[Objective] To study the effect of DNA damage response (DDR) on the replication of porcine epidemic diarrhea virus (PEDV). [Methods] Specific inhibitors were used to detect whether DDR pathway was involved in PEDV replication. The comet assay was employed to observe the DNA damage caused by PEDV infection in Vero cells. The changes in the expression levels of proteins in the DDR pathway and cell cycle of PEDV-infected Vero cells were determined by Western blotting and flow cytometry, respectively. [Results] The ATM inhibitor KU55933 significantly inhibited the replication of PEDV, with the virus titer decreasing from (5.50±0.25) log₁₀ TCID₅₀/mL to (3.15±0.15) log₁₀ TCID₅₀/mL. PEDV infection caused DNA damage in Vero cells during 12–60 h. ATM, ATR, Chk1, Chk2, and p53 were activated by PEDV infection of Vero cells. Especially, p-Chk2 and p-p53 showcased high expression during virus replication. In addition, PEDV infection led to the stagnation of Vero cells in the S phase. During virus replication, the expression of Cyclin B1 was first downregulated and then upregulated significantly. [Conclusion] PEDV perhaps utilized DNA damage pathway hijacks the ATM-Chk2 to manipulate the cell cycle and promote self-replication. The results provided a basis for elucidating the replication and infection mechanisms of PEDV and developing new potential antiviral targets.

Acarbose, an α-glucosidase inhibitor, regulates the postprandial blood glucose level by competitively inhibiting the activities of sucrase, maltase, and glucamylase in the intestine, serving as an ideal drug ingredient with blood glucose-lowering activity. Acarbose is mainly produced by the fermentation of Actinoplanes sp., and its biosynthetic pathway is mainly divided into four modules: C₇-cyclitol synthesis, deoxyglucosamine synthesis, maltose integration, and extracellular transport of acarbose and its homologues (carbophore cycle). This paper reviewed the advances in the research fields mentioned above, aiming to provide ideas for further exploring the biosynthetic pathways of acarbose, catalytic mechanisms of related enzymes, and molecular modification of fermentation strains.

[Objective] Rivers and lakes are important and closely linked aquatic ecosystems, in which microorganisms are important organic components and participate in the transformation of various substances and energy flow. Comparing the bacterial and fungal communities and their co-occurrence networks between rivers and lakes is the key to a deeper understanding of the biogeochemical cycling in aquatic ecosystems of the Qaidam Basin. [Methods] We analyzed the diversity, structures, driving factors, and co-occurrence networks of bacterial and fungal communities in six rivers and four lakes of the Qaidam Basin by next-generation sequencing and statistical analysis methods. [Results] The abundance and diversity of bacteria and fungi in rivers were higher than those in lakes (Wilcoxon, P < 0.01). The most dominant bacterial phylum was Proteobacteria in both rivers and lakes (rivers: 6.0%–63.0%; lakes: 8.0%–61.0%), while the most dominant fungal phylum varied between rivers and lakes, being Ascomycota (0.5%–75.0%) in rivers and unclassified_k_Fungi (3.0%–87.0%) in lakes. The structures of bacterial and fungal communities differed between rivers and lakes (bacteria: R=0.599, P=0.001; fungi: R=0.435, P=0.001). Altitude (Alt), chlorophyll a (Chl-a), and total nitrogen (TN) were significant factors shaping bacterial community structures, while dissolved oxygen (DO), pH, and temperature (Temp) were significant drivers shaping fungal community structures in different aquatic ecosystems. The stability of bacterial and fungal communities varied significantly between habitats. Specifically, bacterial communities were more stable in rivers than in lakes, while fungal communities were more stable in lakes than in rivers. [Conclusion] The bacterial and fungal communities varied between rivers and lakes in the Qaidam Basin, demonstrating spatial heterogeneity. This study can provide data support for the in-depth study of the differences and connections of the microbial community characteristics between rivers and lakes in the Qaidam Basin. Moreover, it lays a theoretical foundation for the protection and management of water resources in this region.

[Objective] Eukaryotic plankton are key components of a freshwater ecosystem, playing an important role in the food web. This study aims to explore the community dynamics and assembly mechanisms of three differently size-fractionated eukaryotic plankton communities (0.2–200, 0.2–3, and 3–200 μm) in two deep subtropical reservoirs (Shidou Reservoir and Tingxi Reservoir) in Xiamen. [Methods] From 2015 to 2018, samples were collected from both reservoirs in four seasons. The V9 region of eukaryotic 18S rRNA gene was amplified and sequenced to investigate the dynamic changes of eukaryotic plankton communities in the reservoirs. [Results] Overall, the temporal dynamics of dominant phyla of total eukaryotic plankton (0.2–200 μm) showed a strong correlation with that of micro-eukaryotic plankton (3–200 μm) and a weak correlation with that of pico-eukaryotic plankton (0.2–3 μm). Turnover was the main factor driving the temporal dynamics of eukaryotic plankton community composition in the two reservoirs. The proportions of the total number of sequences of the turnover species were higher in Shidou Reservoir than in Tingxi Reservoir in 2016 and 2017, while the opposite pattern was observed in 2018. Deterministic processes played a stronger role in the pico-eukaryotic plankton community assembly in Shidou Reservoir than in Tingxi Reservoir. The concentration of cyanobacterial chlorophyll a was weakly correlated with the eukaryotic plankton community in Tingxi Reservoir, while it was significantly correlated with the eukaryotic plankton community (especially the pico-eukaryotic plankton community) in Shidou Reservoir. [Conclusion] The pico-eukaryotic plankton community was more sensitive to cyanobacterial biomass than the micro-eukaryotic plankton community. The dynamics of the micro-eukaryotic plankton community largely determined the dynamics of the total eukaryotic plankton community. In the context of global changes, efforts should be made to monitor differently size-fractionated eukaryotic plankton and analyze the dynamics of community structure and functions for better understanding and protection of the reservoir ecosystem health and water quality.

Heterotrophic nitrification and aerobic denitrification microorganisms (HNADMs) can complete both nitrification and denitrification under aerobic conditions, which paves a new way for biological nitrogen removal. Researchers have discovered that some HNADMs maintain high nitrogen removal efficiency in extreme environments, exhibiting high application potential in the nitrogen removal of atypical wastewater. However, the available studies on HNADMs in extreme conditions remain in the initial stage. This article introduces the diversity, physiological and biochemical characteristics, and the complexity of metabolic pathways of HNADMs. Particularly, it reviews the research progress in HNADMs regarding the tolerance mechanisms to extreme temperature, pH, high salt, oligotrophic, and heavy metal stress conditions, nitrogen removal efficiency of simultaneous nitrogen and phosphorus removal, degradation of complex organic matter, and antibiotic resistance. Furthermore, the application status of HNADMs in extreme environments is summarized. Finally, the bottlenecks in the application of HNADMs in extreme environments are prospected. The review is expected to provide basic data for the application of HNADMs in complex wastewater treatment.

[Objective] To study the plant disease-inhibiting and growth-promoting effects and identify the antimicrobial components of Streptomyces levis L2. [Methods] Morphological features and the phylogenetic tree based on the 16S rRNA gene sequences were employed to identify the strain L2 isolated from the rhizosphere of drought-tolerant Echinochloa crusgalli. The antimicrobial components produced by the strain were identified by chromatography and high-resolution mass spectrometry. The whole genome of the strain was sequenced by Illumina in combination with Nanopore. antiSMASH was employed to search for the biosynthetic gene clusters. [Results] Streptomyces levis L2 and its fermentation broth inhibited the growth of Gram-positive bacteria and phytopathogenic fungi, and the strain produced a large transparent zone on the CAS (chrome azurol sulphonate) plate and could produce indole-3-acetic acid (IAA). The antimicrobial components of the strain showed the m/z of 537.102 0 [M+H]⁺ (calcd for C₂₇H₂₀O₁₂, 537.103 5, 2.2×10^–6) and 523.086 3 [M+H]⁺ (calcd for C₂₆H₁₈O₁₂, 523.087 8, 2.9×10^–6), which were consistent with the exact masses of α-rubromycins, β-rubromycins and γ-rubromycins, with the errors less than parts per 5 million. Their HPLC retention time were in agreement with that of standard rubromycins. The whole genome of L2 had a length of 8.8 Mb and carried 32 biosynthetic gene clusters for secondary metabolites including rubromycins. [Conclusion] S. levis L2 exhibited excellent plant disease-inhibiting and growth-promoting properties, thus could be further developed as biocontrol agents. It produces the antimicrobial components rubromycins and its biosynthetic gene clusters contained 6 more modification genes than the previously published gene clusters for rubromycins and several genes with unknown functions.

Deep-sea cold seeps are formed by the leakage of hydrocarbons such as methane, creating unique eco-environments that foster novel and phylogenetically diverse prokaryotes, eukaryotes, and viruses. Cold seep microorganisms obtain energy and substances through chemosynthesis, driving the biogeochemical cycles of elements such as carbon, sulfur, and nitrogen, thereby maintaining the stability of the cold seep ecosystem. Cold seep habitats contain rich microbial genetic resources, especially enzymes and secondary metabolites produced under extreme conditions, which exhibit dehalogenating, nitrogen-fixing, and antimicrobial activities, with potential applications in agriculture, drug development, and environmental protection. Additionally, cold seep microorganisms are closely related to the environmental impact assessment of natural gas hydrate extraction and play a significant role in global climate change. To effectively develop the microbial genetic resources in deep-sea cold seeps, researchers should combine in situ sampling, sequencing, and culture methods with environmental parameter monitoring to explore the ecological roles and evolutionary mechanisms of these microorganisms, delve into their genetic resources, and investigate microbial responses during hydrate extraction. Such efforts will provide a scientific basis for comprehensively developing microbial genetic resources and hydrate resources in deep-sea cold seeps.

[Objective] To explore the environmental drivers of prokaryotic microbial communities and carbon-fixing microbial groups in the upper and lower reaches of the Xiaolangdi Reservoir of the Yellow River during the dry season. [Methods] Water and surface sediment samples were collected from the upper and lower reaches of Xiaolangdi Reservoir during the dry season (November, 2020), and the physiochemical factors were measured. The composition of prokaryotic microbial communities and their carbon fixation functions were investigated by high-throughput sequencing of bacterial and archaeal 16S rRNA genes and PICRUSt2 prediction. The composition of carbon-fixing microbial groups was analyzed by high-throughput sequencing of cbbL and cbbM. [Results] Proteobacteria (24.74%), Actinobacteria (17.55%), and Firmicutes (11.43%) were the dominant bacterial phyla. Crenarchaeota (63.26%), Thermoplasmatota (18.29%), and Halobacterota (11.31%) were the dominant archaea. Proteobacteria (13.14%), Cyanobacteria (1.70%), and Actinobacteria (0.76%) were the dominant phyla of cbbL-carrying carbon-fixing microorganisms. Proteobacteria (3.52%), Actinobacteria (0.03%), and Gemmatimonadota (0.02%) were the dominant phyla of cbbM-carrying carbon-fixing microorganisms. The main environmental drivers of the bacterial community structure were temperature (T), turbidity, chemical oxygen demand (COD), and total ammonia nitrogen, which, however, had mild influences on archaea and carbon-fixing microbial groups. In bacteria, the relative abundance of the reductive tricarboxylic acid cycle (rTCA), the dicarboxylate-hydroxybutyrate cycle (DC/4HB), the 3-hydroxypropionate bi-cycle (3HP), and the Calvin-Benson-Bassham (CBB) were higher than that of other detected carbon fixation pathways. Notably, the relative abundance of the hydroxypropionate-hydroxybutylate cycle (3HP/4HB) in the upper reaches was significantly higher than that in the lower reaches. In archaea, the relative abundance of carbon fixation pathways such as rTCA, DC/4HB, and incomplete rTCA was higher, and the abundance of the Wood-Ljungdahl pathway (WL) in the lower reaches was markedly higher than that in the upper reaches of the Xiaolangdi Reservoir. Turbidity was a key factor affecting the abundance of the bacterial 3HP and incomplete rTCA, while temperature, dissolved oxygen, turbidity, COD, and total phosphorus were the main factors affecting the abundance of carbon fixation pathways in archaea. [Conclusion] This study revealed the environmental drivers of prokaryotic microbial communities and carbon-fixing microbial groups in the upper and lower reaches of the Xiaolangdi Reservoir during the dry season. The results contribute to a deeper understanding of the microbial carbon fixation process and the environmental driving mechanisms in the Yellow River during the dry season.

[Objective] Cold seeps and hydrothermal fields are typical chemosynthetic ecosystems in the ocean. With distinctive physicochemical properties, they harbor unique microbial communities. Dimethylsulfoniopropionate (DMSP), one of the most abundant organic sulfur-containing compounds on Earth, is synthesized and degraded by a variety of marine bacteria, which plays an important role in driving carbon and sulfur cycles in the ocean. In this study, we isolated and identified DMSP-synthesizing and degrading bacteria from the F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough and analyzed their diversity and distribution, aiming to expand the understanding of these bacteria in the ocean. [Methods] Water, sediment, and animal samples were collected at different depths from both the F-cold seep of the South China Sea and the Yaeyama Knoll hydrothermal field of the Okinawa Trough. Three enrichment media (l-methionine addition and high salinity and low nitrogen for DMSP-synthesizing bacteria; DMSP addition for DMSP-degrading bacteria) and the 2216E medium were used for the enrichment and isolation of bacteria. The taxonomic status of strains was determined by 16S rRNA gene sequencing, and the abilities of representative strains to synthesize or degrade DMSP were assessed. [Results] A total of 874 culturable strains were obtained. Gammaproteobacteria emerged as the dominant class in the three media, and Marinobacter was the most abundant genus. The number and diversity of culturable strains obtained from cold seep samples after enrichment were higher than those from the hydrothermal field. The 14 strains of DMSP-synthesizing bacteria from the cold seep belonged to 7 genera, including 5 Thalassospira strains carrying the DMSP synthesis gene mmtN and 2 Pseudooceanicola strains carrying dsyB. A total of 130 DMSP-degrading bacterial strains were obtained from the cold seep, belonging to 39 genera, among which Glutamicibacter was the most abundant genus (24 strains) without known genes associated with DMSP degradation. There was only 1 strain of DMSP-synthetizing bacteria and 18 strains of DMSP-degrading bacteria from the hydrothermal field, both were much fewer than those from the cold seep. The strains with DMSP cleavage pathway accounted for 98.6% of the total DMSP-degrading strains (148), among which 55 strains had strong cleavage activity and were mainly Actinobacteria. Among the 40 strains with strong DMSP-degrading activity, 9 strains contained known cleavage genes and 3 strains contained known demethylation genes. [Conclusion] Abundant DMSP-synthesizing and -degrading bacteria exist in F-cold seep of the South China Sea and hydrothermal fields of the Okinawa Trough, including a variety of bacterial groups carrying potential novel DMSP synthesis/degradation genes. This study provides a basis for further understanding the microbial-driven organosulfur cycling in chemosynthetic ecosystems.

In the context of global warming, the rising frequency of extreme weather events, including high temperatures, rainstorms, and droughts, will directly or indirectly increase the risks of pathogenic microorganisms entering drinking water systems and source waters. This is attributable to an increase in terrestrial inputs or alterations to the conditions that facilitate microbial survival and growth. It is therefore imperative to give priority to the issue of drinking water biosafety. The development of novel pathogen detection methods and risk assessment models enables a more comprehensive understanding and assessment of the microbiological risks associated with drinking water in watersheds under climate change. This review outlines the sources of microbiological risks associated with drinking water in watersheds experiencing extreme climatic conditions and summarizes various microbial contaminations and their risks to human health. Furthermore, it emphasizes the significance of high-throughput quantitative microbial risk detection methods and assessment models in the control of microbiological risks to drinking water. Finally, it provides novel insights into the effective management and control of pathogenic microorganisms in drinking water under climate change.