Halogenated organic compounds (HOCs) have gained increasing attention due to their potential toxicity, environmental persistence, and bioconcentration. The marine environment is a major source and sink of HOCs, not only accumulating large amounts of anthropogenic HOCs but also containing a wide range of naturally produced HOCs. Microbial reductive dehalogenation is a key strategy for the remediation of HOCs pollution, in which organohalide-respiring bacteria (OHRB) play a pivotal role in the bioremediation and geochemical cycling of HOCs. This article provides an overview of the sources and distribution of HOCs in the marine environment as well as the mechanisms of reductive dehalogenation by anaerobic microorganisms. It systematically reviews the research progress in reductive dehalogenating bacteria that have been isolated from the marine environment and the reductive dehalogenases, aiming to provide a reference for the bioremediation of HOCs in the marine environment and lay a theoretical foundation for clarifying the biogeochemical cycle of halogens in the marine environment. Additionally, this article explores the differences in the properties of marine and terrestrial dehalogenating bacteria and their potential connections, which are important for elucidating their evolution and environmental adaptation in different ecosystems.

China has a large livestock and poultry industry. The frequent occurrence of diseases caused by the spread of bacterial pathogens not only cause serious economic losses of this industry but also threaten public health and safety since some pathogens can cause zoonoses. This article provides an overview of the prevalent bacterial pathogens attacking the livestock and poultry industry in China in recent years and summarizes the current development and application of vaccines for domesticated animals in China. This review is expected to provide a theoretical basis for the prevention and control of bacterial diseases attacking the livestock and poultry industry in China.

Microbial surfactants (biosurfactants) are diverse and have rich functions, demonstrating broad application prospects in enhanced oil recovery. This article provides an overview of the yields, temperature and salt tolerance, critical micelle concentrations, micelle diameters, adsorption capacity, wettability, oil displacement performance, and field applications of oil-displacing biosurfactants such as rhamnolipid, sophorolipid, and lipopeptides. In addition, this article analyzes the challenges in application costs, application scenarios, and oil displacement mechanisms, and proposes the key problems to be addressed and future development directions.

In recent years, the regulation mechanism of lipid metabolism by gut microbiota has become a focus of research. Changes in gut microbiota have been discovered in the mouse models of obesity and lipid metabolism disorders. Adjusting gut microbiota by fecal microbiota transplantation and probiotics can alleviate lipid metabolism disorders. This review focuses on the regulatory effect of gut microbiota on lipid metabolism and expounds the regulatory effects on cardiovascular diseases, nervous system diseases, non-alcoholic fatty liver disease, obesity, and type 2 diabetes mellitus. Finally, this paper explores the therapeutic prospects of regulating gut microbiota in the treatment of lipid metabolism disorders.

Actinomycetes are essential sources of secondary metabolites with diverse chemical structures and bioactivities. Lichen is a unique system of fungi and algae. In addition to lichenized fungi and algae, there are also a large number of endophytic fungi and actinomycetes in the lichen ecosystem, which have garnered increasing attention due to their unique ability to produce secondary metabolites. It is of great significance to study the secondary metabolites of lichen-derived actinomycetes for the discovery of active lead compounds and the development and utilization of medicinal microbial resources. This article reviews the research progress in the secondary metabolites and activities of lichen-derived actinomycetes in recent 30 years.

Antibiotics serve a critical function in preventing and treating infectious diseases. However, their misuse has resulted in the development and persistence of resistance among microorganisms, driven by selective pressure. Carbapenems, vital antibacterial agents, were once considered the last resort for combating severe Gram-negative bacterial infections. Yet, the emergence of carbapenemases has led to a rapid rise in the detection rate of carbapenem-resistant Gram-negative bacteria worldwide, posing a significant threat to global public health security. This review focuses on the global epidemiology of carbapenem-resistant bacteria and the detection methods of clinically relevant resistance genes, providing reference for the rational use of antibiotics and effective control of drug resistance transmission.

[Background] Zearalenone (zearalenone, ZEN), a toxin produced by Fusarium, poses a serious risk to human health and animal production performance as it can disrupt the reproduction and damage the immune system of the body. The lactonase ZHD101 from Clonostachys rosea, also known as ZEN hydrolase, degrades ZEN into non-toxic products by hydrolysis and can be used as a feed enzyme additive to reduce the mycotoxin exposure in animals. [Objective] The digestive enzymes of animals significantly reduce the efficacy of feed enzyme additives, and it is therefore crucial to investigate the methods enhancing the trypsin resistance of feed enzymes to improve their utilization efficiency. [Methods] Rational design was employed to mutate the key amino acid residues of ZHD101 at the interaction interface with trypsin, thereby weakening the binding affinity of ZHD101 to trypsin and enhancing its trypsin resistance. [Results] Compared with that of the wild type, the half-life of ZHD101^K254Q and ZHD101^K254Q/K262Q in simulated intestinal fluid was prolonged by 61.8% and 57.8%, respectively. The mutated enzymes showcased the best performance at pH 9.0−10.0 and about 40 ℃, with similar enzymatic properties to the wild type. [Conclusion] The rational design of ZHD101 for improving the trypsin resistance enhances the application of this enzyme in the feed industry and provides clues for molecular modification of other feed enzymes.

[Background] Controllable cell proliferation is one of the important strategies for achieving automatic control of fermentation. It can be easily implemented by the controlled supply of key nutrients. [Objective] To analyze the characteristics of l-alanine biosynthesis in the l-lactic acid-producing strain Escherichia coli LG101 and explore the feasibility of taking l-alanine biosynthesis as a node to regulate cell proliferation. [Methods] We employed site-specific recombination to obtain mutants by deleting the corresponding genes (avtA, alaA, alaC) of the l-alanine biosynthesis pathway on the basis of comprehensively analyzing the l-alanine biosynthesis pathway. Shake-flask and bioreactor experiments were carried out to examine the physiological and metabolic differences between the original strain and the mutants. [Results] There were at least three l-alanine biosynthesis pathways in the genome of E.coli, two of which utilized pyruvate (also the precursor for the synthesis of lactic acid) as a precursor. The relevant coding genes were deleted, and mutants LG101A (LG101 DavtA), LG102 (LG101 DalaA DalaC) and LG103 (LG101 DalaA DalaC DavtA) were obtained. In shake-flask culture, the cell proliferation of the mutants LG101A and LG102 was not significantly different from that of the original strain. However, the mutant LG103 was l-alanine auxotrophic, and its proliferation presented a positive dose-dependent correlation with l-alanine supplementation. The physiological and metabolic properties of strain LG103 were further analyzed and evaluated in a 5 L fermenter. The strain LG103 restored cell proliferation after supplementation of l-alanine, and the accumulation of l-alanine (0.12 g/L) in the fermentation broth at the end of fermentation was significantly lower than that (0.92 g/L) of the original strain. [Conclusion] E.coli LG101 over-synthesizes and accumulates l-alanine through the reduction reaction with glutamate and valine as amino donors. The mutants with removal of the corresponding synthetic pathways became l-alanine auxotrophic and their proliferation showcased a dose-dependent relationship with l-alanine supplementation. The findings suggest that l-alanine synthesis can be utilized as a nutrient switch to control cell proliferation during the fermentation of E.coli for production of major compounds such as lactic acid.

[Background] Bacteria are the main drivers in lake ecosystems, and their community structure is highly responsive to the environmental changes in the lake. The special geographical location and high altitude environment of Bangong Lake have shaped a unique microbial ecosystem. However, little is known about the bacteria in this lake. [Objective] To explore the bacterial diversity and distribution pattern in Bangong Lake in the Ali region, we collected samples at 20 sites in the east bank, west bank, center, and bottom of this lake in September 2023. [Methods] The 16S rDNA high-throughput sequencing was performed for the samples, and the α diversity of the microorganisms was measured. The Spearman’s correlation analysis was conducted between the physicochemical properties of water and the α diversity of microorganisms. [Results] A total of 14 886 operational taxonomic units (OTUs) were yielded, indicating 470 genera of 47 phyla. The bacterial community in Bangong Lake was mainly composed of Proteobacteria, Actinomycetota, Bacteroidota, and Verrucomicrobiota. The community had high diversity and richness, with a complex structure. The Spearman correlation coefficient indicated that total phosphorus and electrical conductivity were the main environmental factors affecting the bacteria in Bangong Lake. [Conclusion] This paper clarifies the diversity and distribution pattern of bacteria in Bangong Lake and reveals the water physicochemical factors influencing the bacterial community. The findings provide a reference for studying the dynamics of bacteria after the narrowing or expansion of Bangong Lake in the future.

[Background] Aerobic composting is a common resource utilization method to treat agricultural solid waste, while odorous gases (NH₃ and H₂S) generated during the composting process pose a threat to the health of humans and animals. Microbial deodorization has low costs and good effects, while single strains have poor environmental adaptability and limited effects. [Objective] To develop a combination of efficient deodorizing strains and optimize microbial deodorization conditions to address the foul odor in composting. [Methods] The effects of the deodorizing strain combination on the changes of bacterial community structure during composting were studied by screening of deodorizing microbial strains and temperature-controlled simulated composting. Furthermore, the relevant functional genes were analyzed and annotated. [Results] The maximum release of NH₃ and H₂S from the compost supplemented with the deodorizing strain combination E was only about 40% of that from the compost treated with the commercial microbial agent X. The species classification results show that the phyla with relatively high abundance during composting include Proteobacteria, Actinomycetota, Firmicutes and Bacteroidota. Group E showed higher relative abundance of Proteobacteria and Actinomycetota than groups X and CK. The dominant genera included Pseudomonas, Corynebacterium, and Pseudogracilibacillus, among which Corynebacterium kept being dominant in group E. The annotation results from the KEGG database indicated that the addition of the deodorizing strain combination E promoted the amino acid metabolism in the microbial community during composting. Similarly, functional gene annotation results revealed higher abundance of ammonia assimilation-related genes (gs, gdh, asn, and gln) and the sulfur-containing amino acid synthesis-related gene (cysC), suggesting that the combination E reduced NH₃ and H₂S emissions by facilitating the conversion of nitrogen and sulfur into amino acids and other organic compounds. [Conclusion] The deodorizing strain combination E can effectively inhibit the release of NH₃ and H₂S in the manure composting process, providing microbial resources for the treatment of waste gases generated in the manure resource utilization process.

[Background] Biological soil crusts play a crucial role in windbreak and sand fixation, and oligotrophic microorganisms adaptive to nutrient-poor conditions are the main contributors to crust formation in deserts. [Objective] To investigate the sand-fixing function of Paenarthrobacter sp. AMU7 cultured with different carbon sources and analyze its exopolysaccharides, thus providing elite microbial resources for ecological management of deserts. [Methods] The oligotrophic sand-fixing strain AMU7, isolated and screened from the moss crust sample of Mu Us Sandy Land, was identified by 16S rRNA gene sequencing, morphological observation, and physiological and biochemical tests. Strain AMU7 was cultured in the media with different carbon sources. The crust thickness and pressure-bearing capacity were measured with a vernier caliper and a pressure gauge, respectively, to evaluate the effect of strain AMU7 in promoting crust formation. The exopolysaccharides in fermentation broth samples under different treatments were measured by the phenol-sulfuric acid method and the sand-fixing effects were determined, on the basis of which the types and location of the sand-fixing substances produced by strain AMU7 were determined. [Results] Strain AMU7 was identified as Paenarthrobacter sp. AMU7. With glucose as the carbon source, strain AMU7 formed stable crusts with the thickness consistently exceeding 1.74 cm. The 24 h pressure-bearing capacity of the crusts produced by the fermentation broth of strain AMU7 was stably over 25 N higher than that by the glucose synthetic medium (control), which indicated that strain AMU7 significantly enhanced the compressive strength of the crust. The sand-fixing substances of Paenarthrobacter sp. AMU7 were not secondary metabolites secreted in large quantities during the stable growth phase, but exopolysaccharides produced in the extracellular mucous layer formed during the rapid proliferation and growth of bacterial cells. Moreover, the content of exopolysaccharides was higher in the mucous layer during the early logarithmic growth phase. [Conclusion] Paenarthrobacter sp. AMU7 has an efficient sand-fixing capability, demonstrating significant application potential in the ecological management of deserts.

[Background] Amid the aggravating environmental pollution, increasing organisms are endangered by nuclear radiation, chemical pollution, and biological pollution, which seriously disrupts the balance of ecosystems. Deinococcus radiodurans with remarkable performance of DNA repair can survive in various extreme environments. PprI acts as a switch in the DNA repair process in D.radiodurans, and the heterologous expression of this protein can significantly enhance the survival rates of other eukaryotes and prokaryotes in extreme conditions. The available studies on PprI molecules are predominantly conducted with biochemical methods, and the real-time dynamic observation on reactions of single PprI molecules in living cells remains underdeveloped. [Objective] We explored the dynamics of PprI at the single-molecule level before and after DNA damage and revealed the role of PprI in DNA repair, aiming to enhance our understanding of the DNA repair mechanism in D.radiodurans. [Methods] The PprI molecules of D.radiodurans were labeled with the photo-activated fluorescent protein mMaple3. The low-density mMaple3 fluorescent protein was continuously activated by single-particle tracking photoactivated localization microscopy (sptPALM) based on total internal reflection fluorescent (TIRF) microimaging to realize the single-molecule localization and tracking of PprI in living cells, on the basis of which the molecular dynamics of PprI molecules before and after DNA damage was clarified. [Results] By analyzing the distribution of the apparent diffusion coefficients of PprI molecules, we identified three distinct species: immobile molecules (D^*=0.07 μm²/s), slow-diffusing molecules (D^*=0.21 μm²/s), and fast-diffusing molecules (D^*=0.65 μm²/s). After DNA damage, we observed a significant increase in the proportion of diffusing PprI molecules and a significant decrease in the proportion of immobile molecules. [Conclusion] Using the single-molecule tracking technique, we accurately characterized the movement of PprI molecules, finding that most PprI molecules moved fast after DNA damage. Additionally, DNA damage at the surface released a large proportion of immobile PprI molecules. This study improves the molecular mechanism model of the PprI-mediated DNA repair system and paves a way for studying other DNA repair reactions using single-molecule techniques.

[Background] The plasmid-encoded protein pORF5 is a pivotal virulence factor of Chlamydia trachomatis (Ct), capable of inhibiting oxidative stress and apoptosis. [Objective] To investigate whether pORF5 up-regulates the expression of DJ-1 protein to activate the nuclear factor erythroid 2-related factor 2 (Nrf2)/NAD(P) H: quinone oxidoreductase 1 (NQO1) pathway in the regulation of lipopolysaccharide (LPS)-induced cellular oxidative stress and apoptosis. [Methods] HeLa cells were treated with different concentrations of pORF5 for different time periods. Western blotting was employed to determine the expression level of DJ-1. The reactive oxygen species (ROS) assay kit and flow cytometry were employed to examine the effects of pORF5 on LPS-induced oxidative stress and apoptosis. The expression of DJ-1 protein in HeLa cells was down-regulated by siRNA-DJ-1, and the cellular ROS fluorescence intensity was observed under a fluorescence microscope. Corresponding assay kits were used to measure the levels of superoxide dismutase (SOD) and malondialdehyde (MDA) in each group. After pretreatment with the Nrf2 inhibitor ML385 for 1 h, HeLa cells were stimulated with pORF5 alone or combined with LPS, and the expression levels of the apoptosis-related proteins B-cell lymphoma-2 (Bcl-2) and Bcl-2-associated X protein (Bax) were determined. Western blotting was employed to evaluate the effect of down-regulating the expression of DJ-1 on the Nrf2/NQO1 pathway. [Results] pORF5 up-regulated the expression of DJ-1, and the up-regulatory effect was the strongest after treatment with 10 μg/mL pORF5 for 18 h. pORF5 reduced LPS-induced ROS fluorescence intensity and cell apoptosis rate (P<0.001). The si-DJ-1 group showed increased ROS fluorescence intensity and MDA content but decreased SOD activity (P<0.001). ML385 inhibited pORF5-induced expression of Nrf2 and NQO1 (P<0.001), up-regulated the expression of the pro-apoptotic protein Bax (P<0.05), down-regulated the expression of the anti-apoptotic protein Bcl-2 (P<0.01). The expression of Nrf2 and NQO1 was down-regulated in the si-DJ-1 group (P<0.001, P<0.01). [Conclusion] pORF5 can up-regulate the expression of DJ-1 protein to activate the Nrf2/NQO1 pathway, thereby inhibiting LPS-induced oxidative stress and apoptosis.

[Background] In the context of sustainable agricultural development, complex microbial agents have emerged as a potent means for enhancing plant growth, attributed to the synergistic effects of diverse microorganisms. [Objective] To investigate the rhizosphere complex microbial agent of Dicranopteris dichotoma regarding the effects on the growth and rhizosphere microbial community structure of mung bean seedlings. [Methods] Four plant growth-promoting strains isolated from the rhizosphere soil of D.dichotoma were used to formulate two complex microbial agents: BBF and BFF. The agents were inoculated into the rhizosphere of mung bean seedlings, and the physiological parameters and soil physicochemical characteristics of the mung bean seedlings were evaluated after 36 days of cultivation. The community structure and diversity of rhizosphere microorganisms were assessed by 16S rRNA gene and ITS amplicon sequencing. [Results] BFF increased the plant height, aboveground fresh and dry weights, and underground dry weight of mung bean seedlings by 29.38%, 81.47%, 175.73%, and 936.49%, respectively. BBF increased the aboveground fresh weight and dry weight of mung bean seedlings by 92.64% and 179.67%, respectively. High-throughput sequencing results revealed that both BFF and BBF significantly boosted the bacterial diversity and richness, while reducing the fungal diversity. At the phylum level, the two agents increased the relative abundance of Myxococcota while decreasing that of Zygomycota. At the bacterial genus level, the two agents decreased the relative abundance of Rhodanobacter while increasing that of Mucilaginibacter and Bradyrhizobium; at the fungal genus level, the two agents increased the relative abundance of Cryptococcus while decreasing that of Mortierella and Gliocladiopsis. Functional prediction indicated that the application of complex microbial agents notably enhanced bacterial nitrogen fixation in the rhizosphere, increased the relative abundance of pathogenic-saprophytic-symbiotic fungi, and decreased the relative abundance of saprophytic and saprophytic-symbiotic fungi. [Conclusion] Inoculating complex microbial agents increases soil nutrients, regulates rhizosphere microbial community structure and diversity, boosts beneficial bacterial count, and suppresses pathogen presence, thus creating a favorable environment for the root growth and promoting the growth and development of mung bean seedlings. These findings offer new theoretical support for the growth of mung bean seedlings and establish a basis for applying complex microbial agents in agricultural production.

[Background] The distribution of endophytic fungi in plants is affected by environmental changes and growth stages. Investigating the shifts in these fungal communities and understanding their interactions during plant growth and storage enhances our ability to harness the positive effects of fungi on plants. [Objective] To investigate the characteristics and variations of endophytic fungal communities in Psidium guajava fruits during different developmental stages, and provide a scientific basis for the in-depth research and utilization of endophytic fungal resources of this plant and the post-harvest control of diseases. [Methods] High-throughput sequencing of ITS was employed to compare the composition of endophytic fungal communities in P.guajava fruits during different developmental stages. [Results] A total of 1 582 892 high-quality endophytic fungal sequences were obtained, involving 566 OTUs belonging to 281 genera, 161 families, 70 orders, 26 classes of 7 phyla. The diversity and abundance of endophytic fungi in P.guajava fruits increased over time before fruit ripening and then decreased as fruit continued to ripen and decay. Ascomycota was the dominant phylum, with the relative abundance being 99.34%, 96.35%, 91.63%, 65.22%, and 100.00% at the flowering, young fruit, fruit expansion, fruit ripening, and fruit decay stages, respectively. The relative abundance of dominant genera was in a descending order of Neopestalotiopsis (39.34%), Colletotrichum (26.54%), and Cladosporium (18.58%). The dominant genera varied among different developmental stages, with Gibberella, Cladosporium, Neopestalotiopsis, and Didymella being dominant at the flowering, young fruit, fruit expansion, and fruit ripening stages, respectively, and Neopestalotiopsis (49.76%) and Colletotrichum (50.00%) being dominant at the decay stage. The topological characteristics of the endophytic fungal network were influenced by different developmental stages. The strongest interaction occurred at the fruit expansion stage and the weakest at the flowering stage. The reciprocal relationship between species was stronger than the competitive one. [Conclusion] P.guajava fruits contained a rich endophytic fungal community, whose composition and interactions varied considerably at different developmental stages. The findings provide reference for the excavation of fungal resources in P.guajava fruits.

[Background] Phosphorus is one of the essential nutrients for crop growth, and phosphorus deficiency in soil can reduce the yields of crops such as maize. Phosphate-solubilizing bacteria can convert insoluble inorganic or organic phosphorus in the soil into soluble phosphorus, which is easily absorbed by crops. This process helps improve soil quality and subsequently promote crop growth. [Objective] To isolate and identify efficient phosphate-solubilizing bacteria from the black soil in northeast China, enhance soil quality, and promote maize growth, providing elite microbial strains for the development of microbial inoculants suited to the black soil environment in northeast China. [Methods] The culture method was employed to isolate microbial strains, and then the phosphate-solubilizing ability and indole-3-acetic acid secretion ability of the isolates screened out were characterized. The effects of phosphate-solubilizing bacteria on soil quality were studied based on the physicochemical properties of soil. Furthermore, pot experiments were carried out to study the effects of the strains on maize growth. [Results] A total of 16 phosphate-solubilizing bacterial strains were isolated from the black soil in northeast China. Among them, Staphylococcus sp. GL-HT-43 and Enterobacter sp. W-H-13 were applied to the black soil planted with maize, which significantly increased maize plant height, biomass, and chlorophyll content. Additionally, the two strains notably increased the levels of inorganic carbon, organic carbon, organic matter, and total phosphorus in the black soil. These results suggested that GL-HT-43 and W-H-13 had advantages in reducing fertilizer dependency, promoting maize growth, and enhancing the fertility of black soil. [Conclusion] The efficient phosphate-solubilizing bacterial strains GL-HT-43 and W-H-13 promote maize growth and improve the quality of black soil. These strains demonstrate great potential for the development of phosphate-solubilizing microbial inoculants.

[Background] Multifaceted factors contribute to the occurrence of root rot, posing challenges to the management of the disease. Bacterial consortia characterized by robust functionality and structural integrity emerge as viable candidates for the sustainable management of root rot. [Objective] To optimize the proportions of strains in the bacterial consortium and elucidate its disease-preventing and plant growth-promoting effects, thus establishing a foundation of the large-scale application of the bacterial consortium in agricultural practice. [Methods] We employed orthogonal design to optimize the structure of the bacterial consortium that had been obtained. The Topsis comprehensive analysis was conducted to evaluate the inhibitory effects on pathogens and the phosphorus-solubilizing, nitrogen-fixing, and potassium-solubilizing capabilities of each treatment, on the basis of which the optimal composition of the bacterial consortium was obtained. Furthermore, indoor pot experiments and field trials were conducted to assess the performance of the optimized consortium in preventing root rot and promoting plant growth, and the changes in nutrient content of rhizosphere soil were measured. [Results] The optimal bacterial consortium, designated as ‘Tuweiwei No. 4’ (SYP006:SYP033:SYP092:SYP202:SYP400=4:2:3:1:4), demonstrated significant control effect on root rot in Solanum lycopersicum and Capsicum annuum, with inhibition rates of 48.9% and 60.9%, respectively. Additionally, greenhouse pot experiments revealed that the plant height, stem diameter, and fresh weight of S.lycopersicum and C.annuum plants treated with the bacterial consortium increased (P<0.05). Meanwhile, the treatment with the bacterial consortium reduced the pH and salt content and increased the available nitrogen, available phosphorus, and available potassium in rhizosphere soil. Moreover, the treatment increased bacteria and actinomycetes and decreased fungi in the rhizosphere soil. The application of the consortium in the field exhibited the control efficacy of 47.94% on root rot and increased the yield of C.annuum by 7.65%. In the cultivation of Lilium davidii var. unicolor, the consortium achieved the control efficacy of 63.43% and increased the plant height (P<0.05). In the cultivation of Lycium barbarum, the consortium inhibited root rot with the efficacy of 56.11% and increased the yield by 119.99%. The optimal dose for application in the field was 10 L/667 m². [Conclusion] The bacterial consortium ‘Tuweiwei No. 4’ exhibited good performance in controlling root rot, promoting crop growth, improving soil nutrient content, and regulating soil microecology.

[Background] Increasing the straw degradation efficiency is a key path to improve soil quality and curbing soil degradation. [Objective] To screen out the strains with strong degradation effect on straw, optimize the culture conditions and mine the functional genes of the strain. [Methods] Soil samples were collected from a low-temperature and arid area in northern China. The hydrolysis circle assay, cell density assay, and enzyme activity measurement were employed to screen the isolates and characterize the strain screened out. Field degradation experiments were carried out, and functional genes of the strain were mined by whole genome sequencing. [Results] Bacillus stercoris HS6-2 with strong stress tolerance was isolated. In the field, this strain showed the straw degradation rates of 55.74% and 84.77% after rooting for 30 and 180 days, respectively, which were 25.2% and 11.99% higher than those in the control. Under the optimized conditions, the strain showed the endo-cellulase, exo-cellulase, and filter paper enzyme activities of 3.63, 12.27, and 3.48 U/mL, respectively. The results of whole genome sequencing showed that the CAZy family members were encoded by 189 genes, including 71 glycoside hydrolases, some of which were involved in lignocellulose degradation. [Conclusion] HS6-2 as a mildly halophilic and basophilic strain with tolerance to drought and low temperatures demonstrates good application potential in straw degradation, which provides technical support for the research and development of microbial agents serving straw returning.

[Background] Continuous cropping is a common phenomenon in agricultural production. Continuous cropping causes an imbalance of micronutrients and disturbs the microbial community structure in the rhizosphere soil of plants. Accordingly, plants are susceptible to pests and diseases. [Objective] To expose the variation trends and drivers of distinct biological communities in the rhizosphere soil of Panax notoginseng during continuous cropping and the occurrence of root rot. [Methods] We compared the bacterial, fungal, and protist communities in the rhizosphere soil samples of healthy and diseased P.notoginseng growing for different years and the relationships between soil microbial communities with soil factors. [Results] The soil samples presented pH<7.0, with the content of cadmium (Cd) and arsenic (As) exceeding the standard limits. Cadmium was significantly enriched in the soil samples of 3-year-old P.notoginseng. The results of α-diversity analysis showed that the disease of 2-year-old P.notoginseng significantly reduced the diversity of bacteria and fungi, and the disease of 1- and 3-year-old P.notoginseng significantly reduced the diversity of protist. The principal coordinate analysis showed that the β-diversity of bacterial, fungal, and protist communities in the rhizosphere soil of P.notoginseng exhibited significant differences before and after the infection with root rot, with the fungal community showing the most apparent differences. In the protist community, consumers were richer than parasites and phototrophs in the soil samples. The analysis of variance showed a considerable decrease in the abundance of consumers in the soil samples of diseased 3-year-old P.notoginseng. The co-occurrence network of fungal pathogens with bacteria and protist showed more interspecific associations between fungal pathogens and protist, with consumers being dominant in the protist community. The correlation analysis showed that available potassium had larger effects on bacteria and fungi. Cd, had more significant effects than As on the bacterial, fungal, and protist communities. [Conclusion] The differences in bacterial, fungal, and protist communities in rhizosphere soil and the interactions between microorganisms and physicochemical properties of soil result in the occurrence of root rot in the field with continuous cropping of P.notoginseng.

[Background] Endophytic microorganisms in the roots can promote the seedling growth and improve the environmental adaptability of orchids. [Objective] To reveal the structures of endophytic microbial communities in three medicinal orchids (Coelogyne occultata, Arundina graminifolia, and Gymnadenia conopsea) and screen out functional strains. [Methods] Illumina MiSeq high-throughput sequencing was employed to analyze the structures of endophytic microbial communities in the roots of the three orchids. Conventional methods were adopted to isolate the endophytic bacteria and fungi from the roots, and the functional microorganisms were screened. [Results] The endophytic microbial communities of C.occultata and A.graminifolia clustered into one group at the genus level. In C.occultata, A.graminifolia, and G.conopsea, the dominant endophytic bacterial genera were Mycobacterium (Coe: 70.65%), Burkholderia-Caballeronia-Paraburkholderia (Aru: 26.35%), and Gordonia (Gym: 6.65%), respectively; the dominant endophytic fungal genera were Fusarium (Coe: 21.07%), unclassified Helotiales (Aru: 46.74%), and Morchella (Gym: 91.21%), respectively. Bacterial isolates Pseudomonas nunensis Coeb11, Rahnella sikkimica Coeb32, and Rouxiella silvae Coeb22 had the functions of dissolving phosphorus, fixing nitrogen, and secreting indole-3-acetic acid. The hyphae of the fungal isolate Cladophilophora chaetospira Aruf26 could colonize the cells of Dendrobium officinale as the dark septate endophyte. [Conclusion] This study revealed the structures of endophytic microbial communities in the roots of three medicinal orchids and screened the functional microorganisms. The findings provide a scientific basis for the protection of medicinal orchids, biomimetic cultivation under forests, and development and utilization of functional microorganisms.

[Background] A mangrove forest is a special plant community distributed in the intertidal zone of tropical and sub-tropical regions, where a large number of microorganisms exist in the sediments, serving as potential sources for screening agents for the control of plant diseases. [Objective] To screen fungal strains antagonizing Phytophthora parasitica from the microorganisms isolated from mangrove sediments. [Methods] Fungal strains were isolated from the sediments of Xiamen Wuyuan Bay mangrove wetland and then identified based on the similarity of ITS sequences. The dual culture method was employed to select the Trichoderma strains with high activities of inhibiting P.parasitica. The effects of different fermentation conditions on the sporulation of selected strains were examined. [Results] The fungi isolated from the sediments of Xiamen Wuyuan Bay mangrove wetland belonged to 15 genera of 2 phyla. The inhibitory activities of Trichoderma harzianum M312 and Trichoderma virens M552 against P.parasitica were higher than those of other Trichoderma strains. The two strains (M312 and M552) should be cultured at 25 ℃ and 31 ℃, respectively, pH 7.0, and low salinity for high sporulation. [Conclusion] T. harzianum M312 and T.virens M552 screened from the sediments of Xiamen Wuyuan Bay mangrove wetland could be used as candidate fungi for the biocontrol against tobacco black shank, while the fermentation conditions need to be optimized before commercial application.

[Background] Plant growth-promoting rhizobacteria can accelerate nutrient cycling in the soil and improve the structure of soil microbial communities to enhance soil fertility. [Objective] To reveal the diversity of drought-tolerant actinomycetes in the rhizosphere of maize in Panxi Plateau, China and screen out plant growth-promoting drought-tolerant actinomycetes. [Methods] Drought-tolerant actinomycetes were isolated and screened from the rhizosphere soil of maize in the field with tobacco-maize rotation in Panxi Plateau, China. BOXA1R cluster analysis was performed to assess the diversity of drought-tolerant actinomycetes, and 16S rRNA gene sequencing was employed to determine their phylogenetic positions. The abilities of the isolates to produce ACC deaminase and siderophores, degrade cellulose, solubilize phosphorus, and inhibit pathogens were evaluated. The drought-tolerant strains capable of efficiently promoting plant growth were selected for drought stress experiments on maize seedlings. [Results] A total of 31 strains of drought-tolerant actinomycetes were isolated and identified. BOXA1R cluster analysis revealed that these strains belonged to Streptomyces, Nocardioides, Tsukamurella, Gordonia, and Amycolatopsis, among which Streptomyces was the dominant genus. Among the 31 isolates, 25.80%, 32.25%, 9.68%, and 74.19% could produce siderophores, solubilize phosphorus, degrade cellulose, and produce ACC deaminase, respectively. Strains SICAU-37 and SICAU-70 exhibited inhibitory effects on the pathogenic fungi Magnaporthe oryzae, Phytophthora nicotianae, and Cercospora zeina, with the ratios of the inhibitory zone diameter to the colony diameter being greater than 2 against all the three fungal species. Notably, strains SICAU-37 and SICAU-70 with prominent plant growth-promoting and antifungal properties were selected for drought stress experiments. Upon identification, these two strains were determined to be Tsukamurella tyrosinosolvens and Amycolatopsis dendrobii, respectively. Under drought conditions, SICAU-70 effectively promoted the growth of maize seedlings, increasing the plant height and fresh shoot weight by 9.44% and 33.42%, respectively. [Conclusion] The fields with tobacco-maize rotation in Panxi Plateau harbor diverse and rich plant growth-promoting drought-tolerant actinomycetes, which have application potential.

[Background] Sesame (Sesamum indicum L.) is an important oilseed crop susceptible to the infection by Alternaria alternata, which reduces the yield and subsequently impacts the security and quality of sesame. [Objective] This study investigated the differential metabolites and pathways in the sesame capsules infected by A.alternata, aiming to unveil the effects of this disease on sesame capsules. [Methods] Non-targeted metabolomics and multivariate statistical analysis were employed to analyze the metabolite differences and metabolic pathway changes in sesame capsules after infection by A. alternata. [Results] The metabolomic analysis revealed a total of 247 differential metabolites categorized into 11 classes in the capsule peel and seeds. Compared with the control group, A.alternata infection led to the up-regulation of 126 and 231 metabolites and down-regulation of 27 and 118 metabolites in the peel and seeds, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differential metabolites indicated that A.alternata infection significantly affected the amino acid, carbohydrate, and nucleotide metabolism in the peel and seeds, thereby impacting sesame quality. [Conclusion] A.alternata infection affects the quality of sesame by influencing amino acid and carbohydrate metabolism in the capsule peel and seeds. This study provides clues for revealing the disease mechanism and managing this pathogen, thereby contributing to agricultural sustainability.

[Background] The main cause of food spoilage is the contamination by foodborne pathogens. The antimicrobial peptides (AMPs) produced by lactic acid bacteria can effectively inhibit the growth of foodborne pathogens. [Objective] To isolate and purify the antimicrobial substances produced by Lactiplantibacillus plantarum J50 and carry out genomics analysis. [Methods] The antimicrobial substances were identified by a variety of enzyme treatments, purified by organic solvent extraction, gel filtration chromatography, and semi-preparative high performance liquid chromatography, and characterized by liquid chromatography-mass spectrometry. After artificial synthesis, the stability and minimum inhibitory concentration were measured. Finally, genomic analysis was carried out on the strain. [Results] The antimicrobial substances produced by strain J50 were identified to be AMPs. The purified AMPs were characterized as SGAGY (N→C), with the relative molecular weight of 453.44 Da. They exerted antimicrobial effects at pH≤5.5, demonstrated strong thermostability and ultraviolet irradiation stability and the minimum inhibitory concentration of 0.7–1.6 g/L on Gram-positive and Gram-negative foodborne pathogens. Genomic analysis showed that the SGAGY was a non-ribosomal peptide, and J50 carried the genes involved in the synthesis of plantaricin EF. [Conclusion] Strain J50 can produce at least two AMPs, with a broad antimicrobial spectrum, demonstrating a potential value for application in the food industry.

[Background] The LuxS/autoinducer-2 (AI-2) quorum sensing system regulates bacterial adaptation to environmental changes by secreting signal molecules. Exopolysaccharides (EPS) play a crucial role in protecting cells from external environmental stress and damage. However, the relationship between the LuxS/AI-2 system and EPS production remains unclear. [Objective] To investigate the relationship between AI-2 activity and EPS production in Limosilactobacillus fermentum 2-1 cultured under different conditions. [Methods] The phenol-sulfuric acid method and Vibrio harveyi BB170 bioluminescence assay were employed to determine the EPS yield and AI-2 activity, respectively, of L.fermentum 2-1 cultured under different conditions. [Results] The cell growth of L.fermentum 2-1 was the fastest during the early stages of culture, after which the cell density gradually stabilized. The AI-2 activity peaked at the time point of 7 h and then decreased. The EPS production presented a trend of first rising and then declining, reaching the peak of (204.30±15.98) mg/L at the time point of 16 h, which was significantly higher than that at other time points. Both elevated (44 ℃) and declined (23 ℃, 30 ℃) temperatures inhibited the cell density, AI-2 activity, and EPS production. Acidic conditions favored AI-2 secretion but inhibited cell growth and EPS production. AI-2 activity and EPS production were positively correlated with inoculum size within the range of 1%−3%. Changes of the carbon source altered the cell density, AI-2 activity, and EPS production. Addition of exogenous AI-2 at a final concentration of 100 μmol/L promoted EPS production in L.fermentum 2-1 (P<0.05). [Conclusion] Under certain conditions, there is a positive correlation between AI-2 activity and EPS production in L.fermentum 2-1.

[Background] Pyrazines are closely related to the flavor of Maotai-flavor Baijiu. [Objective] To screen out the Bacillus strains with high yields of pyrazines for Baijiu production and provide a basis for improving the quality of Maotai-flavor Baijiu. [Methods] After primary screening and secondary screening, strain J1 with a high yield of pyrazines was screened out from 50 strains of Bacillus in the brewing process of Maotai-flavor Baijiu. The strain was identified by 16S rRNA gene sequencing. The conditions of pyrazine production by this strain were optimized by single factor and orthogonal experiments. Finally, the fermentation performance of the strain was evaluated by simulated fermentation and in-situ fermentation. [Results] Strain J1 was identified as Bacillus amyloliquefaciens. The optimum fermentation conditions were as follows: inoculum concentration of 10⁷ CFU/mL, Saccharomyces cerevisiae to J1 ratio of 1:100, inoculation of J1 two days after inoculation of S.cerevisiae, and the fermentation temperature raised to 50 ℃. Under these conditions, the content of pyrazines reached 322.48 mg/L. The simulation experiment showed that the strain J1 produced rich pyrazines. The content of pyrazines in the Baijiu obtained by in-situ fermentation was 480.87 mg/L, which was about 10 times that of the control group. [Conclusion] This study can provide a basis for improving the quality of Maotai-flavor Baijiu.

[Background] Enterococcus casseliflavus is an opportunistic pathogenic bacterium with wide distribution in the nature, while there are few studies about this bacterium in forest musk deer. [Objective] We isolated, identified, and sequenced a strain of E.casseliflavus from the liver of a death forest musk deer, aiming to lay a foundation for the prevention and treatment of related diseases in forest musk deer. [Methods] Biochemical tests, drug susceptibility tests, 16S rRNA gene analysis, and bacterial load tests were conducted for the isolate. The results of whole genome sequencing were used to annotate gene functions and analyze genetic evolution. [Results] The isolated strain was identified based on 16S rRNA gene analysis and average nucleotide identity as E.casseliflavus, which was consistent with the results of biochemical tests. The strain was named Dec0527. The strain was resistant to cephalexin, aztreonam, amikacin, and tobramycin, and it was sensitive to doxycycline, tetracycline, chloramphenicol, sulfamethoxazole trimethoprim, some β-lactams, aminoglycosides, and quinolones. The bacterial load test results showed that the invasiveness of strain Dec0527 to the liver was significantly higher than that to the heart, lung, spleen, and kidney. The genome length of this strain was 3 345 060 bp, with the G+C content of 42.55%. Strain Dec0527 carried a variety of virulence genes such as ebpC, tufA, groEL, cpsA, cap8E, and psaA, as well as the genes for resistance to vancomycin and ciprofloxacin. The resistance genes of strain Dec0527 against aminoglycosides, macrolides, and β-lactams were not completely consistent with the drug resistance. In addition, the genome of the strain Dec0527 had 2 circular plasmids and a relatively complete phage region. [Conclusion] We isolated a strain of E. casseliflavus from the liver of a dead forest musk deer and sequenced and analyzed the whole genome of this strain, providing a reference for the prevention and control of diseases in forest musk deer.

[Background] Bovine respiratory disease complex (BRDC), a bovine respiratory disease characterized by bronchopneumonia, is caused by interactions of multiple pathogens and factors. The main bacterial pathogens causing BRDC include Mannheimia haemolytica (Mh), Pasteurella multocida (Pm), and Histophilus somni (Hs). [Objective] To understand the distribution and serotypes of Mh and Pm associated with BRDC in China. [Methods] We employed PCR to detect Mh and Pm in 698 samples (359 nasal swabs, 321 tracheal swabs, and 18 lung tissue samples) collected from 698 cattle across 54 farms in 16 provincial-level administrative regions including Henan, Hunan, Hubei, Zhejiang, Anhui, Shandong, Ningxia, Gansu, Guizhou, Heilongjiang, and Inner Mongolia from July 2022 to January 2024. Bacterial isolation and serotyping were performed on the positive samples. [Results] The positive detection rates of Mh and Pm in the samples were 2.15% (15/698, 95% CI: 1.2%–3.5%) and 10.32% (72/698, 95% CI: 8.2%–12.8%), respectively. Co-infection was detected in 5 (0.72%, 95% CI: 0.2%–1.7%) samples. From the positive samples, 8 strains (1 of serotype A1, 3 of serotype A2, and 4 of serotype A6) of Mh and 21 strains (17 of serotype A:L3 and 4 of serotype A:L6) of Pm were isolated. The multi-locus sequence typing (MLST) results for Mh showed that 5 out of 8 strains were of sequence type (ST) 1 (serotypes A1 and A6), and 3 strains were of ST2 (serotype A2). The 21 strains of Pm included 17 strains of ST1 (serotype A:L3) and 4 strains of ST7 (serotype A:L6). [Conclusion] This study isolated and identified the main bacterial pathogens causing BRDC in cattle with respiratory symptoms in specific regions and revealed the prevalent serotypes, virulence genes, and resistance genes. These findings lay a foundation for the development of related vaccines and offer theoretical support for the prevention and control of BRDC.

[Background] Bovine respiratory syndrome seriously affects the health of cattle and has a serious impact on the breeding industry. Mannheimia haemolytica, as the main pathogenic bacteria of bovine respiratory tract, often causes bovine respiratory disease (BRD) when the immunity of cattle is low. At present, Mannheimia haemolytica is mostly controlled by vaccine. [Objective] To analyze the bioinformatics function and immunogenicity of ChaN protein and lay a foundation for the development of subunit vaccines. [Methods] NCBI BLAST was used to screen the potential antigens of Mannheimia haemolytica, and online tools such as Expasy ProtParam, Expasy Protscale, and TMHMM-2.0 were used to analyze their antigenic characteristics. RT-qPCR was conducted to determine the mRNA level of ChaN in M.haemolytica cultured for different time periods. The recombinant ChaN (rChaN) was obtained by prokaryotic expression, and the reactivity of rChaN was examined by Western blotting with the M.haemolytica- positive bovine serum. Mice were vaccinated with different doses of rChaN emulsified with white oil as the adjuvant, and the immunogenicity of rChaN was evaluated. Indirect ELISA was employed to measure the antibody titer. Seven days after the third vaccination, mice were subjected to intraperitoneal injection of the pathogen strain Mh95, and the protective effect of rChaN was tested. [Results] ChaN was a hydrophilic soluble protein with no transmembrane domain, an open reading frame, 16 epitopes, and 23 B cell epitopes. The mRNA level of ChaN was the highest in the logarithmic phase, moderate in the stationary phase and lag phase, and the lowest in the decline phase, showing differences in the four phases (P<0.001). ChaN reacted with the M.haemolytica-positive bovine serum. After immunization with 40 μg ChaN+white oil, the IgG level kept rising. IgG subtyping results showed that ChaN mainly caused the body to produce IgG1 and IgG2b. After mice were injected intraperitoneally with Mh95 strain on day 7 after the third immunization, the survival rate of mice in the 40 μg ChaN+white oil group was 90%, which was higher than those in the commercial vaccine, blank control, PBS, and white oil groups. The survival rates of mice in the blank control, PBS, and white oil groups were less than 20% within 7 days. [Conclusion] ChaN has good reactogenicity and immunogenicity and thus can be used as a potential immunogenic protein of M.haemolytica for subsequent research. The results provide a scientific basis for developing subunit vaccines against M.haemolytica.

[Background] Hyperuricemia is a purine metabolism disorder caused by an imbalance between uric acid production and excretion. The gut microbiota plays a significant role in purine metabolism, degrading approximately one-third of uric acid. Accordingly, gut probiotics have garnered wide attention for their potential of lowering uric acid levels and alleviating hyperuricemia. [Objective] To isolate human-derived uric acid-degrading bacteria and identify the genes and functions potentially involved in uric acid degradation. [Methods] After in vitro enrichment and acclimatization with uric acid, a strain capable of degrading uric acid was isolated from the feces of healthy individuals with normal low uric acid levels. Morphological observation, biochemical tests, 16S rRNA gene sequencing, bioinformatics analysis, and identification were then carried out for this strain. In addition, whole-genome sequencing and functional gene mining were performed. [Results] A Gram-positive bacterium (M2a) with a high uric acid degradation rate of 82.73% was isolated and identified as Lacticaseibacillus paracasei. Whole-genome sequencing revealed that M2a carried nine genes associated with uric acid degradation. [Conclusion] M2a can efficiently degrade uric acid, providing a scientific basis and bacterial resource for the future development and utilization of microbial preparations for treating uric acid-related disorders.

[Background] Previous transcriptomics studies suggested that the RNA polymerase sigma factor (sigW) and the anti-sigma factor W (rsiW) might be involved in the manganese stress response of Bacillus safensis. [Objective] To investigate the effects of sigW and rsiW deletion on the motility, biofilm formation, and manganese-oxidizing ability of B.safensis ST7. [Methods] We employed homologous recombination to construct the sigW- and rsiW-deleted mutant strains of B.safensis ST7. Furthermore, we compared the motility, biofilm formation, manganese oxidation, and expression of flagellum formation-related genes between the wild type and the mutant strains. [Results] The deletion of sigW and rsiW had no significant effect on the growth of ST7 cultured without manganese stress, whereas it retarded the growth of ST7 under manganese stress. Compared with the wild type, ∆sigW showed reduced motility and manganese-oxidizing ability and enhanced biofilm formation, while ∆rsiW showed reduced motility and enhanced biofilm formation and manganese-oxidizing ability. In addition, the expression levels of genes (flim, flgd and flii) related to flagellum formation were downregulated in ∆sigW and ∆rsiW. [Conclusion] sigW and rsiW can promote the flagellum formation, motility, and growth and co-regulate the manganese-oxidizing ability of B.safensis.

Under the guidance of the student-centered, outcome-based, and constant improvement philosophy of professional accreditation of engineering education, we carried out the multiple blended teaching reform of Environmental Engineering Microbiology, which involved blended teaching, flipped classroom, teaching with practice cases and research cases, and supplementation with hot research topics. With the teaching objective achievement degree as the indicator, the overall achievement degrees of teaching objectives and individual students were assessed. Then, the indicators such as the final examination score, the MOOC examination score, and students’ ability to solve problems were analyzed. A questionnaire survey was conducted at the end of the course teaching to evaluate the teaching effect. The results showed that the teaching objectives and the indicators corresponding to teaching objectives, such as final examination score and students’ ability, increased as the teaching reform was deepening, which indicated the teaching reform achieved expected effects. The application of MOOC and flipped classroom influenced the teaching effect obviously. In the future, efforts should be made to improve students’ ability of knowledge application and integrate theoretical courses with experimental courses.

The undergraduates majoring in biological sciences (teacher training) possess both specialized and systematic microbiological knowledge and the dual identity of current students and future teachers. In view of the needs for enhancing microbial literacy in the society, we practiced project-based teaching of Microbiology with microbial science activities as a carrier. The results showed that this new teaching approach improved the knowledge understanding of students, teaching performance, personal value shaping, and social responsibility implementation. Moreover, the results of this project can provide new ideas for science popularization in the public.

Fungi are largely associated with human life. As an important branch of life sciences, Mycology should be of the same importance as Zoology and Botany that study animal and plants, respectively, in the liberal arts education in colleges and universities. However, it is often neglected, and general courses related to Mycology have not been well developed in most colleges and universities in China. As a result, the public and the government managers have lacked basic understanding about this group of organisms for a long time. Accordingly, the potential utilization of fungi in the national economy and development has not been fully explored, and the importance of fungi in biodiversity conservation and environment protection has also not been fully presented in China. This study discussed the teaching contents, approaches, and effectiveness concerning the general course development of Mycology, based on the practical experience in Yangzhou University, Zhejiang University, and Jilin Agricultural University, aiming to promote and popularize Mycology as a general course in the liberal arts education system in colleges and universities.