Frontiers in Microbiology最新文献

Background: Macrolide resistance genes (erm and mef families) and heavy metal resistance genes (cadA) are increasingly disseminated among streptococci via diverse mobile genetic elements.

Methods: Through whole-genome sequencing of 16 Streptococcus agalactiae isolates resistant to both erythromycin and clindamycin, we identified 19 integrative and conjugative elements (ICEs), a type of self-transfer genetic elements, conferring antibiotic resistance. Among these, a novel composite ICE designated ICESag39 was identified in S. agalactiae Sag39 through comparative analysis with the NCBI database.

Results: ICESag39 measured 113,125 bp in length, and it featured a nested "Russian doll" structure comprising an ICESa2603 family backbone integrated with an internal Tn1806-like ICE. The embedded Tn1806-like ICE contained four variable regions (VR1-VR4) that serve as insertion hotspots; among these, VR3 and VR4 carry erm(TR) from ICESp2907 and the cadmium resistance gene cadA from an uncharacterized genetic element, respectively. Conjugation and excision assays confirmed that ICESag39 transfers at a frequency of 8.2 × 10^-9 and co-transfers both resistance determinants. Under cadmium stress, transconjugants carrying ICESag39 displayed enhanced growth relative to the recipient. Although the internal Tn1806-like ICE was also capable of independent transfer, its efficiency was significantly lower (< 10^-9), and its circular form is undetectable by PCR. Database screening identified 199 structurally similar ICEs (ICESag39-like ICE), 62.8% (125/199) of which co-carried erm(TR) and cadA, underscoring the prevalence of this ICE and its associated resistance traits.

Conclusions: This study characterizes a new composite ICE and elucidates a modular mechanism that facilitates the assembly and dissemination of resistance genes, thereby promoting bacterial genome diversification.

To address the challenges of overflow metabolism and the heavy reliance on manual intervention in high-density Escherichia coli fermentation, this study introduces an AI-driven, autonomous intelligent control system. Using superfolder green fluorescent protein (sfGFP) as a reporter, the research first optimized DO-stat feeding parameters and the induction process, achieving a 52.85% increase in cellular specific fluorescence intensity and significantly enhancing protein expression levels. Subsequently, an artificial neural network (ANN) model was developed and trained to achieve real-time recognition of dissolved oxygen (DO) baselines (R ² = 0.998). This model was integrated with feeding control logic to form the NeuroStat-Ctrl system, enabling fully autonomous control across the entire fermentation lifecycle. Utilizing this system, unattended E. coli fermentation was successfully achieved, with fluorescent protein production further increasing by 5.87% compared to the optimized manual control. Experimental validation demonstrated that the system effectively mitigates feeding deviations inherent in traditional fixed-threshold strategies, prevents metabolic overflow, and enhances process stability and reproducibility. Furthermore, this system provides an efficient, standardized, and intelligent solution for high-throughput strain screening and process validation in parallel bioreactors.

Endophytic fungi are asymptomatic microorganisms that inhabit plant tissues and play pivotal roles in regulating crop growth under field conditions. This review first provides an overview of their taxonomy and ecological functions, emphasizing natural diversity and distribution, then systematically summarizes their core mechanisms: enhancing nutrient uptake, regulating phytohormone biosynthesis, promoting root development, and boosting resistance to abiotic stresses (e.g., drought, salinity). We further discuss the agricultural potential and existing challenges, including stability, persistence, and compatibility with current farming practices. Future research directions are outlined to advance sustainable agriculture, focusing on dissecting molecular interactions between endophytic fungi and crops, optimizing application techniques, and evaluating long-term ecological impacts. This work provides a comprehensive reference for agricultural scientists, ecologists, and researchers to facilitate the practical application of endophytic fungi, encouraging further research, and practical applications in this field.

Introduction: Soil salinization threatens global food security and sustainable land use. Ameliorating coastal saline soils with exogenous amendments is crucial. Bio-organic fertilizer (OF) and nano-carbon (NC) are promising green amendments, but their comparative and combined effects on soil properties and microbial communities are not fully understood.

Methods: A field experiment was conducted in coastal saline soil (Ninghe District, Tianjin, China). Four treatments were established: control (CK, no amendment), OF application, NC application, and combined application of OF and NC (FC). Soil physicochemical properties and microbial community structure (via 16S and ITS rRNA gene sequencing) were analyzed.

Results: The FC treatment most effectively improved soil properties, significantly reducing bulk density, pH, salinity, and sodium adsorption ratio (SAR), while increasing porosity, water content, and nutrient (N, P) availability. Soil bacterial diversity (Ace, Chao1, Shannon indices) increased significantly in all amendment treatments compared to CK, with the highest values in NC and FC treatments. Amendment application altered microbial community composition, enriching specific bacterial taxa (e.g., Firmicutes, Desulfobacterota in FC) and fungal taxa. Redundancy analysis identified soil salinity and pH as key drivers of bacterial community structure, whereas fungal communities showed a distinct, less correlated response pattern.

Discussion: The synergistic application of nano-carbon and bio-organic fertilizer (FC) created a more favorable soil habitat, rapidly ameliorating physicochemical conditions which directionally shaped the bacterial community. Bacterial and fungal communities responded differently to amendments, suggesting divergent assembly mechanisms. The FC strategy demonstrates high potential for the initial restoration of saline-alkali soils by enhancing soil health primarily through rapid physicochemical improvement and modulation of the soil microbiome, particularly bacteria. Future work should focus on functional validation of predicted metabolic shifts and assessment of agronomic outcomes.

Guangxi is one of the regions most affected by HIV-1 in China, yet the fine-scale transmission dynamics and molecular epidemiology remain incompletely characterized. In this study, we integrated molecular transmission network analysis, phylogenetic inference, and spatial analysis to elucidate HIV-1 dispersal patterns and inform precision public health interventions. We analyzed 10,199 HIV-1 pol sequences collected from all 14 cities in Guangxi, encompassing major subtypes including CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B. Molecular networks were constructed using a 1.5% TN93 genetic-distance threshold, and logistic regression was applied to identify factors associated with network clustering. Bayesian phylogenetic and phylogeographic analyses were used to characterize spatiotemporal dissemination patterns. Overall, 75.6% (7,706/10,199) of individuals clustered within molecular networks, with clustering proportions exceeding 60% in every city. Factors independently associated with clustering included viral load >10,000 copies/mL (OR = 1.23, 95% CI: 1.10-1.39), education level of junior high school or below (OR = 1.67, 95% CI: 1.30-2.14), age ≥50 years (OR = 1.38, 95% CI: 1.16-1.63), Zhuang ethnicity (OR = 1.18, 95% CI: 1.08-1.30), and syringe sharing (OR = 1.65, 95% CI: 1.14-2.38). Intercity connections accounted for 48.2% of inferred genetic linkages, with CRF55_01B showing the highest intercity connectivity (60.4%). CRF01_AE displayed the broadest geographic distribution, Nanning and Qinzhou emerged as key connectivity hubs. Phylogeographic analyses suggested that Qinzhou was a major source of dispersal for CRF01_AE and CRF08_BC, whereas Nanning played a central role in the dissemination of CRF07_BC, CRF08_BC, and CRF55_01B. HIV-1 transmission in Guangxi is characterized by high network clustering and pronounced spatial heterogeneity, with distinct hub cities contributing to regional connectivity. These findings provide actionable evidence to support targeted, location-specific HIV prevention and control strategies at both local and regional levels.

Tea (Camellia sinensis L. O. Kuntze) is an important economic crop widely cultivated in tropical and sub-tropical regions, where drought stress often limits its growth and productivity. Soil application of nano-biochar (nBC) and nano-calcium oxide (nCaO) offers a promising approach for enhancing soil health, tea quality, and yield. A pot experiment was executed to explore the synergistic effects of nBC and nCaO on soil enzymatic and microbial activities, N-P-C cycling genes, and the quality and yield of tea seedlings under drought stress. The results showed that, under drought stress, the combined application of nBC and nCaO significantly improved the soil physico-chemical and microbial properties viz. an increase in soil pH (23.29%), soil organic matter (53.18%), soil total carbon (30.56%), available N (63.12%), available P (140.85%), available K (32.92%), microbial biomass carbon (9.90%) and microbial biomass N (8.23%) compared with the control. This may have been due to manifold increase in the expression levels of N-C-P cycling genes such as phoD (5.2-fold), phoC (7.0-fold), narG (3.4-fold) and GH31 (1.8-fold) and relatively higher abundance of archaeal and bacterial communities. Soil urease, acid-phosphatase, nitrate reductase, β-glucosidase, catalase, phosphomonoesterase, and N-acetyl-β-d-glucosaminidase enzyme values were 48.32, 13.34, 100.00, 43.37, 612.5, 61.30, and 43.65% higher, respectively, in soils amended with both nBC and nCaO than in the control under drought stress. Furthermore, co-application of nBC and nCaO significantly enhanced tea quality traits such as caffeine (5.89%), polyphenol (12.24%), total catechins (11.00%) and amino acid (16.17%), as well as yield parameters including plant height (10.43%), leaf area (97.55%) and 10-bud weight (42.53%) relative to the control. Overall, the combined application of nBC and nCaO substantially improved soil enzymatic and microbial activities, as well as tea quality and yield traits, under drought stress.

Secondary fungal infections are increasingly recognized as critical factors in the prognosis of severe acute viral infections, including influenza, SARS-CoV-2, Severe Fever with Thrombocytopenia Syndrome virus, and Dengue. This review outlines the clinical features of fungal complications, proposing a "virus-driven immune reprogramming" framework. It highlights how viral infections disrupt immune barriers, impair the Th17-IL-17 antifungal axis, attenuate platelet immune function, and involve unique pathogen interactions, creating a host immune microenvironment that is more susceptible to fungal invasion. Understanding these immune-injury mechanisms underscores the clinical importance of earlier surveillance of secondary fungal disease and informs the development of mechanism-guided therapeutic approaches to improve patient outcomes.

Introduction: Aerobic methanotrophs and non-methanotrophic methylotrophs drive methane cycling in oxic freshwater lakes. Most knowledge about biological aerobic methane oxidation (MOx) comes from ex situ rate experiments, laboratory cultures, and static measurements of natural abundances.

Methods: We investigated the link between MOx rate constants measured with a novel in situ incubation device and the microbial community in Jordan Lake, a methane-rich freshwater lake in NC, USA. We coupled relative abundances of 16S rRNA genes and quantitative PCR of particulate methane monooxygenase subunit A (pmoA) to methane, oxygen, temperature, and in situ MOx rate constants, all collected using the novel iBag in situ incubation system.

Results: In 16 incubations spread across 13 months, Methylococcaceae, whose cultured members are obligate aerobic methanotrophs, strongly and inversely correlate with naturally-varying oxygen but not with methane. Non-methanotrophic methylotrophs and facultative aerobic methanotrophs are more abundant (up to 15.4% of amplicons), but do not correlate with either dissolved gas. Methylococcaceae correlate better than all other families in the methane-oxidizing community with the first-order MOx rate constants obtained from the in situ incubation data. Changes in the methane-oxidizing community across incubations were inconsistent between experiments but replicable within parallel incubations. The lack of response of the methanotrophic community to ammonium and organic carbon additions suggest these are not limiting.

Discussion: Our results suggest Methylococcaceae primarily drive MOx in Jordan lake, despite often not being the most abundant methanotrophic group, and that high oxygen concentrations may suppress this group independently of their association with lower methane concentrations.

Background: This study established and optimized a food-grade solid-state fermentation (SSF) process using Aspergillus oryzae to biotransform ginsenosides in five-year-old white ginseng roots.

Methods: Through single-factor and orthogonal tests, optimal SSF conditions were identified. UPLC-QTOF-MS/MS analysis was used to characterize ginsenoside profile changes. In an ethanol-induced injury model using GES-1 gastric epithelial cells, the fermented extract was evaluated for cytoprotective effects.

Results: Optimal SSF conditions were fermentation time of 8 days, inoculum size of 2.5%, and temperature of 28°C. UPLC-QTOF-MS/MS analysis revealed significant remodeling of protopanaxatriol (PPT)-type ginsenosides, with ginsenoside Rf and PPT increasing by 3.55-fold and 5.03-fold, respectively (p < 0.05). In the ethanol-induced injury model using GES-1 gastric epithelial cells, the fermented extract demonstrated dose-dependent anti-inflammatory, antioxidant, and anti-apoptotic effects without cytotoxicity. We hypothesize that the extracellular glycosidase activity of A. oryzae mediates the sequential deglycosylation leading to the observed PPT-type enrichment, although the specific enzymes involved require further identification. Overall, these results provide a proof-of-concept for a food-safe SSF platform tailored to whole white ginseng roots. This process effectively remodels the ginsenoside profile to enrich cytoprotective PPT-type compounds, supporting its potential for nutraceutical development.