, and reduce the secretion of IL-6 (significantly at both 24 h and 48 h) and IL-1β (significantly at 48 h) in macrophages, but has no significant effect on the secretion of TNF-α.

Objective Saline-alkali soil is an important farmland resource in China. This study explored the effects of a bio-organic fertilizer fortified with a functional strain isolated from the crop rhizosphere of saline-alkali soil on the growth and the grain yield and quality of peanut plants in saline-alkali soil. The results are expected provide a solution for the development of specific microbial organic fertilizers for saline-alkali soil. Methods We first compared the rhizosphere bacterial communities of peanut plants growing in low-salt stress and non-salt stress soils, and identified the potential taxa improving the salt tolerance of plants that were enriched in the peanut rhizosphere under low-salt stress. A strain named HS6 capable of enhancing the salt tolerance of peanut plants was isolated from the rhizosphere soil of peanut plants. It was preliminarily identified as Bacillus paralicheniformis HS6. A microbial organic fertilizer was prepared by combining this strain with organic fertilizer. A field experiment was carried out in coastal saline-alkali land, including a control treatment (CK: decomposed organic fertilizer) and treatment 1 (T1: decomposed organic fertilizer supplemented with the cells of strain HS6). The growth and yield-related indicators of peanut plants were determined by counting and weighting, and the quality of peanuts was determined by the Kjeldahl method and the Soxhlet extraction method. Results The soil salt concentration higher than 0.3% significantly inhibited the growth of peanut plants. The principal component analysis revealed a significant difference in the peanut rhizosphere bacterial communities between low-salt stress (0.3%) and non-salt stress soils. Under low-salt stress, 22 differential taxa, mainly including Bacillaceae, were positively enriched in the peanut rhizosphere. The application of the organic fertilizer prepared with strain HS6 significantly promoted the growth, enhanced the biomass accumulation, and increased the number of nodules of peanut plants. The number of peanut nodules of T1 was 5 times that of CK. Moreover, the functional microbial fertilizer improved the yield and quality of peanuts. Compared with CK, T1 decreased the crude protein content of peanuts by 13.84%, while increasing the crude fat content of peanuts by 5.63%. Conclusion Low-salt stress can promote the enrichment of functional microbial taxa capable of enhancing salt tolerance in the peanut rhizosphere. The microbial organic fertilizer fortified with the functional strain enriched in the rhizosphere under salt stress can significantly improve the yield and quality of peanuts, demonstrating the potential to serve as a special microbial fertilizer for saline-alkali soil.

Objective To investigate the effect of yeast dietary fiber (YDF) on arsenic-induced apoptosis in Saccharomyces cerevisiae and decipher the possible mechanism. Methods The relative survival rate, apoptosis, and antioxidant indicators were determined by the spread plate method, spectrophotometry, fluorescence microscopy, and RT-qPCR. Results The exposure to arsenic significantly decreased the relative survival rate, elevated the intracellular reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and induced apoptosis. However, in the presence of YDF (0.5 mg/mL or 1.0 mg/mL) and arsenic, the arsenic-induced toxic effects were effectively attenuated, which was evidenced by increases in the relative survival rate, content of glutathione, activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPX), and relative expression of antioxidant enzyme genes (SOD1, CTA1, CTT1, and GPX2). Moreover, the treatment with both YDF and arsenic lowered the ROS and the MDA levels, significantly down-regulated the relative expression levels of pro-apoptotic genes (AIF1, NMAⅢ, and NUC1), and significantly reduced apoptotic cells compared with the treatment with arsenic alone. Conclusion YDF regulates the antioxidant system to attenuate the arsenic-induced cytotoxicity, thereby alleviating the arsenic-induced apoptosis.

Viruses are known as the most abundant and diverse biological entities on Earth and regarded as key ecological drivers in ecosystems. The discovery of giant viruses has challenged the conventional understanding of virology and the definition of life with their microscale-virions, megabase-genome sizes, and remarkably numerous eukaryote-specific genes, which were once considered to be hallmark genes of cellular life but barely seen in viruses. Therefore, these biological characteristics of giant viruses blur the boundary between viruses and cellular life. Metagenomics studies have revealed that giant viruses are globally distributed in marine, freshwater, and soil ecosystems, and their geographical distribution is influenced by environmental factors such as temperature, latitude, and host range. Giant virus genomes include core metabolic genes, which enhance environmental adaptability by regulating host metabolism. In addition, giant viruses may even be involved in the horizontal transfer of antibiotic resistance genes. We review the research progress in giant viruses in terms of their diversity, biogeographic distribution, ecological relationships with hosts and intracellular parasites, reprogramming of host cell metabolic systems, driving forces in biogeochemical cycles, and potential impacts on human health to explore the ecological roles of giant viruses from multiple dimensions. This review aims to revolutionize our knowledge of viruses by revealing the ecological significance of giant viruses and their roles in global biogeochemical cycles.

Objective To confirm the function of the farnesyl diphosphate (FPP) cyclase encoded by orf2064 in Streptomyces exfoliatus UC5319. Methods orf2064 was expressed in Escherichia coli, and the recombinant protein was purified and assayed with FPP as the substrate. The reaction products were detected by GC-MS. An FPP-overproducing E. coli strain was engineered for heterologous expression of orf2064. The fermentation products were analyzed by GC-MS, and the target compound was isolated and structurally characterized by nuclear magnetic resonance spectroscopy (NMR). In addition, orf2064 was heterologously expressed in Streptomyces, and the fermentation products were analyzed by GC-MS. Results GC-MS revealed that both the in vitro reaction of the recombinant protein ORF2064 and the heterologous expression products in E. coli and Streptomyces consistently produced a compound with identical retention time and [M⁺] of m/z 204. Subsequent isolation, purification, and NMR analysis confirmed this compound as calarene. Conclusion The FPP cyclase encoded by orf2064 in S. exfoliatus is identified as an calarene synthase.

In recent years, as the antibiotic resistance of bacteria is aggravating, bacterial infections have brought severe challenges to disease prevention and control. Rapid and accurate identification of bacteria and their basic characteristics is extremely important for disease prevention and control, medical diagnosis, and scientific research. Compared with conventional detection methods such as plate culture counting, polymerase chain reaction (PCR), and adenosine triphosphate bioluminescence (ATP) bioluminescence, single-cell Raman spectroscopy has shown advantages and broad application prospects in bacterial classification and identification, bacterial pathogenicity and antibiotic resistance detection, and bacterial viability evaluation. This paper reviews the application of single-cell Raman technology in the field of bacteria, aiming to provide technical and application reference for practitioners engaged in the research on bacteria and Raman technology.

Objective To investigate the community structure, network complexity, and stability of soil bacteria harboring the alkaline phosphatase gene (phoD) under the application of organic amendments, elucidating their regulatory mechanisms in microbially mediated soil phosphorus (P) transformation and availability. Methods We conducted the experiment within a 13-year long-term maize field trial located in Ya’an, Sichuan. The experiment comprised three mineral P fertilizer treatments: 0, 75, and 150 kg/hm² (designated as P0, P1, and P2, respectively). In 2018, a split-plot design was implemented with organic amendment treatments, where mineral P application was reduced by 30% and supplemented with pig manure (P0+M, 70% P1+M, and 70% P2+M treatments). The phoD-harboring bacterial community structure was characterized by high-throughput sequencing and bioinformatic analyses, which revealed the effects of organic amendments with varying P supply levels on phoD-harboring bacterial communities and their regulation of soil available P. Results As the P supply level increased, both mineral and organic amendments significantly increased the content of soil organic matter (SOM), Olsen-P, and organic P (Po), while significantly decreasing soil pH. P levels and organic amendments markedly altered the community composition and network characteristics of phoD-harboring bacteria. Under low-P conditions (P0, P0+M), Bradyrhizobium icense emerged as both the dominant and indicator species, with its relative abundance decreasing significantly as P application increased. Under P-amended treatments (P1, P2, 70% P1+M, and 70% P2+M), Bradyrhizobium diazoefficiens and Roseateles depolymerans became the predominant species, exhibiting significant increases in relative abundance with higher P inputs. Notably, the relative abundance of all the three dominant species under the application of organic amendments was higher than that in corresponding inorganic P treatments. Furthermore, organic amendments increased the network nodes and connectivity links compared with corresponding mineral P treatments. Random forest analysis further identified B. icense as the strongest predictor of soil available P. The stability of phoD-harboring bacterial networks showed no significant difference across treatments. However, after the removal of dominant species, the network stability declined significantly in all treatments. Conclusion Organic amendments increase the relative abundance of dominant species within the phoD-harboring bacterial community across different P supply levels. They enhance the network complexity of phoD-harboring bacteria, thereby improving the network stability of these bacterial communities and ultimately influencing the availability of soil P.

Objective To systematically understand the antibiotic resistance and the distribution of resistance genes of intestinal antibiotic-resistant bacteria in Corvidae species on plateaus. Methods The conventional culture method and sequencing were employed to analyze 71 intestinal samples from five typical Corvidae species in plateau cities. Results A total of 70 bacterial strains were isolated, belonging to 25 species, 14 genera of 3 phyla. The highest number of strains was isolated from the medium containing sulfamethoxazole and the intestinal samples of Corvus macrorhynchos, with Enterococcus and Enterococcus mundtii being the dominant genus and species, respectively. The Kirby-Bauer disk diffusion test revealed that the isolated strains had the highest resistance rate to polymyxin antibiotics, and all the strains exhibited multidrug resistance, with nearly 40% being superbugs resistant to 10 or more antibiotics. Among the seven major categories of resistance genes, carbapenem resistance genes showed the highest detection rate, with tetD being the most frequently detected resistance gene. The detection rates of integrons and gene cassettes were both low. Conclusion Avian species of Corvidae exhibit high diversity and widespread prevalence of multidrug-resistant bacterial strains in their intestinal microbiota. Antibiotic resistance genes are widely present within these strains and exhibit significant transmission potential. As a result, they serve as veritable reservoirs and vectors for antibiotic-resistant bacteria and resistance genes, posing challenges and threats to human public health, medical care, and environmental safety. This study fills the gap in research on intestinal antibiotic-resistant bacteria and their antibiotic resistance in Corvidae birds, providing a scientific basis for subsequent assessments of the transmission risk of antibiotic resistance mediated by wild birds and the formulation of prevention and control strategies.

The β-barrel assembly machinery (BAM) complex is an essential apparatus that is responsible for the assembly of β-barrel outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria. Its functional defects can lead to bacterial death, and thus it is established as a new target for antibacterial drug development. The subunit composition of the BAM complex varies across different bacterial species and in Escherichia coli, it is composed of a core subunit BamA and auxiliary lipoproteins BamB-E. BamA, as a member of the Omp85 family, mediates the folding and release of substrate OMPs through the dynamic conformational changes of its β-barrel structure that are regulated by lipoproteins. In the present review, we summarized recent progress in distinguishing the minimal functional unit, complete functional unit, and other functional units of the BAM complex in E. coli. Moreover, by reviewing the drug screening studies targeting the BAM complex, we provided an overview of new strategies to combat the drug resistance of Gram-negative bacteria.