[Objective] To evaluate the biocontrol and growth-promoting effects and reveal the antifungal mechanisms of the pepper endophyte Bacillus velezensis XY40-1, thus providing elite bacterial strains and technical support for the development of biocontrol agents for pepper Phytophthora blight. [Methods] Plate confrontation, in vivo inoculation assay, and microscopic observation were employed to determine the biocontrol and growth-promoting effects of B. velezensis XY40-1 on pepper. Genomics and metabolomics methods were adopted to determine the antifungal metabolites of the strain and the synthesis pathways of substances involved in antifungal effects, on the basis of which the antifungal mechanisms were explored. [Results] Strain XY40-1 exhibited strong inhibitory effects on six pathogenic fungi: Phytophthora capsici, Sclerotium rolfsii, Colletotrichum scovillei, Alternaria alternate, Fusarium oxysporum, and F. solani, that infected pepper, and it demonstrated broad-spectrum resistance. The strain suspension at 10⁷ CFU/mL showcased the control effect of 66.13%. Moreover, it possessed the abilities to solubilize phosphorus and potassium and fix nitrogen, thus promoting the growth of pepper seedlings. XY40-1 carried a large number of genes involved in the synthesis of ketone and terpenoid antibiotics, which enabled it to produce extracellular metabolites such as nogalamycin, megalomicin, rifaximin, avermectin ala, avermectin, and ansamitocin P-3 to inhibit pathogenic fungi. The synthesis and degradation of ketone bodies, as well as the biosynthetic pathways of terpenoid skeletons and antibiotics, contributed to the antagonistic function of XY40-1. The core metabolic pathway was the biosynthesis of secondary metabolites. [Conclusion] B. velezensis XY40-1, an endophyte of pepper, possesses excellent biocontrol and growth-promoting effects on pepper, being a multifunctional and high-quality strain for the biocontrol of pepper diseases.

The nitrogen fixation in legume root nodules is of great significance for sustainable agricultural development and natural eco-environment protection. The growth period of root nodules can be divided into young, active, and senescence stages. Root nodule senescence is a complex physiological process involving the interactions of multiple genes and environmental factors. The functions and lifespan of root nodules can be altered by regulating nitrogenase activity and leghemoglobin gene expression levels. Biotic and abiotic stresses can accelerate the senescence of root nodules and reduce the biomass and productivity of leguminous plants. This article expounds the mechanism of morphological, physiological, biochemical, and molecular changes of root nodules during senescence and summarizes the biotic and abiotic factors that affect root nodule senescence. Furthermore, the measures for delaying the senescence of root nodules are discussed. These measures will prolong the symbiotic nitrogen fixation, improve the nitrogen utilization efficiency, and increase the overall nitrogen supply for seed filling of leguminous plants, thereby enhancing food security and reducing the adverse effects of chemical fertilizers on the environment.

[Objective] To explore the regulatory role of the metalloregulator ZntR in metal homeostasis and clarify the effects of ZntR on the oxidative stress resistance and virulence of Vibrio parahemolyticus. [Methods] Growth curve analysis and intracellular metal content quantification were performed to investigate the regulatory effect of ZntR on the metal homeostasis in V. parahaemolyticus. The effects of ZntR on the oxidative stress resistance and virulence of V. parahaemolyticus were explored by the growth curve analysis and the competitive infection assay in the zebrafish model, respectively. The genes regulated by ZntR were identified by RNA sequencing. [Results] The zntR-deleted strain (ΔzntR) exhibited growth defects under zinc, nickel excess and iron restriction conditions, and the growth defects were related to zinc homeostasis disturbance. The overexpression of zntA in ΔzntR promoted the growth under zinc, nickel excess and iron restriction conditions. In the case of zinc excess, ΔzntR demonstrated weakened resistance to H₂O₂-induced oxidative stress. The virulence of ΔzntR was attenuated in a competitive infection assay in the zebrafish model. RNA sequencing revealed that ZntR regulated the expression of several virulence genes. [Conclusion] ZntR modulates zinc homeostasis and improves oxidative stress resistance and virulence of V. parahaemolyticus.

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.

[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 construct a recombinant vaccinia virus strain WR that expresses dual reporters (luciferase Fluc and red fluorescent protein mCherry). [Methods] Firstly, the gRNA CRISPR/Cas9 plasmid targeting the J2R region of WR and the plasmid pJSE-Fluc/mCherry carrying the dual reporter genes were constructed. Then, the CRISPR/Cas9 gene editing tool was used to insert the dual reporter genes into the TK region, and thus the recombinant vaccinia virus strain rWR-Fluc/mCherry (rWR) was constructed. The location and sequence of insertion in rWR were analyzed by PCR and sequencing. The recombinant strain rWR was characterized by mCherry/Fluc activity and plaque assays. The recombinant strain rWR was subcultured for 12 passages, and the expression levels of the dual reporter genes and E3L were determined to reveal the genetic stability of the strain. To analyze the replication dynamics of the virus in Vero and HeLa cells, we determined the cytopathic effect (CPE), TCID₅₀, and dual reporter expression of rWR and the wild type (WR) in the infected cells. Furthermore, we evaluated the inhibitory effects of ST-246 as a positive drug on both rWR and WR in vitro by the plaque assay, qPCR, and dual reporter activity measurement. [Results] Fluc and mCherry were accurately inserted into the TK region of WR. The Vero cells infected with rWR showed the activities of dual reporters and the plaque morphology consistent with that of WR. After 12 passages, the dual reporter activities and E3L expression were stably detected in rWR, which indicated that rWR was successfully constructed and genetically stable. The CPE, TCID₅₀, and dual reporter activity in Vero and HeLa cells indicated that replication peaked 48–72 h post-infection with rWR, which was consistent with the replication dynamics of WR. The median effective concentration (EC₅₀) of ST-246 against rWR was in agreement with that against WR, and the EC₅₀ (2–7 nmol/L) obtained by the plaque assay, qPCR, and dual reporter activity measurement showed good consistency (r > 0.500 0 and P < 0.05). [Conclusion] A recombinant vaccinia virus strain rWR simultaneously expressing Fluc and mCherry was successfully constructed, and it was genetically stable. This strain might be used as an in vitro system for rapid screening and characterization of anti-orthopoxvirus drugs with simple operation.

[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.

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.

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.