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2019, 46(3):548-562. DOI: 10.13344/j.microbiol.china.180149Abstract:
[Background] Plant growth-promoting rhizobacteria can promote plant growth and improve stress tolerance. There are special microbial habitats on tea rhizosphere and some beneficial microorganisms with growth-promoting effects could be easily acquired. [Objective] To ascertain taxonomic status and study growth-promoting characteristics of four PGPR strains isolated from tea rhizosphere, and further screen superior PGPR strain. [Methods] These four strains were identified based on morphological, physiological and biochemical characteristics, homology alignments of 16S rRNA gene sequences. The plant growth-promoting characteristics of isolates were studied. Phosphorus contents were analyzed with Mo-Sb colorimetry. ACC (1-Aminocyclopropane-1-carboxylic acid) deaminase activity was measured by colorimetric method. Also, siderophere secreting capacity and IAA content were determined by quantitative test of CAS (Chrome zaurol S) medium and method of Salkowski, respectively. In pot experiments, plant growth-promoting effects were analyzed by measuring shoot heights and fresh weights of tested plants (including Chinese cabbage, swamp cabbage, amaranth and rice). [Results] The strain KKS-6-N1 was identified as Agrobacterium radiobacter, KKS-7-N7 identified as Pseudomonas aeruginosa, GD3 identified as Pseudomonas hunanensis, and GD12 identified as Bacillus flexus, respectively. In these four strains, nitrogen-fixing strains KKS-6-N1 and KKS-7-N7 produced siderophore, KKS-7-N7 also had the abilities of phosphorus-dissolving and IAA secreting as high as 101.29 mg/L. The other two strains, potassium-solubilizing strain GD3 still dissolved phosphorus, its ACC deaminase activity was 8.09 μmol/(mg·h) and relative content of siderophore was 0.31. whereas GD12, which had dissolved potassium and fixed nitrogen, was found to secret ACC deaminase of 14.46 μmol/(mg·h). In pot experiments, shoot heights and fresh weights of Chinese cabbage, swamp cabbage and amaranth were increased obviously by inoculation of these four strains, especially GD3 is the most excellent among them. [Conclusion] Pseudomonas hunanensis GD3, which isolated from tea rhizosphere, could strongly promote plant growth. And it is possible to develop as an excellent microbial fertilizer.2010, 37(12):1825-1829.Abstract:
Real-time quantitative PCR is a commonly used method to analyse the gene expression profile, it is important to select an appropriate reference gene for normalization of experimental data when using this method. In our study, we used two statistical methods to evaluate the gene expression stabilities of five reference genes (ldh, recA, rpoB, gapdh and 16S rRNA) under the different growth phases of Lactobacillus helveticus H9. The results showed that the best reference gene was ldh which was the most stable gene would be used for normalization of real-time quantitative PCR experiments data.GUO Lei , ZHU Wen-Cheng , LIU Wei-Wei , DING Guo-Wei , ZHANG Yue-Qian , ZHANG Shou-Lu , QIU Yue , XIE Yu2013, 40(6):951-958.Abstract:
[Objective] To identify marine fungus HN4-13 isolated from Lianyungang coastal sea sediments with antibacterial activity and to optimize the fermentation conditions of synthesizing antibacterial active substances. [Methods] Strain HN4-13 was identified based on its morphological characters and internal transcribed spacer (ITS) sequence; The optimization of fermentation conditions for antibacterial production by strain HN4-13 were investigated by the one-factor-at-a-time method and the orthogonal design method. [Results] Strain HN4-13 was identified as Aspergillus flavipes, and the optimal fermentation conditions can be recognized as follows: 4% sucrose, 0.5% peptone, 0.1% KCl, 0.06% NaH2PO4, 1% inoculation concentration, 28 °C, 160 r/min for 9 days. [Conclusion] The results provide the clues for further separation and purification of the antibacterial active metabolites derived from strain HN4-13.4 Isolation, Identification and Characterization of Aeromonas hydrophila from Hemorrhagic Grass carpDENG Guo-Cheng , JIANG Xiao-Yan , YE Xing , LIU Ming-Zhi , XU Shu-Ying , LIU Li-Hui , BAI Yue-Qiang , LUO Xia2009, 36(8):1170-1177.Abstract:
Two strains of infectious bacteria and a GCRV-like virus were isolated from grass carp which seemed to be infected by both virus and bacteria in Guangdong and Fujian provinces. CIK cells were inoculated with tissue fluid filtrated from the diseased fish. GCRV-like virus particles and virus inclusion body were observed in the cytoplasm of the infected cells under electron microscope. Artificial infection experiments showed that healthy grass carp died after infected with both the bacteria strains and virus-infected cell culture supernatant. Bacteria morphology, characteristics, physiology and biochemistry assays were used to identify the isolated bacteria. The characteristics of the two strains isolated were in accordance with those of Aeromonas hydrophila. PCR was performed to identify the bacteria. Both 16S rRNA gene and gryB gene of the two strains possessed high similarity with those of A. hydrophila registered in GenBank. AerA and ahpA genes could be amplified in both strains which indicated that both of them possessed strong pathogenicity. The two strains were therefore identified to be virulent strains of A. hydrophila. The diseased grass carp analyzed was supposed to be mixed infected by both A. hydrophila and virus.XU Xiaorong , HUANG Zhipu , YU Hong , XU Yuxiao , ZHANG Bing , ZHANG Ketao , LIU Chaojin , ZHAO Qing , ZHANG Xiaomei2022, 49(10):4048-4065. DOI: 10.13344/j.microbiol.china.220180Abstract:
[Background] Yunnan boasts abundant Cordyceps species resources and the natural Cordyceps species community contains diverse endophytic fungi, which can be used for mining antimicrobial.[Objective] To investigate the diversity of entomogenous fungi and the endophytic fungi in Dashao village, Songming county, Yunnan province, and screen strains with antimicrobial activities. [Methods] Entomogenous fungi and the endophytic fungi were isolated from Cordyceps species samples with tissue separation method. They were identified and the diversity was analyzed based on morphological observation and sequencing of ITS, nrSSU,nrLSU, tef-1α, rpb1, and rpb2. The activities against 7 pathogenic bacteria and 5 plant pathogenic fungi were tested by plate confrontation assay.[Results] A total of 86 natural Cordyceps species samples were collected, which belonged to 7 species in 5 genera in 3 families:Cordyceps (1 species), Beauveria (2 species), and Samsoniella(2 species) in Cordycipitaceae, Metapochonia (1 species) in Clavicipitaceae, and Ophiocordyceps (1 species) in Ophiocordycipitaceae. Meanwhile, 26 strains of endophytic fungi in 9 genera of 9 families were isolated from the samples, among which Trichoderma(38%) and Fusarium (19%) dominated. In addition, 20 strains, which were selected from entomogenous fungi and endophytic fungi according to their origins and taxonomy, were tested for the antimicrobial activities. Results demonstrated that 11 strains showed activities against two or more pathogenic bacteria, and 13 strains against more than one plant pathogenic fungi. Trichoderma sp. Y3-1 and Fusarium sp. WZ3-1 demonstrated broad-spectrum antimicrobial activities. [Conclusion] The Dashao village in Songming county of Yunnan province enjoys rich resources of entomogenous fungi and endophytic fungi and the isolated fungi show activities against diverse pathogens. This study enriches the diversity of entomogenous fungi in Yunnan province, providing not only data support for the development and utilization of entomogenous fungi and the endophytic fungi in Yunnan province but also strains for mining active substances from them.YAO Yi , Lü Yu-Cai , GONG Yan-Li , DENG Zhi-Wei , LI Ning , GUO Jin-Ling , TIAN Yi-Hong , GONG Da-Chun2017, 44(10):2361-2369. DOI: 10.13344/j.microbiol.china.160934Abstract:
[Objective] To explore synergy mechanism of cellulose biodegradation and relationships among the bacterial consortium, we took an approach of artificial constructing composite consortia. [Methods] Some strains were isolated from a microbial community which could ferment lignocellulose to produce biogas at high temperature. One of strains was identified as Bacillus licheniformis by sequencing nearly complete 16S rRNA gene. The strains’ combination, which consisted of the Bacillus licheniformis and Clostridium thermocellum strain CTL-6, had strong filter paper cellulose degradation ability. [Results] Throughout the 9-day co-cultivation, the cumulative degradation amount of filter paper was 484.6 mg and relative degradation ratio was as high as 93.2%. Overall, the variation of pH decreased firstly and then gradually increased. The initial pH of the culture solution was 7.00. The pH dropped to the lowest value (about 6.57) in 3 d. At the end of the culture period (9 days), the pH was 7.73. The combination could produce cellulase and hemicellulase, and two kinds of enzyme activity all represented the rising trend. The maximum of cellulase activity and hemicellulase activity were 0.32 and 0.57 U/mL, respectively, on the day 9. Lactic acid, formic acid, acetic acid, propionic acid and butyric acid were detected by HPLC during the co-culture. Among the five organic acids, the propionic acid and butyric acid had higher metabolism yield and the maximum concentrations were 1 068.8 and 1 477.3 mg/L, respectively. In addition to propionic acid, the concentration change trends of other 4 organic acids had no significant correlation with the change of the filter paper degradation. The total concentration variation of the five organic acids was in accordance with the variation of pH. This result indicated that it probably existed some not-detected acidic substances, the concentration variation of which played a decisive role in the pH variation of the co-culture system. [Conclusion] Bacillus licheniformis could effectively promote the cellulolytic activity of Clostridium thermocellum CTL-6, and the strains’ combination could also be used to artificially construct composite microbial which was able to convert cellulose to produce methane.2020, 47(6):1776-1786. DOI: 10.13344/j.microbiol.china.190828Abstract:
[Background] The occurrence of?rice panicle browning disease is more common in Heilongjiang province, and it can reduce production and quality of rice. [Objective] To identify the pathogen of rice panicle browning in Heilongjiang province. [Methods] Samples of?rice panicle browning were collected from different rice producing areas. The pathogens were isolated. The pathogens were confirmed pathogenicity according to Koch’s postulates, and identified by morphologic and molecular biological characteristics. [Results] Four isolates were obtained. The symptoms of rice panicle inoculated by the four fungi were similar to that observed under natural conditions. Based on morphologic characteristics and rDNA ITS sequences analysis, four pathogens were identified as Fusarium graminearum Schwabe, Alternaria alternata (Fr.) Keissler, Nigrospora oryzae Petch and Epicoccum nigrun Link. Dominant pathogens could change in different years. [Conclusion] The identification of pathogenic fungi causing rice panicle browning in Heilongjiang province could be references to develop disease management strategies.2007, 34(4):0773-0776.Abstract:
Denitrification plays an important role in wastewater treatment systems for the reason that the nitrate or nitrite was reduced, and some gases such as NO, N2O or N2 were released. The application of denitrification in wastewater, the mechanism of denitrification, and the effect factors of denitrification were introduced in this paper. The communities of Denitrifying bacteria, and some key enzymes of denitrification were also introduced. The discovery of aerobic denitrifying bacteria, autotrophic denitrifying bacteria, and denitrifying Phosphorus-removing Bacteria were also mentioned in this paper.2013, 40(6):921-927.Abstract:
[Objective] In order to improve the acetoin production efficiency by Bacillus subtilis CCTCC M 208157. [Methods] The processes of acetoin fermentation were investigated under various pH conditions in a 7 L fermentor. [Results] The effects of pH on cell growth and acetoin production showed that the optimum pH for acetoin production and cell growth were 4.5 and 5.5, respectively. Based on the above results, a two-stage pH control strategy was developed: the pH was controlled at 5.5 for the first 16 h, and then decreased to 4.5 for the remaining time. [Conclusion] With this optimized pH control strategy, the production of acetoin had a significant improvement. Moreover, the production, conversion rate from glucose and productivity of acetoin were achieved at 32.7 g/L, 0.41 g/g and 0.91 g/(L·h), respectively, which were 41%, 42% and 69% higher than that from the strategy without pH control.2008, 35(1):131-136.Abstract:
Obtaining soil bacterial DNA of good quality is a key step in soil bacterial ecology study. A quick, efficient, sensitive and stably method of DNA extraction from soil were established by combining strongpoints of two kits ( Soilmaster kit and DNA IQTM kit). In addition, the 16S rDNA gene and T-RFLP (Terminal restriction fragment length polymorphism) were used in the analysis of soil bacterial community diversity and the result show that T-RFLP is a powerful tool for bacterial community study.2015, 42(2):436-436. DOI: 10.13344/j.microbiol.china.158002Abstract:2008, 35(6):0967-0976.Abstract:
Based on the data of the ISI “Journal Citation Report” in 2006 edition, a statistics for the 88 microbiology science journals has been made. The results showed that these 88 learned journals were published in 16 countries with 3 languages, especially English. And the main countries were United States, England, Netherlands and Japan. The average data of articles and total cites of the 88 journals were 165 and 5226.64, respectively. Moreover, the average data of impact factor and immediacy factor were 3.154, 0.45 and 5.84, respectively. Finally, fifty-five learned journals with impact factor over 2.0 were introduced from these journals to be referenced.2007, 34(5):0836-0838.Abstract:
A mathematical model, describing the population growth under limited conditions, was developed based on the time dependent changes of the specific growth rate. This model could simulate the lag growth phase, the exponential growth phase and the stationary growth phase of the population growth of many kinds of biology or their organs or cells. This model had less parameters, and all the parameters had clear physiological meanings and were easy to be calculated.2014, 41(6):1094-1108. DOI: 10.13344/j.microbiol.china.130856Abstract:
[Objective] Xylose fermentation is crucial in lignocellulosic ethanol production. Acetic acid generated during pretreatment process seriously inhibits xylose fermentation of yeast strain. The effect of differential expression of transaldolase gene (TAL1), one key gene in oxidative pentose phosphate pathway (PPP), on xylose utilization as well as acetic acid tolerance of genetically engineered xylose-fermenting strain NAPX37 was studied. [Methods] The promoter of TAL1 gene (PTAL1) of the strain NAPX37 was separately replaced with three promoters, PTDH3, PAHP1 and PUBI4, through homologous recombination. By subsequent sporulation, spore segregation and mating, three homozygotes in which PTAL1 were replaced with PTDH3, PAHP1 or PUBI4 were constructed. The fermentation capacity and acetic acid tolerance of the three homozygotes and the original strain NAPX37 were compared through batch fermentation using xylose or the mixture of glucose and xylose as carbon source. [Results] Three promoters, PTDH3, PAHP1 and PUBI4, increased the transcription level of TAL1 gene differentially, which not only improved xylose consumption rate and acetic acid tolerance significantly, but also improved glucose consumption rate under the condition of 60 mmol/L of acetic acid. When xylose was used as sole carbon source without acetic acid or when mixed sugar was used, the strain with PAHP1-controlled TAL1 gene showed better fermentation results than strains with PTDH3- or PUBI4-controlled TAL1 gene, indicating the expression level of PAHP1-controlled TAL1 gene was most appropriate. When xylose was used as sole carbon source under the condition of 30 mmol/L of acetic acid, the strain with PUBI4-controlled TAL1 gene showed best fermentation results among all strains, indicating the most suitable expression level of PUBI4-controlled TAL1 gene. [Conclusion] Three promoters, PTDH3, PAHP1 and PUBI4, overexpressed TAL1 gene, which improved xylose fermentation rate and acetic acid tolerance of strain NAPX37 differentially. However, the fermentation condition affected the level of improvement.ZHU Jing , HU Dan , LIU Li-Na , ZHANG Jin-Hai , ZHANG Feng-Yu , HAO Li-Na , GENG Mei-Ling , ZHENG Feng , ZHU Jin , PAN Xiu-Zhen , WANG Chang-Jun2013, 40(6):1058-1067.Abstract:
[Objective] To explore the mechanism of signaling pathways Streptococcus suis serotype 2 infected monocytes/macrophages leaded, discuss the role of capsular sialic acid component played in Streptococcus suis activate macrophage TLR2-AKT-NF-κB signaling pathway. [Methods] RAW264.7 as the target cell line, RT-PCR, Western blotting, immunofluorescence and ELISA were applied to detect different infection time of wild type strain, sialic acid knockout strain and sialic acid complementary strain on macrophages TLR2 mRNA transcription level, AKT phosphorylation level, NF-κB activation level, as well as TNF-α secretion level. Pretreat with TLR2 blocking agent and PI-3K inhibitor on macrophages, detect the expression level above. [Results] Sialic acid knockout strain activates signal transduction pathways selectively. RT-PCR results show that TLR2 mRNA expression levels began to increase at 1 h, 1.5 h reached its peak then slowly decline. Western blotting showed that TLR2 protein expression level reached its peak at 7 h, 9 h decline. Level of p-AKT is stable at its peak during 1.5?5 h, 7 h decline. Immuno fluorescence showed high level of NF-κB activation-nuclear translocation at 15 min. ELISA results indicate TNF-α secretion level was significantly higher than the other two strains after 10 h. TLR2 blocking agent and PI-3K inhibitor significantly suppressed the activation degree of three strains. [Conclusion] Capsular sialic acid could inhibit activation of the TLR2-AKT-NF-κB signaling pathway to some extent, thus participate in bacteria evading the host immune defense.2009, 36(2):0261-0266.Abstract:
Phage display is a widely used gene engineering high technology. Through the display of exogenous peptides or proteins fused specific coat protein on the surface of phages, it is possible to construct proteins or peptides libraries and screen interesting proteins, peptides and antibodies successfully. Most commonly used phage display technology is phagemid/helper phage system, in which helper phages are essential for the replication and assembly of phagemid particles. In this review, in combination with the newest research dynamic status, we summarize phagemid/helper phage double-genome system. We mainly emphasized the features and mutation mechanisms of different helper phages. We also made some prospects for the future directions, in the meanwhile, we also expect that our experience can provide some help for further maturity of the technology.2010, 37(1):0103-0111.Abstract:
Numerous virus families utilize endocytosis to infect host cells, mediating virus internalization as well as traf?cking to the site of replication. The endocytic pathways utilized include clathrin-mediated endocytosis, caveolae, macropinocytosis and non-clathrin, non-caveolae pathways. The tools to study endocytosis and, consequently, virus entry are becoming more effective and speci?c as the amount of information on endocytic component structure and function increases. Now, the use of inhibitory drugs, although still quite common, often leads to non-speci?c disruptions in the cell. Molecular inhibitors in the form of domi-nant–negative proteins and siRNA have surpassed the use of chemical inhibitors in terms of speci?city to in-dividual pathways. This review focuses on the experimental approaches taken to examine virus entry and provides some examples on a variety of virus families.2010, 37(10):1519-1524.Abstract:
Bacteriocins are antibacterial proteins produced by bacteria that can kill or inhibit closely related bacteria. Many lactic acid bacteria (LAB) produce a high diversity of different bacteriocins. Though these bacteriocins are produced by LAB found in numerous fermented and non-fermented foods, nisin is currently the only bacteriocin widely used as a food preservative. Compared with antibiotics, bacteriocins are ribosomally synthesized. Their transcript must be modified before becoming active and are translocated to the outside of the cell by a transporter system. Bacteriocins inhibit target cells by acting on the membrane, while the cell synthesizing the bacteriocin has immunity to its product. Therefore, bacteriocins should be safely and effectively used to control the growth of target pathogens, make it have wide applications in many food systems.Du Xiong-Feng , Li Shu-Zhen , FENG Kai , He Qing , Wang Zhu-Jun , Wu Yue-Ni , Wang Dan-Rui , Peng Xi , Wang Shang , Deng Ye2020, 47(9):2789-2806. DOI: 10.13344/j.microbiol.china.200465Abstract:
[Background] Microorganisms in grassland soils are important for ecosystem functioning and stability maintaining. To discover the profile of microbes along the soil vertical depths is essential for our understanding about microbial contributions in grassland ecosystems. [Objective] To comprehensively investigate the vertical patterns of total prokaryotic quantity, diversity and interaction networks in 0?80 cm soil profiles. [Methods] Based on the quantitative PCR and high-throughput sequencing on 16S rRNA gene in a typical agropasture grassland, Inner Mongolia, the total microbial quantity and diversity were cautiously measured. Besides, the molecular ecological network approach (MENA) was used to explore the changes of microbial species interactions. [Results] The quantity and diversity of prokaryotes decreased with depths, as well as the variations of community. Along the soil vertical depths, the close association among microbes would gradually become sparse and the network structures become simpler. In addition, Acidobacteria was one of top abundant phyla, and network analysis revealed that some species in Acidobacteria were the keystone taxa in this grassland ecosystem. These species might play an important role in maintaining the stability of soil ecological functions. [Conclusion] The quantity, diversity and interactions of prokaryotes showed highly consistent with vertical patterns. The quantity and diversity of prokaryotes is negatively correlated with the soil depth, and the variation of community structure will gradually expand at deep soils. Meanwhile the interactions among species in molecular network are decreasingly weakened. These results provide important insights into the dynamic change of microbial community, and are valuable for the ecological protection of grasslands in typical agropasture area.-
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