Abstract:

Abstract:Coastal wetlands are crucial blue carbon ecosystems and play an indispensable role in regulating global climate change and preserving biodiversity. Microorganisms are key drivers of biogeochemical cycles, maintaining ecosystem functions and stability by coupling carbon, nitrogen, and sulfur cycles. Synthetic microbial ecology aims to understand microbial interaction mechanisms and environmental applications. In view of the critical issues in coastal wetlands, this paper focuses on the theoretical studies of synthetic microbial ecology and explores the applications of microbiome engineering in reducing greenhouse gas emissions and enhancing carbon sinks, providing scientific and technological support for mitigating global climate change.

Abstract: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.

Abstract:Vitamin B₁₂ (VB₁₂) is an essential nutrient and growth cofactor for the majority of organisms. It exerts influence not only on the structure of microbial communities and marine primary productivity but also on the global biogeochemical cycles, thus justifying its designation as a “hard currency” in marine ecosystems. Ammonia-oxidizing archaea (AOA), initially isolated from the ocean in 2005, are distinguished by their chemolithoautotrophic characteristics. Genomic, metabolomic, and culture studies have demonstrated that AOA are among the few microbial groups capable of synthesizing VB₁₂ in the ocean. This capability is crucial for maintaining microbial community stability and biogeochemical functions. This review summarizes the measurement methods and distribution characteristics of VB₁₂ in the ocean and the pathways through which AOA produce VB₁₂. It discusses the importance of AOA in marine VB₁₂ supply and outlines the future research directions for VB₁₂ production by AOA.

Abstract:[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.

Abstract: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.

Abstract:Dissolved organic matter (DOM) in the ocean encompasses complex and diverse organic compounds, and heterotrophic bacteria, the main DOM decomposers, also exhibit high biodiversity. The interactions between heterotrophic bacteria and DOM play an important role in biogeochemical cycles, which, however, are not fully understood. [Objective] To explore the dynamics of microbial communities with the addition of marine-derived concentrated DOM. [Methods] DOM with a molecular weight exceeding 1 kDa and enriched from coastal seawater was introduced into microcosm culture systems. Illumina amplicon sequencing, dissolved organic carbon (DOC) concentration measurement, and bacterial isolation were performed on different days of incubation. [Results] The addition of DOM significantly influenced bacterial community composition, inducing more pronounced changes in the high-DOM group. Specifically, the relative abundance of Campylobacterota, Nitrosococcales, and Nitrincolaceae increased in the high-DOM group on days 3, 10, and 30, respectively. The alpha diversity and evenness of the microbial community decreased during days 0−3 and increased during days 10−30, with a transition point occurring between days 3 and 10. The network analysis revealed that the high-DOM group exhibited a more tightly interconnected and complex network than the control group. In addition, bacterial isolates from the culture systems added with different concentrations of DOM were distinct. The specific genera of different DOM treatments were identified, which may be key groups in DOM degradation. [Conclusion] The addition of DOM triggers the succession of microbial community structures within microcosm culture systems, and the community composition may be associated with specific DOM components, which influence the direction of community succession. Furthermore, the varying DOM concentrations select for culturable bacteria with diverse survival strategies. This study provides a basis for enriching our understanding about the mechanisms underlying microbial responses to marine-derived DOM.

Abstract:Cable bacteria are a new group of filamentous electroactive microorganisms with the ability of long-distance electron transfer (LDET), playing an important role in the geochemical cycling of elements. Their unique structural and functional characteristics make them like “biological cables”. Since the first discovery in marine sediments in 2012, cable bacteria have attracted widespread attention. They have shown unique ecological potential in maintaining the health of aquatic ecosystems, environmental restoration, and climate regulation. Focusing on the “biological cable” structures and functions of cable bacteria, this paper reviews their filamentous structural characteristics, electrogenic sulfur oxidation characteristics, diversity and distribution characteristics, and LDET mechanism in sediments, and summarizes their influences on the cycling of key elements such as S, C, N, and P and the migration and transformation of metal ions. In addition, this paper summarizes the interactions of cable bacteria with other organisms and their roles in the natural restoration of ecosystems and analyzes the existing problems and future development directions, with a view to providing a reference for further giving play to the role of “biological cables” in the natural restoration of ecosystems.

Abstract:Cyanobacteria have garnered great attention as important players in the marine hydrosphere and the source of bioactive compounds. Type IV pili (TFP) play a crucial role in cyanobacteria by participating in various physiological functions such as substrate surface movement, phototaxis, and natural transformation. With the continuous advancements in the visualization of pili, we have gained a deeper understanding of the TFP-mediated cell behaviors of cyanobacteria. We review the recent progress and applications of visualization of pili in the research on the twitching, phototaxis, and natural transformation of cyanobacteria. This review is expected to improve our understanding of the TFP-mediated cell behaviors and the ecological function and significance of cyanobacteria in the hydrosphere. Additionally, it provides new insights for developing TFP-based regulation on cell behaviors of cyanobacteria.

Abstract:[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.

Abstract: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.

Abstract:[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.

Abstract:Although the large scale of industrial nitrogen fixation and chemical nitrogen fertilizer application have increased crop yields and alleviated food crisis, the excess discharge of nitrogen nutrients have affected the environment and human health. The treatment of nitrogen contamination is largely dependent on the nitrogen cycle driven by microorganisms. In the last three decades, researchers have discovered the inorganic nitrogen metabolism pathways such as anaerobic ammonia oxidation (Anammox), complete ammonia oxidation (Comammox), and direct ammonia oxidation (Dirammox). Shewanella, a genus of known bacteria with abundant respiration pathways, are ubiquitous in natural habitats and have potential applications in both microbial fuel cells and environmental bioremediation. In this review, we described the modulation mechanisms of denitrification and dissimilatory nitrate reduction to ammonium pathways in Shewanella from the nitrate reductase systems, regulation of the cyclic AMP (cAMP) receptor proteins (Crp), and modulation and switching of nitrate reduction pathways, aiming to give insights into the microbial-driven nitrogen cycling mechanism in the hydrosphere and the development of novel biotechniques and bioreactors for the removal and mitigation of nitrogen pollution.

Abstract:Higher alcohols, major metabolic byproducts produced by Saccharomyces cerevisiae during winemaking, are intricately regulated by a multilevel system. While the enzymatic machinery and their encoding genes involved in the metabolic pathways of higher alcohols in S. cerevisiae have been largely elucidated, the transcriptional regulation underlying this process remains poorly understood. This paper, building upon a summary of the metabolic pathways and regulatory strategies of higher alcohols metabolism in yeast, focuses on the transcription factors Aro80p, GATA and Leu3p implicated in the regulation of higher alcohols metabolism in yeast and their mechanisms of action. The review aims to give theoretical insights into a comprehensive understanding of the transcriptional regulation of higher alcohols metabolism in yeast and facilitate the breeding of yeast strains with moderate production of higher alcohols.

Abstract: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.

Abstract: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.

Abstract:Marine mammals mainly include Cetacea living in the water, Sirenia primarily inhabiting water, and Pinnipedia which are amphibious. All these animals are rare and included in the list of national second-class or higher protected animals. Microorganisms play crucial roles in nutrient absorption, assisting the digestive process, and enhancing immune function of mammals, being an indispensable component of the host. The unique living conditions and diets of marine mammals result in significant differences in their microbiomes compared with terrestrial mammals. As a result, our knowledge about the microbiomes derived from terrestrial mammals is not applicable to marine mammals. Therefore, understanding the structures and functions of marine mammal microbiomes is essential for comprehending the interactions between marine mammals and their living environment and enhancing conservation efforts. This paper summarizes the recent advances in research on the microbiomes of marine mammals, discusses relevant technical methods, and highlights worthy scientific issues in future research.

Abstract:Cyclic adenosine monophosphate (cAMP) is a second messenger widely present in eukaryotes. It is synthesized by adenylate cyclase (AC) and regulates downstream protein activity by binding to protein kinase A, thereby regulating fungal growth and development, virulence, cell wall integrity, environmental stress responses, and sexual/asexual reproduction. This article introduces the research progress of the cAMP signaling pathway in phytopathogenic fungi and the cooperation of this pathway with other signaling pathways in regulating cellular processes. At the same time, it elucidates the role of the cAMP signaling pathway in the infection of plant phytopathogenic fungi. This review is expected to provide reference for screening the agents for inhibiting phytopathogenic fungi that target the genes or proteins in the cAMP pathway. Additionally, the cAMP signaling pathway could be targeted to prevent and control the growth, development, and pathogenicity of phytopathogenic fungi in the future.

Abstract: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.

Abstract:[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.

Abstract:[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.

Abstract:[Objective] To investigate the biosynthetic potential of the endophyte Streptomyces sp. SZC001 in Sinomenium acutum and explore the unknown active natural products. [Methods] SZC001 was isolated by surface sterilizing method and its full-length genome sequence was obtained by third-generation and second-generation sequencing. Then, the biosynthetic potential of SZC001 was evaluated by antiSMASH analysis. Fermentation was carried out with four media, and the compounds were separated and identified by silica gel column chromatography, high-performance liquid chromatography, high-resolution mass spectrometry and nuclear magnetic resonance. The CCK-8 assay was employed to examine the cytotoxicity of the target compounds. [Results] The strain was identified as Streptomyces sp. SZC001, with a genome length of 9 109 166 bp and the G+C content of 71.08%. The antiSMASH analysis showed that the genome of the strain contained a total of 31 biosynthetic gene clusters (BGCs), among which 17 BGCs had less than 40% similarity with the known BGCs. The strain produced several anthracyclines in four media, and the two most abundant compounds 1 and 2 were isolated and identified. Compound 1 is the known compound ε-rhodomycinone and compound 2 is a new compound η-rhodomycinoe, which is derived from α₂-rhodomycinone by derivatization of the hydroxyl group at the C-10 position and transfer of the hydroxyl group at the 6-position to the 11-position of the backbone. Both compounds 1 and 2 showed relatively strong inhibitory effects on two tumor cell lines, with IC₅₀ of 1.55–4.59 μmol/L. [Conclusion] SZC001 is a strain that holds the potential for the exploration of active natural products. The anthracyclines produced by the strain exhibit anti-tumor activities and warrant further development and utilization. This study enriches ε-rhodomycinone derivatives, furnishing a foundation for the subsequent exploitation of the endophytic resources of S. acutum.

Abstract:[Objective] To explore the effects of rice-crab co-culture on physicochemical indicators and microbial community structure of soil in the Yellow River irrigation area of Ningxia and thus provide a theoretical basis for promoting rice-crab farming in the Yellow River irrigation area in northwest China. [Methods] The physicochemical indicators of soil were measured, and high-throughput sequencing of 16S rRNA gene amplicons was employed to reveal the microbial community structure in the fields with only rice planting (CK) and rice-crab co-culture (EG) by introduction of crabs into the ditches around rice plots. [Results] EG had higher soil pH, total nitrogen (TN), and soil organic matter (SOM) and lower total salt content than CK from April to August. The TN, available phosphorus (AP), and SOM in EG were significantly higher than those in CK in June and July. In terms of microbial community structure characteristics, EG significantly altered the bacterial community structure in soil, increasing the bacterial diversity and abundance in April, and August. EG had higher cumulative relative abundance of the top 20 bacterial phyla than CK from April to August. The dominant phylum of both CK and EG from April to August was Proteobacteria. At the genus level, EG increased the relative abundance of Pseudomonas and decreased the relative abundance of Thiobacillus and Methanosaeta. The comparison showed that EG had stronger effect on the bacterial community structure than the sampling month. Correlation analysis shows that TN is the main factor affecting the relative abundance of soil bacteria, and it is significant (P<0.05). [Conclusion] Compared with traditional rice monoculture (CK), sampling rice crab intercropping (EG) enhances soil fertility, increases the relative abundance of Proteobacteria and Pseudomonas in the soil, and helps improve soil fertility and nutrient cycling efficiency, as well as clean up pollutants in soil and water bodies.

Abstract:[Objective] To study the therapeutic effect of Bifidobacterium adolescentis strains with strong antioxidant capacity on a mouse model of ulcerative colitis (UC). [Methods] The B. adolescentis strains with strong antioxidant capacity were screened based on 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging rate, reducing capacity, and hydrogen peroxide tolerance. Subsequently, we established a mouse model of dextran sulfate sodium (DSS)-induced colitis to investigate the alleviating effects of the B. adolescentis strains with strong antioxidant capacity on UC. [Results] Among the 26 strains of B. adolescentis, TH02767, TH03658, and TH03664 demonstrated strong antioxidant capacity. Only TH02767 showed an alleviating effect on UC in terms of disease activity index and spleen index in the mouse model (P<0.05). Moreover, the intervention with TH02767 lowered the levels of tumor necrosis factor-α, interleukin-6, interleukin-1β, and myeloperoxidase (P<0.05), while enhancing the production of interleukin-10 (P<0.05) in the colon. In addition, TH02767 modulated gut microbiota in the mice by reducing the relative abundance of Deferribacterota and increasing the relative abundance of Bacteroidetes. At the genus level, it increased the relative abundance of Muribaculum and Muribaculaceae (P<0.05). [Conclusion] B. adolescentis TH02767 screened out in this study for its robust antioxidant capacity not only ameliorates the clinical symptoms associated with DSS-induced colitis in mice but also significantly reduces the levels of pro-inflammatory cytokines and modulates the gut microbiota.

Abstract:[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.

Abstract:[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.

Abstract: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.

Abstract:[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.

Abstract:A mutant (G₉-72) of Halomonas campaniensis exhibiting high ectoine production was obtained by ultraviolet (UV) mutagenesis. The mutation sites, molecular variations, and high ectoine production mechanism of this mutant remain unknown. [Objective] To investigate the mutation sites and genetic variations of G₉-72 compared with the wild type strain XH26 and identify the potential causes of ectoine accumulation outbreak. [Methods] PacBio Sequel II was used for whole-genome sequencing, and the mutation sites in the genome of the mutant were identified based on the sequencing results. The amino acid metabolic pathways were analyzed to reveal the association between mutated genes and ectoine synthesis, and the results were verified by RT-PCR. [Results] The genome of strain XH26 was 4.11 Mb, encoding 3 927 genes. Compared with strain XH26, G₉-72 showed 35 mutation sites, including 18 single nucleotide polymorphism mutations, 14 insertion mutations, and 3 deletion mutations. The mutated genes argF, coaBC, and livH, which encoded ornithine transcarbamylase (100.00% similarity with ArgF proteins in NCBI database), phosphopantothenoylcysteine decarboxylase (99.28% similarity with CoaBC proteins in NCBI database), and branched-chain amino acid ABC transporter permease (96.27% similarity with LivH proteins in NCBI database), were implicated in the synthesis of fumaric acid, citric acid and the absorption and transport of branched-chain amino acids, respectively. The increased flow of upstream metabolites may be the key reason for the sharply increased accumulation of ectoine in the mutant. RT-PCR verified 20 genes related to the ectoine metabolic pathway, and the transcriptional expression levels were consistent with the expected analysis. [Conclusion] The overexpression of genes argF, coaBC, and livH enhanced the anabolic flow of ectoine, which contributed to a significant increase in ectoine accumulation in the mutant. This finding provides a reference point for subsequent studies on the reaction mechanisms of enzymes in the mutant and the fermentation production.

Abstract:[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.

Abstract:[Objective] To reveal the dynamics of bacterial communities in surface water and groundwater in the densely populated area of the Jianghan Plain across seasons and explore the underlying factors causing the temporal variations. [Methods] Water samples were collected from both surface water and groundwater in the densely populated area of the Jianghan Plain, and metagenomic sequencing was employed to investigate the seasonal variations of bacterial communities. The variations in environmental factors, bacterial community structure, and bacterial community assembly processes in the surface water and groundwater were compared considering rainy and dry seasons. [Results] For the surface water, the salinity (P<0.01) and conductivity (P<0.01) during the rainy season were lower than those during the dry season, while no significant seasonal variation was observed in turbidity. For the groundwater, the turbidity was higher in the rainy season than in the dry season (P<0.05), while neither salinity nor conductivity showcased seasonal variations. The Shannon index of bacteria in the surface water in the rainy season was higher than that in the dry season (P<0.01), whereas that in the groundwater presented no significant seasonal difference. The principal coordinates analysis and permutational multivariate analysis of variance (P=0.001) revealed significant seasonal variations in bacterial communities between surface water and groundwater. The Mantel test showed no significant correlations between the bacterial community in the groundwater and environmental factors during the dry season, while other communities were significantly correlated with at least one environmental factor. The neutral community model, modified stochasticity ratio (MST), and β nearest taxon index all indicated that stochastic processes exerted stronger effects on the bacterial community in the surface water during the rainy season than during the dry season, and the trend was similar but not significant for the bacterial community in the groundwater. The migration rate of surface water was higher during the rainy season than during the dry season, whereas that of groundwater showed an opposite trend. (5) The seasonal variations in the diversity of antibiotic resistance genes exhibited a negative correlation with MST (ρ=−0.164, P=4.942E−2) in the surface water, whereas the correlation was positive in the groundwater (ρ=0.393, P=1.452E−6). [Conclusion] The temporal dynamics of bacterial communities in surface water and groundwater in the densely populated area of the Jianghan Plain showed notable differences. These differences can potentially be attributed to distinct basic properties between surface water and groundwater, frequent environmental disturbances during the rainy season, and water exchange processes between surface water and groundwater.