The first human Pegivirus (HPgV-1) and the second human Pegivirus (HPgV-2) are the only two human Pegiviruses that have been identified until now. They share some common features including similar viral genome structure and low pathogenicity, while they also represent unique biological characteristics. HPgV-1 is called "good virus" because of its ability to slow down disease progression and reduce disease severity when co-infecting with HIV and Ebola virus. In addition, HPgV-1 was recently found to be related with lymphoma and neurological diseases. Therefore, HPgV-1 might be a possible breakthrough point in the treatment of refractory diseases caused by HIV and other viruses. HPgV-2 was firstly discovered from the plasma of a hepatitis C virus (HCV)-infected patient in 2015 and was found to always co-infect with HCV but hardly infect healthy people. However, the underlying mechanism of HPgV-2 and HCV co-infection remains to be elucidated. Distinct from most of RNA viruses, HPgV-2 exhibits low genomic diversity with high sequence identity and low intra-host variation, which give the implication of HPgV-2 as an excellent model for studying the mechanisms of viral genome variations. In conclusion, the human Pegiviruses are worthy of sustaining attention and study.

[Objective] To observe the effects of supplementing compound probiotics on the structure of gut microbiota, content of short-chain fatty acids (SCFAs), and levels of inflammatory cytokines in Chinese wrestlers. [Methods] Eighteen non-sports undergraduates from Shandong Sport University were recruited as a control group, while 30 Chinese wrestlers served as the experimental group. Both groups received oral compound probiotics for 8 weeks. Venous blood and stool samples were collected before and after the intervention. Enzyme-linked immunosorbent assay (ELISA) was used to measure inflammatory cytokines levels in plasma. The structural characteristics of gut microbiota were analyzed using 16S rRNA gene sequencing of the V3−V4 region, and gas chromatography-mass spectrometry (GC-MS) was employed to determine SCFAs content in stool samples. [Results] Prior to the intervention, the experimental group exhibited lower levels of interleukin-1 (IL-1), interleukin-6 (IL-6), and C reactive protein (CRP) (P < 0.001, P < 0.01, P < 0.01), and higher levels of interleukin-10 (IL-10) compared to the control group (P < 0.001). After 8 weeks of probiotic supplementation, plasma levels of IL-6 and CRP in the Chinese wrestlers further declined (P < 0.01, P < 0.05). Before the intervention, the abundance of Bifidobacterium adolescentis was higher in Chinese wrestlers than that in the control group (P < 0.01). Following 8 weeks of supplementation, Chinese wrestlers showed an increased abundance of Collinsella (P < 0.01), a decreased abundance of Faecalibacterium (P < 0.01), and reduced α-diversity in gut microbiota (P < 0.01). Prior to the intervention, there was no significant difference in SCFAs content between the two groups. After 8 weeks of intervention with compound probiotics, the content of acetic acid and butyric acid in the stool samples increased in both the control group (P < 0.01, P < 0.05) and the experimental group (P < 0.05). The correlation analysis results indicated a positive correlation between B. adolescentis abundance and plasma IL-10 level (r=0.233, P=0.037) and negative correlations of B. adolescentis and C. aerofaciens abundance with plasma IL-6 level (r=−0.499, P=0.000; r=−0.366, P=0.001) in Chinese wrestlers. Additionally, there was a positive correlation between C. aerofaciens abundance and the butyric acid content in stool samples of Chinese wrestlers (r=0.243, P=0.032). [Conclusion] The 8 weeks intervention with compound probiotics effectively reduced pro-inflammatory cytokine levels and increased anti-inflammatory cytokine levels in plasma. Furthermore, it enhanced the abundance of butyric acid-producing bacteria in the gut microbiota, promoting the production of SCFAs, and improving anti-inflammatory capacity.

Inhibitors including sugar degradation products (e.g., 5-hydroxymethylfurfural and furfural) and phenols (e.g., 4-hydroxybenzoic acid and vanillin) from lignin degradation are inevitably formed in the pretreatment process of lignocellulose raw materials, exerting a negative impact on the fermentation efficiency. [Objective] To improve the tolerance of yeast to inhibitors in cellulose hydrolysates and ensure the efficient production of industrial biomass ethanol. [Methods] The model strain W303-1A was domesticated with the inhibitor furfural and p-hydroxybenzoic acid alone or in combination. The growth curves and ethanol fermentation performance of the domesticated strain and the original strain were compared under different inhibitor concentrations. We then conducted high-throughput genome resequencing of both the domesticated and original strains to identify the mutations in genes related to the glucose metabolism and drug resistance, thereby analyzing the variation points related to inhibitor tolerance. [Results] In the medium containing 2.0 g/L furfural, the ethanol yield of F-2 was 19.40 g/L, which was 2 times higher than that of the original strain. In the medium containing 1.6 g/L furfural and p-hydroxybenzoic acid, the highest ethanol yield of B-2 was 20.22 g/L, 7.6 times that of the original strain. Then, high-throughput genome resequencing of the original and domesticated strains revealed several mutations in the genes encoding ethanol dehydrogenase, fructose-1, 6-diphosphate aldolase, and pyruvate dehydrogenase in the glucose metabolism pathway. The mutations of YAP1 (transcriptional activator involved in oxidative stress response and REDOX homeostasis), PDR5 (pleiotropic ABC transporter tolerant to multiple chemicals), and RPN4 (zinc finger protein) genes played an important role in the inhibitor tolerance of Saccharomyces cerevisiae. [Conclusion] The findings provide more targets for further optimization and construction of model strains.

Truffles must be symbiotic with plants to form ectomycorrhiza (ECM), which facilitates the formation of fruiting bodies by mutually beneficial exchanges of substances. [Objective] To elucidate the flow of substances between Tuber sinense and Pinus yunnanensis in a symbiosis relationship. [Methods] Liquid chromatography-mass spectrometry (LC-MS) was employed to analyze the metabolite profiles of freshly harvested T. sinense (SL) and P. yunnanensis roots (SG). [Results] In SL and SG, 1 304 and 1 516 substances were detected respectively, including 399 SL-specific substances (SLSs) and 611 SG-specific substances (SGSs). There were 294 common differential substances, including 93 up-regulated substances (DEMs-up) and 201 down-regulated substances in SL. The network correlation analysis revealed that 92 of the 100 substances with the relative content ≥2.0 (40 SLSs and SGSs and 60 DEMs-up) displayed significant correlations. Twenty-nine associated substances in SLSs and SGSs and 19 substances in DEMs-up were enriched in 15 important pathways, which mainly involved secondary metabolite biosynthesis, amino acid biosynthesis and metabolism, and vitamin biosynthesis and metabolism. [Conclusion] A network correlation existed between T. sinense and P. yunnanensis pine roots metabolites. Some substances in truffles and pine roots, including adenosine 3′, 5′-cyclic monophosphate (cAMP), phytosterol, and indole-3-acetic acid, had regulatory effects on the development of fruiting bodies. The findings provided a theoretical basis for further studying the potential signaling molecules associated with fruiting body development and elucidating the symbiotic mechanism between T. sinense and pines. Additionally, this study laid a practical basis for screening the substances promoting the growth of mycorrhizal seedlings and fruiting bodies and for large-scale artificial cultivation of truffles.

Microbially enhanced coalbed methane production has become a research hotspot of coalbed methane production in recent years. Methanogens, the essential microorganisms in coalbed methane production, are usually strictly anaerobic and sensitive to oxygen. [Objective] To understand the changes in the methane production and composition of the anaerobic microbiome after exposure to oxygen, we conducted the enrichment culture of coalbed formation water collected from different regions along the east edge of Ordos Basin in China for air exposure experiments. Our findings are expected to provide scientific support for the future in-situ utilization of large-scale anaerobic fermentation products in coalbed methane production. [Methods] We used the enrichment cultures of coalbed formation water collected from Hancheng (HC), Baode (BD), and Linfen (LF) for air exposure for a series of time schedules within 24 h. The air-exposed enrichment cultures were re-inoculated and cultured. The methane production and community succession were analyzed to evaluate the microbiome tolerance to the aerobic condition. [Results] The microorganisms in all the three regions were still active after 24 hours of air exposure and showed the methane production comparable to that before air exposure. The dominant groups involved in the hydrolysis, acidification, and acetoxylation mainly included Firmicutes, Synergistetes, Proteobacteria, and Bacteroidetes. Methanogenic archaea were mainly Methanosarcina, Methanofollis, and Methanobacterium, belonging to Euryarchaeota. [Conclusion] After 24 hours of air exposure, the methane-producing capacity of the microbiome from the coalbed formation water was not affected and was comparable to that before air exposure. The microbiome did not showcase obvious succession, while the relative abundance of different groups changed accordingly. Our study can give scientific support for the in-situ industrial application of anaerobic enrichment culture from deep coalbed seams during coal degrading in methane production.

[Objective] To explore the formation process of multi-species biofilms in paddy soils developed from different parent materials mediated by soil minerals, thus providing a scientific basis for revealing the interaction mechanisms between soil components and multi-species biofilms. [Methods] The multi-species biofilms were extracted from reddish clayey soil and acidic purple soil, and kaolinite and goethite were used as the mineral media. Modern biological microscopy, high-throughput sequencing, and infrared spectroscopy were employed to study the mineral-mediated formation process, structural changes, and bacterial community structure of the biofilm. [Results] Based on the high-throughput sequencing technology of 16S rRNA gene, the flora in the multi-species biofilms in the paddy soils developed from the two parent materials was dominated by Chloroflexi, Acidobacteria, Proteobacteria, Nitrospirae, and Desulfobacterota. Compared with the control without mineral addition, goethite and kaolinite significantly inhibited the formation of the multi-species biofilm dominated by Chloroflexi in the acidic purple soil, decreasing the biofilm biomass by 18.38% and 17.30%, respectively. In the reddish clayey soil dominated by Acidobacteria, goethite and kaolinite promoted the multi-species biofilm formation to varying degrees. Kaolinite demonstrated more significant promotion effect, increasing the biofilm thickness, the secretion of polysaccharides in the biofilm by 7.69%, and the biofilm biomass by 18.99%. [Conclusion] Kaolinite stimulated bacterial production of extracellular substances, promoted the multi-species biofilm formation in reddish clayey soil, and inhibited the multi-species biofilm formation in acidic purple soil. Goethite inhibited the multi-species biofilm formation in acidic purple soil. Compared with kaolinite, goethite is likely to cause cell inactivation. This study further revealed the interaction mechanism between soil components and multi-species biofilms, and the results provided a scientific theoretical basis for promoting the sustainable development of soil health.

Campanumoea lancifolia (Roxb.) Merr. is a new plant species with both medicinal and edible values, demonstrating broad prospects for development and utilization. However, as its cultivation area expands, root rot has become increasingly severe. In the fields with severe root rot, the losses can reach up to 40%, accounting for 75% to 90% of the losses caused by all diseases affecting C. lancifolia. Root rot directly leads to declines in fruit yield and quality, affecting the commercial value of the fruits and reducing farmers' incomes. Thus, it is urgent to address the root rot in C. lancifolia. [Objective] To isolate and identify the pathogens causing root rot in C. lancifolia and investigate the inhibitory effects of essential oils extracted from four aromatic medicinal plants on the growth of these pathogens. [Methods] Pathogens were isolated from C. lancifolia plants displaying typical root rot symptoms by the tissue culture method. The pathogens were identified based on morphological and molecular evidence and verified according to Koch's postulates. Essential oils were extracted from four aromatic medicinal plants by steam distillation. The Oxford cup method was employed to examine the inhibitory effects of the essential oils on the pathogens, and the 96-well plate method was used to determine the minimum inhibitory concentrations (MICs) of the essential oils. [Results] Four pathogenic strains were isolated and identified from the roots of diseased C. lancifolia plants. Re-inoculation of these pathogens induced root rot symptoms consistent with those observed in the field. The pathogens were identified as Fusarium oxysporum, Fusarium solani, Colletotrichum liriopes, and Stagonosporopsis pogostemonis. The essential oils exhibited strong inhibitory effects on these pathogens, with inhibition rates ranging from 32.94% to 95.29%. Additionally, the MICs of the four essential oils against the pathogens ranged from 0.031 mg/mL to 4.000 mg/mL. [Conclusion] This study demonstrates that F. oxysporum, F. solani, C. liriopes, and S. pogostemonis are pathogenic to C. lancifolia. This is the first report of F. solani, C. liriopes, and S. pogostemonis causing root rot in C. lancifolia. Furthermore, the essential oils extracted from the selected four aromatic plants exhibited strong inhibitory effects on the pathogens causing root rot in C. lancifolia, which coincides with the theory of aromatic plants dispelling pathogens in traditional Chinese medicine. The findings lay a scientific foundation for the development of botanical pesticides against root rot in C. lancifolia and the eco-friendly cultivation of this plant.

Staphylococcus aureus is one of the common pathogens causing infections. It can attach media or implant surfaces to form biofilms, which makes it difficult to be tackled and leads to the generation of drug resistance, posing a great challenge to clinical treatment. Therefore, it is urgent to develop novel antimicrobials. Pillar[5]arenes, a new class of supramolecular macrocyclic hosts, attracting wide attention due to their highly rigid and symmetrical architectures and controllable cavity sizes, which afford the limitless possibility to create antimicrobial agents with various functional groups and biological activities.[Objective] To synthesize triphenylphosphine pillar[5]arene (TPP) and determine its antibacterial activities and drug resistance with Staphylococcus aureus ATCC 6538, Staphylococcus aureus subsp. aureus (S. subsp. aureus) ATCC 29213, and methicillin-resistant S. aureus ATCC 43300. [Methods] The minimal inhibitory concentration (MIC) and minimal bacteriocidal concentration (MBC) were determined to evaluate the antibacterial activity of TPP. The effects of TPP on biofilm formation were quantified by crystal violet staining, and the content of extracellular polysaccharides in the biofilm was determined by the phenol-sulfuric acid assay. The strain resistance to TPP was examined. [Results] TPP exhibited inhibitory effects on the three strains tested, with a MIC of 15.63 μg/mL for the three strains and a MBC of 125.00 μg/mL for both S. aureus and S. subsp. aureus. However, TPP was unable to kill MRSA even at a concentration of 125.00 μg/mL. The biofilm inhibition rates of TPP at MIC were as high as 72.9%, 69.2%, and 71.8% for the three strains, respectively. The content of extracellular polysaccharides decreased with the increase in the concentration of TPP. S. aureus did not develop resistance to TPP after 20 generations. [Conclusion] This study clarified the antibacterial performance of TPP, providing a theoretical basis for the further development and utilization of TPP in the medicine field.

Microorganisms have survived and evolved in continuously changing and energy-limited environments for billions of years. Compared with those cultured in laboratories with abundant organic substrates, the microorganisms in natural oligotrophic environments exhibit significant differences in physiological states, gene expression, and protein synthesis. Under extreme and low-energy environmental stress, microorganisms utilize a range of substances such as hydrogen, ferrous ions, minerals, and organic remnants as energy or electron sources. They adjust their gene expression, metabolic pathways, and physiological states through various mechanisms to enhance energy utilization efficiency, adapt to nutrient-scarce conditions, sustain metabolic activities and population survival, and drive material transformation and element cycling. Understanding the physiological states of microorganisms in natural environments and their adaptive mechanisms to low-energy supply is crucial for revealing the microbial origins, evolution, growth, metabolism, dormancy, and the minimum energy requirements for life. This review introduces the formation, evolution, and distribution of natural low-energy environments (i.e., environments deficient in electron donors and carbon sources), as well as the physiological states and survival strategies of microorganisms in these variable low-energy environments. The research in this field advances microbial remediation technology development, extreme environment protection, and bio-mining technology development, representing a frontier in geomicrobiology.