Objective To compare the compositional differences, assembly characteristics, and ecological roles of generalist and specialist microeukaryotes between the dry and rainy seasons in the lower reaches of the Yarlung Zangbo River and to clarify how spatial heterogeneity and seasonal hydrological fluctuations influence microeukaryotic diversity. Methods Water samples were collected from 34 paired sampling sites in May 2022 (dry season) and July 2023 (rainy season). Environmental factor measurements, 18S rRNA gene high-throughput sequencing, and multivariate statistical analyses were conducted to examine the assembly processes, environmental responses, species associations, and state-transition characteristics of the generalist and specialist subcommunities. Results A total of 14 828 high-quality amplicon sequence variants (ASVs) were obtained, with 10 240 and 8 737 detected in the dry and rainy seasons, respectively. In the dry season, 146 generalists and 933 specialists were identified, whereas 526 generalists and 1 420 specialists were identified in the rainy season. The relative abundance of generalists and specialists was 6.29% and 73.18% in the dry season and 4.45% and 77.49% in the rainy season, respectively. The composition of generalists and specialists differed significantly in both seasons, and beta diversity was mainly driven by species turnover. Stochastic processes generally dominated community assembly, although the relative contributions of ecological processes differed between the two ecological strategy groups. In the rainy season, dispersal limitation weakened in specialists, whereas the contribution of deterministic processes increased in generalists, mainly due to increased homogeneous selection. Binary-state speciation and extinction (BiSSE) parameters indicated that specialists had higher state-transition rates, suggesting faster state turnover under contrasting seasonal conditions. Spatial and water physicochemical factors jointly drove community differentiation and niche divergence, with latitude, turbidity, and chemical oxygen demand as the main explanatory variables. Co-occurrence network analysis showed that both groups contributed to maintaining network complexity and stability, while network simplification was more pronounced after specialists were removed. Conclusion Generalist and specialist microeukaryotes in the lower reaches of the Yarlung Zangbo River showed marked differences in community assembly across seasonal transitions. Their distribution was jointly shaped by spatial heterogeneity, hydrological connectivity, and environmental filtering. Specialists contributed more strongly to network connectivity and may play a more important role in maintaining community resilience than generalists.

Yuncheng Salt Lake located in the southwest of Shanxi Province is one of the three major sodium sulfate inland salt lakes in the world, harboring rich microbial resources, while there is still a lack of systematic research on the archaeal diversity in this salt lake. Objective To explore the diversity of archaea in soil sediments of Yuncheng Salt Lake and analyze the influences of environmental factors on the diversity. Methods Soil physical and chemical analysis was carried out on 54 samples from 18 sampling sites in Yuncheng Salt Lake, and the effects of environmental factors on the archaeal diversity were analyzed by amplicon high-throughput sequencing. Results Amplicon analysis showed that Halobacteriota, Thermoproteota, Nanobdellota, Thermoplasmatota, and Asgardarchaeota were the main taxa. Among them, Halobacteriota and Thermoproteota were the dominant groups of archaea in the soil sediments of Yuncheng Salt Lake. The analysis of diversity and community composition showed that there were obvious differences in archaeal communities among different sampling sites. Redundancy analysis showed that total nitrogen, total carbon, ammonium nitrogen, and SO₄^2- had the greatest effect on the archaeal diversity in soil sediments, followed by nitrate nitrogen, Cl^-, Mg²⁺, and Na⁺, while Ca²⁺, total phosphorus, and total potassium had mild effects. Conclusion The archaeal community in soil sediments of Yuncheng Salt Lake has high diversity and is closely related to environmental factors. This study enriches the biological information of archaeal resources in soil sediments of Yuncheng Salt Lake and provides a theoretical basis for the mining and research of archaeal resources in salt lakes.

Objective Efficient carbon-fixing microorganisms are a critical functional resource for achieving the “dual carbon” goals. However, the unstable carbon fixation performance makes natural strains difficult to directly meet industrial application needs. The molecular mechanisms underlying the enhancement of carbon fixation performance by atmospheric and room temperature plasma (ARTP) mutagenesis remain unclear. Methods Five carbon-fixing bacterial strains preserved in our laboratory were used as the starting strains. Through ARTP mutagenesis combined with directed screening and carbon-fixing enzyme activity tracking, a genetically stable and efficient carbon-fixing mutant B4-5 was constructed. Whole-genome sequencing, combined analysis of single nucleotide polymorphism (SNP) and insertion/deletion (InDel), and metabolic characterization were employed to systematically elucidate the carbon fixation enhancement mechanism. Results The mutant B4-5 showed increases of 33.16%, 72.54%, and 72.61% in key carbon-fixing enzyme activity, carbon assimilation amount, and carbon assimilation rate, respectively, with the Calvin cycle serving as the core carbon fixation pathway. Whole-genome comparison revealed that the genome of the mutant was highly collinear with that of the parent strain (similarity>98.50%), indicating that there were no large-scale chromosomal structural variations in the genome of the mutant. The combined analysis of SNP and InDel identified four key mutation sites (spoⅡE, nprR, glnQ, and murB) related to carbon fixation performance, and these sites optimized carbon source allocation, coordinated carbon-nitrogen metabolism balance, and reprogrammed carbon flux. Finally, a cascade mechanism of genomic micro-variation-metabolic regulation-phenotype enhancement was established. Conclusion This study clarifies the regulatory mechanism underlying the enhancement of carbon fixation metabolism by ARTP mutagenesis, providing a theoretical basis and engineered strain resources for the development of microbial carbon neutralization technologies.

Objective The ecosystem of alpine lakes in northwestern Yunnan Province is well-preserved, while the microbial communities and functional characteristics in the sediments remain unclear. This study aims to elucidate the vertical distribution patterns of microbial communities in alpine lake sediments within this region and their functional differentiation in carbon, nitrogen, and sulfur cycling. Methods Three adjacent alpine lakes (Taiji Lake, Tiancai Lake, and Rencai Lake) in Laojunshan National Park, Lijiang City, Yunnan Province were selected. Samples were collected from four depths (0-1, 10-11, 20-21, 30-31 cm) of sediment cores and subjected to metagenomic sequencing. Medium and high-quality metagenome-assembled genomes (MAGs) were recovered through binning analysis, with taxonomic annotation conducted against the GTDB database. Meanwhile, functional gene annotation was performed against the CAZymes and KEGG databases to characterize the vertical stratification of community structure and biogeochemical cycling functions. Results A total of 478 MAGs (belonging to 27 bacterial phyla and 9 archaeal phyla) were obtained. Approximately 95.0% of these MAGs could not be identified at the species level, indicating that there were a large number of uncultured microbial groups in the sediments. The bacterial communities exhibited distinct succession with depth. The surface layer was dominated by Cyanobacteriota and Bacteroidota, while the middle and lower layers were mainly occupied by Pseudomonadota and Chloroflexota. The archaeal community was mainly composed of Nanobdellota, Thermoproteota, and Halobacteriota, and exhibited increasing stability with sediment depth. Carbohydrate-active enzymes (CAZymes) in the surface layer were mainly enzymes (e.g., glycosyl transferases GT51 and glycoside hydrolases GH59) targeting readily degradable carbon sources, while those in deeper layers were mainly enzymes (e.g., carbohydrate-binding modules CBM38 and auxiliary activity family AA6) acting on recalcitrant carbon sources. Nitrogen and sulfur cycling functions also exhibited a distinct vertical hierarchical structure. The bacteria primarily participated in nitrogen and sulfur cycling processes in surface sediments, whereas archaea predominated in deeper sediment layers. Conclusion The microbial communities in the sediments of alpine lakes in northwestern Yunnan Province exhibited distinct vertical distribution patterns related to carbon, nitrogen, and sulfur cycling, reflecting the influences of the sediment redox gradient and the organic matter composition on microorganisms. This study provides a new perspective for understanding the microbial ecology and biogeochemical cycling process in alpine lakes.

Porcine enteric coronaviruses (PECs) include porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV). Infections with PECs can cause severe diarrhea in pigs, particularly newborn piglets, resulting in high mortality rates and posing a serious threat and economic loss to the global swine industry. Such infections induce oxidative stress to activate various transcription factors and alter their transcriptional pathways, thereby affecting cellular metabolism and the viral life cycle. This leads to cellular dysfunction and further promotes viral replication, forming a vicious cycle. The oxidative stress associated with PECs is considered one of the potential common pathogenic mechanisms. This review summarizes the information about the oxidative stress induced by infections with PECs and emphasizes that antioxidant strategies represent one of the effective approaches to counteract such infections.

Objective To investigate changes in ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 (Agap2) expression during hepatic fibrosis progression following hepatitis E virus (HEV) infection and preliminarily explore the association between chronic HEV infection and Agap2 expression. Methods A BALB/c mouse model of HEV infection was established through inoculation in tail vein and subjected to RNA sequencing. HEV infection and Agap2 expression in the liver tissue were detected via immunohistochemistry, immunofluorescence assay, and real-time qPCR. Results Agap2 expression was upregulated following HEV infection (24 hpi group: P=0.000 3, 48 hip group: P=0.001 9). Chronic HEV infection induced hepatic fibrosis in mice, and Agap2 expression in the mouse liver was positively correlated with HEV load (r=0.797 4, P<0.000 1). Similarly, in vitro experiments demonstrated that Agap2 expression was upregulated in HEV-infected Huh 7.5.1 cells (r=0.968 3, P=0.002 4) and LX-2 cells (r=0.683 5, P=0.006 5), showing a positive correlation with HEV load. Conclusion The results demonstrate that Agap2 expression is positively correlated with HEV load during hepatic fibrosis progression after chronic HEV infection. Agap2 may serve as a potential molecular target for the treatment of HEV-associated hepatic fibrosis.

Objective Transient receptor potential vanilloid 4 (TRPV4), a non-selective cation channel, is deeply involved in the physiological and pathological regulation of multiple organ systems, while the comprehensive influencing mechanism of its mutation on animal intestines and intestinal flora is not clear. This study explored the regulatory effects of Trpv4 exon 8 c.1491+1G>A mutation on intestinal barrier integrity and flora-metabolic microenvironment in mice, aiming to provide an experimental basis for analyzing the interaction mechanisms between host genes and intestinal flora. Methods Trpv4 exon 8 c.1491+1G>A gene-edited mice previously constructed in our laboratory were taken as the research objects, and the expression levels of Trpv4 and TRPV4 in the intestinal tissue were determined by qPCR and Western blotting, respectively. Pathological sections were prepared for observation of the structural changes of the intestinal tissue. The 16S rRNA gene high-throughput sequencing was conducted to reveal the structural differences of intestinal flora. Non-targeted metabolomics based on LC-MS was employed to examine the changes of fecal metabolites, and the correlations between flora and metabolites were analyzed. Results Trpv4 editing led to the abnormal expression of Trpv4 and TRPV4 in the intestinal tissue of mice, which resulted in the structural abnormality of the intestinal tissue and the impairment of intestinal barrier function. In addition, the gene-edited mice exhibited an imbalance in intestinal flora, with significantly increased relative abundance of Bacteroidota, a significantly decreased Bacillota/Bacteroidota (F/B) ratio, and reduced abundance of common commensal bacteria such as Staphylococcus. Metabolomic analysis indicated that the gene-edited mice presented disordered lipid metabolism and abnormalities in immune-related metabolites. The abundance of Bacteroidota was positively correlated with lipid metabolites, while that of Desulfovibrio and Enterobacter was negatively correlated with lipid and immune metabolites. Conclusion Trpv4 exon 8 c.1491+1G>A gene-edited mice exhibited impaired intestinal barrier function, along with alterations in intestinal flora structure and the metabolic microenvironment. This study provides basic data for elucidating the interactions between specific gene mutations and the gut microbiota and offers theoretical support for the development of diagnostic and therapeutic strategies for Trpv4-related diseases.

Objective To establish a mouse model that effectively simulates the key clinical features of porcine Senecavirus A (SVA) infection, providing a crucial experimental tool for elucidating its pathogenesis and evaluating prevention and control products. Methods Five-week-old SPF C57BL/6J wild-type (WT) mice and type I interferon receptor-deficient (C57BL/6J ^IFNR-/- ) mice were inoculated via intraperitoneal, subcutaneous, and intramuscular routes. Blood and tissue samples were collected on days 1, 3, and 5 post-infection (dpi) for analysis of gross pathology, histopathology, viral load, and dynamic determination of inflammatory cytokines at the mRNA level. Results Compared with the mock-infected control group, both mouse strains developed gross lesions (e.g., swollen inguinal lymph nodes, yellowish livers, splenomegaly) and histopathological lesions (e.g., cortical disintegration of lymph nodes, hepatocellular necrosis, atrophy of splenic white pulp, and renal tubular necrosis). However, these lesions were more severe in C57BL/6J ^IFNR-/- mice. Viral RNA was widely distributed in tissues of both groups but was significantly higher in the C57BL/6J ^IFNR-/- group. Notably, viremia was undetectable in WT mice, whereas in C57BL/6J ^IFNR-/- mice, the virus was detected in whole blood as early as 1 dpi, peaked at 3 dpi, and then declined rapidly. Inflammatory cytokine analysis revealed significantly higher mRNA levels and protein levels of IL-1β and IL-6 in C57BL/6J ^IFNR-/- mice than in WT mice. Conclusion The C57BL/6J ^IFNR-/- mouse model successfully simulates, for the first time, the transient viremia characteristic of porcine SVA infection. It comprehensively replicates key features, including the multi-organ viral distribution, high viral load, and self-limiting recovery, providing a more effective animal model for delving into the pathogenic mechanism of SVA and evaluating vaccines and antiviral drugs.

Objective To investigate the effects of combined application of organic and inorganic fertilizers on soil nutrient content and microbial community structures and functions in soybean fields, thus providing a scientific basis for rational fertilization and high-quality, high-yield soybean production. Methods Four fertilization treatments—control (CK: no fertilization), inorganic fertilizer (CF: compound fertilizer), organic fertilizer (OF: dry chicken manure), and combined organic-inorganic fertilizers (OCF: dry chicken manure+compound fertilizer)—were established. During the experiment, soil organic matter (SOM), alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), available potassium (AK), and microbial community structures and functions were measured to investigate the relationships between microbial communities and soil nutrients. Results Different fertilization treatments influenced soil nutrients in soybean fields. Compared with CK, the OCF treatment increased the soil SOM, AN, AP, and AK by 60.67% (P<0.05), 68.09% (P<0.001), 15.18 folds (P<0.001), and 59.54% (P<0.01), respectively, and it also increased soil pH. Amplicon sequencing indicated that different fertilization measures did not alter the community composition of soil microorganisms but changed the relative abundance of different phyla and genera. Compared with CK, the OCF treatment increased the relative abundance of Basidiomycota and Mortierellomycota by 5.62 folds and 4.51%, respectively, while decreasing that of Ascomycota by 38.35%. The OCF treatment reduced fungal community richness and diversity (P<0.05). The alpha diversity analysis revealed that both bacterial and fungal diversity decreased after organic fertilizer application, with fungal alpha diversity showing the most significant reduction (P<0.05). Functional prediction indicated that amino acid metabolism exhibited the highest relative abundance among metabolic pathways in bacterial communities, suggesting that the OCF treatment promoted metabolic processes centered on nitrogen assimilation and protein synthesis, facilitating bacterial participation in soil nutrient transformation. Under the OF treatment, symbiotropic fungi exhibited the highest relative abundance, which suggested that organic fertilizer promoted the ecological functions of fungi in soil nutrient cycling. Conclusion Combined application of organic and inorganic fertilizers modulates soil pH, mitigates soil acidification, and enhances soil nutrient content. Fungal communities exhibit greater sensitivity to organic fertilizer application, which significantly reduces their diversity and stimulates the proliferation of certain pathogenic fungi. Conversely, inorganic fertilizer suppresses the relative abundance of pathogenic fungi. Thus, the combined application of organic and inorganic fertilizers demonstrates distinct advantages in balancing soil nutrient supply with microbial community structure and optimizing soil microbial functional composition. This approach provides theoretical foundations and practical guidance for achieving efficient, green, and sustainable fertilization management in soybean fields.

The general stress response (GSR) is a global regulatory strategy developed by bacteria to adapt to diverse environmental stresses by coordinating a suite of physiological and metabolic changes, thereby enabling survival in fluctuating conditions. The alternative sigma factor RpoS (σ^S) serves as a central GSR regulator in bacteria and is crucial for bacterial responses to various stress conditions. Such regulators in bacteria are conserved, while polymorphic variations in rpoS are prevalent across numerous natural isolates and acclimated strains. This polymorphism reflects the adaptive trade-off mechanism formed by bacteria during the evolutionary process, positioning RpoS as a key model for investigating fitness trade-offs in bacteria. This review summarizes the functions and polymorphisms of RpoS and explores the potential environmental drivers underlying its polymorphism.