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.

Colorectal cancer (CRC), a common malignant neoplasm of the digestive system globally, demonstrates pathological progression that is intricately linked not only to dysbiosis of the gut microbiota but also to the oral microbial ecosystem. The emerging concept of the “oral-gut axis” offers novel insights into the regulation of microbial interactions across different organs. Recent research indicates that Peptostreptococcus, a predominant genus within the oral microbiome, exhibits spatiotemporal correlations with the initiation and progression of CRC. This genus may influence intestinal microecological changes and CRC pathogenesis through the “oral-gut axis”. We explore the microbial interactions between oral and intestinal ecosystems, examining the multidimensional associations between specific Peptostreptococcus species (such as P. stomatis and P. anaerobius) and CRC development. Key considerations include the population heterogeneity of these species among CRC patients with varying clinical profiles, their dynamic evolution during the adenoma-carcinoma sequence, and their spatial distribution across different pathological stages. We synthesize mechanistic evidence illustrating the role of Peptostreptococcus in promoting tumorigenesis by enhancing cancer cell proliferation, inducing epithelial-mesenchymal transition, and remodeling the tumor microenvironment. Additionally, this article assesses the clinical potential of Peptostreptococcus as predictive biomarkers and therapeutic targets for CRC. Finally, we propose future directions for the development of targeted microbial intervention strategies against oral-derived pathogens, with the aim of stimulating scientific interest and encouraging further investigation in this emerging research area.

Heterotrophic nitrifying-aerobic denitrifying (HN-AD) bacteria can simultaneously complete nitrification and denitrification processes under aerobic conditions, significantly simplifying wastewater treatment procedures. These strains exhibit rapid growth, tolerance to extreme environments, and are widely applied in various wastewater treatments. This review summarizes the nitrogen removal pathways of HN-AD bacteria and highlights the potential of novel immobilization carriers (composite materials, magnetic nanocarriers, and biochar) for nitrogen removal across diverse wastewater sectors. It focuses on elucidating the fundamental principles, application cases, current research status, and future prospects of emerging immobilization technologies, including biomimetic mineralization immobilization, electrospun fiber immobilization, and 3D printing carrier immobilization. The enhanced effects of novel immobilization strategies on improving nitrogen removal efficiency and system stability are discussed. Finally, challenges and future prospects for HN-AD bacterial immobilization technology during fabrication and application are outlined.

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.

In recent years, the widespread application of new technologies such as viral metagenomics has expanded our understanding of viral diseases in giant pandas. In addition to the previously reported infections with canine distemper virus, rotavirus, and parvovirus, the viruses carried by giant pandas exhibit increasing diversity and unique genetic variation characteristics. The growing population size and density of giant pandas post serious challenges to the population biosecurity, especially the prevention and control of viral diseases. To better understand the epidemiological characteristics of viral diseases in giant pandas, as well as the current status of the prevention and control for the development of effective strategies, we review the studies about viral diseases in giant pandas. This paper systematically elucidates the infection characteristics and hazards of major viral pathogens, as well as diagnostic methods, treatment measures, and preventive strategies. Additionally, the paper explores the bottlenecks and challenges encountered in developing and applying vaccines for giant pandas and the difficulties faced in viral disease research and proposes future research directions and recommendations, aiming to provide a scientific basis for preventing and controlling viral diseases in giant pandas.

Amino acids serve as indispensable components and nutrients for living organisms, while recent studies have revealed that amino acid metabolism in pathogenic bacteria plays a pivotal role in their pathogenic processes. This review summarizes current research on the roles of different amino acids in facilitating the pathogenicity of pathogenic bacteria. Specifically, we highlight how Salmonella enterica utilizes l-aspartate to achieve colonization and dissemination within the inflamed intestine, and how branched-chain amino acids indirectly regulate the virulence of Staphylococcus aureusvia the global transcriptional regulator CodY. Additionally, we briefly outline the vital roles of amino acid metabolism throughout the infection processes of pathogenic bacteria. In-depth research into how amino acid metabolism promotes pathogenic processes will deepen our understanding of the underlying mechanisms and provide a theoretical basis for developing novel antibacterial strategies.

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 Screening fungi with the ability to degrade polyacrylamide (PAM) and analyzing the characteristics of their degradation products can provide a basis for clarifying the degradation mechanism. Methods Fungi capable of degrading PAM were screened from bauxite sludge and used to construct a composite fungal community, with the degradation products and morphological characteristics being determined under optimized conditions. Results The results showed that the three strains of fungi screened out were Trichoderma asperellum, Aspergillus flavus, and Aspergillus niger, which showed the degradation rates of 27.35%, 25.20%, and 23.04%, respectively, for PAM. The degradation conditions were optimized by the response surface method as initial pH 5.5, inoculum amount of 5.1%, and incubation temperature of 32 ℃, under which the fungal complex constructed with T. asperellum and A. flavus showed the PAM degradation rate of 45.44%, a viscosity reduction rate of 84.57%, and laccase and urease activities of 13.90 U/mL and 17.70 U/mL, respectively. A large number of hollows and cavities were formed on the surface of PAM after degradation. In addition, mycelial biofilm was observed on the surface. The degradation products showed -COOH and -OH functional groups. Conclusion The above results suggest that the fungal complex may degrade PAM into small molecules through the synergistic effects of mycelial physical erosion and extracellular enzymes.

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.

Objective To explore the application of hutC sequence analysis in the identification of Burkholderia cepacia complex (Bcc) at the species level. Methods We compared the sequences of hutC and the amino acid sequences of the encoded proteins and conducted phylogenetic analysis to theoretically assess the feasibility of using hutC for species-level identification of Bcc. Primers targeting the hutC of Bcc were designed, and the amplification conditions were optimized. With those of standard strains as templates, the hutC sequences of representative Bcc species were amplified. The sequencing results were compared with NCBI sequences for phylogenetic analysis to validate the theoretical hypothesis. Additionally, single nucleotide polymorphism analysis of hutC sequences was performed to identify species-level characteristic barcodes of Bcc. Results The hutC gene was relatively conserved between Bcc and non-Bcc. With the designed primers and amplification conditions, a 692 bp fragment of hutC was successfully amplified from 12 Bcc standard strains. Except for one strain with taxonomic errors, the remaining 11 strains had the comparison results consistent with those from the culture collection centers. The phylogenetic analysis based on hutC showed that different Bcc species could be clustered with high bootstrap values. A 12 nucleotide characteristic barcode of hutC was identified, which can rapidly distinguish different species of Bcc. Conclusion The gene hutC can serve as a new housekeeping gene target for accurate identification of Bcc at the complex and species levels.

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.

Helicobacter pylori infection is a major causative factor for chronic gastritis and gastric cancer, while current antibiotic therapies are facing increasingly severe resistance. Probiotics have emerged as a promising approach for anti-H. pylori research due to their high safety. Notably, certain Lactobacillus strains have been demonstrated to effectively alleviate H. pylori-induced inflammatory responses, yet their underlying molecular regulatory mechanisms remain unclear. Objective To investigate the molecular mechanism by which Lactiplantibacillus plantarum ZJ316 inhibits the H. pylori-induced inflammatory response by modulating the p38 mitogen-activated protein kinase (MAPK) signaling pathway in the host cells and assess the regulatory effect of this strain on gastric microecological homeostasis, thus providing a theoretical basis for the development of probiotic therapeutics targeting H. pylori. Methods We integrated cell experiments (human gastric adenocarcinoma cell line AGS) and animal experiments (C57BL/6 mice) and employed Western blotting (to determine the phosphorylation level of p38 MAPK), transcriptome sequencing and RT-qPCR (to analyze differential gene expression), ELISA [to determine the levels of inflammatory cytokines interleukin (IL)-8 and IL-10], 16S rRNA gene sequencing (to unveil the gastric flora structure), and hematoxylin-eosin staining (to observe gastric mucosal damage) to systematically study the intervention effect of L. plantarum ZJ316 on H. pylori infection. Results At the cellular level, L. plantarum ZJ316 inhibited H. pylori-induced p38 MAPK phosphorylation, with the inhibition rates of 21.95% and 33.72% at the time points of 1 h and 2 h, respectively (P<0.01). It down-regulated the expression of pathway genes such as MAP3K8 and FOS, and lowered the mRNA levels of the pro-inflammatory cytokines interferon-γ, tumor necrosis factor-α, and IL-6 by 43.26%, 35.95%, and 51.91%, respectively (P<0.01). The combination of this strain with adezmapimod, a p38 MAPK-specific inhibitor, further enhanced the inhibitory effect. In animal experiments, L. plantarum ZJ316 significantly attenuated gastric mucosal pathological injury and inflammatory response, and 16S rRNA gene sequencing revealed that ZJ316 reduced the relative abundance of pathogenic Pseudomonadota and significantly increased the relative abundance of Bacillota [(54.8±9.9)% vs. (27.8±5.9)%, P<0.01] in the stomach. When ZJ316 was combined with adezmapimod, the relative abundance of Bacteroidota was elevated [(58.5±5.2)% vs. (47.8±6.9)%, P<0.05], and specific beneficial genera such as Alistipes were synergistically enriched (an increase of 69.52% compared with the H. pylori group). Conclusion L. plantarum ZJ316 alleviated the inflammatory response triggered by H. pylori infection by inhibiting the p38 MAPK pathway and remodeled the gastric microecological structure. The findings provide a theoretical basis for the inhibition of H. pylori-induced inflammation by lactobacilli and the development of probiotic-based functional foods.

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 Developing plant-microbe combined techniques is significant for addressing the problem of declining cropland quality in China and enriching the approaches for biological remediation of degraded soils. Methods The plant growth-promoting traits of Burkholderia sp. YQ9 were determined by assessing its cellulase, protease, and ammonia production. Subsequently, a pot experiment was conducted to evaluate the effects of different dilutions of Burkholderia sp. YQ9 inoculant and culture medium on the growth of white clover (Trifolium repens) and the physicochemical properties of the rhizosphere soil. Furthermore, high-throughput sequencing was employed to analyze the impacts of different treatments on the structure of the rhizosphere microbial community. Results Burkholderia sp. YQ9 exhibited plant growth-promoting traits, being capable of producing cellulase, protease, and ammonia. White clover improved the pH environment of the rhizosphere soil. Application of the original inoculant of Burkholderia sp. YQ9 promoted white clover growth, significantly enhancing the content of soluble protein and soluble sugar in the shoots and leaves, as well as the levels of available phosphorus and available potassium in the rhizosphere soil, thereby facilitating organic matter decomposition. Analysis of microbial alpha diversity in the rhizosphere soil revealed that both the original inoculant of Burkholderia sp. YQ9 and the culture medium significantly reduced the richness, diversity, and evenness of both fungal and bacterial communities in the rhizosphere soil and altered the composition of the soil microbial community. The correlation analysis further indicated that the microbial community in the rhizosphere soil was correlated with white clover growth and soil physicochemical properties. Conclusion Burkholderia sp. YQ9 not only promoted the growth of white clover but also modified the composition of the rhizosphere microbial community and improved the soil fertility. These findings provide microbial augmentation-based technical support for enhancing cropland quality.

Objective The formation of neutrophil extracellular traps (NETs) induced by influenza A virus (IAV) subtype H1N1 was investigated both qualitatively and quantitatively. Methods Mouse bone marrow neutrophils were isolated, purified, and characterized. NETs were induced in vitro using lipopolysaccharide (LPS) and phorbol 12-myristate 13-acetate (PMA). Additionally, IAV groups with three different titers: one hundred 50% tissue culture infective doses (100 TCID₅₀), 50 TCID₅₀, and 25 TCID₅₀ as well as the normal control group were established, and the intracellular nucleoprotein (NP) mRNA expression levels of the IAV groups were detected using reverse transcription quantitative polymerase chain reaction (RT-qPCR). The effect of each factor on neutrophils was assessed by measuring the concentration of circulating cell-free DNA (cfDNA) in the supernatant of each group using the quantitative SYTOX Green staining method. The NETs structure in each group of cells was observed under a fluorescence microscope after Hoechst 33342 staining. An immunofluorescence assay was performed to detect the expression levels of NET characteristic markers citrullinated histone H3 (CitH3), peptidylarginine deiminase 4 (PAD4), myeloperoxidase (MPO), and neutrophil elastase (NE) proteins, as well as the nuclear co-localization and fluorescence intensity of PAD4 with CitH3, and MPO with NE in each group. The levels of reactive oxygen species (ROS) were determined by using a fluorescent probe assay, and the levels of intracellular CitH3 protein formation were determined by using Western blotting. Results The activity of neutrophils isolated from mouse bone marrow reached 98%, with purities of ≥87%. The expression levels of NP mRNA in the IAV groups were significantly higher than those in the control group. Compared with the control group, the cfDNA levels of the PMA, LPS, and IAV groups were significantly increased, with significant increases in the web-like structures of NETs. The immunofluorescence assay showed that the relative expression levels of MPO, NE, PAD4, and CitH3 proteins were elevated to varying degrees, with the co-localization of PAD4/CitH3 or MPO/NE increased after IAV infection. Moreover, the peak of MPO protein expression was observed before that of NE protein, whereas CitH3 expression paralleled that of PAD4 protein. Additionally, the ROS level was elevated, and the level of CitH3 protein formation was also significantly increased. Conclusion Stimulation of neutrophils by IAV (H1N1) induces NET formation, which may be related to the increased intracellular ROS and PAD4 levels.

Agrobacteriumtumefaciens, a classic model organism for plant-microbe interaction research, is a valuable transgenic tool for plants. Phenolic acids secreted by plants after injury can affect the infection of the host by A. tumefaciens. Objective This study investigated the transcription factor PcaR of A. tumefaciens regarding its effects on the metabolism of simple phenolic acids, regulation of the target gene, and effect on the bacterial tumorigenicity in host plants. Methods The A. tumefaciens strain with atu4546 knockout (Δatu4546) and the complement strain C-Δatu4546 were constructed via the suicide plasmid pEX18Km and the plasmid pUCA19 with a strong promoter, respectively. Both Δatu4546 and C-Δatu4546 were tested for growth with p-hydroxybenzoic acid or protocatechuic acid as the sole carbon source and tumorigenicity on carrot stems and Kalanchoe pinnata leaves. In the wild-type strain C58 and Δatu4546, the reporter gene was in situ inserted into the downstream region of the metabolic target gene atu4549. The regulatory link between atu4546 and the target gene was examined based on the β-galactosidase activity. To investigate the self-regulation of PcaR, we constructed the atu4546 self-promoter reporter plasmid. To identify the binding sites of PcaR, we constructed the upstream promoter region reporter plasmid of the target gene to remove or replace the predicted binding sites and then determined the β-galactosidase activity. Results The knockout of atu4546 did not affect the growth of A. tumefaciens on sucrose, but led to the inability to use p-hydroxybenzoic acid or protocatechuic acid as the sole carbon source. The growth was restored after atu4546 was complemented. The tumor weights of carrot stems and K. pinnata leaves infected by Δatu4546 decreased by 34.90% and 52.58%, respectively, and the number of colonies per 0.1 g tumor decreased by 72.19% and 80.54%, respectively. The knockout of atu4546 led to a 102.04% increase in its own promoter activity, which suggested that atu4546 negatively regulated its own expression. Atu4546 boosted the expression of the atu4547-atu4549 gene cluster, as evidenced by a 74.86% decrease in β-galactosidase activity downstream of the target gene in Δatu4546 compared with that in the wild type. The promoter region sequence alteration experiment identified GTGCGATATATACGAAC as the binding site of PcaR. Conclusion This study shows that the transcription factor PcaR is involved in phenolic acid catabolism, negatively regulates itself and stimulates the transcription of the downstream gene pcaIJF. The binding site of PcaR to the target gene is GTGCGATATACGAAC. The knockout of PcaR attenuates the pathogenicity of A. tumefaciens. This study reveals the dual regulation mechanism in the phenolic acid metabolism-pathogenic signaling pathway and expands the theoretical cognition of plant-microbe interactions.

Objective To address the environmental pollution caused by polyethylene terephthalate (PET), we screened functional bacterial strains capable of degrading PET and analyzed their growth and degradation characteristics, aiming to provide theoretical support and microbial resources for PET bioremediation. Methods Bacterial strains capable of degrading PET were isolated from the soil samples collected around a landfill site. The selected strain was identified based on morphological characteristics, physiological and biochemical properties, and 16S rRNA gene sequencing. The surface morphology and chemical group changes of PET films before and after degradation were analyzed by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and water contact angle (WCA) measurements. The types and concentrations of degradation products were quantified via high-performance liquid chromatography (HPLC). Results A PET-degrading strain, designated YH-1, was successfully isolated and identified as a member of the Cellulosimicrobium sp. genus based on 16S rRNA analysis. The optimal growth conditions for strain YH-1 were 35 °C, pH 7.0, and 1% salinity, and the strain exhibited robust growth within the ranges of pH 6.0-10.0 and 1%-4% salinity. After 6 days of incubation, YH-1 achieved a PET weight loss rate of 1.90%. HPLC revealed that terephthalic acid (TPA) and bis(2-hydroxyethyl) terephthalate (BHET) were the main degradation products, with concentrations of 3.87 mg/L and 4.70 mg/L, respectively. SEM images showed obvious surface roughening and cracking of the PET film after degradation, while FTIR revealed changes in functional groups. WCA measurements showed a reduction in contact angle from 79.385° to 65.052°, indicating enhanced hydrophilicity of the degraded PET film surface. Conclusion Strain YH-1 demonstrates good environmental adaptability and PET degradation potential. It can disrupt the PET film surface and generate typical degradation products. The findings lay a foundation for further development of PET-degrading microbial resources and exploration of degradation mechanisms.

Objective To investigate the effect of inoculating the associative nitrogen-fixing bacteria strain Paraburkholderia RBCS-17 on the root-associated bacterial community of sugarcane. Methods We employed 16S rRNA gene high-throughput sequencing combined with QIIME 2-based bioinformatics analysis to investigate the effects of inoculating Paraburkholderia RBCS-17 on the alpha diversity, beta diversity, composition, and co-occurrence network of the root-associated bacterial community of sugarcane. Results Inoculating Paraburkholderia RBCS-17 did not significantly affect the diversity but significantly changed the structure of the root-associated bacterial community. Further studies showed that the inoculation significantly increased the relative abundance of Burkholderia, Dyella, and Pseudomonas, while reducing the relative abundance of certain potentially detrimental bacteria such as Ralstonia. In addition, the inoculation altered the key module composition of the bacterial co-occurrence network in sugarcane roots, which suggested that inoculation might influence potential bacterial interactions. Conclusion Inoculating the associative nitrogen-fixing bacterial strain Paraburkholderia RBCS-17 modified the root-associated bacterial community structure of sugarcane, promoting the enrichment of potentially beneficial bacteria while suppressing potentially harmful ones. These findings provide new insights into the intricate interactions among associative nitrogen-fixing bacteria, host plants, and indigenous bacteria.

Objective Nitrous oxide (N₂O)-reducing microbes are the only known microbial group capable of eliminating N₂O. The abundance, diversity, community structure, and influencing factors of their functional gene (nosZ) are critical for N₂O removal. Cunninghamia lanceolata is a widely planted timber species in southern China, and its rhizosphere represents a hotspot for both N₂O production and reduction. However, the spatial distribution pattern of nosZ Ⅰ genes and their driving factors in the rhizosphere soils of C. lanceolata plantations remain unclear. Methods We investigated the rhizosphere soils of C. lanceolata plantations from five state-owned forest farms—Qiujiashan, Wuyi, Guanzhuang, Xiayang, and Xiapu—in Fujian Province. Quantitative PCR and amplicon sequencing were employed to analyze the abundance, diversity, and community structure of nosZ Ⅰ genes and to identify their key environmental drivers. Results Dissolved organic carbon concentrations in rhizosphere soils ranged from 6.91 mg/kg to 23.52 mg/kg, being significantly lower in Guanzhuang and Xiayang than in Wuyi, Qiujiashan, and Xiapu. The nosZ I gene abundance ranged from 4.76×10⁶ copies/g to 36.50×10⁶ copies/g, reaching 36.50×10⁶ copies/g and 29.08×10⁶ copies/g in Guanzhuang and Xiayang, respectively, which significantly exceeded those in Qiujiashan, Wuyi, and Xiapu. Dissolved organic carbon emerged as the primary driver of nosZ I gene abundance, which implied that low dissolved organic carbon may promote the proliferation of N₂O-reducing bacteria. The Shannon index of nosZ I genes ranged from 4.41 to 5.67, being significantly higher in Xiayang than in Wuyi and Xiapu and the lowest in Xiapu. Total carbon was the key factor affecting the Shannon index. The nosZ I community structures in Qiujiashan, Guanzhuang, and Xiapu were similar, whereas that of Xiayang was significantly different from the others. Soil pH was identified as the main driver of community structure, and Xiayang had a significantly higher pH than the other sites. The dominant bacterial class in the rhizosphere soils of all five forest farms was Gammaproteobacteria. Xiayang had significantly lower relative abundance of Gammaproteobacteria but significantly higher relative abundance of Alphaproteobacteria than other farms. Conclusion Soil carbon content and pH are key environmental factors regulating the abundance, diversity, and community structure of N₂O-reducing bacteria in the rhizosphere soils of C. lanceolata plantations, potentially influencing N₂O removal and mitigation potential. Therefore, the management strategies for C. lanceolata plantations should consider regulating soil carbon content and pH to optimize N₂O mitigation effects and alleviate global climate change.

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 investigate the effects of the antidepressant mirtazapine on the microbial resistome in complex intestinal environments. Methods We employed read mapping and metagenomic assembly to analyze the antibiotic resistance genes (ARGs) and their bacterial hosts based on metagenomic sequencing data of fecal and cecal content samples. Results A total of 29 classes of ARGs, comprising 610 subtypes, were identified. Bacitracin-, tetracycline-, and vancomycin-class ARGs were the predominant types. Chronic restrain stress (CRS) increased the total abundance of ARGs, significantly elevating the abundance of high-risk ARGs belonging to aminoglycoside, MLS (macrolide-lincosamide-streptogramin), and tetracycline classes (e.g., tetM, tetO, and tet40). Oral administration of mirtazapine exhibited initial microbiota-dependent effects on the resistome. It increased the total abundance of ARGs in healthy rats but decreased that in depressed rats. In addition, mirtazapine significantly enhanced the abundance of vancomycin-, aminoglycoside-, and mupirocin-class ARGs in healthy rats, as well as the tetracycline resistance gene tetP and multidrug resistance gene ompR in depressed rats. Bacillota, Bacteroidota, and Pseudomonadota were the dominant phyla of gut microbiota and served as the primary bacterial hosts of ARGs. Bacillota, as the main host phylum for aminoglycoside and MLS-class ARGs, showed increased abundance after CRS treatment, which was a key factor driving the significant enrichment of these two ARG classes. Furthermore, CRS increased the proportion of pathogenic bacteria such as vancomycin-resistant enterococci. Lactobacillus and Blautia were identified as potential hosts of tetP and ompR, respectively. The significant increases in the abundance of Lactobacillus and Blautia in the intestines of depressed rats after oral mirtazapine administration were critical factors for the marked enrichment of tetP and ompR. Conclusion CRS increases gut microbiota resistance risks by elevating the abundance of high-risk ARGs and pathogenic bacteria carrying ARGs. The effects of oral mirtazapine on the gut resistome are dependent on the initial microbiota composition. This study provides insights into the relationship between non-antibiotic drugs and gut microbiota resistance, offering important implications for the prevention and control of antibiotic resistance transmission.

Objective To investigate the effects of changes in single factors such as pH, metal ions, and NaCl concentration in the MG medium on the growth of Virgibacillus salexigens DSM 11483 and the yield of 5-hydroxyectoine (5-HE), optimize the culture conditions, and explore the mixed culture conditions of Halomonas campaniensis XH26 with V. salexigens DSM 11483 and the change in the yield of 5-HE. Methods We used a spectrophotometer was used to monitor the biomass (OD₆₀₀) of bacteria. The HPLC method was used to measure the yields of ectoine and 5-HE. The one-sample t-test was conducted to analyze the difference significance of the experimental data. Results The optimal culture conditions for V. salexigens DSM 11483 were as follows: pH 9.0, FeSO₄·7H₂O concentration of 1.00 mmol/L, and NaCl concentration of 2.0 mol/L. In this medium, the yields of ectoine and 5-HE were 200.4 mg/L and 80.0 mg/L, respectively. After “feeding” V. salexigens DSM 11483 with 40.0 mmol/L ectoine and culturing for 72 h, the yield of 5-HE reached 1 373.5 mg/L, which was 17.2 times that in the control group. After 72 h of mixed culture of H. campaniensis XH26 cultured for 24 h with V. salexigens DSM 11483 cultured for 36 h, the yields of ectoine and 5-HE were 1 535.1 mg/L and 168.7 mg/L, respectively, which were 7.7 times and 2.1 times the yield of V. salexigens DSM 11483 in pure culture. Conclusions The mixed culture of halophilic bacteria can make full use of their respective advantages to improve the synthesis and transformation efficiency of ectoine, demonstrating further research value.

Objective To investigate the mechanism by which the endophytic fungus Trichoderma harzianum Rifai help the seedlings of the rare medicinal plant Camphora migao (H. W. Li) Y. Yang, Bing Liu & Zhi Yang to defend against drought stress. Methods We simulated different drought stress gradients using the potted weighing method after inoculation of C. migao seedlings with T. harzianumvia rhizosphere injection and investigated the plant growth, physiological, and biochemical indexes. Results Under different drought conditions, inoculation with T. harzianum significantly increased the growth indexes such as biomass, plant height, and root growth of C. migao seedlings, compared with the uninoculated control group. Furthermore, T. harzianum significantly increased the activities of antioxidant enzymes and the content of osmotically regulation substances, reduced the malondialdehyde content, and elevated the content of photosynthetic pigments in the seedling leaves, which effectively mitigated the drought stress effects on the growth and development of C. migao seedlings. Conclusion T. harzianum improved the physiological responses of C. migao seedlings to drought stress by regulating osmotic balance and maintaining the stability of antioxidant system.

Objective To isolate lactic acid bacteria (LAB) with the ability to degrade milk fat, providing a theoretical foundation and technical support for dairy fermentation process optimization and probiotic development. Methods Primary screening employed media with butter as the main carbon source, followed by secondary screening using media with butter as the sole carbon source. The target strains were validated via carbon-free media. The selected strains underwent chromogenic assays for lipase characterization. Fermentation properties were assessed through viable count, acidity, acid value, and free fatty acid measurements. Probiotic potential was evaluated via acid/bile salt tolerance and cholesterol reduction assays. Results Through primary screening, secondary screening, and validation, ten strains with the ability to degrade milk fat were selected. Among them, a strain with faster growth than the others was identified as Lactobacillus delbrueckii grx601 through morphological and molecular biological characterization. This strain exhibited high lipase activity during logarithmic and stationary phases, with intracellular and extracellular enzyme activities of 14.14 U/mL and 11.45 U/mL, respectively. Enzymatic characterization showed that the optimal substrate for intracellular and extracellular lipases was p-nitrophenol palmitate, with the optimal reaction conditions of pH 7.0 and 40 ℃. The relative activity remained above 50% at 5% NaCl, which indicated certain salt tolerance. The fermentation characteristic experiment showed that L. delbrueckii grx601 significantly increased the acidity, acidity value, and free fatty acid content during the fermentation process. Moreover, the survival rates of L. delbrueckii grx601 in artificial simulated solutions with pH 3.0 and 0.30% bile salt were 83.87% and 47.70%, respectively, which indicated acid/bile salt tolerance of the strain. In addition, the cholesterol degradation rate of the strain was 7.95%. Conclusion L. delbrueckii grx601 was successfully isolated and characterized as a potent milk fat-degrading strain. Its high intra/extracellular lipase activity, favorable enzymatic properties, robust fermentation performance, and probiotic attributes (acid/bile salt tolerance, cholesterol reduction) indicate significant potential for dairy fermentation and probiotic applications.

Objective To isolate multifunctional phosphate-solubilizing bacteria (PSB) exhibiting psychrophilic adaptation and saline-alkaline tolerance in response to the ecological challenge of phosphorus limitation in saline-alkaline soils in cold regions, evaluate their phosphate-solubilizing efficiency and environmental adaptability, and preliminarily investigate their phosphate-solubilizing mechanisms. Methods We used an inorganic phosphorus-selective medium to isolate bacterial strains from saline-alkaline soils in Baicheng, Jilin Province. The phosphate-solubilizing capacity was quantitatively determined through the molybdenum-antimony colorimetric method. Taxonomic identification was performed through morphological characterization and phylogenetic analysis based on 16S rRNA gene sequences. The phosphate solubilization conditions were optimized via multi-parameter gradient optimization. HPLC was employed to quantify organic acid metabolites. Phenol-sulfuric acid assay and crystal violet staining were employed to characterize biofilm formation and extracellular polysaccharide (EPS) synthesis. Results The isolated strain Pseudomonas psychrophila MPP2402 demonstrated broad-spectrum environmental adaptability, maintaining stable growth at 5-30 ℃, pH 7.0-10.0, and 0.2-0.8 mol/L NaCl. The strain achieved 574.66 mg/L soluble phosphorus (14.8% increase) under optimal conditions: 15 ℃, pH 7.0, 0.4 mol/L NaCl, 1% inoculum density, and 5 g/L Ca₃(PO₄)₂. MPP2402 may exert the phosphate-solubilizing effect through the secretion of organic acids such as succinic acid (51.53 μg/mL), oxalic acid (22.84 μg/mL), tartaric acid (15.11 μg/mL), and malic acid (5.93 μg/mL), which worked in concert to solubilize phosphate. Additionally, the strain utilized EPS to construct a biofilm barrier and regulated the viable count in adverse environments such as low-temperature and saline-alkaline conditions. Conclusion The successful isolation of MPP2402 establishes a foundational resource for developing efficient saline-alkaline tolerant microbial agents and improving soil nutrient management in cold-region ecosystems.

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.

Porcine hemagglutinating encephalomyelitis virus (PHEV), a member of the betacoronavirus genus, is widespread in swine herds and the only known coronavirus causing neurological diseases in pigs. Objective To characterize the genomic features and phylogenetic relationship of a PHEV strain isolated from China. By investigating the biological properties of the virus, we assessed its epidemiological status and identified genetic variation patterns and evolutionary trends, providing a scientific basis for developing targeted prevention and control strategies. Methods RT-PCR detection was performed on suspected PHEV-positive samples collected from a large pig farm in Jiangsu Province, China, followed by virus isolation. The isolated virus was validated by indirect immunofluorescence assay (IFA), transmission electron microscopy (TEM), and whole genome sequencing. Phylogenetic analysis was performed based on the complete genome, S gene, HE gene, and NS2 gene. Results A PHEV strain, designated as PHEV JS-2025, was successfully isolated from the brain tissue sample. IFA showed strong red fluorescence signals in the cytoplasm, and TEM revealed typical coronavirus particles with a diameter of approximate 150 nm. The strain showed vigorous propagation in HRT-18 cells, reaching the peak viral titer at 72 h, with a 50% tissue culture infectious dose (TCID₅₀) of about 10^4.3 TCID₅₀/mL. PHEV JS-2025 could infect HRT-18, NPTR, and LLC-PK1 cells, and to a lesser extent, human intestinal Caco-2 cells. Whole genome sequencing revealed that the genome of PHEV JS-2025 was 30 044 bp in length, with over 94.9% nucleotide sequence identity to 14 reference PHEV strains, clustering within the rvPHEV-L-1 lineage. Of note, a mutation in the NS2 gene caused a premature termination at amino acid 19, resulting in the functional loss of the NS2 protein. Conclusion A novel PHEV strain JS-2025 from Jiangsu Province was successfully isolated and identified. This strain exhibits unique cellular tropism and can infect human intestinal cell lines, showing a risk of cross-species transmission. The truncated NS2 gene may affect the pathogenic mechanism of this strain. This study aids in understanding the genetic evolutionary characteristics and epidemiological features of PHEV and has implications for the prevention and control of PHE.

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 We compared the rhizosphere microbial interaction network structure and keystone taxon identification arising from distinct network construction algorithms, aiming to clarify the characteristics and advantages of each algorithm in inferring microbial interactions and identifying keystone taxa, thereby providing a theoretical basis for methodological selection. Methods Taking the rhizosphere microbial community of Camphora migao (a rare plant) as the model system, we constructed molecular ecological networks with three mainstream algorithms: sparse correlations for compositional data (SparCC), random matrix theory (RMT), and co-occurrence network (CoNet). We comprehensively compared network structural features and keystone taxon identification across algorithms by integrating PICRUSt2 functional prediction with keystone taxa-environmental factor correlation analysis. Results Network construction algorithms significantly influenced the topological properties of networks. SparCC generated highly modular networks (relative modularity index, RM=1.31) with distinct interaction segregation (edge connectivity=0). RMT produced a single-module structure (RM=0.78) and homogeneous connectivity (closeness centralization index=0.22). Integration of 26.0% negative correlations in CoNet reduced modularity (RM=0.95), increased network diameter (33.22 steps), and decreased robustness. Keystone taxon identification was method-dependent. Specifically, CoNet, SparCC, and RMT identified 224.00, 44.00, and 19.00 keystone taxa, respectively, with<9.2% cross-method overlap. Rhizobiales and Acidobacteriales were consistently identified as core keystone taxa by all methods, demonstrating cross-algorithm stability. The correlation analysis with environmental factors confirmed that these shared taxa significantly correlated with β-glucosidase activity, validating their role in cellulose degradation and highlighting methodological consistency in identifying key ecological processes. Conclusion The three algorithms exhibited complementary strengths: CoNet resolved complex competitive interactions; SparCC reliably assessed functional stability; RMT uncovered core functional modules. The correlation analysis with environmental factors validated the cellulose degradation function of keystone taxa, with high cross-method consistency in core ecological process identification. Our work provides a theoretical foundation for elucidating plant-microbe interactions and optimizing microbial network construction.