[Objective] Coastal wetland ecosystems, situated at the interface of freshwater and seawater, are characterized by the seepage of groundwater with high Fe²⁺ concentrations into the surface layers of sediments, which forms wetland runoff. This runoff, combined with periodic tidal flooding, creates an oxic-anoxic interface conducive to the bio-oxidation of Fe²⁺ by Fe-oxidizing bacteria. However, there is a lack of comprehensive assessment of Fe-oxidizing bacterial communities in coastal wetland ecosystems. [Methods] We measured the basic environmental parameters such as the oxygen penetration depth in the sediments of five coastal wetland sites in Xisha Wetland Park in Chongming, Shanghai and Dongsha Beach in Zhujiajian Island in Zhoushan, Zhejiang. The community composition and distribution of bacteria and Fe-oxidizing bacteria were comprehensively deciphered by 16S rRNA gene amplicon sequencing. [Results] Dongsha Beach in Zhujiajian Island exhibited deeper oxygen penetration (reaching more than 10 mm) than Xisha Wetland in Chongming. The non-metric multidimensional scaling (NMDS) results indicated that the bacterial community structure was primarily influenced by environmental conditions that varied with geographical location, while the community structure of Fe-oxidizing bacteria was influenced by both the geographical location of the sampling sites and the oxygen penetration depth of the sediments. The dominant bacteria in Xisha Wetland and Dongsha Beach wereCyanobacteria,Gammaproteobacteria,Bacteroidetes,Alphaproteobacteria, andActinobacteria. The dominant genera of Fe-oxidizing bacteria wereGallionella,Rhodobacter,Lepthothrix, andSideroxydans. [Conclusion] We studied the Fe-oxidizing bacteria in the sediments of Xisha Wetland in Chongming and Dongsha Beach in Zhujiajian Island and discovered that the composition of Fe-oxidizing bacterial communities was closely linked to the oxygen penetration depth variations caused by different types of wetland sediments.

[Objective] To reveal the dynamic changes of soil microbial community and nutrient cycling process in the artificial grass squares dominated by pioneering plants such asLeymus secalinus andCarex praeclara in the alpine sandy land. [Methods] Metagenomic sequencing and qPCR were performed for the structure analysis, functional gene annotation, and absolute abundance determination of soil microbial communities, which were combined with soil physico-chemical factors for redundancy analysis. [Results] The artificial establishment of grass squares increased the total nitrogen by 20%–68%, available phosphorus by 10%–247%, and organic carbon by 19%–56% in sandy soils. Furthermore, it increased the bacterial and fungal abundance by 17%–81% and 2%–95%, respectively. Specifically, it increased the relative abundance of plant growth-promoting bacteria, such asSphingomonas,Bradyrhizobium,Nitrospira,Solirubrobacter, andNocardioides. Furthermore, the artificial establishment of grass squares enriched theamoCAB gene cluster and thenxrAB gene cluster associated with ammonia oxidation and nitrite oxidation in the nitrogen cycle. In addition, a genetic signature for complete ammonia oxidation was identified. [Conclusion] The artificial establishment of grass squares increases the content of soil nutrients and microbial abundance and promotes the nutrient cycling in alpine sandy areas. Moderate grazing can increase the diffusivity of nitrogen sinks and promote the colonization of native pioneer plants in the sandy ecosystem. The findings provide theoretical references for future restoration of sandy ecosystems in similar high-altitude areas.

[Objective] Currently, there are few studies on microorganisms in Antarctic ice cores, and the available studies mostly employ the pure culture and high-throughput sequencing methods, with limited knowledge about the microbial diversity. We studied the microbial community composition of the meltwater at −183 m depth of the Dalk Glacier in eastern Antarctica, aiming to provide a reference for the development of extremophiles in Antarctica. [Methods] We employed the culture, single-cell sorting, and high-throughput sequencing methods to study the microbial community composition in the meltwater at −183 m depth of the Dalk Glacier. [Results] We obtained bacterial isolates belonging to 94 genera, 19 orders of 10 phyla, in whichProteobacteria,Alphaproteobacteria, andSphingomonas were the dominant phylum, order, and genus, respectively. This result indicated high microbial diversity in the meltwater. The culture, single-cell sorting, and high-throughput sequencing yielded 25 bacterial strains, 24 bacterial strains, and 55 183 sequences (116 operational taxonomic units), respectively. The dominant taxa were different among the three methods. By the culture and single-cell sorting methods, we identified 7 bacterial strains with the 16S rRNA gene identity less than 98.65% compared with their closest relatives in GenBank, of which two strains had the identity less than 95.00% identity. Accordingly, we inferred that there may be two potential new genera and five potential new species. [Conclusion] We studied the microbial diversity in the meltwater of the Dalk Glacier in eastern Antarctica by using the culture, single-cell sorting, and high-throughput sequencing method and discovered rich bacterial species in the meltwater. Each method has its own advantages and limitations. This means that when studying microbial diversity, more comprehensive information about the composition of the microbial community can be obtained by combining different methods. The results of this study can serve as a reference for further research on the genetic resources in Antarctica.

[Objective] Microbial prospecting for oil and gas, characterized by high resolution, high signal-to-noise ratio, minimal environmental interference, low costs, and short time consumption, garners increasing attention from exploration experts. However, in most cases, microbial prospecting is based on laboratory culture and analysis, which cannot accurately and comprehensively reflect thein-situ dynamic changes of microbiota in oil and gas resources in the geological history. In this study, we compared the microbial community structure and developmental characteristics between the gas-producing zone and the background zone in Hangjinqi Gas Field, aiming to identify the surface microbial anomalies related to oil and gas. [Methods] We conducted the bacterial 16S rRNA gene sequencing for the soil samples collected from Xinzao and Shiguhao areas of Hangjinqi. Furthermore, we compared the microbial diversity, analyzed the impacts of physicochemical parameters on microbial distribution, and identified microbial anomalies. The co-occurrence network analysis was employed to explore the assembly process and functional composition of microbial community in the surface soil above the reservoir. [Results] In the Hangjinqi area,Actinobacteria andProteobacteria were dominant, accounting for 72.47% of the total microbial abundance. The correlation analysis of environmental factors with microbial abundance showed that the distribution of microorganisms in this area was not significantly correlated with environmental factors. The microbial community structure presented significant differences between the gas-producing area and the background area. The co-occurrence network analysis of the gas-producing area revealed non-randomness and connectivity in the microbial community, indicating deterministic factors play a dominant role in the construction of microbial communities. Modular co-occurrence network analysis revealed the formation of specific functional modules within the microbial community, and different modules possibly served different functions. [Conclusion] By comparing the microbial diversity between the gas-producing and background area of Hangjinqi area, we identified the indicator genera in the gas-producing fields of Xinzao and Shiguhao. Furthermore, the co-occurrence network analysis identifiedGemmatimonas,Solirubrobacter,Pseudonocardia,Brevibacillus,Aeromicrobium, andNocardioides as the key taxa in the gas-producing area, which were associated with the main functional modules of carbon and nitrogen cycling and organic matter degradation, contributing to the degradation of hydrocarbons in the surface soil of the gas-producing area.

The conventional rescue system of newcastle disease virus (NDV) contains a cDNA clone plasmid and three helper plasmids expressing NDV: nucleocapsid protein (NP), phosphoprotein (P) and polymerase protein (L), respectively. These four plasmids have to be transfected into the same host cell simultaneously to complete the assembly of the virus, which is relatively inefficient. [Objective] To improve the rescue efficiency of NDV, this study aims to establish a two-plasmid rescue system. [Methods] The expression cassettes of NP, P, and L genes were constructed and sequentially cloned into the eukaryotic expression vector pCI to generate a single-helper plasmid, named pCI-NPL, capable of co-expressing NP, P, and L proteins. During this process, the genomic cDNA of the NDV LaSota strain was incorporated downstream of the CMV promoter in the pCI expression vector. Simultaneously, the reporter gene EGFP was inserted into the genome between the P and M genes, accompanied by the introduction of a hammerhead ribozyme sequence at the 5′ end and a hepatitis delta virus ribozyme sequence at the 3′ end. This culminated in the development of the full-genome transcriptional plasmid termed pCI-LaSota-EGFP. The two plasmids pCI-LaSota-EGFP and pCI-NPL were co-transfected as a two-plasmid system into BHK-21 cells to rescue the recombinant virus rLaSota-EGFP. The biological characteristics of the virus were then examined. [Results] RT-PCR, fluorescence microscopy, Western blotting, and growth characterization confirmed that rLaSota-EGFP was correctly constructed and expressed the foreign gene. The rescued recombinant virus rLaSota-EGFP had similar biological characteristics to wild-type (WT) LaSota. [Conclusion] A novel two-plasmid rescue system for NDV based on the CMV promoter was successfully established, laying a foundation for the efficient rescue of recombinant NDV and other paramyxoviruses.

[Background] Bacteria ofEnterobacteriaceae are the main pathogens of foodborne and clinical infections, posing a threat to human and animal health. The numerical identification method using API 20E as the "gold standard" is one of the main identification methods forEnterobacteriaceae. However, the existing numerical identification methods have problems such as laborious sample addition, low accuracy, and high prices. [Objective] To develop a semi-automatic, high-precision, and low-cost biochemical kit for identifying the bacteria ofEnterobacteriaceae based on the numerical identification method. [Methods] On the basis of the theoretical model and supporting software of the numerical identification system forEnterobacteriaceae established by our team, we designed and optimized 24 biochemical matrix trace formulations. Furthermore, a semi-automatic freeze-drying identification strip was developed. Using the commercialized numerical identification strip API 20E, MALDI-TOF MS, and 16S rRNA gene sequencing as the controls, we evaluated the performance of the developed biochemical kit that integrated semi-automatic biochemical identification strips and online analysis software. [Results] The biochemical spectra of 458 strains ofEnterobacteriaceae were obtained, with the overall identification accuracy of 98.5% at the genus level and 96.5% at the species level. The kit only needed twice sample addition to obtain the identification results, with the price only 4.46% that of API 20E. The shelf life of the product was 7 days, and the biochemical experiments had repeatability. [Conclusion] We develop a semi-automatic biochemical kit for identification ofEnterobacteriaceae based on the numerical identification method, which has simple operation, a low cost, and high accuracy. This study provides technical support for the identification ofEnterobacteriaceae and the development of biochemical products for numerical identification of other families and genera of bacteria.

[Objective] The biofloc-based culture system (BFS) ofPenaeus vannamei is a new ecological shrimp production mode based on the concept of cultivating and regulating the microbial community in the aquaculture system. However, the characteristics and assembly processes of microbial communities in different habitats of the BFS remain unclear. [Methods] The 16S rRNA gene sequencing was employed to explore the bacterial community composition in three different habitats (water, bioflocs, and shrimp gut) of the BFS. SourceTracker and the neutral model were adopted to explore the characteristics and assembly processes of bacterial communities in different habitats. [Results] The bacterial community diversity and composition varied significantly in the three habitats, and the structures and composition of bacterial communities were similar between bioflocs and shrimp gut. SourceTracker results showed that 98.76% of bacterial taxa in the shrimp gut were sourced from bioflocs, and only 0.83% were derived from water.Ruegeria existed in all the three habitats, with the relative abundance of 1.72%, 7.34%, and 6.00% in water, bioflocs, and shrimp gut, respectively. The unique amplicon sequence variants (ASVs) showed the maximal number of 89 in water, mainly belonging toMariculis andOwenweeksia. Bioflocs contained 56 ASVs, which were mainlyRheinheimera. Only 10 ASVs were present in the shrimp gut, mainly belonging toRoseobacter. The bacterial communities in water, bioflocs, and shrimp gut were all fit to the neutral model, which indicated that the bacterial communities in the three habitats were dominated by the neutral process. [Conclusion] The microbial communities in different habitats of the BFS were significantly different, and the intestinal bacteria of shrimp mainly came from bioflocs. The assembly processes in the three habitats were dominated by neutral processes. The results provide a theoretical basis for regulating the microbial community in the BFS.

Hepatitis E virus (HEV) is a major zoonotic pathogen that causes acute viral hepatitis worldwide. HEV has high genetic diversity, and the incidence of various genotypes or subtypes is strongly correlated with host species, geographic location, and prevention and control methods. HEV strains HEV-3, comprising 3a–3i subtypes, were present in Europe and America, whereas HEV-3 and HEV-4 were prevalent in Asia. The epidemic strains in China have evolved from HEV-1 to HEV-4. Recent studies have shown that gene recombination, amino acid mutations, and synonymous codon usage patterns are part of the mechanisms underlying HEV evolution. In particular, amino acid mutations are the main driving force for the continued prevalence of the virus. This paper reviews the classification, global epidemic characteristics, and evolutionary mechanism of HEV, aiming to provide a reference for the prevention and control of hepatitis E and vaccine development.

The roles of gut microbiota and its metabolites in the pathogenesis and rehabilitation of neurodegenerative diseases, gastrointestinal diseases, and musculoskeletal systemic diseases in the elderly are receiving increasing attention. Gut microbiota and its metabolites can regulate the functions of the cranial nervous system and the musculoskeletal system through various pathways, involving the immune, endocrine, and nervous systems. Conversely, the gut, brain, and musculoskeletal system can act on the intestinal system via inflammatory, metabolic, and mitochondrial pathways to regulate the gut microbiota. Accordingly, bidirectional signaling mechanisms are formedvia the gut-brain, gut-muscle, and gut-brain-muscle axes, which affect the organism health. This review summarizes that gut microbiota establishes gut-brain-muscle interconnections mainly through metabolites, intestinal permeability, and immune-neural pathways, providing new ideas for improving the brain neuroplasticity and muscle health.

Listeria monocytogenes, a major zoonotic food-borne intracellular pathogen, is ubiquitous in the natural environment and easily contaminates animal-derived food products. The consumption of the contaminated food can cause severe listeriosis in both humans and animals, with the mortality rate reaching up to 30%. The antimicrobial therapy is the only feasible approach for treatingL.monocytogenes infection sinceL.monocytogenes is susceptible to multiple antimicrobials. However, the reports of multidrug-resistant strains are increasing due to the selective pressure exerted by the irrational use of antimicrobials or disinfectants. The antimicrobial resistance mechanisms ofL.monocytogenes are complex. Efflux pump proteins are crucial in bacteria and participate in various biological processes. Specifically, they can influence bacterial sensitivity to antibiotics, facilitate the efflux of toxic compounds, and affect bacterial virulence. Over the last two decades, scholars have conducted research on the efflux pumps-mediated resistance ofL.monocytogenes, identifying several efflux pump proteins associated with the efflux of antibiotics or toxic compounds. Additionally, some efflux pumps are involved in the virulence expression process ofL.monocytogenes. This paper reviews the research advances in the functions and regulatory mechanisms of efflux pumps in multidrug-resistantL.monocytogenes. It provides a theoretical foundation for probing into the environmental adaption mechanisms ofL.monocytogenes, curbing the spread of this pathogen, and identifying new drug targets for combating infections.