Abstract:[Background] D(−)-tartaric acid is a non-natural organic acid, which has great application potential in health care products, food, and tumor drug synthesis. At present, D(-)-tartaric acid is produced from cis-epoxysuccinic acid (ESH) hydrolyzed by cis-epoxysuccinic acid hydrolase[CESH(D)] through biotransformation. This method is simple and mild but has bottleneck problems such as low enzyme conversion efficiency of CESH(D). [Objective] To improve the enzyme activity, temperature, and pH stability of CESH(D) through genetic engineering. [Methods]Directional evolution and semi-rational design were used to modify CESH(D) in vitro to screen out forward mutants with high throughput. Then the enzymatic properties were studied, including the enzyme activity, the influence of temperature and pH on the catalytic efficiency of the enzyme, the temperature and pH stability of the enzyme, and enzymatic kinetics analysis. Finally, the primary mechanism of mutation sites affecting catalytic activity was analyzed using molecular docking. [Results] Four positive mutants L231P/N226S, V77I, D183E, and T223S were screened out. The specific enzyme activity of the four mutants was increased by 2.2, 1.6, 1.5, and 1.4 folds of the wild-type enzyme, respectively. The temperature stability and pH stability of L231P/N226S mutant were significantly higher as compared with the wild-type CESH(D), and its catalytic activity was 1.6 folds at 55℃, and 1.2 folds at pH 6.0 as compared with the wild-type enzyme, respectively. Kinetic analysis showed that the affinity of L231P/N226S mutant and T223S mutant to ESH substrates was significantly increased, with K_m values of 20 mmol/L and 21 mmol/L, respectively, which were 18% and 16% lower than that of the wild-type enzyme, respectively. Finally, the results of molecular docking showed that the mutated site promoted the interaction between enzyme and substrate mainly by changing the substrate binding pocket, thus affecting enzyme activity. [Conclusion] Through experiments, CESH(D) mutants with good temperature and pH stability and significantly improved catalytic activity were obtained. The mechanism of mutation site affecting enzyme activity is preliminarily analyzed in this research, which lays a foundation to study the relationship between the structure and function of CESH(D) and its further improvement.

Abstract:[Background] Coral reef ecosystem is extremely important in the marine ecosystem, in which the actinomycetes are the important line of defense against various pathogens. Therefore, coral-associated actinomycetes are important resources for molecules with antibacterial activity, indicating tremendous medicinal potential.[Objective] To isolate the culturable actinomycetes from samples of Xisha stone corals and screen out the strains with good antibacterial activity. [Methods] Coral-associated actinomycetes were isolated by dilution separation method and identified by phylogenetic analysis of 16S rRNA gene sequence. The antibacterial activity test was conducted by the plate confrontation method, and the target strain was identified. The salinity tolerance test was carried out by plating the strain on ISP2 solid medium with different concentrations of NaCl, and the thermostability and photostability of the fermentation products were tested by the plate confrontation method. The genome of the target active actinomycete was sequenced by Nanopore and Illumina sequencing, and the types of biosynthetic gene clusters of secondary metabolites were analyzed online by antiSMASH. [Results] A total of 104 culturable actinomycetes were isolated from 6 samples of Xisha stone corals, and 27 actinomycetes were obtained after removing duplicates according to colony morphology and sample source. The 16S rRNA gene sequencing of the 27 strains was performed, and they were identified as Salinispora (25 strains), Streptomyces (1 strain), and Gordonia (1 strain) according to sequence alignment and phylogenetic tree analysis. The results of activity screening showed that Salinispora sp. SH098 had the optimal antibacterial activity during the antibacterial activity test. Salinispora sp. SH098 did not grow in the salt-free medium and its salt-tolerant range was 2%-5%. Its fermentation products showed good thermostability and photostability. The whole genome sequence analysis showed that 21.93% of the gene sequences of strain SH098 were related to the biosynthesis of secondary metabolites. The structure types of predicted metabolites were diverse, which needed to be further explored. [Conclusion] This is the first report on Salinispora spp. with anti-agricultural pathogenic bacteria activity from Xisha stone corals in China, which enriches the obligate marine actinomycetes resources from the Xisha islands of China. It provides new resources for the development of new microecological agents applied to mariculture and also lays a foundation for mining antibacterial active substances.

Abstract:[Background] 4-hydroxybenzoic acid and its esters are precursors for various aromatic compounds. They are, however, difficult to be decomposed in the nature, causing environmental pollution. These pollutants migrate to the ocean along with ocean current, damaging the marine ecological environment.[Objective] To screen a 4-hydroxybenzoic acid esters-degrading strain from the marine environment, predict the metabolic pathways of 4-hydroxybenzoic acid esters by whole-genome sequencing and annotation analysis, and analyze the key enzymes in the pathways and the functions of the enzymes. [Methods] We isolated the 4-hydroxybenzoic acid esters-degrading strain through enrichment culture. We used gene cloning technology to express the genes encoding key enzymes in the metabolic pathways of 4-hydroxybenzoic acid esters in Escherichia coli and explored the activities and enzymological characteristics of the recombinant proteins. [Results] A strain (B1 strain) was screened out from the seabed sediment and identified as Citricoccus nitrophenolicus by 16S rRNA sequencing. B1 can grow with diverse 4-hydroxybenzoic acid esters, and the growth status was the best when methyl ester was the only carbon source. Genes encoding carboxylesterase and monooxygenase were successfully expressed in E. coli. The optimal reaction conditions of recombinant carboxylesterase were pH 8.0 and 30℃ (30 min). The activity of recombinant monooxygenase depended on coenzyme, and Mg²⁺, Mn²⁺, Zn²⁺, and Fe³⁺ can enhance the activity of monooxygenase. As further identified by fluorescent quantitative PCR, z13175 and z09075 were genes encoding carboxylesterase. In the absence of oxygen, B1 strain carried out anaerobic respiration and reduced nitrate to nitrite.[Conclusion] Carboxylesterase and monooxygenase are key enzymes in the conversion of 4-hydroxybenzoic acid esters to protocatechuic acid, which play an important role in the biodegradation of the esters.

Abstract:[Background] Mn(Ⅱ)-oxidizing bacteria can precipitate and oxidize Mn(Ⅱ) to form solid manganese oxides, which have attracted much attention in the field of biogeochemistry and environmental remediation. However, most of the studied Mn(Ⅱ)-oxidizing model strains originated from the ocean, and fewer Mn(Ⅱ) oxidizing bacteria from soil sources were involved. [Objective]To enrich the available source of soil-derived Mn(Ⅱ) oxidizing bacteria, and also provide a new strain for the potential application of bixbyite-type Mn₂O₃.[Methods] In this study, Pseudomonas aeruginosa L3, was isolated from a ceased smelting industrial park at Zhuzhou, Hunan Province, and a systemic assay was conducted on its isolation and purification, identification, growth curves, pH alteration, Mn(Ⅱ) oxidation, and structure of manganese oxide. [Results] The cell suspension, the supernatant after centrifugation, and the pyocyanin extracted from the cell suspension all exhibited the ability to oxidize Mn(Ⅱ). In particular, the supernatant showed a stronger ability for Mn(Ⅱ) oxidation than the cell suspension. The X-ray diffraction (XRD) spectrum was further used to record the crystalline phase of manganese oxide produced by P. aeruginosa L3. The result showed that the manganese oxide had two characteristic peaks at 2θ=32.951° and 55.189°, indicating that its crystalline structure was the poorly-crystalline bixbyite-type Mn₂O₃.[Conclusion] P. aeruginosa L3 has a high Mn(Ⅱ) tolerance and oxidation ability, and the supernatant has a higher Mn(Ⅱ) oxidation ability than the cell suspension. Its Mn(Ⅱ) oxidation process may be associated with pyocyanin, and the Mn oxides are similar to poorly-crystalline bixbyite-type Mn₂O₃.

Abstract:[Background] The sodium in albite poses a challenge to mineral processing and utilization. [Objective] To screen an efficient albite-decomposing strain and to remove the sodium in albite. [Methods] With albite as the sole sodium source, a stable strain with strong decomposition ability was screened from the soil of salt lake in Inner Mongolia. Then, it was identified based on morphological observation, physiological and biochemical characteristics, and 16S rRNA gene sequencing. The phylogenetic tree was constructed and the growth curve was plotted. Moreover, the influence of culture conditions of the growth of the strain was investigated. [Results] An efficient albite-decomposing strain was screened out and identified as Acinetobacter johnsonⅡ, with the logarithmic phase of the 3rd−11th hours. The optimal culture conditions are as follows:initial pH 9.0, temperature of 25℃, 2% salt, shaker speed at 150 r/min, inoculum of 5%, liquid volume of 100 mL/250 mL, beef extract as the sole carbon source, and peptone as the sole nitrogen source. [Conclusion] It is reported for the first time that A. johnsonⅡ has the ability to decompose albite, which provides a strain for biological removal of sodium.

Abstract:[Background] In the treatment of wastewater containing nitrate, common microorganisms cannot efficiently remove nitrate while having a high removal rate for total nitrogen, which results in the use of multiple bacteria or complex processes.[Objective] To efficiently and safely remove nitrate nitrogen and total nitrogen from water. [Methods] An efficient aerobic denitrifying bacterium was isolated from activated sludge and sequenced for the 16S rRNA gene. The response surface methodology was employed to optimize the factors affecting nitrogen removal. Further, the denitrification capacity and characteristics of the strain for nitrate-containing wastewater were studied. [Results] An efficient aerobic denitrifying bacterium SY-D-22 was isolated from activated sludge and identified as Staphylococcus. The best denitrification efficiency of the strain was achieved under pH 8.18, C/N ratio of 13.39, 31.43℃, and 130 r/min. With sodium citrate as the sole carbon source, strain SY-D-22 rapidly removed nitrogen under aerobic conditions, demonstrating the nitrate nitrogen (100 mg/L) removal rate up to 100% and the total nitrogen removal rate of 95.34%. [Conclusion] Staphylococcus SY-D-22 was isolated from the activated sludge. After the denitrification conditions were optimized by response surface methodology, the removal rates of the strain for nitrate nitrogen and total nitrogen was up to 100.00% and 95.34%, respectively. This strain is capable of removing nitrate nitrogen and nitrite nitrogen.

Abstract:[Background] The associated bacteria have complex interactions with cyanobacteria.[Objective] To study the effect of associated bacteria on the growth of freshwater Synechococcus. [Methods] The diversity of the bacteria associated with Synechococcus was analyzed by high-throughput sequencing. The associated bacteria were isolated by plate streaking and identified based on morphological characteristics and 16S rRNA gene sequence. The impact of associated bacteria on the growth of Synechococcus FACHB-7942 was analyzed by determining the concentration of chlorophyll-a by co-culturing Synechococcus and their associated bacteria of different concentrations. Rice seed germination test was carried out to verify the growth-promoting function of the associated bacteria. [Results] The dominant genera of the associated bacteria of freshwater Synechococcus were Porphyrobacter, Rhizobium, Aquimonas, and Mesorhizobium. Two associated bacterial strains, JQ1 and JQ2, were isolated and identified as species of Rhizobium and Peribacillus, respectively. Through co-cultivation Synechococcus with different concentrations of associated bacteria and rice seed germination test, it was confirmed that JQ1 and JQ2 exerted growth-promoting effect when the ratios of bacteria to cyanobacteria were 5:1 and 15:1, respectively. JQ1 significantly improved the germination rate of rice seeds compared with JQ2, and both strains played a role in improving the seedling quality and root development. [Conclusion] The associated bacterial strains JQ1 and JQ2 at appropriate concentrations can significantly promote the growth of Synechococcus, and the application of associated bacteria in rice can improve the germination and promote the growth of rice.

Abstract:[Background] Via oxydehydrogenation of polyvinyl alcohol (PVA), polyvinyl alcohol dehydrogenase (PVADH) plays an important role in the biodegradation of PVA.[Objective] pvadh gene was extracted from the PVA-degrading Bacillus cereus sp. DG01 for the expression of PVADH in Pichia pastoris and specificity of the enzyme for degrading different PVA species was explored. The findings are expected to guide the application of PVADH in PVA degradation.[Methods] The 1 965 bp pvadh as obtained by reverse-transcription PCR amplification. pPIC9K-cpvadh plasmid was constructed for expression in P. pastoris GS115. Methanol was employed to induce the expression of the protein which was then isolated and purified. The enzymatic properties and degradation specificity were investigated. [Results] The activity of crude PVADH solution yielded under optimal fermentation conditions reached 54.55 U/mL. The purified PVADH had the specific activity of 173.42 U/mg, molecular weight of 67.1 kDa, and isoelectric point of 6.06, and the optimum temperature and pH for PVADH were 41 ℃ and pH 7.5, respectively. The half-life of PVADH was more than 4 h at 27-32 ℃ and pH 7.0-8.0, and 1 mmol/L Ca²⁺ can activate the enzyme. K_mvalues of PVADH for the three substrates PVA1799, PVA1788, and PVA2488, were 1.49 mg/mL, 1.17 mg/mL, and 1.21 mg/mL, separately. [Conclusion] Heterogeneous expression in P. pastoris is a simple method to obtain PVADH and the purification features ease of implementation. The yielded PVADH has stable enzymatic properties and high efficiency in degrading the PVA with low alcoholysis degree.

Abstract:[Background] Temperature plays an important role in shaping soil microbial communities at large scales, but there is a paucity of research on large-scale soil microbial diversity in different temperature zones around the globe. [Objective] To clarify the difference in composition and function of large-scale soil microbes among different temperature zones.[Methods] We used metagenomic technology to analyze the composition and function of soil microbial communities in different temperature zones. [Results] The species diversity of bacteria rose with the increase of latitude of temperature zones, and that of fungi was the highest in temperate zone and lowest in cold zone with absolute dominance of Candida. The abundance of species in the microbial communities also varied greatly among the three temperature zones, with different dominant and special genera. Particularly, the abundance of Pseudomonas and Bacillus was significantly different among the three temperature zones and it increased with the rise of the latitude. However, the abundance of Streptomyces, Geodermatophilus, Rubrobacter, and Micromonospora decreased with increase of latitude of temperature zones. In terms of function, it was found that gene functions related to posttranslational modification, protein turnover, chaperones, intracellular trafficking, secretion, vesicular transport, and cell motility may play an important role in cold tolerance of microorganisms. [Conclusion] This study found that soil microorganisms differed significantly in species diversity, community composition, and function among temperature zones and identified bacteria, fungi, and functions significantly affected by changes in temperature zones, contributing to a large-scale study of the geographic patterns of soil microbial diversity and their formation mechanisms.

Abstract:[Background] The extreme habitats of the Qinghai-Tibet Plateau (QTP) harbor rich microbial resources and are important sources of microbial drugs, with abundant microbial resources remaining to be exploited.[Objective] A Streptomyces strain Qhu-G9 isolated from Gobi soil of the QTP was identified by polyphasic taxonomy, and its biosynthesis potential of secondary metabolites was analyzed. [Methods] The taxonomic status of Streptomyces Qhu-G9 was determined by 16S rRNA gene amplification, sequencing, and phylogenetic analysis, combined with polyphasic taxonomy based on genome sequencing and morphological, physiochemical, and cytochemical characteristics. [Results] Qhu-G9 had the highest similarity (99.22%) with the type strains Streptomyces dioscori A217^T and S. auranttⅡacus NBRC 13017^T, which, combined with morphological characteristics, indicated that Qhu-G9 belonged to Streptomyces. However, the phylogenetic tree constructed based on the 16S rRNA gene sequence displayed that Qhu-G9 branched independently. Moreover, the physiochemical and cytochemical characteristics of this strain were quite different from those of the most similar model bacteria. We then employed genome sequencing to evaluate the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between Qhu-G9 and the model bacteria. The dDDH and ANI values were the highest between Qhu-G9 and S. auranttⅡacus NBRC 13017^T, reaching 36.65% and 88.21%, respectively, both of which were lower than those determining a novel species. The results further confirmed that Qhu-G9 was a novel species of Streptomyces and named as S. haixigobicum sp. nov. Qhu-G9. In addition, antiSMASH revealed a large number of gene clusters for the biosynthesis of known and unknown secondary metabolites in the Qhu-G9 genome. [Conclusion] Qhu-G9 isolated from Gobi soil of the QTP is a novel Streptomyces species and has great potential for the production of active secondary metabolites.

Abstract:[Background] Archaea, the pioneer on the surface of carbonatite, promote the chemical weathering of carbonatite and the formation of soil and play an essential part in biogeochemical process of elements. [Objective] To reveal the structure and ecological functions of the archaeal community on the carbonatite surface weathered for different time.[Methods] A total of 18 samples were collected from the surface of abandoned carbonatite tombstones (weathered for 19-213 years) in Huaxi District, Guizhou Province, and the structural and functional characteristics of archaeal community were analyzed by metagenomic sequencing. [Results] The dominant archaeal phylum was Euryarchaeota, followed by Thaumarchaeota, unclassified Archaea, Bathyarchaeota, and Crenarchaeota. At the genus level, Methanosarcina, Methanothrix, Methanoperedens,Nitrosocosmicus, Nitrososphaera and others unidentified genera were dominant. C/N, C/P and N/P were the main environmental factors that significantly affected the archaeal community on the carbonatite surface. In addition, archaeal community on the surface of carbonatite had diverse functions, particularly metabolism. Euryarchaeota and Thaumarchaeota were the dominant functional groups in the cycling of C, N, and S. The weathering degree of carbonatite significantly increased and the relative abundance of Euryarchaeota and Crenarchaeota obviously decreased over time. Moreover, the relative abundance of Thaumarchaeota had no significant change over time. [Conclusion] In summary, we believed that the survival strategy of the archaeal community changed from an r-strategy (Euryarchaeota) to a K-strategy (Thaumarchaeota) with the weathering.

Abstract:[Background] Medicinal plants harbor abundant fungal endophytes, producing host-related secondary metabolites with a variety of biological activities. [Objective] To analyze the diversity of endophytic fungi in the roots of medicinal species Ampelopsis japonica (Thunb.) Makino and isolate strains producing chemicals with anti-acne activity. [Methods] The taxonomic diversity of fungal endophytes was analyzed based on high-throughput sequencing and tissue isolation. The activity of metabolites of the endophytes against acne-associated pathogens was tested with agar diffusion method and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined by broth microdilution.[Results] The endophytic fungi from the roots of A. japonica belonged to 93 genera, 73 families, 45 orders, 22 classes, and 8 phyla. The dominant genera were Tainosphaeria (20.86%) and Fusarium (15.38%). With the tissue isolation method, 83 fungal strains (12 genera) were isolated, among which Penicillium (24.10%), Trichoderma (14.46%),Cadophora (13.25%), and Fusarium (12.05%) dominated. The results of anti-acne bacteria activities of 17 representative strains showed that the strains with activities against Propionibacterium acnes and Staphylococcus aureus accounted for 11.76% and 23.53%, respectively. The fermentation broth of the endophytic Fusarium oxysporum BLR17 displayed obvious inhibitory effect on both pathogens. The MIC of its crude ethyl acetate extract against P. acnes and S. aureus was 7.81 μg/mL and 62.5 μg/mL, respectively, and the MBC was 7.81 μg/mL and 62.5 μg/mL, separately. [Conclusion] The endophytic fungi of A. japonica had high diversity and contained a certain proportion of anti-acne species resources. F. oxysporum BLR17 is expected to be a resource strain for screening the anti-acne bioactive compounds, which is worthy of further study.

Abstract:[Background] Plant growth-promoting rhizobacteria are beneficial bacteria inhabiting the rhizosphere of plants, with a promising prospect of application in the development of microbial fertilizers. [Objective] We isolated the plant growth-promoting rhizobacteria from the rhizosphere of the endangered plant Cercidiphyllum japonicum and evaluated their effects on C. japonicum seedlings. We then chose the strain with the greatest growth-promoting effect on C. japonicum seedlings, characterized its plant growth-promoting properties, and carried out strain identification, whole genome sequencing and plant growth-promoting related gene analysis. [Methods] The plant growth-promoting rhizobacteria capable of solubilizing organophosphate, inorganic phosphorus, and potassium were isolated with the corresponding selective media. The inoculation assay was employed and the strain with the greatest growth-promoting effect on C. japonicum seedlings was selected to verify the abilities for potassium solubilization, IAA and ACC deaminase production. The strain was identified based on cell morphology observation, 16S rRNA gene sequence analysis and the average nucleotide identity of the whole genome sequence. Furthermore, the genes conferring plant growth promotion and heavy metal resistance in the genome of this strain were identified by genome functional annotation and comparative genomics analysis. [Results] Three, two, and two strains capable of solubilizing organophosphate, inorganic phosphate, and potassium, respectively, were isolated from the rhizosphere soil of C. japonicum. Among them, the potassium-solubilizing bacterial strain LWK2 had the best performance of promoting the growth of C. japonicum seedlings. Strain LWK2 can produce IAA and ACC deaminase and was identified as a strain of Burkholderia pyrrocinia. The whole genome of LWK2 consisted of two chromosomes and a plasmid, with the lengths of 3 713 209, 3 026 422, and 880 277 bp and the GC proportions of 66.50%, 66.37%, and 65.69%, respectively. The genes associated with IAA, siderophore, pyrrolnitrin biosynthesis, ACC deaminase production, and phosphorus solubilization were identified in the LWK2 genome. These genes are ubiquitous in the other 13 strains of Burkholderia spp. with plant growth-promoting activities, while the IAA synthesis pathways and the enzymes catalyzing the reactions vary between different strains. In addition, the LWK2 genome carried the genes involved in the resistance to heavy metals, including copper, cobalt-zinc-cadmium, and arsenic. Heavy metal resistance experiments showed that LWK2 was resistant to CuSO₄, ZnSO₄, CdCl₂, and CoCl₂, with the maximum tolerance concentrations of 4, 10, 3, and 1 mmol/L for these four heavy metal salts, respectively.[Conclusion] B. pyrrocinia LWK2 isolated from C. japonicum rhizosphere has plant growth-promoting properties. It can significantly promote the growth of C. japonicum seedlings, demonstrating the potential of application in the development of microbial fertilizers for the endangered plant C. japonicum. The whole genome sequencing of LWK2 enriches the genome data of plant growth-promoting B. pyrrocinia. The identification of the genes associated with plant growth promotion and heavy metal resistance in the LWK2 genome is critical for further elucidating the plant growth-promoting mechanism of LWK2 and expanding its application in the development of plant growth-promoting agents used in the environment with heavy metal stress.

Abstract:[Background] Some microorganisms, with high production of extracellular polysaccharide, can help improve saline-alkali soil and promote crop growth. [Objective] To screen saline-alkali-tolerant and extracellular polysaccharide-producing microorganisms for the development of microbial agents which can improve saline-alkali soil. [Methods] We screened strains which reproduce in saline-alkali soil, produce extracellular polysaccharide, and have the ability to solubilize phosphate and release potassium from rhizosphere soil of plants in coastal saline-alkali area. The eligible strain was identified based on morphological observation, physiological and biochemical indexes, 16S rRNA gene and gyrB gene sequencing. Then we analyzed growth of the strain and the production of extracellular polysaccharide under saline-alkali stress. In addition, the influence of the strain on the proportion of aggregates with different particle sizes in saline-alkali soil was investigated, and the effect on growth indexes of tomato in saline-alkali soil and soil indexes was examined. [Results] From 727 strains in coastal saline-alkali soil, strain GBW HF-98 was screened out, which, with strong reproductive ability in saline-alkali soil, produced extracellular polysaccharide and had the ability to solubilize phosphate and release potassium. The strain was identified as Bacillus subtilis subsp. inaquosorum and it can tolerate pH 10.0 stress and NaCl concentration of up to 110 g/L. It significantly improved the proportion of aggregates with different particle sizes in soil with mild and moderate salinity. The high dose of this strain (T2 group) increased the strong seedling index, root dry weight, dry weight of whole plant, stem diameter, and plant height of tomato in soil with moderate salinity by 33.8%, 59.3%, 37.2%, 12.3%, and 15.6%, respectively, as compared with the control (P<0.05). Moreover, it significantly reduced pH, total salt content, and soil bulk density by 8.9%, 27.9%, and 17.9%, respectively, and significantly raised soil available phosphorus content and available potassium content by 36.0% and 17.4%, separately (P<0.05).[Conclusion] GBW HF-98, with high production of extracellular polysaccharide, can remarkably promote the growth of tomato in moderately saline-alkali soil and improve the soil. Thus, it can be used for the development of microbial agents for the improvement of saline-alkali soil.

Abstract:[Background] As a lactic acid-producing probiotic candidate, Enterococcus faecium is widely used in animal breeding owing to the satisfactory biological characteristics. However, a few studies of the influence of E. faecium on intestinal metabonomics are available. [Objective] To explore the effect of E. faecium on intestinal metabonomics and inflammatory factors of Penaeus monodon (giant tiger prawn) and thus to lay a theoretical basis for the application of E. faecium as a probiotic in prawn culture. [Methods] A total of 400 giant tiger prawns were randomly classified into four groups. For three groups (experimental groups) of them, E. faecium was added into the feed at 10⁷, 10⁸, and 10⁹ CFU/g, respectively. For the remainder, no E. faecium was added to the feed, and this group was regarded as control. The experiment lasted 28 days. Then, the content of immunoglobulin IgM, phenol oxidase (PO), interleukin-6 (IL-6), and complement fragment 3a (C3a) in P. monodon was measured, and the changes of intestinal metabolites were studied by LC-MS. On this basis, differential metabolites and related metabolic pathways were analyzed.[Results] The addition of E. faecium had positive effect on the inflammatory factors of P. monodon. It increased the content of IgM, PO, and C3a and reduced the content of IL-6 in P. monodon. A total of 165 differential metabolites between the control group and the experimental groups were identified, which were mainly lipids and lipid-like molecules, organic acids and derivatives, organic oxygen compounds, organic heterocyclic compounds, nucleosides, nucleotides and analogues, etc. The differential metabolites were involved in 37 metabolic pathways, including arachidonic acid metabolism, α-linolenic acid metabolism, choline metabolism, and pyrimidine metabolism (P<0.05), and arachidonic acid metabolism α-linolenic acid metabolism, choline metabolism, pyrimidine metabolism, and glycerophosphatide metabolism topped the pathways in the number of metabolites.[Conclusion] E. faecium has positive effect on lipid metabolism, amino acid metabolism, nucleotide metabolism, and inflammatory factors in the intestine of P. monodon, which lays a theoretical foundation for the application of E. faecium in shrimp culture, and has important significance and application prospects.

Abstract:[Background] Bacterial fruit blotch (BFB) is a serious quarantine disease caused by Acidovorax citrulli on the plants of Cucurbitaceae. Type Ⅲ secreted effectors (T3SEs) are known as the key pathogenic factors in the pathogen, while little is known about their roles and functioning mechanisms. [Objective] To identify the T3SE gene aopW of A. citrulli and analyze the way that the protein affects plant immunity, so as to lay a foundation for further understanding the role of aopW in the pathogenic mechanism of A. citrulli. [Methods] Bioinformatics tools were used to analyze the sequence of the gene. Fluorescence quantitative PCR was performed to determine the expression of aopW and the relationship in the expression between aopW and disease resistance genes. Gene mutagenesis and gene function complementation were employed to explore the gene functions through the analysis of pathogen pathogenicity and host accumulation of reactive oxygen species. Hypersensitive response (HR) induced by AopW and the subcellular localization of AopW in the non-host plant were investigated by transient expression technique. [Results] There was a binding site with the type Ⅲ secretion system (T3SS) core gene in the promoter region of aopW gene, and the protein encoded by aopW had no signal peptide or transmembrane domain. AopW was homologous to harpin. The expression of aopW in the mutants of T3SS core genes hrpG/hrpX was significantly down-regulated. After aopW was deleted, the pathogenicity of the mutant decreased, while the accumulation of reactive oxygen species in the host increased. AopW was mainly located in the cytoplasm and cytoplasmic membrane and induced HR in Nicotiana benthamiana. Moreover, AopW affected the pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) signaling pathway and the expression of the genes involved in hormone signaling pathways.[Conclusion] The AopW of A. citrulli is a harpin of the T3SE family, which plays a role as a toxic factor in the interaction of A. citrulli with the host cucumber. It may be involved in the PAMP-triggerred plant PTI and hormone signaling pathways and induce cell necrosis in N. benthamiana.

Abstract:[Background] Rhizosphere microbial community is closely related to the root rot of Panax notoginseng (PN). However, PN with root rot under natural forest is rarely reported. [Objective] To compare rhizosphere microbial community of PN with root rot under natural forest and in the field and to lay a basis for the control of root rot and wild cultivation of PN. [Methods] Rhizosphere soil of PN with root rot under the natural forest and in the field was respectively collected, and species composition and diversity of soil bacterial and fungal communities were analyzed based on high-throughput sequencing. Moreover, we determined soil physicochemical properties and enzyme activity. [Results] The composition of bacterial and fungal communities in the rhizosphere soil was different between PN with root rot under natural forest and that in the field. The rhizosphere soil of PN under natural forest had abundant Basidiomycota, Acidobacteria, and Verrucomicrobia species, while that of PN in the field boasted abundant Ascomycota, Proteobacteria, and Chloroflexi species. At the genus level, Fusarium was dominant in the rhizosphere soil of PN under natural forest, with relative abundance of 17.30%, and Plectosphaerella dominated the rhizosphere soil of PN in the field, with relative abundance standing at 22.55%. The relative abundance of Candidatus Bacilloplasma in non-PN rhizosphere soil under natural forest was 8.05%, while the figure was quite low for rhizosphere soil of PN (0−1.25%). The organic matter content, enzyme activity, and microbial diversity in the rhizosphere soil of PN with root rot in the field were lower than those under natural forest (P<0.05). Redundancy analysis (RDA) suggested significant differentiation of soil bacterial and fungal communities in the rhizosphere soil of PN under natural forest and in the field, which was closely related to the soil organic matter content and enzyme activity. [Conclusion] The rhizosphere microbial composition of PN with root rot under natural forest was significantly different from that in the field. For the cultivation of PN in the field, efforts should be made to improve soil organic matter content, enzyme activity, and microbial diversity. In addition to pathogenic Fusarium, Plectosphaerella should be emphasized in the cultivation of PN.

Abstract:[Background] With the rapid development of animal husbandry, it becomes a challenging task to utilize animal manure and reduce the pollution caused by it. Aerobic composting, as an effective way to utilize manure, has become the focus of research. [Objective] By screening microorganisms with efficient nitrogen conversion capabilities for use in reducing nitrogen losses in aerobic composting, thus improving fertility and reducing pollution. [Methods] We isolated and identified the strain NS-1 with strong ammonia-oxidizing capacity from the heterotrophic nitrifying bacteria in cow dung. Furthermore, we cultured the strain NS-1 under different conditions to investigate its ammonia-oxidizing capacity. [Results] The strain NS-1 was identified as Alcaligenes aquatilis based on morphological characteristics and 16S rRNA sequence. When being cultured in the medium with sodium succinate as the carbon source, the C/N ratio of 15, and pH 7.0 at 35℃, strain NS-1 demonstrated significantly improved ammonia-oxidizing capacity. The validation experiment showed that strain NS-1 completely removed 1 230.694 7 mg/L ammonia nitrogen within 32 h, with the removal efficiency of 100% and the removal rate of 38.46 mg/(L·h).[Conclusion] The strain NS-1 with excellent ammonia-oxidizing capacity is of great significance for reducing nitrogen loss in the composting process. This study provides microbial materials and technical support for the production of high-quality bio-organic fertilizer.

Abstract:[Background] Endophytic bacteria coexist with the host for a long time, posing an impact on the growth and development of the host. Pueraria montana is an important plant with both medicinal and edible values. The research on the endophytic bacteria of this plant is of practical significance. [Objective] To isolate and identify the endophytic bacteria from the roots of Pueraria. montana var. lobata growing in Guangxi and analyze their growth-promoting effect, so as to learn the community structure and growth-promoting effects of endophytic bacteria from the medicinal and edible plants, and provide references for revealing the role of endophytic bacteria in the production and quality formation of medicinal and edible plants and the development and utilization of endophytic bacterial resources. [Methods] Six different media were used to isolate the endophytic bacterial strains from the root nodules, root system, and root callus of Pueraria montana var. lobata. The 16S rRNA gene sequencing was employed to explore the distribution characteristics and genetic diversity of the endophytic bacteria. The physiological and biochemical tests were carried out to determine the nitrogen-fixing activity, phosphorous-solubilizing properties, siderophore production, and indole acetic acid (IAA) secretion of the isolated strains. [Results] A total of 223 strains were isolated from the root nodules, root system, and root callus of Pueraria montana var. lobata. These isolates were phylogenetically classified into 19 genera, 10 families, 4 classes of 2 phyla based on their 16S rRNA gene sequences. Bacillus, Pseudomonas, Agrobacterium, Enterobacter were the predominant taxa. The number and community structure of the endophytic bacteria varied between tissues. Specifically, the number of the endophytic bacteria was in the order of root nodules>root system>root callus and the diversity in the order of root callus>root system>root nodules. Furthermore, the bacterial communities were also distinct from various culture media showed different richness. There were 6 strains with nifH gene, 15 strains with four growth-promoting properties including nitrogen fixation, phosphorous solubilizing, siderophore production, and IAA secretion, and 17 strains with three growth-promoting properties were selected from the tested strains. [Conclusion] The endophytic bacteria in the roots of Pueraria montana var. lobata from Guangxi are genetically diverse, with the distribution varying between tissues and multiple growth-promoting properties.

Abstract:[Background] Traditional milk curd and sour cream butter (Urimo) are the most popular food in Inner Mongolia, which contains abundant lactic acid bacteria resources to be developed and utilized urgently. [Objective] The diversity and distribution characteristics of lactic acid bacteria in traditional homemade milk curd and Urimo samples were analyzed to provide resources and theoretical basis for breeding and utilization of superior strains. [Methods]Lactic acid bacteria were isolated and purified by spread plate method. The phylogenetic relationship, genetic differentiation and community structure of these strains were illustrated based on the sequences of gene 16S rRNA and the species was identified. [Results] A total of 81 strains of lactic acid bacteria were isolated from the traditional homemade samples, mainly belonging to 13 species such as Pediococcus acidilactici, Pediococcus pentosaceus, Lactobacillus brevis, Lactobacillus helveticu, Lactobacillus paracasei, Lactobacillus diolivorans, Lactobacillus otakiensis, Lactobacillus plantarum, Lactobacillus kefir,Lactococcus lactis, Enterococcus faecalis, Enterococcus faecium and Enterococcus durans. Among them, Enterococcus faecium and Lactococcus lactis were the dominant species of milk curd and Urimo, respectively. The single microbial community structure, low nucleotide polymorphism (π), long genetic distance (Dxy), and low gene flow index (Nm) among these lactic acid bacteria were confirmed here. [Conclusion] The biodiversity of lactic acid bacteria in milk curd and Urimo was high, and no correlation was found between species and geographical distribution. There was a strong genetic stability because of the low frequency of gene recombination and exchange in the evolutionary history of lactic acid bacteria.

Abstract:[Background] Among dairy productsin northern Xinjiang, raw cheese harbors a variety of microorganisms and is a valuable source of high-quality food-grade microorganisms. However, the rich microbial resources contained therein are facing the risk of being lost. [Objective] To establish the growth curves of 41 strains of lactic acid bacteria isolated from raw cheese and characterize their tolerance to low pH environment and probiotic characteristics. [Methods] Forty-one strains of lactic acid bacteria isolated from raw cheese were cultured with simulated gastric fluid and the media containing 0.3%, 0.5%, and 1.0% bovine bile salt. [Results] Among the 41 strains of lactic acid bacteria, 6 strains (QM-5, QM-27, UM-12, UM-18, NM-11, and NM-14) grew well at pH 2.0, 2.5, 3.0, 3.5, and 4.0. In the medium at pH 2.0, QM-5 strain maintained a survival rate above 50% and the viable count more than 10⁸ CFU/mL. The lactic acid bacteria isolated from raw cheese has strong resistance to acid and bile salt and can survive in the gastrointestinal environment. Furthermore, the 41 strains had inhibitory effects on Escherichia coli, Staphylococcus aureus, and Bacillus subtilis. [Conclusion] Three dominant strains with antibacterial activity and comprehensive tolerance to acid, simulated gastric fluid, and bile salt were screened out.

Abstract:[Background] Under normal physiological conditions, ribosomal protein SA is mainly expressed in cells and involved in a variety of cell functions. In the occurrence of infectious diseases, RPSA expresses in the cell membrane and mediates the infection of microorganisms. [Objective] To comprehensively reveal the role of RPSA in infection of hosts by Streptococcus suis serotype 2 (SS2). [Methods] The available cerebrospinal fluid and serum proteomics database (piglets with meningitis induced by SS2 and healthy piglets) was used, and bioinformatics methods were employed to screen the differentially expressed proteins (DEPs) in cerebrospinal fluid and serum and the involved signaling pathways were summarized. The host cells were stimulated by enolase (ENO) in vitro, and the changes of mitochondrial membrane potential, Ca²⁺ concentration, and reactive oxygen species were detected to reveal the effect of RPSA-mediated SS2-ENO on the main functions of the energy-generating organelle mitochondria in host cells. [Results] RPSA and related proteins were mainly enriched in energy-related pathways such as metabolism and glycolysis/gluconeogenesis after SS2 infection. SS2-ENO stimulation resulted in decreased mitochondrial membrane potential and increased Ca²⁺ level and ROS level in host cells. Blockade of RPSA alleviated the influence of ENO on mitochondrial membrane potential, ROS and Ca²⁺ concentration. [Conclusion] RPSA mediates the SS2 virulence factor ENO to damage host cell mitochondria. This study enriches the mechanism of RPSA in SS2 infection and provides a theoretical basis for the prevention and treatment of SS2 meningitis.

Abstract:[Background] Insects are the animal group with the most species and the most abundant gut microbiota resources in the world. The microorganisms in insect gut have the ability to produce active secondary metabolites, which is an important source of active natural products.[Objective] To identify the secondary metabolites produced by Streptomyces sp. BPA71 isolated from the gut of the medicinal insect Blaps rynchopetera and determine their biological activities. [Methods] The crude fermentation extract of the strain was separated and purified by column chromatography with silica gel and Sephadex LH-20. Oxford cup method was employed to determine the antimicrobial activity, and the antimicrobial active part was determined. The compound structure was identified by comparison of data from ESI-MS, ¹H NMR, and ¹³C NMR. The minimum inhibitory concentration (MIC) and antitumor activity were determined by microbroth dilution method and MTS method, respectively.[Results] Four known compounds were purified from the crude fermentation extract of BPA71 and identified as methyl 2-furoate (1), pyrroloformamide A (2), pyrroloformamide B (3), and methyl 2-(1H-indol-3-yl) acetate (4). Compound 2 had broad-spectrum antimicrobial activity. In addition, it demonstrated significant inhibitory activities on five tumor cell lines, including cervical cancer cell line HeLa, lung cancer cell line A549, liver cancer cell line SMMC-7721, breast cancer cell line MDA-MB-231, and colon cancer cell line SW480. [Conclusion] Streptomyces sp. BPA71 from the gut of B. rynchopetera can produce rich bioactive substances. The findings of this study lay a foundation for further mining the active natural products of Streptomyces from the gut of B. rynchopetera and enriched our understanding of the gut microbiota of B. rynchopetera.

Abstract:[Background] Senecavirus A (SVA) is a novel pathogen that causes an infectious viral disease in pigs. SVA, a member of the genus Senecavirus of the family Picornaviridae, has a single-stranded positive-sense RNA genome. SVA can infect pigs of all ages, causing neonatal mortality and blisters on the feet and in or around the mouth of pigs. Innate immunity is the first line of host defense against viral invasion, while the role of the mechanism of the interaction between SVA and host innate immune responses remains unknown.[Objective] To investigate the role of the 2C protein of SVA in innate immune responses. [Methods] RT-qPCR and Western blotting were employed to analyze the effect of 2C protein on cytokine expression and signaling pathway in host PK-15 cells overexpressing 2C protein or were infected with SVA. [Results] The infection of SVA significantly up-regulated the expression of interferon beta (IFNβ), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in host PK-15 cells. Meanwhile, SVA infection resulted in the phosphorylation of TANK-binding kinase 1 (TBK1) and Nuclear factor-kappa B (NF-κB). Further studies revealed that 2C protein activated TBK1 and NF-κB and induced the expression of IFNβ, TNF-α, and IL-6. In addition, 2C protein activated the stimulator of interferon genes (STING), a key protein against DNA virus infection. The knockout of STING suppressed the phosphorylation of TBK1 and NF-κB as well as the expression of IFNβ, TNF-α, and IL-6. [Conclusion] This study preliminary reveals that the 2C protein of SVA activates STING to induce the innate immune responses. The findings uncover the regulatory role of STING in the RNA virus SVA-mediated immune response, which provide a theoretical basis for the research and development of antiviral drugs and vaccines.

Abstract:[Background] Salmonella enterica is a common foodborne enteric pathogen that infects humans and animals and causes food poisoning, typhoid fever and other diseases. In recent years, antibiotic abuse has aggravated the antibiotic resistance of S. enterica, and it is urgent to develop new anti-infectives. After the contact with the intestinal epithelium, S. enterica can deliver several effector proteins into the host cells through the type Ⅲ secretion system (T3SS). The effector proteins can manipulate many common cellular processes, including host immune responses, cytoskeletal dynamics, vesicle transport, and signaling pathways, which facilitate the infection in the host cells. T3SS, composed of more than 20 proteins, is a protein transport nanomachine ubiquitous in most Gram-negative bacterial pathogens and symbionts. Its structure and function are highly conserved in diverse pathogens. The SctV family protein, one of the most conserved components of T3SS, is located at the core part of T3SS and involved in energy supply and effector secretion of T3SS. The mutation of key residues in SctV results in the failure of S. enterica invasion. [Objective] To obtain the anti-virulence T3SS inhibitors with the SctV family proteins of Salmonella as the targets by virtual screening. [Methods] The in vitro interaction assay, secretion assay, bacterial growth curve assay, and bacterial invasion assay were combined to analyze and validate the inhibitory effect of candidate molecules. [Results] The compounds C4 (pneumocandin B0) and C5 (purpurin) significantly inhibited the secretion of T3SS effectors and further prevented S. Typhimurium from invading NCM460 cells. Instead of binding to the intracellular part of SctV, C4 and C5 employed other mechanisms to inhibit the virulence of S. Typhimurium. [Conclusion] How C4 inhibits the secretion of T3SS effectors remains unclear. C5 may down-regulate the expression of the regulator gene hilD to inhibit the secretion of T3SS effectors and further hinder the invasion of S. Typhimurium into NCM460 cells. This work provides new targets and ideas for the development of novel anti-infectives targeting T3SS. Moreover, it provides a theoretical basis for the optimization and modification of subsequent T3SS anti-virulence inhibitors.

Abstract: Abstract:[Background] Pseudomonas aeruginosa, a Gram-negative bacterium, is a common opportunistic pathogen of nosocomial infection. Cyclic di-guanosine monophosphate (c-di-GMP), a secondary messenger ubiquitous in bacteria, plays a role in regulating the physiological and biochemical functions of bacteria. PA2072 is a gene involved in c-di-GMP metabolism in P. aeruginosa PAO1. [Objective] To investigate the biological functions of PA2072 in P. aeruginosa PAO1. [Methods] The suicide vectors carrying the full length and different domains of PA2072 were constructed by common molecular cloning technology. Three mutant strains of PA2072 were obtained and studied. The swimming, swarming, and twitching motility, as well as the biofilm formation, of the strains was studied. Congo Red staining was further employed to determine the c-di-GMP levels of the strains. [Results] PA2072 mutant strains and complement strains were successfully constructed. The deletion of PA2072 affected the biofilm formation, and the individual domains of PA2072 also played a role in biofilm formation. The motility tests showed that PA2072 was involved in the regulation of bacterial motility. Compared with the wild-type PAO1 strain, PA2072-delected strains displayed red lawn, which indicated an increased level of intracellular c-di-GMP. [Conclusion] The deletion of PA2072 affects the phenotypes of P. aeruginosa, which might be because of the changes in c-di-GMP level. Our work lays a foundation for further characterization of the biological functions of PA2072.

Abstract:[Background] Microbial transformation is an important means for structural modification of natural products. Many microorganisms can transform ginsenoside compounds into saponins with high activity by modifying the structure of different positions.[Objective] To screen a strain that can transform ginsenoside Rb₁ into rare ginsenosides with high pharmacological activity. [Methods] A total of 36 fungal strains were isolated from rhizosphere soil and stem of Panax notoginseng and purified. Primary screening of saponin transformation activity was performed with β-glucosidase method, followed by a second screening with ginsenoside Rb₁ as substrate. The transformation products were analyzed by TLC, HPLC, and MS. [Results] A strain F17 with high transformation activity of ginsenoside Rb₁ was screened out and it was identified as Pestalotiopsis biciliata based on morphological observation and ITS sequence analysis. It can transform ginsenoside Rb₁ into ginsenoside Rd and rare ginsenosides F₂ and C-K through the pathway of Rb₁→Rd→F₂→C-K. [Conclusion] This study provides a new strain for transformation of rare ginsenosides F₂ and C-K.

Abstract:[Background] Kluyveromyces marxianus with a complete xylose metabolic pathway can utilize xylose in lignocellulose. The study of its sugar transporter genes may solve the problem of how to efficiently transport xylose.[Objective] To explore the functions of the sugar transporter genes of K. marxianus GX-UN120 obtained according to the function prediction of KLMA_70145 and KLMA_80101 in K. marxianus DMKU3-1042. [Methods] Km_SUT2 and Km_SUT3 were respectively expressed in Saccharomyces cerevisiae EBY.VW4000. We then observed the growth characteristics of different recombinants in the media with different carbon sources to evaluate the transport capacity of corresponding transporters. [Results] The sugar transporter Km_SUT2 improved the ability of host cells to transport xylose, arabinose, sorbose, ribose, lactose and glucose, while the cells did not have the ability to transport mannose, fructose, sucrose or galactose. Similarly, the sugar transporter Km_SUT3 can transport xylose, arabinose, sorbose, galactose, ribose, lactose and glucose, while it cannot transport mannose or fructose. In the medium with glucose, the utilization of carbon sources by the recombinants was inhibited, while the inhibition on the transport of xylose and ribose by Km_SUT3 was weaker than that by Km_SUT2. [Conclusion] The transporters Km_SUT2 and Km_SUT3 in K. marxianus GX-UN120 can promote the transport of monosaccharides such as xylose. More significantly, Km_SUT3 enables the recombinant to utilize both glucose and xylose under the condition of low glucose concentration, while the transport of xylose by Km_SUT2 is entirely inhibited by glucose.

Abstract:Triterpenes, a major group of key components in the medicinal and edible Ganoderma lucidum in China, have crucial pharmacological activities. Liquid fermentation is the most promising way to produce the triterpenes as this method enables short growth cycle, has controllable environmental conditions, yields target products of stable quality, and is suitable for large-scale production. The metabolic pathway of triterpenes, fermentation process parameters, and dissolved oxygen are the key to the liquid fermentation of G. lucidum for triterpenes. In this study, we summarized the effect of metabolic pathways for triterpene biosynthesis and the related enzymes (genes), liquid fermentation process, and dissolved oxygen control regulated fermentation parameters on the biosynthesis of triterpenes, as well as the future research directions, hoping to serve as a reference for the regulation and high-yield production of triterpenes by submerged liquid fermentation.

Abstract:Foodborne pathogen infection is the primary factor causing foodborne diseases, which seriously endangers human health. Inflammasomes assemble multiprotein complexes by recognizing receptors to sense danger signals of invading pathogenic factors, thereby inducing inflammatory responses, which is an important defense line in the innate immune system. The NLRP3 inflammasome is an important intracellular inflammatory response platform that senses the invasion of pathogenic microorganisms and plays a crucial role in the innate immune response. Foodborne pathogen infection often causes abnormal activation of the NLRP3 inflammasome, which mediates the occurrence and development of a variety of inflammatory diseases. Therefore, the NLRP3 inflammasome is often taken as the target in the research on inflammation. In this review, we summarize the activation mechanisms of NLRP3 inflammasome by foodborne pathogens and their metabolites, as well as the mechanisms of natural products and dietary functional substances in inhibiting NLRP3 inflammasome activation, aiming to provide new ideas for the treatment of inflammatory diseases and the development of functional compounds that alleviate the inflammatory response induced by pathogenic bacteria.

Abstract:Two-step fermentation is the main method for the industrial production of vitamin C (Vc). The mechanism for the production of Vc precursor 2-keto-l-gluonic acid (2-KLG) in the second step with mixed bacteria composed of companion strain and 2-KLG-producing Ketogulonigenium vulgare has been a research focus. It has become a common method to reveal the interactions of various components in biological systems through high-throughput genomics, transcriptomics, proteomics, metabolomics and other omics. In this paper, we summarized the research on the use of omics in elucidating the interactions between two bacteria in fermentation of Vc, the relief of oxidative stress, companion active substances, quorum sensing in K. vulgare, exogenous additives, and genetic modification of K. vulgare to promote 2-KLG production, providing ideas for further exploration and research.

Abstract:It has been revealed that bacterial small non-coding RNAs are post-transcriptional regulatory molecules that tune important processes in bacterial physiology, such as the metabolism, virulence, and antibiotic resistance. In this paper, we review sRNAs' regulation of bacterial virulence and antibiotic resistance, which is of significance for revealing the post-transcriptional mechanism of bacterial virulence and drug resistance.

Abstract:The prevalence of nontuberculous mycobacteria (NTM) infection has been increasing worldwide in recent years, posing a threat to public health. Drinking water distribution systems (DWDSs) represent an important reservoir and a primary transmission route for NTM. However, the growth factors and control measures of NTM remain elusive in DWDSs. This review summarizes the growth and transmission features of NTM and analyses the influence of environmental and engineering factors (disinfectant, organic carbon, pipe material, and temperature) and biotic factors (biofilm, amoeba, and bacteria) on the abundance and diversity of NTM. Further, we summarize the control approaches towards NTM and their effectiveness in DWDSs from source to taps and identify the research gaps and further research needs.

Abstract:Plant bacterial wilt is a soil-borne disease that can cause huge economic losses. The pathogen, Ralstonia solanacearum species complex (RSSC), can synthesize virulence factors through a complex virulence regulatory network and secrete them into the intercellular matrix or cytoplasm of plant cells, thereby causing disease and withering of host plants. This paper elaborates on the main virulence genes and regulatory networks of RSSC, including the motility (flagella and fimbriae), bacterial secretion systems (T2SS, T3SS, and T6SS), virulence regulatory systems (Phc, Prh, Vsr, Peh, and Sol), virulence factors (CWDEs, T3Es, and EPS), the quorum sensing signal AHL, and phytohormones. We summarized the latest research progress and depicted the relevant regulation network, aiming to provide a reference for further research on the pathogenic mechanism of plant bacterial wilt.

Abstract:Biological nitrogen removal is one of the important links in the nitrogen cycle of the earth dominated by microorganisms, mainly including nitrification, denitrification, and anaerobic ammonia oxidation (anammox). Under the combined action of microorganisms, organic nitrogen and ammonia nitrogen in sewage are transformed into nitrogen through a series of actions in sewage. The cost-effective and environment-friendly treatment has been widely applied all over the world. Quorum sensing (QS) is mediated by signal molecules to regulate the behaviors of microorganisms by changing the density of bacteria and the surrounding environment. Many studies have confirmed that the regulation of QS signal molecules has application potential in biological nitrogen removal. This paper introduced various types of signal molecules, summarized the application and detection methods of various signal molecules from the aspects of genomics and practical application, and introduced in detail the role of acyl homoserine lactones (AHLs) in biological nitrogen removal. However, the deficiency was that the study of signal molecules only stayed in the laboratory stage and only studied the effect of a single signal molecule on biological nitrogen removal. In the future, signal molecules can be applied to actual sewage to study the interaction of multiple signal molecules and QS phenomenon among multiple microorganisms.

Abstract:Microbiology is a compulsory course and a core professional course for brewing engineering, bioengineering, biotechnology and other majors. To meet the teaching goal of cultivating innovative talents with scientific inquiry ability, the teaching team has deeply reformed the course of Microbiology and built a first-class undergraduate course. The team comprehensively improved students' scientific inquiry ability through implementing the concept of student-centered teaching and scientific research back-feeding teaching, exploring the educating value of the curriculum, carrying out the ideological and political education, building a full set of online teaching resources at Massive Open Online Courses (MOOCs), constructing the teaching mode of foundation consolidation-training of problem analyzing and solving ability-symposium, improving students' learning mode, reforming the system for evaluating the learning process, and guiding students to participate in the science and technology innovation competition. This practice could foster innovative talents with scientific inquiry ability for the society and provide reference for constructing first-class courses in engineering colleges and universities.

Abstract:[Background] Soil microorganisms play a crucial role in the response of terrestrial ecosystem to global warming.[Objective] To unravel the status quo, hotspots, and frontiers of research on the response of soil microorganisms to global warming and to clarify the knowledge structure in this field. [Methods] Based on the 3 189 papers on the response of soil microorganisms to global warming published in Science Citation Index Expanded of Web of Science from 1999 to 2021, the annual number of papers in this field, cited frequency of the papers, authors, affiliations, countries, subjects, and keywords were visualized by Vosviewer and CiteSpace.[Results] The number of papers shows an overall increasing trend:first slow increase, then steady increase, and finally rapid increase in detail. The highly cited papers are all published in top international journals, the research outcomes of which have high academic influence. As for interdisciplinary research and collaboration, Environmental Science, Ecology, and Soil Science are the main disciplines, and Multidisciplinary Sciences occupies an important position in this field. Moreover, professors Luo Yiqi, Schuur, and Zhou Jizhong are the core scholars in this field. Cooperation among the authors in the same research team is common. The main affiliations are the Chinese Academy of Sciences, University of California, and the US Department of Energy, with close cooperation among the affiliations. Besides, China, the US, and Europe are the main forces in this field and frequent cooperation among countries in this filed is observed. The research focus is that global warming changes the community structure, diversity, and physiological and biochemical functions of soil microorganisms, further influencing geochemical cycle. The research frontiers are the mechanism of action and regulatory mechanism of soil microorganisms in release of soil carbon pool. [Conclusion] The response and adaptation mechanism of soil microorganisms in different ecosystems to global warming are different. A few studies of microbial carbon function-related genes and interaction of multiple environmental factors are available. Therefore, efforts should be made to carry out research on specific ecosystems and large-scope large-scale long-term positioning research, strengthen the research on microbial carbon degradation- and carbon fixation-related genes, and emphasize the impact of the interaction of multiple environmental factors on soil microbial ecological processes.